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{"total": 415, "projects": {"MIKE": "default", "SIP": "4.17-Python-2.7.9", "HDF5": "1.10.0-patch1-intel-2016.01-mic", "p4vasp": "0.3.29-GNU-4.9.3-2.25", "Automake": "1.15-GNU-5.1.0-2.25", "netcdf": "4.3.0", "bullxde": "2.0", "APR-util": "1.5.4-foss-2015g", "ScaLAPACK": "2.0.2-OpenBLAS-0.2.14-LAPACK-3.5.0", "BerkeleyUPC": "2.16.2-gompi-2015b", "BWA": "0.7.5a-foss-2015g", "openmpi": "1.8.1-icc", "matlab": "R2014a-EDU", "sympy": "0.7.6-intel-2016.01-Python-2.7.9", "kbproto": "1.0.7-intel-2016a", "lsprepost": "4.2", "prace": "20160107-intel-2016.01", "mpt": "2.12", "Bison": "3.0.4-GCC-4.9.3", "totalview": "8.13", "Wine": "1.7.29-GNU-5.1.0-2.25", "opari2": "1.1.2-icc", "MAP": "5.0.1", "libyaml": "0.1.6-intel-2015b", "mercurial": "2.9.1", "beopest": "13.3", "perfsuite": "1a5.3", "PSBLAS-ext": "1.0-4-GCC-4.9.3-2.25", "OSPRay": "0.9.1", "S4MPLE": "1.0.0", "libxslt": "1.1.28-intel-2015b", "hwloc": "1.11.5-GCC-6.3.0-2.27", "libunistring": "0.9.3-intel-2015b", "QGIS": "2.12.3-foss-2015g", 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"opencl-rt": "4.5.0.8", "samtools": "0.1.19", "ictce": "8.3.5", "Python": "3.5.2-intel-2017.00", "make": "3.82-intel-2015b", "Mono": "4.2.2.10-intel-2016.01", "FreeFem++": "3.45-intel-2015b", "SAMtools": "1.3-foss-2015g", "SQLite": "3.13.0-intel-2017a", "HPL": "2.1-intel-2015b", "OpenDX": "4.4.4-foss-2015g", "Autoconf": "2.69-GNU-5.1.0-2.25", "RStudio": "0.98.1103", "globus": "globus", "fontsproto": "2.1.3-intel-2016a", "SDE": "7.41.0", "gzip": "1.6-intel-2015b", "gsl": "1.16-icc", "tcl": "8.5.15", "TotalView": "8.15.4-6-linux-x86-64", "MPICH": "3.2-GCC-5.3.1-snapshot-20160419-2.25", "GSL": "2.1-intel-2015b", "libXfixes": "5.0.1-intel-2016a", "OpenFOAM": "3.0.0-intel-2016.01", "SCons": "2.3.6-Python-2.7.9", "iccifort": "2017.1.132-GCC-6.3.0-2.27", "plasma": "2.6.0", "phonopy": "1.11.6.7-intel-2015b-Python-2.7.11", "libXdmcp": "1.1.2-intel-2016a", "Mercurial": "3.7.3-foss-2015g-Python-2.7.9", "xproto": "7.0.28-intel-2016a", "FLTK": "1.3.2-intel-2015b", "hpg-variant": "1.0.0", "libdrm": 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"13.0", "PerformanceReports": "6.0.6", "netcdf-cxx": "4.2", "impi": "2017-BETA.ENG", "Lmod": "7.2.2", "libmatheval": "1.1.11-intel-2015b", "GLib": "2.40.0-GCC-4.4.7-system", "QCA": "2.1.0-foss-2015g", "scite": "3.4.3", "Tk": "8.6.5-intel-2017a", "hpg-fastq": "1.0.0", "SnpEff": "4.1_G", "libpthread-stubs": "0.3-intel-2016a", "bzip2": "1.0.6-intel-2017a", "cmake": "2.8.11-mic", "gnuplot": "4.6.5", "gettext": "0.19.6-intel-2017.00", "VDE2": "2.3.2-GCC-4.4.7-system", "Advisor": "2017", "glproto": "1.4.17-intel-2016a", "ORCA": "3_0_3-linux_x86-64", "llvm": "3.6.0", "papi": "5.4.0-mic", "Serf": "1.3.8-foss-2015g", "libxc": "2.2.1-intel-2015b", "libtool": "2.4.6-GCC-6.3.0-2.27", "libffi": "3.2.1-GCC-4.4.7-system", "libmesh": "0.9.3-petsc-3.4.4-icc-impi-mkl-opt", "opencl-sdk": "4.6.0.92", "GMP": "6.1.1-intel-2017.00", "PETSc": "3.6.3-intel-2015b-Python-2.7.11", "OpenMPI": "2.0.2-GCC-6.3.0-2.27", "netCDF": "4.4.1-intel-2017a", "Hypre": "2.10.1-intel-2015b", "renderproto": "0.11-intel-2015b", "oscar-modules": "1.0.3"}}
!!! Hint "Cluster Acronyms"
A - Anselm • S - Salomon • U - uv1 at Salomon
| Module </br><input id="searchInput" placeholder="🔍 Filter" style="width: 8rem; border-radius: 0.2rem; color: black; padding-left: .2rem;"> | Versions | Clusters |
| ------ | -------- | -------- |
| ABINIT | 7.10.1-foss-2015b</br>7.10.1-intel-2015b</br>8.2.2-intel-2017a</br>8.6.1-intel-2017a</br>8.6.1-intel-2017a-test | `US-`</br>`US-`</br>`-SA`</br>`-S-`</br>`-S-` |
| absl-py | 0.1.10-Py-3.6 | `-SA` |
| ABySS | 2.0.2-foss-2018a</br>2.0.3-foss-2018a | `-SA`</br>`-S-` |
| ACE | 6.3.3 | `-S-` |
| ACTC | 1.1-intel-2017a | `-S-` |
| adams | 2013.2 | `--A` |
| adios | 1.8.0 | `--A` |
| Advisor | 2016_update2</br>2017_update3</br>2017_update5 | `-S-`</br>`-SA`</br>`-S-` |
| advisor_xe | 2013.5</br>2015.1.10.380555 | `--A`</br>`--A` |
| aislinn | 20160105-Python-2.7.9-gompi-2015e | `-S-` |
| ALAMODE | 0.9.8-intel-2017a | `-SA` |
| almost | 2.1.0-foss-2015b</br>2.1.0-foss-2015g</br>2.1.0-foss-2016a</br>2.1.0-intel-2015b | `-S-`</br>`-SA`</br>`-SA`</br>`-S-` |
| ALPScore | 2.1.1-intel-2017b | `--A` |
| Amber | 14</br>18-intel-2017b | `-S-`</br>`-S-` |
| Anaconda2 | 4.4.0 | `-SA` |
| Anaconda3 | 4.4.0 | `-SA` |
| ANSYS | 16.1</br>18.2-intel-2017a</br>19.0-intel-2017b</br>19.1-intel-2017c | `-S-`</br>`-S-`</br>`-S-`</br>`-SA` |
| ant | 1.9.3-Java-1.7.0_79</br>1.9.7-Java-1.8.0_121 | `-S-`</br>`--A` |
| APR | 1.5.2</br>1.5.2-foss-2015g | `-SA`</br>`-SA` |
| APR-util | 1.5.4</br>1.5.4-foss-2015g | `-SA`</br>`-SA` |
| Armadillo | 7.500.0-foss-2016a-Python-3.5.2 | `-SA` |
| arpack-ng | 3.3.0-foss-2016a</br>3.3.0-intel-2015b</br>3.3.0-intel-2017.00</br>3.4.0-intel-2017.00</br>3.5.0-intel-2017a | `-SA`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-SA` |
| ASE | 3.15.0-Py-3.6</br>3.15.0-Python-2.7.13-base</br>3.15.0-Python-2.7.13-base-test</br>3.15.0-Python-3.6.1-base-test | `-SA`</br>`--A`</br>`-S-`</br>`-S-` |
| asn1crypto | 0.24.0-Py-2.7 | `-S-` |
| astor | 0.6.2-Py-3.6 | `-S-` |
| astroid | 1.5.3-Python-2.7.13-base | `-SA` |
| asv | 0.2.1-Py-2.7</br>0.2.1-Py-3.6 | `-S-`</br>`-S-` |
| ATK | 2.18.0</br>2.20.0 | `-S-`</br>`--A` |
| ATLAS | 3.10.1-GCC-4.9.3-2.25-LAPACK-3.4.2</br>3.10.3-GCC-6.3.0-2.27-LAPACK-3.6.1</br>3.10.3-GCC-7.1.0-2.28-LAPACK-3.6.1 | `--A`</br>`-SA`</br>`-S-` |
| attrs | 17.4.0-Py-2.7</br>17.4.0-Py-3.6 | `-S-`</br>`-S-` |
| Autoconf | 2.69</br>2.69-foss-2015g</br>2.69-foss-2016a</br>2.69-intel-2015b</br>2.69-intel-2017.00</br>2.69-intel-2017a</br>2.69-GCCcore-6.4.0</br>2.69-GCC-6.3.0-2.27</br>2.69-GNU-4.9.3-2.25</br>2.69-GNU-5.1.0-2.25 | `-SA`</br>`-S-`</br>`--A`</br>`--A`</br>`--A`</br>`-SA`</br>`-S-`</br>`--A`</br>`--A`</br>`--A` |
| Automake | 1.15</br>1.15-foss-2016a</br>1.15-intel-2015b</br>1.15-intel-2017.00</br>1.15-intel-2017a</br>1.15-GCC-6.3.0-2.27</br>1.15-GNU-4.9.3-2.25</br>1.15-GNU-5.1.0-2.25</br>1.16.1 | `-SA`</br>`--A`</br>`--A`</br>`--A`</br>`-SA`</br>`--A`</br>`--A`</br>`--A`</br>`-S-` |
| Autotools | 20150215</br>20150215-foss-2016a</br>20150215-intel-2015b</br>20150215-intel-2017.00</br>20150215-intel-2017a</br>20150215-GCC-6.3.0-2.27</br>20150215-GNU-4.9.3-2.25</br>20150215-GNU-5.1.0-2.25</br>20180311 | `-SA`</br>`--A`</br>`--A`</br>`--A`</br>`-SA`</br>`--A`</br>`--A`</br>`--A`</br>`-S-` |
| backports_abc | 0.5-Py-2.7 | `-S-` |
| Bash | 4.2-intel-2015b</br>4.3</br>4.4-intel-2017b</br>4.4-GCC-6.3.0-2.27 | `US-`</br>`-SA`</br>`USA`</br>`USA` |
| Bazel | 0.4.4</br>0.4.4-GCC-4.8.3</br>0.4.4-GCC-4.9.3</br>0.4.5-GCC-4.8.3</br>0.5.0-GCC-4.9.3-tf</br>0.5.1-GCC-7.1.0-2.28</br>0.7.0-GCC-6.3.0-2.27</br>0.7.0-GCC-7.1.0-2.28 | `--A`</br>`--A`</br>`--A`</br>`--A`</br>`-SA`</br>`-SA`</br>`-SA`</br>`-S-` |
| BCFtools | 1.6-intel-2017a</br>1.8-intel-2017a | `-S-`</br>`-S-` |
| bcl2fastq2 | 2.20.0-intel-2017a-Python-2.7.13 | `-S-` |
| bcrypt | 3.1.4-Py-2.7 | `-S-` |
| beopest | 12.0.1</br>12.2</br>13.3 | `--A`</br>`--A`</br>`--A` |
| BeoPEST | 14.02-GCC-6.3.0-2.27 | `-S-` |
| BerkeleyUPC | 2.16.2-gompi-2015b | `-S-` |
| binutils | 2.25</br>2.25-GCCcore-4.9.3</br>2.25-GCCcore-5.3.0</br>2.25-GCCcore-5.3.1-snapshot-20160419</br>2.25-GCC-4.9.3</br>2.25-GCC-4.9.3-binutils-2.25</br>2.25-GCC-5.1.0-binutils-2.25</br>2.26</br>2.26-GCCcore-5.3.0</br>2.26-GCCcore-5.4.0</br>2.27</br>2.27-GCCcore-6.3.0</br>2.28</br>2.28-GCCcore-6.3.0</br>2.28-GCCcore-6.4.0</br>2.28-GCCcore-7.1.0</br>2.30</br>2.30-GCCcore-8.1.0 | `--A`</br>`-SA`</br>`-S-`</br>`-S-`</br>`--A`</br>`USA`</br>`USA`</br>`--A`</br>`-SA`</br>`-SA`</br>`USA`</br>`USA`</br>`USA`</br>`--A`</br>`USA`</br>`USA`</br>`--A`</br>`-SA` |
| Bison | 2.5-intel-2015b</br>2.7</br>2.7-foss-2015b</br>2.7-foss-2015g</br>3.0.2</br>3.0.4</br>3.0.4-foss-2016a</br>3.0.4-intel-2015b</br>3.0.4-intel-2016.01</br>3.0.4-GCCcore-4.9.3</br>3.0.4-GCCcore-5.3.0</br>3.0.4-GCCcore-5.4.0</br>3.0.4-GCCcore-6.3.0</br>3.0.4-GCC-4.9.3</br>3.0.4-GCC-4.9.3-binutils-2.25</br>3.0.4-GCC-5.1.0-binutils-2.25 | `-SA`</br>`-SA`</br>`-S-`</br>`-SA`</br>`--A`</br>`-SA`</br>`-SA`</br>`--A`</br>`-S-`</br>`--A`</br>`--A`</br>`--A`</br>`USA`</br>`--A`</br>`--A`</br>`--A` |
| BLCR | 0.8.5 | `U--` |
| bleach | 1.5.0-Py-3.6</br>2.1.2-Py-3.6 | `-S-`</br>`-S-` |
| blender | 2.71 | `--A` |
| BoltzTraP2 | 18.1.1-Py-3.6</br>18.1.2-Py-3.6 | `-S-`</br>`--A` |
| Boost | 1.58.0-foss-2015g-Python-2.7.9</br>1.58.0-gompi-2015e-Python-2.7.9</br>1.58.0-ictce-7.3.5-Python-2.7.9</br>1.58.0-intel-2015b-Python-2.7.9</br>1.58.0-intel-2016.01-Python-2.7.9</br>1.58.0-Python-2.7.9</br>1.59.0-intel-2015b</br>1.59.0-intel-2015b-Python-2.7.11</br>1.59.0-intel-2016.01</br>1.60.0-foss-2015g-Python-2.7.9</br>1.60.0-intel-2015b-Python-2.7.11</br>1.60.0-intel-2016a</br>1.61.0-foss-2016a</br>1.61.0-foss-2016a-serial</br>1.61.0-foss-2017a-serial</br>1.63.0-foss-2015g-Python-3.6.1</br>1.63.0-foss-2016a-Python-2.7.13</br>1.63.0-foss-2017a-Python-2.7.13</br>1.63.0-foss-2017a-Python-3.6.1</br>1.63.0-intel-2017a</br>1.63.0-intel-2017a-Python-2.7.11</br>1.63.0-intel-2017a-Python-2.7.13</br>1.66.0-foss-2017a-Py-2.7</br>1.66.0-foss-2018a-Py-2.7</br>1.66.0-intel-2017b-serial</br>1.66.0-intel-2018a</br>1.67.0-intel-2017c-serial</br>1.68.0-intel-2017c-serial | `-SA`</br>`-S-`</br>`-S-`</br>`US-`</br>`-S-`</br>`-S-`</br>`--A`</br>`-S-`</br>`-S-`</br>`-SA`</br>`-S-`</br>`--A`</br>`-S-`</br>`-SA`</br>`-S-`</br>`-S-`</br>`--A`</br>`-SA`</br>`-S-`</br>`USA`</br>`-SA`</br>`-S-`</br>`-S-`</br>`-SA`</br>`-SA`</br>`-SA`</br>`-S-`</br>`-S-` |
| bowtie2 | 2.2.3 | `--A` |
| bullxde | 2.0 | `--A` |
| bullxmpi | bullxmpi_1.2.4.1 | `--A` |
| bupc | 2.16.2 | `--A` |
| BWA | 0.7.5a-foss-2015g</br>0.7.17-intel-2017a | `-S-`</br>`-S-` |
| byacc | 20120526</br>20120526-foss-2015b</br>20120526-foss-2015g</br>20120526-foss-2016a</br>20120526-intel-2015b</br>20150711-intel-2015b</br>20170509 | `-SA`</br>`-S-`</br>`-SA`</br>`-SA`</br>`-SA`</br>`--A`</br>`-S-` |
| bzip2 | 1.0.6</br>1.0.6-foss-2015b</br>1.0.6-foss-2015g</br>.1.0.6-foss-2015g</br>1.0.6-foss-2016a</br>1.0.6-foss-2017a</br>1.0.6-gompi-2015e</br>1.0.6-ictce-7.3.5</br>1.0.6-intel-2015b</br>1.0.6-intel-2016.01</br>1.0.6-intel-2016a</br>1.0.6-intel-2017.00</br>1.0.6-intel-2017a | `USA`</br>`US-`</br>`USA`</br>`--A`</br>`-SA`</br>`-S-`</br>`-S-`</br>`-S-`</br>`USA`</br>`-SA`</br>`--A`</br>`--A`</br>`-SA` |
| Caffe | 1.0-foss-2016a-CUDA-8.0.44-Python-2.7.13 | `--A` |
| cairo | 1.12.18</br>1.12.18-foss-2015b</br>1.14.6</br>1.14.8</br>1.14.12 | `-SA`</br>`-S-`</br>`-S-`</br>`USA`</br>`-SA` |
| CASMcode | 0.2.1-foss-2016a | `-S-` |
| CentOS | 6.9</br>6.9-GPU</br>6.9-MIC</br>7.4</br>7.4-GPU</br>7.4-MIC</br>7.5</br>7.5-intel</br>7.5-intel-ESPRESO</br>7.5-VARROC | `-SA`</br>`--A`</br>`-S-`</br>`-SA`</br>`--A`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-` |
| cereal | 1.2.1 | `-S-` |
| certifi | 2018.1.18-Py-2.7</br>2018.1.18-Py-3.6 | `-S-`</br>`-SA` |
| cffi | 1.11.5-Py-2.7 | `-S-` |
| CGAL | 4.8.1-intel-2017a</br>4.12-intel-2017a | `USA`</br>`-SA` |
| chicken | 4.8.0.6 | `--A` |
| ChronusQ | 20180802-intel-2017c | `-S-` |
| Clang | 3.7.0-GNU-5.1.0-2.25</br>5.0.0-GCC-6.3.0-2.27 | `-S-`</br>`-SA` |
| click | 6.7-Py-3.6 | `-SA` |
| Clp | 1.16.10-intel-2017a | `-SA` |
| CMake | 3.3.1-foss-2015g</br>3.3.1-foss-2016a</br>3.3.1-intel-2016.01</br>3.3.1-GCC-4.9.3-2.25</br>3.4.1-foss-2016a</br>3.4.1-intel-2015b</br>3.5.2</br>3.5.2-foss-2016a</br>3.5.2-intel-2016a</br>3.6.2</br>3.7.2</br>3.7.2-intel-2017a</br>3.7.2-GCCcore-6.3.0</br>3.8.1</br>3.9.0</br>3.9.1</br>3.11.1-GCCcore-6.4.0</br>3.11.4-GCC-6.3.0-2.27 | `--A`</br>`--A`</br>`-S-`</br>`--A`</br>`--A`</br>`--A`</br>`-SA`</br>`-SA`</br>`--A`</br>`--A`</br>`--A`</br>`USA`</br>`--A`</br>`--A`</br>`-SA`</br>`--A`</br>`-SA`</br>`-SA` |
| cmake | 2.8.11</br>2.8.11-mic | `--A`</br>`--A` |
| CNTKCustomMKL | 3.0 | `-S-` |
| Code_Saturne | 3.0.5 | `--A` |
| COMSOL | 51-COM</br>51-EDU</br>52-COM</br>52-EDU | `-S-`</br>`-S-`</br>`USA`</br>`USA` |
| comsol | 43b-COM</br>43b-EDU</br>44-COM</br>44-EDU</br>50-COM</br>50-EDU | `--A`</br>`--A`</br>`--A`</br>`--A`</br>`--A`</br>`--A` |
| CORALbenchmark | 1.00-foss-2016a | `-S-` |
| Coreutils | 8.30-GCCcore-8.1.0 | `-S-` |
| CP2K | 2.6.0-intel-2015b</br>5.1 | `-S-`</br>`-SA` |
| cp2k-mpi | 2.5.1-gcc | `--A` |
| cryptography | 2.3-Py-2.7 | `-S-` |
| cube | 4.2.3-gcc</br>4.2.3-icc | `--A`</br>`--A` |
| Cube | 4.3.4</br>4.3.4-intel-2015b</br>4.3.5</br>4.3.5-intel-2017a | `--A`</br>`-S-`</br>`-S-`</br>`-S-` |
| CUDA | 7.5.18</br>8.0.44</br>8.0.61</br>9.0.176</br>9.1.85</br>9.2.88 | `USA`</br>`--A`</br>`US-`</br>`--A`</br>`USA`</br>`--A` |
| cuDNN | 5.1-CUDA-7.5.18</br>5.1-CUDA-8.0.44</br>7.0.5-CUDA-9.0.176</br>7.41-CUDA-9.1.85</br>7.41-CUDA-9.2.88 | `--A`</br>`--A`</br>`--A`</br>`--A`</br>`--A` |
| cURL | 7.37.1</br>7.45.0-foss-2015b</br>7.47.0-intel-2017.00</br>7.49.1-intel-2017a</br>7.51.0</br>7.51.0-intel-2017.00</br>7.53.1</br>7.53.1-GCCcore-6.3.0</br>7.56.1</br>7.61.1-GCC-6.3.0-2.27 | `--A`</br>`US-`</br>`-S-`</br>`--A`</br>`--A`</br>`-S-`</br>`USA`</br>`USA`</br>`-S-`</br>`-S-` |
| cycler | 0.10.0-Py-3.6 | `-S-` |
| Cython | 0.27.3-Py-2.7</br>0.27.3-Py-3.6 | `-SA`</br>`-SA` |
| darshan-runtime | 3.1.4-foss-2017a</br>3.1.4-intel-2017b | `-SA`</br>`-SA` |
| darshan-util | 3.1.4-foss-2017a</br>3.1.4-intel-2017b | `-SA`</br>`-SA` |
| dask | 0.17.0-Py-3.6 | `-SA` |
| dataspaces | 1.4.0 | `--A` |
| DCW | 1.1.2 | `-S-` |
| DDT | 4.2</br>5.0.1 | `-S-`</br>`-S-` |
| Debian | 8.0</br>8.0-GPU | `-SA`</br>`--A` |
| decorator | 4.2.1-Py-3.6 | `-SA` |
| deMonNano | 4.3.6 | `-SA` |
| digimat | 5.0.1 | `--A` |
| Digimat | 5.0.1-COM</br>5.0.1-EDU | `-S-`</br>`-S-` |
| Discovery_Studio | 4.0 | `--A` |
| dist-keras | 0.2.1-Py-3.6 | `-S-` |
| DMTCP | 2.5.1</br>2.5.2</br>3.0 | `USA`</br>`US-`</br>`-S-` |
| Doris | 4.06beta2-intel-2017a</br>5.0beta-foss-2017a</br>5.0beta-foss-2017a-test | `-SA`</br>`-S-`</br>`-S-` |
| dotNET-Core-Runtime | 2.0.7</br>2.1.4 | `-SA`</br>`-S-` |
| dotNET-Core-SDK | 2.0.7-2</br>2.1.200</br>2.1.402 | `--A`</br>`-SA`</br>`-S-` |
| Doxygen | 1.8.11</br>1.8.11-intel-2017a</br>1.8.13-GCCcore-6.3.0</br>1.8.14-GCC-6.3.0-2.27 | `-SA`</br>`USA`</br>`USA`</br>`-S-` |
| duplicity | 0.7.17-Py-2.7 | `-S-` |
| DynaPhoPy | 1.15-intel-2017a-Python-2.7.13-base</br>1.15-Python-2.7.13-base</br>1.16.3-Py-3.6 | `-SA`</br>`-S-`</br>`-SA` |
| dytran | 2013.0.1 | `--A` |
| EasyBuild | 3.1.2</br>3.2.0</br>3.3.0</br>3.4.1</br>3.5.0</br>3.5.1</br>3.5.2</br>3.6.0</br>3.6.1</br>3.6.2</br>3.7.0</br>3.7.1 | `-S-`</br>`US-`</br>`--A`</br>`--A`</br>`--A`</br>`--A`</br>`--A`</br>`--A`</br>`--A`</br>`-SA`</br>`-S-`</br>`-S-` |
| Eigen | 3.2.9</br>3.3.3</br>3.3.4</br>3.3.5-GCC-6.3.0-2.27 | `--A`</br>`-SA`</br>`--A`</br>`-S-` |
| Elk | 4.3.6-intel-2017a</br>4.3.6-intel-2017a-openmp | `-S-`</br>`-S-` |
| elmer | 7.0-r6695-dbg</br>7.0-r6695-opt | `--A`</br>`--A` |
| Embree | 2.16.2-intel-2017a</br>3.2.0-intel-2017a | `-SA`</br>`-S-` |
| enum34 | 1.1.6-Py-2.7 | `-S-` |
| ETSF_IO | 1.0.4-intel-2017a | `-S-` |
| eudev | 3.1.5-foss-2016a</br>3.1.5-intel-2016a | `-S-`</br>`-S-` |
| expat | 2.1.0</br>2.1.0-foss-2015b</br>2.1.0-foss-2015g</br>2.1.0-intel-2015b</br>2.1.0-intel-2017.00</br>2.2.0</br>2.2.6-GCC-6.3.0-2.27 | `-SA`</br>`US-`</br>`-SA`</br>`-S-`</br>`-S-`</br>`USA`</br>`-S-` |
| fasteners | 0.14.1-Py-2.7 | `-S-` |
| fastqc | 0.11.2 | `--A` |
| FastQC | 0.11.3 | `US-` |
| fds | 5.5.3</br>5.5.3-omp</br>6.svn | `--A`</br>`--A`</br>`--A` |
| FEFLOW | 7.0-intel-2017a</br>7.1-intel-2017a</br>7.1u06-intel-2017a | `-S-`</br>`-S-`</br>`-S-` |
| FFmpeg | 3.0.2</br>3.1.3-intel-2017a | `--A`</br>`-S-` |
| ffmpeg | 2.4</br>2.4-foss-2015g</br>2.4-intel-2015b | `-SA`</br>`-S-`</br>`-S-` |
| FFTW | 2.1.5-gompi-2015b</br>2.1.5-iimpi-7.3.5-GNU-5.1.0-2.25</br>3.3.4-gompi-2015b</br>3.3.4-gompi-2015e</br>3.3.4-gompi-2015g</br>3.3.4-gompi-2016.04</br>3.3.4-gompi-2016a</br>3.3.4-intel-2015b</br>3.3.4-intel-2016.01</br>3.3.5-foss-2016a</br>3.3.5-gompi-2016a</br>3.3.5-intel-2016.01</br>3.3.5-intel-2016a</br>3.3.5-intel-2017.00</br>3.3.5-intel-2017a</br>3.3.6-foss-2017a</br>3.3.6-gompi-2017a</br>3.3.6-gompi-2017b</br>3.3.6-intel-2017a</br>3.3.7-gompi-2018a</br>3.3.7-GCC-6.3.0-2.27 | `-S-`</br>`-S-`</br>`US-`</br>`US-`</br>`USA`</br>`-SA`</br>`-SA`</br>`USA`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`USA`</br>`-SA`</br>`-S-`</br>`USA`</br>`-SA`</br>`USA`</br>`-SA`</br>`-SA` |
| fftw2 | 2.1.5-gcc</br>2.1.5-icc | `--A`</br>`--A` |
| fftw2-mpi | 2.1.5-gcc</br>2.1.5-icc | `--A`</br>`--A` |
| fftw3 | 3.3.3-gcc</br>3.3.3-icc | `--A`</br>`--A` |
| fftw3-mpi | 3.3.3-gcc</br>3.3.3-icc | `--A`</br>`--A` |
| FIAT | 1.6.0-intel-2015b-Python-2.7.9</br>1.6.0-intel-2015b-Python-2.7.11</br>1.6.0-intel-2016.01-Python-2.7.9 | `-S-`</br>`-S-`</br>`-S-` |
| fixesproto | 5.0</br>5.0-foss-2015g</br>5.0-foss-2016a</br>5.0-intel-2016a | `-SA`</br>`-S-`</br>`-S-`</br>`-S-` |
| Flask | 0.12.2-Py-3.6 | `-S-` |
| flex | 2.5.35-intel-2015b</br>2.5.38-GCC-4.8.3</br>2.5.39</br>2.5.39-foss-2015b</br>2.5.39-foss-2015g</br>2.5.39-foss-2016a</br>2.5.39-intel-2015b</br>2.5.39-GCCcore-4.9.3</br>2.5.39-GCC-4.9.3</br>2.5.39-GCC-4.9.3-binutils-2.25</br>2.5.39-GCC-5.1.0-binutils-2.25</br>2.6.0</br>2.6.0-intel-2017a</br>2.6.0-GCCcore-5.3.0</br>2.6.0-GCCcore-5.4.0</br>2.6.3</br>2.6.3-GCCcore-6.3.0</br>2.6.4 | `-SA`</br>`-S-`</br>`-SA`</br>`-S-`</br>`-SA`</br>`-SA`</br>`--A`</br>`--A`</br>`--A`</br>`--A`</br>`--A`</br>`USA`</br>`-SA`</br>`--A`</br>`--A`</br>`USA`</br>`-SA`</br>`USA` |
| FLTK | 1.3.2</br>1.3.2-intel-2015b</br>1.3.4 | `--A`</br>`-S-`</br>`-SA` |
| fontconfig | 2.11.1</br>2.11.1-foss-2015b</br>2.11.1-intel-2015b</br>2.11.94-intel-2017.00</br>2.12.1-libpng-1.6.29</br>2.12.1-GCCcore-6.3.0-libpng-1.6.29</br>2.13.0-libpng-1.6.34 | `USA`</br>`-S-`</br>`-S-`</br>`-S-`</br>`USA`</br>`-SA`</br>`-SA` |
| fontsproto | 2.1.3</br>2.1.3-foss-2015g</br>2.1.3-foss-2016a</br>2.1.3-intel-2016a</br>2.1.3-intel-2017a | `-SA`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-` |
| Forge | 5.1-43967</br>5.7</br>6.0.5</br>6.0.6</br>6.1.2</br>7.0</br>7.0.1</br>7.0.2</br>7.0.3</br>7.0.4</br>7.0.5</br>7.0.5-test</br>7.0.6</br>7.1</br>18.2.3 | `-SA`</br>`--A`</br>`-SA`</br>`-SA`</br>`-SA`</br>`-S-`</br>`--A`</br>`-SA`</br>`-SA`</br>`-SA`</br>`-SA`</br>`--A`</br>`-SA`</br>`-SA`</br>`-S-` |
| foss | 2015b</br>2015e</br>2015g</br>2016.04</br>2016a</br>2017a</br>2017b</br>2018a | `US-`</br>`US-`</br>`USA`</br>`-SA`</br>`-SA`</br>`USA`</br>`-SA`</br>`-SA` |
| FOX | 1.6.51-foss-2015g | `-S-` |
| FreeFem++ | 3.45-intel-2015b | `-S-` |
| freeglut | 3.0.0-intel-2017a</br>3.0.0-intel-2017a-Mesa-18.1.3 | `-SA`</br>`-S-` |
| freetype | 2.5.3</br>2.5.3-foss-2015b</br>2.5.3-foss-2015g</br>2.5.3-intel-2015b</br>2.5.5-intel-2015b</br>2.6.2-intel-2016a</br>2.6.2-intel-2017.00</br>2.6.3</br>2.6.3-foss-2016a</br>2.6.3-intel-2016a</br>2.7.1-libpng-1.6.29</br>2.8</br>2.9.1-libpng-1.6.34 | `-SA`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-SA`</br>`-S-`</br>`-S-`</br>`USA`</br>`-SA`</br>`-SA` |
| FriBidi | 1.0.2 | `-SA` |
| gast | 0.2.0-Py-3.6 | `-S-` |
| gatk | 2.6-4 | `--A` |
| GATK | 2.6-5-Java-1.7.0_79</br>3.5-Java-1.7.0_79</br>4.0.2.1-Java-1.8.0_144</br>4.0.3.0-Java-1.8.0_144 | `US-`</br>`-S-`</br>`-SA`</br>`-S-` |
| gcc | 4.8.1 | `--A` |
| GCC | 4.4.7-system</br>4.7.0</br>4.8.3</br>4.9.3</br>4.9.3-2.25</br>4.9.3-binutils-2.25</br>4.9.3-tf</br>5.1.0-binutils-2.25</br>5.1.1-knc</br>5.3.0-2.25</br>5.3.0-2.26</br>5.3.1-snapshot-20160419-2.25</br>5.4.0-2.26</br>6.3.0-2.27</br>6.4.0-2.28</br>7.1.0-2.28</br>8.1.0-2.30 | `USA`</br>`--A`</br>`-SA`</br>`USA`</br>`-SA`</br>`USA`</br>`-SA`</br>`USA`</br>`-S-`</br>`-S-`</br>`-SA`</br>`-S-`</br>`-S-`</br>`USA`</br>`-S-`</br>`USA`</br>`-S-` |
| GCCcore | 4.9.3</br>5.1.1-knf</br>5.3.0</br>5.3.1-snapshot-20160419</br>5.4.0</br>6.3.0</br>6.4.0</br>7.1.0</br>8.1.0 | `-SA`</br>`-S-`</br>`-SA`</br>`-S-`</br>`-SA`</br>`USA`</br>`USA`</br>`USA`</br>`-SA` |
| GDAL | 1.9.2-foss-2015g</br>2.0.2-intel-2017.00</br>2.1.0-foss-2015g</br>2.1.0-GCC-6.3.0-2.27</br>2.1.0-GNU-5.1.0-2.25-intel-2015b</br>2.1.3-Python-2.7.13</br>2.3.2-GCC-6.3.0-2.27-Py-2.7 | `--A`</br>`-S-`</br>`--A`</br>`--A`</br>`-S-`</br>`USA`</br>`-S-` |
| Gdk-Pixbuf | 2.32.3</br>2.35.1 | `-S-`</br>`--A` |
| GEOS | 3.5.0</br>3.5.0-foss-2015g</br>3.6.1-Python-2.7.13</br>3.7.0-GCC-6.3.0-2.27-Py-2.7 | `-SA`</br>`-S-`</br>`USA`</br>`-S-` |
| gettext | .0.19.2</br>0.19.2</br>0.19.2-foss-2015g</br>0.19.2-intel-2015b</br>0.19.4</br>0.19.6</br>0.19.6-foss-2016a</br>0.19.6-intel-2017.00</br>0.19.8</br>0.19.8.1 | `--A`</br>`-SA`</br>`-SA`</br>`-S-`</br>`USA`</br>`-S-`</br>`-SA`</br>`--A`</br>`USA`</br>`USA` |
| gflags | 2.1.2 | `--A` |
| Ghostscript | 9.21-intel-2017a | `-SA` |
| gimkl | 2.11.5 | `--A` |
| gimpi | 2.11.5 | `--A` |
| git | 2.17.0-GCC-6.3.0-2.27</br>2.18.0 | `--A`</br>`-S-` |
| GL2PS | 1.4.0-intel-2017a | `-SA` |
| GLib | 2.40.0</br>2.40.0-foss-2015g</br>2.40.0-intel-2015b</br>2.52.0</br>2.56.1</br>2.57.1 | `USA`</br>`-S-`</br>`-S-`</br>`USA`</br>`--A`</br>`-SA` |
| glibc | 2.14</br>2.17</br>2.19 | `-S-`</br>`-S-`</br>`-SA` |
| GLM | 0.9.7.2-intel-2017a | `-SA` |
| GLOBUS | globus | `--A` |
| globus | globus | `-S-` |
| glog | 0.3.4 | `--A` |
| GLPK | 4.61-intel-2017a | `-SA` |
| glproto | 1.4.16-foss-2015g</br>1.4.17-foss-2016a</br>1.4.17-intel-2016a</br>1.4.17-intel-2017a | `-S-`</br>`-S-`</br>`-S-`</br>`-S-` |
| GMP | 5.0.5</br>5.0.5-foss-2015b</br>5.0.5-foss-2015g</br>5.0.5-intel-2015b</br>6.0.0a</br>6.0.0a-intel-2015b</br>6.0.0a-GNU-4.9.3-2.25</br>6.0.0a-GNU-5.1.0-2.25</br>6.1.0-foss-2016a</br>6.1.0-intel-2015b</br>6.1.0-intel-2017.00</br>6.1.0-GCC-4.9.3-2.25</br>6.1.1</br>6.1.1-foss-2017a</br>6.1.1-intel-2017a</br>6.1.2 | `-SA`</br>`-S-`</br>`-SA`</br>`-S-`</br>`-SA`</br>`--A`</br>`-S-`</br>`-S-`</br>`--A`</br>`-SA`</br>`--A`</br>`-S-`</br>`USA`</br>`-S-`</br>`-SA`</br>`USA` |
| GNU | 4.9.3-2.25</br>5.1.0-2.25</br>5.1.0-2.25-intel-2015b</br>6.3.0-2.27 | `USA`</br>`USA`</br>`-S-`</br>`-SA` |
| gnuplot | 4.6.5</br>5.0.6-intel-2017a</br>5.0.6-GCC-6.3.0-2.27</br>5.2.3</br>5.2.4-GCC-6.3.0-2.27 | `--A`</br>`-S-`</br>`-S-`</br>`--A`</br>`-S-` |
| Go | 1.11.1 | `-S-` |
| GObject-Introspection | 1.47.1</br>1.52.0</br>1.56.1 | `-S-`</br>`-SA`</br>`-SA` |
| gompi | 2015b</br>2015e</br>2015g</br>2016.04</br>2016a</br>2017a</br>2017b</br>2018a | `US-`</br>`US-`</br>`USA`</br>`-SA`</br>`-SA`</br>`USA`</br>`-SA`</br>`-SA` |
| gperf | 3.0.4-foss-2015g</br>3.0.4-foss-2016a</br>3.0.4-intel-2016a</br>3.0.4-intel-2017a</br>3.1 | `-S-`</br>`-S-`</br>`-S-`</br>`-SA`</br>`-S-` |
| gperftools | 2.7-GCC-6.3.0-2.27 | `-SA` |
| GPI-2 | 1.1.1-gompi-2015e</br>1.1.1-gompi-2015e-MPI | `-S-`</br>`-S-` |
| gpi2 | 1.0.2</br>1.1.0</br>1.1.1 | `--A`</br>`--A`</br>`--A` |
| grace | 5.1.23</br>5.1.25-intel-2015b</br>5.1.25-intel-2017a | `--A`</br>`-S-`</br>`--A` |
| Graph500 | 3.0.0-foss-2018a</br>3.0.0-intel-2018a</br>3.0.0rc1-foss-2016a | `-SA`</br>`-SA`</br>`-S-` |
| GraphicsMagick | 1.3.25-intel-2017a | `-SA` |
| GROMACS | 4.6.7-foss-2015g-hybrid-single-PLUMED</br>5.0.4-foss-2015e-hybrid-single-PLUMED</br>5.0.4-foss-2015g-hybrid-single</br>5.0.4-foss-2015g-hybrid-single-PLUMED</br>5.0.4-ictce-7.3.5-hybrid-single</br>5.1.2-foss-2015g-hybrid-single-PLUMED</br>5.1.2-intel-2015b-hybrid-single-cuda</br>5.1.2-intel-2015b-hybrid-single-CUDA-7.5-PLUMED-2.2.1</br>5.1.2-intel-2015b-hybrid-single-CUDA-7.5-PLUMED-2.2.1-test</br>5.1.2-intel-2016a-hybrid</br>5.1.4-foss-2016a-hybrid-single-PLUMED</br>5.1.4-foss-2016a-hybrid-single-PLUMED-v2</br>2016.4-intel-2017c-hybrid-single-PLUMED</br>2016.4-intel-2017c-hybrid-single-PLUMED-2.4.1</br>2016.5-intel-2017b</br>2018.1-intel-2017c-hybrid-single-PLUMED</br>2018-intel-2017b | `-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`--A`</br>`--A`</br>`--A`</br>`--A`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-SA`</br>`-S-`</br>`-SA` |
| grpcio | 1.9.1-Py-3.6 | `-S-` |
| gsl | 1.16-gcc</br>1.16-icc | `--A`</br>`--A` |
| GSL | 1.16-intel-2015b</br>1.16-intel-2016.01</br>2.1-foss-2016a</br>2.1-intel-2015b</br>2.3-foss-2017a</br>2.3-intel-2017a</br>2.4-intel-2017c</br>2.5-intel-2017c</br>2.5-GCC-6.3.0-2.27 | `-SA`</br>`--A`</br>`-S-`</br>`--A`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-` |
| GST-plugins-base | 1.6.4 | `--A` |
| GStreamer | 1.6.4 | `--A` |
| GTK+ | 2.24.28</br>2.24.30 | `-S-`</br>`--A` |
| guile | 1.8.8</br>1.8.8-foss-2015b</br>1.8.8-foss-2015g</br>1.8.8-foss-2016a</br>1.8.8-foss-2017a</br>1.8.8-intel-2015b | `-SA`</br>`-S-`</br>`-S-`</br>`-SA`</br>`-S-`</br>`-SA` |
| gupc | 4.8.0.3 | `--A` |
| gzip | 1.6</br>1.6-foss-2015g</br>1.6-foss-2016a</br>1.6-intel-2015b | `-SA`</br>`-SA`</br>`-SA`</br>`-SA` |
| h5py | 2.4.0-ictce-7.3.5-Python-2.7.9-serial</br>2.7.0-intel-2017a-Python-2.7.13-base</br>2.7.1-Py-2.7</br>2.7.1-Py-3.6 | `-S-`</br>`-SA`</br>`-SA`</br>`-SA` |
| Hadoop | 2.8.0-native | `-S-` |
| HarfBuzz | 1.1.3</br>1.3.1</br>1.7.6</br>1.8.1</br>1.8.1-GCC-6.3.0-2.27 | `-S-`</br>`-SA`</br>`--A`</br>`-S-`</br>`-S-` |
| Harminv | 1.4-intel-2015b | `-S-` |
| HDF5 | 1.8.13-foss-2015g</br>1.8.13-intel-2015b</br>1.8.13-intel-2015b-no-mpi</br>1.8.13-intel-2016.01</br>1.8.14-ictce-7.3.5-serial</br>1.8.15-patch1-foss-2015b</br>1.8.16-foss-2015g</br>1.8.16-foss-2016a</br>1.8.16-foss-2016a-serial</br>1.8.16-intel-2015b</br>1.8.16-intel-2015b-threadsafe</br>1.8.16-intel-2016.01</br>1.8.16-intel-2017.00</br>1.8.17-intel-2017a</br>1.8.18-foss-2017a-serial</br>1.8.18-intel-2017a-serial</br>1.10.0-patch1-intel-2016.01-mic</br>1.10.0-patch1-intel-2017a</br>1.10.0-patch1-intel-2017b-mic-parallel</br>1.10.1-foss-2017a</br>1.10.1-foss-2017a-serial</br>1.10.1-intel-2017b-serial</br>1.10.1-iomkl-2017b</br>1.10.1-GCC-6.3.0-2.27-serial | `-S-`</br>`US-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`US-`</br>`-S-`</br>`-SA`</br>`--A`</br>`USA`</br>`-S-`</br>`--A`</br>`-S-`</br>`USA`</br>`-S-`</br>`-SA`</br>`-S-`</br>`USA`</br>`-S-`</br>`-S-`</br>`-S-`</br>`--A`</br>`-S-`</br>`-SA` |
| hdf5 | 1.8.11</br>1.8.13 | `--A`</br>`--A` |
| hdf5-parallel | 1.8.11</br>1.8.11-gcc</br>1.8.13</br>1.8.13-gcc</br>1.8.13-gcc49 | `--A`</br>`--A`</br>`--A`</br>`--A`</br>`--A` |
| help2man | 1.47.4</br>1.47.4-GCCcore-6.3.0 | `-SA`</br>`-SA` |
| horovod | 0.11.3-Py-3.6 | `--A` |
| hpg-aligner | 1.0.0 | `--A` |
| hpg-fastq | 1.0.0 | `--A` |
| hpg-variant | 1.0.0 | `--A` |
| HPL | 2.1-foss-2015b</br>2.1-intel-2015b | `-S-`</br>`-S-` |
| html5lib | 0.9999999-Py-3.6</br>1.0.1-Py-3.6 | `-S-`</br>`-S-` |
| HTSlib | 1.6-intel-2017a</br>1.8-intel-2017a | `-S-`</br>`-S-` |
| hwloc | 1.5-GCC-4.4.7-system</br>1.11.0</br>1.11.0-GNU-4.9.3-2.25</br>1.11.0-GNU-5.1.0-2.25</br>1.11.1-iccifort-2015.3.187-GNU-4.9.3-2.25</br>1.11.2-GCC-4.9.3-2.25</br>1.11.3-GCC-5.3.0-2.26</br>1.11.4-iccifort-2017.1.132-GCC-5.4.0-2.26</br>1.11.5-GCC-6.3.0-2.27</br>1.11.6-GCC-6.3.0-2.27</br>1.11.7-GCC-6.3.0-2.27</br>1.11.7-GCC-7.1.0-2.28</br>1.11.7-PGI-18.5-GCC-6.3.0-2.27 | `-S-`</br>`-SA`</br>`USA`</br>`USA`</br>`-SA`</br>`-SA`</br>`-SA`</br>`-SA`</br>`USA`</br>`-SA`</br>`USA`</br>`US-`</br>`-S-` |
| HyperLoom | 0.9 | `-S-` |
| hypermesh | 12.0.110 | `--A` |
| HyperWorks | 13.0 | `-S-` |
| hyperworks | 13.0 | `--A` |
| Hypre | 2.10.0b-intel-2015b</br>2.10.0b-intel-2016.01</br>2.10.1-intel-2015b</br>2.11.1-intel-2017a | `-S-`</br>`-S-`</br>`-S-`</br>`-S-` |
| icc | 2013.5.192-GCC-4.8.3</br>2015.3.187</br>2015.3.187-GNU-4.9.3-2.25</br>2015.3.187-GNU-5.1.0-2.25</br>2016.1.150</br>2016.1.150-GCC-4.9.3</br>2016.1.150-GCC-4.9.3-2.25</br>2017.0.098-GCC-5.4.0-2.26</br>2017.1.132-GCC-5.4.0-2.26</br>2017.1.132-GCC-6.3.0-2.27</br>2017.4.196-GCC-6.3.0-2.27</br>2017.4.196-GCC-6.4.0-2.28</br>2017.5.239-GCC-6.3.0-2.27</br>2017.7.259-GCC-6.3.0-2.27</br>2018.1.163-GCC-6.4.0-2.28</br>2018.3.222-GCC-8.1.0-2.30</br>2019.0.117-GCC-6.3.0-2.27 | `-S-`</br>`-S-`</br>`-SA`</br>`USA`</br>`-S-`</br>`-S-`</br>`-SA`</br>`-SA`</br>`USA`</br>`USA`</br>`-S-`</br>`USA`</br>`-SA`</br>`-SA`</br>`-SA`</br>`-SA`</br>`-S-` |
| iccifort | 2013.5.192-GCC-4.8.3</br>2015.3.187</br>2015.3.187-GNU-4.9.3-2.25</br>2015.3.187-GNU-5.1.0-2.25</br>2016.1.150</br>2016.1.150-GCC-4.9.3</br>2016.1.150-GCC-4.9.3-2.25</br>2017.0.098-GCC-5.4.0-2.26</br>2017.1.132-GCC-5.4.0-2.26</br>2017.1.132-GCC-6.3.0-2.27</br>2017.4.196-GCC-6.3.0-2.27</br>2017.4.196-GCC-6.4.0-2.28</br>2017.5.239-GCC-6.3.0-2.27</br>2017.7.259-GCC-6.3.0-2.27</br>2018.1.163-GCC-6.4.0-2.28</br>2018.3.222-GCC-8.1.0-2.30</br>2019.0.117-GCC-6.3.0-2.27 | `-S-`</br>`-S-`</br>`-SA`</br>`USA`</br>`-S-`</br>`-S-`</br>`-SA`</br>`-SA`</br>`USA`</br>`USA`</br>`-S-`</br>`USA`</br>`-SA`</br>`-SA`</br>`-SA`</br>`-SA`</br>`-S-` |
| ictce | 7.3.5</br>8.3.5 | `-S-`</br>`-S-` |
| idna | 2.7-Py-2.7 | `-S-` |
| ifort | 2013.5.192-GCC-4.8.3</br>2015.3.187</br>2015.3.187-GNU-4.9.3-2.25</br>2015.3.187-GNU-5.1.0-2.25</br>2016.1.150</br>2016.1.150-GCC-4.9.3</br>2016.1.150-GCC-4.9.3-2.25</br>2017.0.098-GCC-5.4.0-2.26</br>2017.1.132-GCC-5.4.0-2.26</br>2017.1.132-GCC-6.3.0-2.27</br>2017.4.196-GCC-6.3.0-2.27</br>2017.4.196-GCC-6.4.0-2.28</br>2017.5.239-GCC-6.3.0-2.27</br>2017.7.259-GCC-6.3.0-2.27</br>2018.1.163-GCC-6.4.0-2.28</br>2018.3.222-GCC-8.1.0-2.30</br>2019.0.117-GCC-6.3.0-2.27 | `-S-`</br>`-S-`</br>`-SA`</br>`USA`</br>`-S-`</br>`-S-`</br>`-SA`</br>`-SA`</br>`USA`</br>`USA`</br>`-S-`</br>`USA`</br>`-SA`</br>`-SA`</br>`-SA`</br>`-SA`</br>`-S-` |
| iimpi | 5.5.0-GCC-4.8.3</br>7.3.5</br>7.3.5-GNU-5.1.0-2.25</br>8.1.5-GCC-4.9.3-2.25</br>8.3.5</br>2016.00-GCC-4.9.3</br>2016.01-GCC-4.9.3</br>2016.01-GCC-4.9.3-2.25</br>2017.00-GCC-5.4.0-2.26</br>2017a</br>2017b</br>2017c</br>2018.03</br>2018a</br>2019.01 | `-S-`</br>`-S-`</br>`USA`</br>`-SA`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-SA`</br>`-SA`</br>`USA`</br>`USA`</br>`-SA`</br>`-SA`</br>`-SA`</br>`-S-` |
| imkl | 11.0.5.192-iimpi-5.5.0-GCC-4.8.3</br>11.2.3.187</br>11.2.3.187-gimpi-2.11.5</br>11.2.3.187-iimpi-7.3.5</br>11.2.3.187-iimpi-7.3.5-GNU-5.1.0-2.25</br>11.2.3.187-iompi-2015.03</br>11.3.0.109-iimpi-2016.00-GCC-4.9.3</br>11.3.1.150-iimpi-8.1.5-GCC-4.9.3-2.25</br>11.3.1.150-iimpi-8.3.5</br>11.3.1.150-iimpi-2016.00-GCC-4.9.3</br>11.3.1.150-iimpi-2016.01-GCC-4.9.3-2.25</br>2017.0.098-iimpi-2017.00-GCC-5.4.0-2.26</br>2017.1.132-iimpi-2017a</br>2017.1.132-iompi-2017a</br>2017.1.132-iompi-2017a-2.0.1</br>2017.3.196-iimpi-2017b</br>2017.4.239-iimpi-2017b</br>2017.4.239-iimpi-2017c</br>2017.4.239-iompi-2017b</br>2018.1.163-iimpi-2018a</br>2018.3.222-iimpi-2018.03</br>2019.0.117-iimpi-2019.01 | `-S-`</br>`-S-`</br>`--A`</br>`-S-`</br>`USA`</br>`-S-`</br>`-S-`</br>`-SA`</br>`-S-`</br>`-S-`</br>`-SA`</br>`-SA`</br>`USA`</br>`-SA`</br>`--A`</br>`USA`</br>`-SA`</br>`-SA`</br>`-S-`</br>`-SA`</br>`-SA`</br>`-S-` |
| impi | 4.1.1.036</br>4.1.1.036-iccifort-2013.5.192-GCC-4.8.3</br>5.0.3.048</br>5.0.3.048-iccifort-2015.3.187</br>5.0.3.048-iccifort-2015.3.187-GNU-5.1.0-2.25</br>5.0.3.048-GCC-4.9.3</br>5.1.2.150-iccifort-2016.1.150</br>5.1.2.150-iccifort-2016.1.150-GCC-4.9.3</br>5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25</br>2017.0.098-iccifort-2017.0.098-GCC-5.4.0-2.26</br>2017.1.132-iccifort-2017.1.132-GCC-6.3.0-2.27</br>2017.3.196-iccifort-2017.4.196-GCC-6.3.0-2.27</br>2017.3.196-iccifort-2017.4.196-GCC-6.4.0-2.28</br>2017.3.196-PGI-17.9-GCC-6.3.0-2.27</br>2017.4.239-iccifort-2017.5.239-GCC-6.3.0-2.27</br>2017.4.239-iccifort-2017.7.259-GCC-6.3.0-2.27</br>2018.1.163-iccifort-2018.1.163-GCC-6.4.0-2.28</br>2018.3.222-iccifort-2018.3.222-GCC-8.1.0-2.30</br>2019.0.117-iccifort-2019.0.117-GCC-6.3.0-2.27 | `--A`</br>`-S-`</br>`--A`</br>`-S-`</br>`USA`</br>`--A`</br>`-S-`</br>`-S-`</br>`-SA`</br>`-SA`</br>`USA`</br>`-S-`</br>`USA`</br>`--A`</br>`-SA`</br>`-SA`</br>`-SA`</br>`-SA`</br>`-S-` |
| inputproto | 2.3</br>2.3.1-foss-2016a</br>2.3.1-intel-2016a</br>2.3-foss-2015g</br>2.3-intel-2015b | `-SA`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-` |
| Inspector | 2016_update1 | `-S-` |
| inspector_xe | 2013.5</br>2015.1.2.379161 | `--A`</br>`--A` |
| intel | 13.5.192</br>14.0.1</br>15.2.164</br>15.3.187</br>2014.06</br>2015b</br>2016.00</br>2016.01</br>2016a</br>2017.00</br>2017a</br>2017b</br>2017c</br>2018.03</br>2018a</br>2019.01 | `--A`</br>`--A`</br>`--A`</br>`--A`</br>`-S-`</br>`USA`</br>`-S-`</br>`-SA`</br>`-SA`</br>`-SA`</br>`USA`</br>`USA`</br>`-SA`</br>`-SA`</br>`-SA`</br>`-S-` |
| intelpcm | 2.6 | `--A` |
| intltool | 0.51.0 | `-S-` |
| iomkl | 2017a</br>2017b | `-SA`</br>`-S-` |
| iompi | 2015.03</br>2017.01</br>2017a</br>2017a-2.0.1</br>2017b | `-S-`</br>`-S-`</br>`-SA`</br>`--A`</br>`-S-` |
| IOR | 3.0.1-foss-2016a-mpiio | `-S-` |
| ipaddress | 1.0.22-Py-2.7 | `-S-` |
| ipm | 0.983-icc-impi | `--A` |
| ipp | 9.0.1.150</br>13.5.192</br>14.0.1</br>15.2.164</br>15.3.187</br>2017.1.132-GCC-6.3.0-2.27 | `-S-`</br>`--A`</br>`--A`</br>`--A`</br>`--A`</br>`-S-` |
| ISL | 0.14-GNU-5.1.0-2.25</br>0.15</br>0.15-GCC-4.9.3-2.25</br>0.15-GNU-4.9.3-2.25 | `-S-`</br>`-SA`</br>`-S-`</br>`-S-` |
| isort | 4.2.15-Python-2.7.13-base | `-SA` |
| ispc | 1.6.0</br>1.9.1 | `-S-`</br>`-SA` |
| itac | 8.1.4.045</br>9.0.3.051</br>9.1.2.024 | `--A`</br>`--A`</br>`-S-` |
| itsdangerous | 0.24-Py-3.6 | `-S-` |
| Jansson | 2.11 | `-SA` |
| JasPer | 1.900.1</br>1.900.1-intel-2015b</br>2.0.12-intel-2017a</br>2.0.14-GCC-6.3.0-2.27 | `--A`</br>`-S-`</br>`USA`</br>`-S-` |
| java | 1.7 | `--A` |
| Java | 1.7.0_79</br>1.8.0_51</br>1.8.0_72</br>1.8.0_112</br>1.8.0_121</br>1.8.0_144</br>1.9.0+181 | `USA`</br>`USA`</br>`US-`</br>`-SA`</br>`USA`</br>`-SA`</br>`-SA` |
| Jinja2 | 2.10-Py-2.7</br>2.10-Py-3.6 | `-S-`</br>`-S-` |
| JOE | 4.2 | `-SA` |
| JUnit | 4.11-Java-1.7.0_79</br>4.12-Java-1.8.0_121 | `-S-`</br>`--A` |
| kbproto | 1.0.6</br>1.0.6-foss-2015g</br>1.0.6-intel-2015b</br>1.0.7</br>1.0.7-foss-2016a</br>1.0.7-intel-2016a | `-SA`</br>`-S-`</br>`-S-`</br>`-SA`</br>`-S-`</br>`-S-` |
| Keras | 2.0.5-Tensorflow-1.1.0-CUDA-7.5.18-Python-3.6.1</br>2.0.5-Tensorflow-1.1.0-CUDA-8.0.44-Python-3.6.1</br>2.0.5-Tensorflow-1.1.0-Python-3.6.1</br>2.0.5-Tensorflow-1.2.0-Python-3.6.1</br>2.0.5-Tensorflow-1.3.0-intel-2017b-mkl-Python-3.6.1</br>2.0.5-Theano-1.2.0-Python-3.6.1</br>2.0.8-Tensorflow-1.1.0-CUDA-8.0.44-Python-3.6.1</br>2.1.2-Tensorflow-1.1.0-CUDA-8.0.44-Python-3.6.1</br>2.1.2-Tensorflow-1.2.0-Python-3.6.1</br>2.1.2-Tensorflow-1.2.1-Python-3.6.1</br>2.1.2-Tensorflow-1.6.0rc0-Python-3.6.1</br>2.1.4-Py-3.6-Tensorflow-1.6.0rc0</br>2.1.4-Py-3.6-Tensorflow-1.6.0rc0-CUDA-9.0.176</br>2.1.4-Py-3.6-Theano-1.0.1 | `--A`</br>`--A`</br>`--A`</br>`-S-`</br>`-S-`</br>`-SA`</br>`--A`</br>`--A`</br>`-S-`</br>`--A`</br>`-S-`</br>`-S-`</br>`--A`</br>`-S-` |
| lam | 7.1.4-icc | `--A` |
| LAMMPS | 16Mar2018-intel-2017a</br>17Jan2018-foss-2017a</br>17Jan2018-foss-2017a-CUDA</br>17Jan2018-intel-2017a</br>17Jan2018-intel-2017a-MIC</br>22Jun2018-foss-2017a</br>22Jun2018-intel-2017a</br>22Sep2017-intel-2017a</br>23Oct2017-intel-2017a</br>24Jul2017-intel-2017a</br>28Jun14-intel-2015b | `-S-`</br>`-S-`</br>`--A`</br>`-SA`</br>`-S-`</br>`-S-`</br>`-SA`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-` |
| lammps | 28Jun14 | `--A` |
| LAPACK | 3.7.1-gompi-2017a | `-S-` |
| LAPACKE | 3.5.0-LAPACK-3.5.0 | `-S-` |
| latexcodec | 1.0.5-Py-3.6 | `-SA` |
| LevelDB | 1.18 | `--A` |
| libarchive | 3.3.2 | `-SA` |
| libc | 2.14-6.3.0 | `-S-` |
| libcerf | 1.5 | `-S-` |
| libctl | 3.2.2-intel-2015b | `-S-` |
| libdrm | 2.4.27</br>2.4.27-foss-2015g</br>2.4.67-intel-2016a</br>2.4.68-foss-2016a</br>2.4.68-intel-2016a</br>2.4.75</br>2.4.76 | `-SA`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`USA`</br>`USA` |
| libepoxy | 1.4.3 | `-S-` |
| libevent | 2.1.8 | `-SA` |
| libffi | 3.0.5</br>3.0.13</br>3.0.13-foss-2015b</br>3.0.13-foss-2015g</br>3.0.13-intel-2015b</br>3.1-foss-2015b</br>3.1-intel-2015b</br>3.1-intel-2016.01</br>3.1-GNU-5.1.0-2.25</br>3.2.1</br>3.2.1-foss-2016a</br>3.2.1-foss-2017a</br>3.2.1-intel-2017.00</br>3.2.1-intel-2017a | `--A`</br>`-SA`</br>`-S-`</br>`-S-`</br>`-SA`</br>`-S-`</br>`-SA`</br>`--A`</br>`-S-`</br>`USA`</br>`-SA`</br>`-S-`</br>`-S-`</br>`-SA` |
| libfontenc | 1.1.3</br>1.1.3-foss-2015g</br>1.1.3-foss-2016a</br>1.1.3-intel-2016a | `-SA`</br>`-S-`</br>`-S-`</br>`-S-` |
| libgd | 2.2.3</br>2.2.4</br>2.2.4-intel-2017a</br>2.2.4-intel-2017b</br>2.2.4-GCC-6.3.0-2.27</br>2.2.5 | `-S-`</br>`-S-`</br>`-S-`</br>`-SA`</br>`-SA`</br>`-SA` |
| libgdiplus | 3.12</br>3.12-intel-2016.01</br>3.12-GCC-4.4.7-system | `-SA`</br>`-S-`</br>`-S-` |
| libglade | 2.6.4 | `-S-` |
| libGLU | 9.0.0</br>9.0.0-foss-2015g | `USA`</br>`-S-` |
| libICE | 1.0.9</br>1.0.9-foss-2015g</br>1.0.9-intel-2015b | `-SA`</br>`-S-`</br>`-S-` |
| libICU | 59_1</br>61.1</br>62.1-GCC-6.3.0-2.27 | `-S-`</br>`-S-`</br>`-S-` |
| Libint | 1.1.4-foss-2015b</br>1.1.4-gompi-2015b</br>1.1.4-intel-2015b</br>1.1.6-intel-2017a</br>1.1.6-GCC-6.3.0-2.27 | `-S-`</br>`-S-`</br>`US-`</br>`-S-`</br>`-S-` |
| libjpeg-turbo | 1.3.1-foss-2015b</br>1.3.1-intel-2015b</br>1.4.0</br>1.4.0-foss-2015g</br>1.4.0-intel-2015b</br>1.4.1-foss-2015b</br>1.4.2-intel-2017.00</br>1.5.1</br>1.5.3</br>2.0.0-GCC-6.3.0-2.27 | `-S-`</br>`-S-`</br>`-SA`</br>`-S-`</br>`-S-`</br>`US-`</br>`-S-`</br>`USA`</br>`-SA`</br>`-S-` |
| LIBLINEAR | 2.11-intel-2017a | `-SA` |
| libmatheval | 1.1.8</br>1.1.8-foss-2015b</br>1.1.8-foss-2015g</br>1.1.8-foss-2016a</br>1.1.8-intel-2015b</br>1.1.11</br>1.1.11-foss-2017a</br>1.1.11-intel-2015b | `-SA`</br>`-S-`</br>`-S-`</br>`-SA`</br>`-SA`</br>`-S-`</br>`-S-`</br>`--A` |
| libMesh | 0.9.5-intel-2016.01 | `-S-` |
| libpciaccess | 0.13.1</br>0.13.1-foss-2015g</br>0.13.4-foss-2016a</br>0.13.4-intel-2016a | `-SA`</br>`-S-`</br>`-S-`</br>`-S-` |
| libpng | 1.6.9-intel-2015b</br>1.6.12</br>1.6.12-foss-2015b</br>1.6.12-foss-2015g</br>1.6.12-intel-2015b</br>1.6.12-intel-2016.01</br>1.6.16-intel-2015b</br>1.6.17-foss-2015b</br>1.6.21-foss-2016a</br>1.6.21-intel-2016a</br>1.6.21-intel-2017.00</br>1.6.29</br>1.6.29-GCCcore-6.3.0</br>1.6.34 | `US-`</br>`-SA`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`US-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`USA`</br>`-S-`</br>`-SA` |
| libpthread-stubs | 0.3</br>0.3-foss-2015g</br>0.3-foss-2016a</br>0.3-intel-2015b</br>0.3-intel-2016a</br>0.4 | `-SA`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`USA` |
| libreadline | 6.2-intel-2015b</br>6.3</br>6.3-foss-2015b</br>6.3-foss-2015g</br>6.3-foss-2016a</br>6.3-foss-2017a</br>6.3-gimkl-2.11.5</br>6.3-gompi-2015e</br>6.3-ictce-7.3.5</br>6.3-intel-2015b</br>6.3-intel-2016.01</br>6.3-intel-2017.00</br>6.3-intel-2017a</br>7.0</br>7.0-GCCcore-6.3.0 | `US-`</br>`USA`</br>`US-`</br>`USA`</br>`-SA`</br>`-S-`</br>`--A`</br>`-S-`</br>`-S-`</br>`USA`</br>`-SA`</br>`--A`</br>`-SA`</br>`USA`</br>`-SA` |
| LibreSSL | 2.1.6-intel-2017b | `-S-` |
| librsync | 2.0.2 | `-S-` |
| libSM | 1.2.2</br>1.2.2-foss-2015g</br>1.2.2-intel-2015b | `-SA`</br>`-S-`</br>`-S-` |
| libsmm | 2015-11-10 | `-S-` |
| libsndfile | 1.0.28</br>1.0.28-intel-2017a | `-S-`</br>`USA` |
| LIBSVM | 3.22-intel-2017a | `-SA` |
| LibTIFF | 4.0.3</br>4.0.3-intel-2015b</br>4.0.7</br>4.0.7-GCC-6.3.0-2.27 | `-SA`</br>`-S-`</br>`USA`</br>`-S-` |
| libtool | 2.4.2</br>2.4.2-foss-2015b</br>2.4.2-foss-2015g</br>2.4.2-intel-2015b</br>2.4.6</br>2.4.6-foss-2016a</br>2.4.6-intel-2015b</br>2.4.6-intel-2017.00</br>2.4.6-intel-2017a</br>2.4.6-GCC-6.3.0-2.27</br>2.4.6-GNU-4.9.3-2.25</br>2.4.6-GNU-5.1.0-2.25 | `-SA`</br>`-S-`</br>`-SA`</br>`-S-`</br>`-SA`</br>`-SA`</br>`--A`</br>`--A`</br>`-SA`</br>`-SA`</br>`--A`</br>`--A` |
| libunistring | 0.9.3</br>0.9.3-foss-2015b</br>0.9.3-foss-2015g</br>0.9.3-foss-2016a</br>0.9.3-intel-2015b</br>0.9.6-foss-2017a | `-SA`</br>`-S-`</br>`-S-`</br>`-SA`</br>`-SA`</br>`-S-` |
| libunwind | 1.1-GCC-5.4.0-2.26</br>1.2</br>1.2.1 | `-S-`</br>`-SA`</br>`-SA` |
| LibUUID | 1.0.3 | `-SA` |
| libuv | 1.20.3 | `-S-` |
| libX11 | 1.6.2-foss-2015g-Python-2.7.9</br>1.6.2-intel-2015b-Python-2.7.9</br>1.6.2-Python-2.7.8</br>1.6.2-Python-2.7.9</br>1.6.3</br>1.6.3-foss-2016a</br>1.6.3-intel-2016a</br>1.6.5-intel-2017a | `-S-`</br>`-S-`</br>`-S-`</br>`-SA`</br>`-SA`</br>`-S-`</br>`-S-`</br>`-S-` |
| libXau | 1.0.8</br>1.0.8-foss-2015g</br>1.0.8-foss-2016a</br>1.0.8-intel-2015b</br>1.0.8-intel-2016a</br>1.0.8-intel-2017a | `-SA`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-` |
| libxc | 2.2.0-foss-2015b</br>2.2.0-gompi-2015b</br>2.2.1-intel-2015b</br>2.2.2-intel-2017a</br>3.0.0</br>3.0.0-intel-2017a</br>3.0.0-GCC-6.3.0-2.27</br>4.0.2-intel-2017a</br>4.1.0-intel-2017a | `-S-`</br>`-S-`</br>`US-`</br>`-S-`</br>`-SA`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-` |
| libxcb | 1.10-Python-2.7.8</br>1.11.1</br>1.11.1-foss-2016a</br>1.11.1-intel-2016a</br>1.11-foss-2015g-Python-2.7.9</br>1.11-intel-2015b-Python-2.7.9</br>1.11-Python-2.7.9 | `-S-`</br>`-SA`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-SA` |
| libXdamage | 1.1.4-foss-2015g-Python-2.7.9</br>1.1.4-foss-2016a</br>1.1.4-intel-2016a</br>1.1.4-intel-2017a | `-S-`</br>`-S-`</br>`-S-`</br>`-S-` |
| libXdmcp | 1.1.2</br>1.1.2-foss-2015g</br>1.1.2-foss-2016a</br>1.1.2-intel-2015b</br>1.1.2-intel-2016a | `-SA`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-` |
| libXext | 1.3.2-Python-2.7.8</br>1.3.3</br>1.3.3-foss-2015g</br>1.3.3-foss-2015g-Python-2.7.9</br>1.3.3-foss-2016a</br>1.3.3-intel-2015b</br>1.3.3-intel-2016a | `-S-`</br>`-SA`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-` |
| libXfixes | 5.0.1</br>5.0.1-foss-2015g</br>5.0.1-foss-2016a</br>5.0.1-intel-2016a | `-SA`</br>`-S-`</br>`-S-`</br>`-S-` |
| libXfont | 1.5.1-foss-2015g-Python-2.7.9</br>1.5.1-foss-2016a-freetype-2.6.3</br>1.5.1-intel-2016a</br>1.5.1-intel-2016a-freetype-2.6.3</br>1.5.1-intel-2017a</br>1.5.1-Python-2.7.9 | `-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-SA` |
| libXft | 2.3.2-intel-2015b | `-S-` |
| libXinerama | 1.1.3</br>1.1.3-intel-2015b | `--A`</br>`-S-` |
| libxml2 | 2.9.2</br>2.9.2-foss-2015b</br>2.9.2-foss-2015g-Python-2.7.9</br>2.9.2-intel-2015b</br>2.9.3-foss-2016a</br>2.9.3-intel-2016a</br>2.9.4</br>2.9.4-Python-2.7.13</br>2.9.8-GCC-6.3.0-2.27 | `-S-`</br>`US-`</br>`-S-`</br>`-SA`</br>`-SA`</br>`--A`</br>`USA`</br>`--A`</br>`-S-` |
| libXrender | 0.9.8</br>0.9.8-intel-2015b</br>0.9.9 | `-S-`</br>`-S-`</br>`-SA` |
| libxslt | 1.1.28-intel-2015b</br>1.1.29 | `-S-`</br>`-SA` |
| libxsmm | 1.6.4-intel-2017a</br>1.7.1</br>1.7.1-GCC-6.3.0-2.27 | `-S-`</br>`-S-`</br>`-S-` |
| libXt | 1.1.4-foss-2015g-libX11-1.6.2</br>1.1.4-intel-2015b-libX11-1.6.2</br>1.1.4-libX11-1.6.2</br>1.1.5</br>1.1.5-foss-2015g</br>1.1.5-intel-2017a-libX11-1.6.5 | `-S-`</br>`-S-`</br>`-SA`</br>`--A`</br>`-S-`</br>`-S-` |
| libyaml | 0.1.6-intel-2015b</br>0.1.7 | `-S-`</br>`-SA` |
| libzip | 1.2.0 | `-S-` |
| LicenseChecker | 1.0 | `-S-` |
| likwid | 3.1.1-icc</br>3.1.1-mic</br>3.1.2-gcc</br>3.1.2-icc</br>3.1.2-mic</br>4.1.2-gcc</br>4.1.2-intel | `--A`</br>`--A`</br>`--A`</br>`--A`</br>`--A`</br>`-S-`</br>`-S-` |
| LLVM | 3.7.1-foss-2015g</br>3.7.1-intel-2016a</br>3.8.0-foss-2016a</br>3.8.0-intel-2016a</br>3.8.1-intel-2017a</br>3.9.0-intel-2017.00</br>4.0.0-GCC-6.3.0-2.27</br>5.0.0-GCC-6.3.0-2.27</br>6.0.0-Py-2.7</br>6.0.1-GCC-6.3.0-2.27 | `-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`USA`</br>`-S-`</br>`USA`</br>`-SA`</br>`-SA`</br>`-SA` |
| LMDB | 0.9.18 | `--A` |
| LMGC90 | 2017.rc1-GCC-6.3.0-2.27 | `-S-` |
| Lmod | .6.4.2</br>.7.0.6</br>7.2.2</br>7.3.28</br>7.4.4</br>7.7.7 | `--A`</br>`--A`</br>`-SA`</br>`--A`</br>`--A`</br>`-SA` |
| loom | 0.9-Py-3.6 | `-S-` |
| lsdyna | 7.x.x | `--A` |
| LSMS | 3_rev237-foss-2015g</br>3_rev237-foss-2016a | `-S-`</br>`-S-` |
| lsprepost | 4.2 | `--A` |
| Lua | 5.1.4-8</br>.5.1.4-8</br>5.3.4 | `-SA`</br>`--A`</br>`-S-` |
| lux | 1.3.1 | `--A` |
| lxml | 3.4.4-intel-2015b-Python-2.7.9</br>3.8.0-Python-2.7.13-base</br>4.1.1-Py-2.7</br>4.1.1-Py-3.6 | `-S-`</br>`-SA`</br>`-SA`</br>`-SA` |
| M4 | 1.4.16-foss-2015g</br>1.4.16-intel-2015b</br>1.4.17</br>1.4.17-foss-2016a</br>1.4.17-intel-2015b</br>1.4.17-intel-2017.00</br>1.4.17-GCCcore-4.9.3</br>1.4.17-GCCcore-5.3.0</br>1.4.17-GCCcore-5.4.0</br>1.4.17-GCC-4.9.3</br>1.4.17-GCC-4.9.3-binutils-2.25</br>1.4.17-GCC-5.1.0-binutils-2.25</br>1.4.17-GNU-4.9.3-2.25</br>1.4.17-GNU-5.1.0-2.25</br>1.4.18</br>1.4.18-GCCcore-6.3.0</br>1.4.18-GCCcore-6.4.0 | `-S-`</br>`--A`</br>`USA`</br>`-SA`</br>`--A`</br>`--A`</br>`--A`</br>`--A`</br>`--A`</br>`--A`</br>`--A`</br>`--A`</br>`--A`</br>`--A`</br>`USA`</br>`USA`</br>`-S-` |
| magma | 1.1.0-mic</br>1.3.0-mic | `--A`</br>`--A` |
| make | 3.82</br>3.82-intel-2015b</br>4.2.1 | `-SA`</br>`US-`</br>`-S-` |
| makedepend | 1.0.4</br>1.0.4-foss-2015g</br>1.0.5-foss-2016a</br>1.0.5-intel-2016a | `-SA`</br>`-S-`</br>`-S-`</br>`-S-` |
| Mako | 1.0.4-Python-2.7.13</br>1.0.6-Python-2.7.13</br>1.0.7-Py-2.7 | `--A`</br>`USA`</br>`-S-` |
| MAP | 4.2</br>5.0.1 | `-S-`</br>`-S-` |
| marc | 2011</br>2013.1 | `--A`</br>`--A` |
| Marc | 2013.1.0 | `-S-` |
| Markdown | 2.6.11-Py-3.6 | `-S-` |
| MarkupSafe | 1.0-Py-2.7</br>1.0-Py-3.6 | `-S-`</br>`-S-` |
| MATIO | 1.5.2-intel-2017a | `-SA` |
| MATLAB | 2013a-EDU</br>2015a-COM</br>2015a-EDU</br>2015b-COM</br>2015b-EDU</br>2015b-EDU-test</br>2018a-EDU</br>R2013a-COM</br>R2013a-EDU</br>R2014a-COM</br>R2014a-EDU | `US-`</br>`-S-`</br>`-S-`</br>`-SA`</br>`-SA`</br>`--A`</br>`-S-`</br>`--A`</br>`--A`</br>`--A`</br>`--A` |
| matplotlib | 1.4.3-intel-2015b-Python-2.7.9</br>1.5.1-Python-2.7.13-freetype-2.6.3</br>2.0.2-Python-2.7.13-base</br>2.0.2-Python-3.6.1-libpng-1.6.29</br>2.1.1-Py-2.7</br>2.1.1-Py-3.6 | `-S-`</br>`-SA`</br>`-SA`</br>`-SA`</br>`-SA`</br>`-SA` |
| Maven | 3.3.9 | `USA` |
| maxwell | 3.0 | `--A` |
| mdtest | 1.9.3-intel-2017a | `-S-` |
| Meep | 1.3-intel-2015b | `-S-` |
| memoryscape | 3.4 | `--A` |
| mercurial | 2.9.1 | `--A` |
| Mercurial | 3.5-Python-2.7.9</br>3.7.3-foss-2015g-Python-2.7.9</br>4.4.2-Py-2.7</br>4.7-Py-2.7 | `-S-`</br>`USA`</br>`-S-`</br>`-S-` |
| Mesa | 11.0.8-foss-2015g-Python-2.7.9</br>11.2.1-foss-2016a</br>12.0.2-intel-2017a</br>17.0.2-intel-2017a</br>17.2.6-foss-2017a</br>17.2.6-intel-2017a</br>18.1.3-intel-2017a</br>18.1.3-GCC-6.3.0-2.27 | `-S-`</br>`-S-`</br>`USA`</br>`USA`</br>`-S-`</br>`-S-`</br>`-SA`</br>`--A` |
| METIS | 5.1.0</br>5.1.0-intel-2015b</br>5.1.0-intel-2016.01</br>5.1.0-intel-2016.01-32bitIDX</br>5.1.0-intel-2017.00</br>5.1.0-intel-2017a | `-SA`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`USA` |
| MIKE | 2014</br>2016</br>2016-SP2</br>2016-SP2-test</br>2017</br>MIKE-old | `-SA`</br>`-SA`</br>`-SA`</br>`-S-`</br>`-SA`</br>`--A` |
| mkl | 13.5.192</br>14.0.1</br>15.2.164</br>15.3.187</br>2017.4.239</br>2017.4.239-GCC-6.3.0-2.27</br>2018.1.163 | `--A`</br>`--A`</br>`--A`</br>`--A`</br>`-SA`</br>`-S-`</br>`-S-` |
| MLD2P4 | 2.0-rc4-GCC-4.9.3-2.25 | `--A` |
| modflow-2005 | 1.11.00 | `--A` |
| modflow-nwt | 1.0.9</br>1.0.9-aquaveo | `--A`</br>`--A` |
| Molden | 5.7-intel-2017b | `-S-` |
| Molpro | 2010.1-patch-57-intel2015b | `-S-` |
| molpro | 2010.1-p45-intel | `--A` |
| mono | 3.2.3</br>3.12.1 | `--A`</br>`--A` |
| Mono | 3.12.1-GCC-4.4.7-system</br>4.2.2.10-intel-2016.01</br>4.6.2.16</br>4.8.1.0</br>5.0.0.100 | `-S-`</br>`-S-`</br>`--A`</br>`--A`</br>`USA` |
| monotonic | 1.5-Py-2.7 | `-S-` |
| monty | 1.0.2-Py-3.6 | `-SA` |
| moreutils | 0.62 | `US-` |
| motif | 2.3.4-foss-2015g-libX11-1.6.2</br>2.3.4-intel-2015b-libX11-1.6.2</br>2.3.7 | `-S-`</br>`-S-`</br>`--A` |
| MotionCor2 | 1.0.5-CUDA-8.0.44 | `--A` |
| MPC | 1.0.2 | `-S-` |
| MPFR | 3.1.4-intel-2017a</br>3.1.5 | `USA`</br>`-S-` |
| MPI-LIBLINEAR | 2.1-1-intel-2017a | `-SA` |
| mpi.net | 1.0.0</br>1.0.0-impi</br>1.0.0-mono-3.12.1 | `--A`</br>`--A`</br>`--A` |
| mpi4py | 2.0.0-intel-2017a-Python-2.7.13-base</br>3.0.0-foss-2017a-Python-2.7.13</br>3.0.0-Py-2.7</br>3.0.0-Py-3.6 | `-SA`</br>`-S-`</br>`-SA`</br>`-SA` |
| MPI_NET | 1.2.0-gompi-2015e</br>1.2.0-intel-2016.01 | `-S-`</br>`-S-` |
| MPICH | 3.2.1-GCC-6.3.0-2.27</br>3.2-GCC-4.9.3-2.25</br>3.2-GCC-5.3.0-2.25</br>3.2-GCC-5.3.1-snapshot-20160419-2.25 | `-SA`</br>`--A`</br>`-S-`</br>`-S-` |
| mpmath | 1.0.0-Py-3.6 | `-SA` |
| MPT | 2.12 | `-S-` |
| MUMPS | 5.0.2-intel-2017a-parmetis | `-S-` |
| mvapich2 | 1.9-gcc</br>1.9-gcc46</br>1.9-icc | `--A`</br>`--A`</br>`--A` |
| MVAPICH2 | 2.1-iccifort-2015.3.187-GNU-5.1.0-2.25</br>2.1-GCC-4.4.7-system</br>2.1-GNU-5.1.0-2.25 | `-S-`</br>`-S-`</br>`-S-` |
| mxml | 2.9 | `--A` |
| namd | 2.8 | `--A` |
| NAMD | 2.9-mpi | `-S-` |
| nano | 2.9.6 | `--A` |
| NASM | 2.11.05</br>2.11.05-foss-2015b</br>2.11.05-foss-2015g</br>2.11.05-intel-2015b</br>2.11.06-intel-2015b</br>2.11.08-foss-2015b</br>2.11.08-intel-2017.00</br>2.12.02</br>2.13.03 | `-SA`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`US-`</br>`-S-`</br>`USA`</br>`-SA` |
| nastran | 2013.1.1 | `--A` |
| NCCL | 2.1.4 | `--A` |
| ncurses | 5.9</br>5.9-foss-2015b</br>5.9-foss-2015g</br>5.9-gimkl-2.11.5</br>5.9-gompi-2015e</br>5.9-ictce-7.3.5</br>5.9-intel-2015b</br>5.9-intel-2016.01</br>5.9-GCC-4.9.3-2.25</br>5.9-GNU-4.9.3-2.25</br>6.0</br>6.0-foss-2016a</br>6.0-foss-2017a</br>6.0-intel-2016a</br>6.0-intel-2017.00</br>6.0-intel-2017a</br>6.0-GCCcore-6.3.0</br>6.1 | `-SA`</br>`US-`</br>`USA`</br>`--A`</br>`-S-`</br>`-S-`</br>`USA`</br>`-SA`</br>`--A`</br>`--A`</br>`USA`</br>`-SA`</br>`-S-`</br>`-SA`</br>`--A`</br>`USA`</br>`USA`</br>`-SA` |
| netcdf | 4.2.1.1</br>4.3.0 | `--A`</br>`--A` |
| netCDF | 4.3.2-foss-2015g</br>4.3.2-intel-2015b</br>4.3.2-intel-2016.01</br>4.3.3.1-foss-2015b</br>4.3.3.1-intel-2017.00</br>4.4.0-intel-2017.00</br>4.4.1.1-intel-2017a</br>4.4.1-intel-2017a</br>4.6.1-iomkl-2017b</br>4.6.1-GCC-6.3.0-2.27 | `-S-`</br>`US-`</br>`-S-`</br>`US-`</br>`-S-`</br>`-S-`</br>`USA`</br>`USA`</br>`-S-`</br>`-S-` |
| netcdf-cxx | 4.2 | `--A` |
| netcdf-fortran | 4.2 | `--A` |
| netCDF-Fortran | 4.4.0-intel-2016.01</br>4.4.4-intel-2017a</br>4.4.4-iomkl-2017b | `-S-`</br>`USA`</br>`-S-` |
| netcdf-parallel | 4.3.0 | `--A` |
| Netgen | 6.0-beta-intel-2017a-Python-3.6.1 | `-S-` |
| nettle | 3.2-intel-2017a</br>3.3-foss-2017a</br>3.3-intel-2017a</br>3.3-GCC-6.3.0-2.27 | `USA`</br>`-S-`</br>`USA`</br>`--A` |
| networkx | 1.11-Python-2.7.13</br>2.1-Py-3.6 | `-SA`</br>`-SA` |
| ngsPipeline | 1.0.0 | `--A` |
| NLopt | 2.4.2</br>2.4.2-intel-2017a | `-S-`</br>`USA` |
| NodeJS | 6.10.1-foss-2016a | `-S-` |
| numactl | 2.0.9</br>2.0.10</br>2.0.10-iccifort-2015.3.187-GNU-4.9.3-2.25</br>2.0.10-GNU-4.9.3-2.25</br>2.0.10-GNU-5.1.0-2.25</br>2.0.11</br>2.0.11-GCCcore-5.4.0</br>2.0.11-GCCcore-6.3.0</br>2.0.11-GCC-4.9.3-2.25</br>2.0.11-GCC-5.3.0-2.26</br>2.0.11-GCC-6.3.0-2.27</br>2.0.11-GCC-7.1.0-2.28</br>2.0.11-PGI-18.5-GCC-6.3.0-2.27 | `--A`</br>`-SA`</br>`-SA`</br>`USA`</br>`USA`</br>`-SA`</br>`-SA`</br>`-SA`</br>`-SA`</br>`-SA`</br>`USA`</br>`US-`</br>`-S-` |
| numpy | 1.8.2-intel-2015b-Python-2.7.9</br>1.8.2-intel-2015b-Python-2.7.11</br>1.8.2-intel-2016.01-Python-2.7.9</br>1.8.2-Py-2.7</br>1.9.1-intel-2015b-Python-2.7.9</br>1.12.1-intel-2017a-Python-2.7.11</br>1.13.0-Python-2.7.13-base</br>1.13.3-Py-2.7</br>1.13.3-Py-3.6</br>1.14.2-Py-2.7-test | `-SA`</br>`-SA`</br>`-SA`</br>`-S-`</br>`-S-`</br>`--A`</br>`-SA`</br>`-SA`</br>`-SA`</br>`-SA` |
| NWChem | 6.3.revision2-2013-10-17-Python-2.7.8</br>6.5.revision26243-intel-2015b-2014-09-10-Python-2.7.8</br>6.6.revision27746-intel-2017a-2015-10-20-Python-2.7.13</br>6.6.revision27746-iomkl-2017a-2015-10-20-Python-2.7.13 | `-S-`</br>`-S-`</br>`-SA`</br>`-SA` |
| Octave | 3.8.2-foss-2015g</br>3.8.2-gimkl-2.11.5</br>3.8.2-intel-2015b</br>4.0.0-foss-2015g</br>4.0.1-gimkl-2.11.5</br>4.2.1-intel-2017a</br>4.2.1-intel-2017a-without-X11 | `-S-`</br>`--A`</br>`-S-`</br>`-SA`</br>`--A`</br>`-SA`</br>`-SA` |
| octave | .3.6.4</br>.hg-20130730 | `--A`</br>`--A` |
| Octopus | 8.2-intel-2017a-mpi | `-S-` |
| opari2 | 1.1.2-gcc</br>1.1.2-icc | `--A`</br>`--A` |
| OPARI2 | 1.1.4-intel-2015b</br>2.0</br>2.0.2 | `-S-`</br>`-SA`</br>`-S-` |
| OpenBabel | 2.4.1-Python-2.7.13 | `-SA` |
| OpenBLAS | 0.2.14-gompi-2015e-LAPACK-3.5.0</br>0.2.14-GNU-4.9.3-2.25-LAPACK-3.5.0</br>0.2.14-GNU-5.1.0-2.25-LAPACK-3.5.0</br>0.2.14-LAPACK-3.5.0</br>0.2.15-GCC-4.9.3-2.25-LAPACK-3.6.0</br>0.2.15-GCC-5.1.0-binutils-2.25-LAPACK-3.6.0</br>0.2.15-GCC-5.1.0-binutils-2.25-LAPACK-3.6.0-gompi-2016a</br>0.2.18-GCC-5.3.0-2.26-LAPACK-3.6.0</br>0.2.19-GCC-5.4.0-2.26-LAPACK-3.6.0</br>0.2.19-GCC-5.4.0-2.26-LAPACK-3.7.0</br>0.2.19-GCC-6.3.0-2.27-LAPACK-3.7.0</br>0.2.20-GCC-6.3.0-2.27</br>0.2.20-GCC-6.4.0-2.28 | `US-`</br>`USA`</br>`USA`</br>`-S-`</br>`USA`</br>`--A`</br>`--A`</br>`-SA`</br>`-S-`</br>`-S-`</br>`USA`</br>`USA`</br>`-S-` |
| OpenCL-builder | 2015 | `-S-` |
| opencl-rt | 4.5.0.8 | `--A` |
| OpenCL-runtime | 15.1</br>16.1.1</br>16.1.2 | `-S-`</br>`--A`</br>`-SA` |
| OpenCL-sdk | 7.0.0.2568 | `-SA` |
| opencl-sdk | 4.6.0.92 | `--A` |
| OpenCoarrays | 1.0.0-GNU-5.1.0-2.25</br>1.0.1-GNU-5.1.0-2.25</br>1.4.0-GCC-5.3.0-2.25</br>1.4.0-GCC-5.3.1-snapshot-20160419-2.25</br>1.8.10-GCC-6.3.0-2.27 | `-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-SA` |
| OpenCV | 2.4.9-intel-2015b</br>3.0.0-intel-2015b</br>3.1.0 | `-S-`</br>`-S-`</br>`--A` |
| opencv-python | 3.3.0.10-Python-3.6.1 | `-SA` |
| OpenDX | 4.4.4-foss-2015g | `-S-` |
| openfoam | 2.2.1-gcc481-openmpi1.6.5-DP</br>2.2.1-gcc481-openmpi1.6.5-SP</br>2.2.1-icc-impi4.1.1.036-DP</br>2.2.1-icc-openmpi1.6.5-DP</br>2.2.2-icc-openmpi1.8.1-DP | `--A`</br>`--A`</br>`--A`</br>`--A`</br>`--A` |
| OpenFOAM | 2.2.2-intel-2015b</br>2.3.0-intel-2015b</br>3.0.0-intel-2016.01</br>4.1-intel-2017a</br>5.0-intel-2017a | `US-`</br>`US-`</br>`-S-`</br>`USA`</br>`-SA` |
| OpenJPEG | 2.3.0 | `-S-` |
| openmpi | 1.6.5-gcc</br>1.6.5-gcc46</br>1.6.5-icc</br>1.8.1-gcc</br>1.8.1-gcc46</br>1.8.1-icc | `--A`</br>`--A`</br>`--A`</br>`--A`</br>`--A`</br>`--A` |
| OpenMPI | 1.8.6-GCC-4.4.7-system</br>1.8.8-iccifort-2015.3.187-GNU-4.9.3-2.25</br>1.8.8-GNU-4.9.3-2.25</br>1.8.8-GNU-5.1.0-2.25</br>1.10.2-GCC-4.9.3-2.25</br>1.10.2-GCC-5.3.0-2.26</br>1.10.7-GCC-6.3.0-2.27</br>1.10.7-GCC-6.3.0-2.27-noPBS</br>1.10.7-GCC-7.1.0-2.28</br>1.10.7-PGI-18.5-GCC-6.3.0-2.27</br>2.0.1-iccifort-2017.1.132-GCC-5.4.0-2.26</br>2.0.1-iccifort-2017.1.132-GCC-6.3.0-2.27</br>2.0.2-GCC-6.3.0-2.27</br>2.1.0-GCC-6.3.0-2.27</br>2.1.1-GCC-6.3.0-2.27</br>3.0.0-GCC-6.3.0-2.27</br>3.0.1-GCC-6.3.0-2.27-nvidia</br>3.0.1-GCC-6.3.0-2.27-nvidia-RHEL6 | `US-`</br>`-SA`</br>`USA`</br>`-S-`</br>`USA`</br>`-SA`</br>`USA`</br>`-SA`</br>`US-`</br>`-S-`</br>`-SA`</br>`--A`</br>`USA`</br>`-SA`</br>`USA`</br>`USA`</br>`--A`</br>`--A` |
| openssh-x509 | 6.2p2 | `--A` |
| OpenSSL | 1.0.2n</br>1.0.2n-intel-2017b</br>1.1.0e-intel-2017b | `--A`</br>`-S-`</br>`-S-` |
| ORCA | 3_0_3-linux_x86-64</br>4.0.1.2</br>4_0_1-linux_x86-64 | `--A`</br>`-SA`</br>`-S-` |
| oscar-modules | 1.0.3 | `--A` |
| osm2pgsql | 0.92.0-intel-2017a | `-S-` |
| OSPRay | 1.3.0-intel-2017a</br>1.6.1-intel-2017a | `-SA`</br>`-S-` |
| OTF2 | 1.4-intel-2015b</br>2.0</br>2.0-intel-2015b-mic</br>2.1 | `-S-`</br>`-SA`</br>`-S-`</br>`-S-` |
| otf2 | 1.2.1-gcc</br>1.2.1-icc</br>1.4-gcc</br>1.4-icc | `--A`</br>`--A`</br>`--A`</br>`--A` |
| p4vasp | 0.3.30 | `-S-` |
| packaging | 17.1-Py-3.6 | `-SA` |
| palettable | 3.1.0-Py-3.6 | `-SA` |
| pandas | 0.22.0-Py-3.6 | `-SA` |
| Pango | 1.39.0</br>1.40.5</br>1.40.5-intel-2017a</br>1.42.1-GCC-6.3.0-2.27 | `-S-`</br>`-SA`</br>`-S-`</br>`-S-` |
| PAPI | 5.4.0-intel-2015b</br>5.4.0-mic</br>5.4.0-p-mic</br>5.4.3</br>5.4.3-intel-2015b-mic</br>5.4.3-pic</br>5.5.1 | `-S-`</br>`-S-`</br>`-S-`</br>`-SA`</br>`-S-`</br>`-S-`</br>`-S-` |
| papi | 5.3.0</br>5.3.2</br>5.3.2-mic</br>5.4.0</br>5.4.0-mic | `--A`</br>`--A`</br>`--A`</br>`--A`</br>`--A` |
| parallel | 20141122</br>20150322</br>20150322-GNU-5.1.0-2.25 | `--A`</br>`-S-`</br>`-S-` |
| paramiko | 2.4.1-Py-2.7 | `-S-` |
| ParaView | 5.0.0-binary</br>5.1.2-intel-2017a-mpi</br>5.4.0-intel-2017a-mpi-OSPRay</br>5.4.0-intel-2017a-mpi-OSPRay-OpenGL</br>5.4.0-intel-2017a-mpi-OSPRay-OpenGL2</br>5.4.0-intel-2017a-mpi-OSPRay-TEST</br>5.4.1-intel-2017a-mpi</br>5.5.2-intel-2017a-mpi-OSPRay | `-S-`</br>`USA`</br>`-SA`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-SA`</br>`-S-` |
| paraview | 4.0.1-gcc481-bullxmpi1.2.4.1-osmesa10.0 | `--A` |
| ParMETIS | 4.0.3-intel-2015b</br>4.0.3-intel-2016.01</br>4.0.3-intel-2017a | `-S-`</br>`-S-`</br>`-SA` |
| PatchELF | 0.9 | `-SA` |
| PCRE | 8.36-intel-2015b</br>8.36-intel-2016.01</br>8.37</br>8.37-foss-2015g</br>8.37-gimkl-2.11.5</br>8.37-intel-2016.01</br>8.39-intel-2017.00</br>8.40</br>8.42</br>8.42-GCC-6.3.0-2.27 | `-S-`</br>`-S-`</br>`-SA`</br>`-SA`</br>`--A`</br>`--A`</br>`-S-`</br>`USA`</br>`-SA`</br>`-S-` |
| PCRE2 | 10.22-intel-2017.00 | `-S-` |
| PDT | 3.18.1</br>3.24 | `-S-`</br>`-SA` |
| perfboost | 1.0 | `-S-` |
| perfcatcher | 1.0 | `-S-` |
| PerformanceReports | 5.1-43967</br>6.0.6</br>7.0.6</br>7.1 | `-S-`</br>`-SA`</br>`-SA`</br>`-SA` |
| PerfReports | 5.0.1 | `-S-` |
| PerfSuite | 1a5.3 | `-S-` |
| Perl | 5.16.3-intel-2015b</br>5.20.2-bare</br>5.24.0-GCC-4.9.3-2.25-bare</br>5.26.0-GCC-7.1.0-2.28-bare</br>5.26.1-foss-2017a</br>5.26.1-intel-2017a</br>5.26.1-intel-2017b</br>5.26.2-GCC-6.3.0-2.27 | `US-`</br>`-S-`</br>`--A`</br>`--A`</br>`-SA`</br>`-S-`</br>`-SA`</br>`--A` |
| pest | 13.0 | `--A` |
| petsc | 3.5.3-icc15-impi-mkl-dbg</br>3.5.3-icc15-impi-mkl-opt</br>3.5.3-icc15-impi-mkl-threads-dbg</br>3.5.3-icc15-impi-mkl-threads-opt</br>3.7.3-icc16-impi5-mkl-dbg</br>3.7.3-icc16-impi5-mkl-opt | `--A`</br>`--A`</br>`--A`</br>`--A`</br>`--A`</br>`--A` |
| PETSc | 3.6.1-intel-2015b-Python-2.7.9</br>3.6.1-intel-2016.01-Python-2.7.9</br>3.6.3-intel-2015b-Python-2.7.11</br>3.7.5-intel-2017a-it4i | `-S-`</br>`-S-`</br>`-S-`</br>`-SA` |
| PFFT | 1.0.8-alpha-intel-2017a | `-S-` |
| PGI | 15.7</br>16.10-GNU-4.9.3-2.25</br>17.9-GCC-6.3.0-2.27</br>18.5-GCC-6.3.0-2.27 | `-S-`</br>`-S-`</br>`-SA`</br>`-SA` |
| phono3py | 0.9.14-ictce-7.3.5-Python-2.7.9</br>1.11.13.35-intel-2015b-Python-2.7.9</br>1.11.13.35-intel-2017a-Python-2.7.13</br>1.11.13.35-Py-2.7</br>1.11.13.35-Py-2.7-test</br>1.12.7.46-Py-2.7</br>1.12.9.5-Py-2.7</br>1.13.3-Py-2.7</br>1.13.3-Py-3.6 | `-S-`</br>`-S-`</br>`-SA`</br>`-SA`</br>`-S-`</br>`--A`</br>`-SA`</br>`-S-`</br>`-S-` |
| phonopy | 1.11.6.7-intel-2015b-Python-2.7.9</br>1.11.6.7-intel-2015b-Python-2.7.11</br>1.11.12.5-intel-2015b-Python-2.7.9</br>1.11.12.5-Python-2.7.13-base</br>1.12.4.11-Py-2.7</br>1.12.6.66-Py-2.7</br>1.12.6.66-Py-3.6</br>1.13.2-Py-2.7</br>1.13.2-Py-3.6 | `-S-`</br>`--A`</br>`-S-`</br>`-SA`</br>`-SA`</br>`-SA`</br>`-SA`</br>`-S-`</br>`-S-` |
| PHREEQC | 3.3.12-12704-intel-2017b | `-SA` |
| picard | 1.117</br>1.119</br>2.1.0 | `--A`</br>`-S-`</br>`-S-` |
| pigz | 2.4-GCC-6.3.0-2.27 | `-SA` |
| Pillow | 3.2.0-Python-2.7.13-freetype-2.6.3</br>5.0.0-Py-3.6 | `-SA`</br>`-SA` |
| pixman | 0.32.6</br>0.32.6-foss-2015b</br>0.32.6-intel-2015b</br>0.34.0 | `-SA`</br>`-S-`</br>`-S-`</br>`USA` |
| pkg-config | 0.27.1</br>0.27.1-foss-2015b</br>0.27.1-foss-2015g</br>0.27.1-intel-2015b</br>0.29</br>0.29.1</br>0.29.1-foss-2016a</br>0.29.1-foss-2017a</br>0.29.1-intel-2016a</br>0.29.2</br>0.29-foss-2016a</br>0.29-intel-2016a | `-SA`</br>`-S-`</br>`-S-`</br>`-SA`</br>`-S-`</br>`USA`</br>`-S-`</br>`-S-`</br>`-S-`</br>`USA`</br>`-SA`</br>`-S-` |
| plasma | 2.6.0 | `--A` |
| Platypus | 20170509-Py-2.7 | `-S-` |
| pluggy | 0.6.0-Py-2.7</br>0.6.0-Py-3.6 | `-S-`</br>`-S-` |
| PLUMED | 2.1.3-foss-2015g</br>2.2.1-intel-2015b</br>2.3.0-foss-2016a</br>2.3.0-foss-2017a</br>2.3.5-intel-2017c</br>2.3b-foss-2015g</br>2.3b-foss-2016a</br>2.4.1-intel-2017c</br>2.4.2-intel-2017c | `-S-`</br>`--A`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-SA`</br>`-S-`</br>`-S-` |
| PLUTO | 4.2-intel-2017b-Python-2.7.14 | `-S-` |
| PostgreSQL | 9.6.9-Py-2.7</br>9.6.9-Py-2.7-Py-2.7 | `-SA`</br>`--A` |
| prace | 20160107-intel-2016.01 | `-S-` |
| PRACE | 20150630-intel-2015b</br>prace | `US-`</br>`--A` |
| PragTic | 0.1-GCC-5.3.0-2.25 | `-S-` |
| PrgEnv-gnu | 4.4.6</br>4.4.6-test</br>4.8.1 | `--A`</br>`--A`</br>`--A` |
| PrgEnv-intel | 13.5.192</br>14.0.1</br>15.0.3 | `--A`</br>`--A`</br>`--A` |
| PROJ | 4.8.0-foss-2015b</br>4.9.2-intel-2017.00</br>4.9.3-foss-2017a</br>4.9.3-intel-2017a | `US-`</br>`-S-`</br>`-S-`</br>`USA` |
| PROJ_4 | 4.9.2</br>4.9.2-foss-2015g | `-SA`</br>`-S-` |
| protobuf | 2.5.0</br>3.2.0-foss-2016a</br>3.2.0-GCC-7.1.0-2.28-Python-3.6.1</br>3.2.0-Python-3.6.1</br>3.3.0-foss-2017a</br>3.3.0-GCC-4.9.3-2.25</br>3.4.0-GCC-6.4.0-2.28-Python-3.6.1</br>3.4.0-GCC-7.1.0-2.28-Python-3.6.1</br>3.4.0-Py-3.6</br>3.5.1-Py-3.6 | `-S-`</br>`--A`</br>`-S-`</br>`-SA`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-SA`</br>`-SA` |
| protobuf-python | 3.2.0-GCC-7.1.0-2.28-Python-3.6.1</br>3.4.0-GCC-6.4.0-2.28-Python-3.6.1</br>3.4.0-Py-3.6</br>3.5.1-Py-3.6 | `-S-`</br>`-S-`</br>`-SA`</br>`-SA` |
| PSBLAS | 3.3.4-3-GCC-4.9.3-2.25 | `--A` |
| PSBLAS-ext | 1.0-4-GCC-4.9.3-2.25 | `--A` |
| psycopg2 | 2.7.4-Py-2.7 | `-SA` |
| pudb | 2017.1.4-Py-2.7</br>2017.1.4-Py-3.6 | `-S-`</br>`-S-` |
| pWord2Vec | 2018-01-25-intel-2017a | `-S-` |
| Py | 2.7</br>3.6 | `USA`</br>`-SA` |
| py4j | 0.10.6-Py-3.6 | `-S-` |
| pyasn1 | 0.4.4-Py-2.7 | `-S-` |
| pybtex | 0.21-Py-3.6 | `-SA` |
| PyCairo | 1.10.0-Python-2.7.13-base | `-S-` |
| pycparser | 2.18-Py-2.7 | `-S-` |
| PyDispatcher | 2.0.5-Py-3.6 | `-SA` |
| pydot | 1.2.4-Py-3.6 | `-S-` |
| pyFFTW | 0.10.4-Py-2.7</br>0.10.4-Py-3.6 | `-SA`</br>`-SA` |
| PyGObject | 2.28.6-Python-2.7.13-base | `-S-` |
| PyGTK | 2.24.0-Python-2.7.13-base | `-S-` |
| pylint | 1.7.2-Python-2.7.13-base | `-SA` |
| pymatgen | 2018.1.29-Py-3.6 | `-SA` |
| PyNaCl | 1.2.1-Py-2.7 | `-S-` |
| pyparsing | 2.2.0-Py-2.7</br>2.2.0-Py-3.6 | `-SA`</br>`-SA` |
| PyQt | 4.12-Py-3.6 | `-SA` |
| PyQt5 | 5.10-Py-3.6 | `-SA` |
| pyspark | 2.3.0-Py-3.6 | `-S-` |
| pytest | 3.3.2-Py-2.7</br>3.3.2-Py-3.6 | `-S-`</br>`-S-` |
| python | 2.7.5</br>2.7.6</br>3.3.2</br>3.3.5</br>3.4.2 | `--A`</br>`--A`</br>`--A`</br>`--A`</br>`--A` |
| Python | 2.7.8-intel-2015b</br>2.7.9</br>2.7.9-foss-2015g</br>2.7.9-gompi-2015e</br>2.7.9-ictce-7.3.5</br>2.7.9-intel-2015b</br>2.7.9-intel-2016.01</br>2.7.11-intel-2015b</br>2.7.11-intel-2017a</br>2.7.12-intel-2017a</br>2.7.13</br>2.7.13-base</br>2.7.14-base</br>2.7.14-GCC-6.3.0-2.27-base</br>2.7.15-base</br>3.5.1</br>3.5.2</br>3.5.2-foss-2016a</br>3.5.2-intel-2017.00</br>3.6.1</br>3.6.2-base</br>3.6.4-base</br>3.6.4-GCC-6.3.0-2.27-base</br>3.7.0-base | `-S-`</br>`-SA`</br>`USA`</br>`-S-`</br>`-S-`</br>`USA`</br>`-SA`</br>`-SA`</br>`-SA`</br>`--A`</br>`USA`</br>`-SA`</br>`-S-`</br>`USA`</br>`-SA`</br>`-S-`</br>`-S-`</br>`--A`</br>`--A`</br>`USA`</br>`-SA`</br>`-S-`</br>`-SA`</br>`--A` |
| python-dateutil | 2.6.1-Py-2.7</br>2.6.1-Py-3.6 | `-SA`</br>`-SA` |
| python-meep | 1.4.2-intel-2015b-Python-2.7.9-Meep-1.3 | `-S-` |
| pytz | 2017.3-Py-3.6 | `-SA` |
| PyWavelets | 0.5.2-Py-3.6 | `-SA` |
| PYXAID | 1.0 | `-S-` |
| PyYAML | 3.11-intel-2015b-Python-2.7.9</br>3.12-Py-2.7</br>3.12-Py-3.6</br>3.12-Python-2.7.13-base | `-S-`</br>`-SA`</br>`-SA`</br>`-SA` |
| pyzmq | 16.0.4-Py-2.7 | `-S-` |
| QBOX | r140b-foss-2016a | `-S-` |
| QCA | 2.1.0-foss-2015g | `-S-` |
| QEMU | 2.1.2-GCC-4.4.7-system</br>2.1.2-GCC-4.4.7-system-VDE2</br>2.9.0-GCC-4.4.7-system</br>2.9.0-GCC-4.4.7-system-VDE2</br>2.10.0-GCC-4.4.7-system</br>2.10.0-GCC-4.4.7-system-VDE2 | `US-`</br>`US-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-` |
| qemu | 2.1.0</br>2.1.0-vde2</br>2.1.2</br>2.1.2-vde2</br>2.9.0</br>2.9.0-vde2</br>2.10.0</br>2.10.0-vde2 | `--A`</br>`--A`</br>`--A`</br>`--A`</br>`--A`</br>`--A`</br>`--A`</br>`--A` |
| Qhull | 2015.2 | `-SA` |
| qrupdate | 1.1.2-intel-2017a | `-SA` |
| Qt | 4.8.6</br>4.8.6-foss-2015g</br>4.8.7 | `-SA`</br>`-S-`</br>`-SA` |
| Qt5 | 5.8.0-intel-2017a</br>5.8.0-GCC-6.3.0-2.27</br>5.11.1-GCC-6.3.0-2.27 | `-S-`</br>`USA`</br>`-SA` |
| QuantumESPRESSO | 5.4.0-foss-2015g</br>5.4.0-foss-2017a</br>5.4.0-intel-2017.00</br>6.0-intel-2017a</br>6.1-intel-2017a | `-S-`</br>`-S-`</br>`-SA`</br>`-S-`</br>`-SA` |
| Qwt | 6.1.2-foss-2015g | `-S-` |
| R | 3.0.1</br>3.1.1</br>3.1.1-intel-2015b</br>3.2.3-intel-2016.01</br>3.4.0-intel-2017a</br>3.4.0-intel-2017a-X11-20170314</br>3.4.2-foss-2017a</br>3.4.2-intel-2017a | `--A`</br>`--A`</br>`US-`</br>`-S-`</br>`-S-`</br>`USA`</br>`-S-`</br>`-S-` |
| Racket | 6.1.1-GNU-5.1.0-2.25 | `-S-` |
| racket | 6.0.1 | `--A` |
| ranger | 1.9.1-Py-3.6 | `-S-` |
| RapidJSON | 1.1.0-GCC-6.3.0-2.27 | `-S-` |
| redis | 4.0.11-GCC-6.3.0-2.27 | `-S-` |
| relion | 1.2</br>1.3 | `--A`</br>`--A` |
| RELION | 1.3-intel-2015b</br>2.1-foss-2017a-DP</br>2.1-foss-2017a-SP | `-S-`</br>`--A`</br>`--A` |
| renderproto | 0.11</br>0.11-intel-2015b | `-SA`</br>`-S-` |
| requests | 2.18.4-Py-3.6 | `-SA` |
| Rosetta | 3.10-intel-2017c | `-S-` |
| RStudio | 0.98.1103 | `-SA` |
| ruamel.yaml | 0.15.35-Py-3.6 | `-SA` |
| ruby | 2.0.0-p247 | `--A` |
| Ruby | 2.1.5-intel-2015b</br>2.3.1</br>2.3.3</br>2.4.2 | `-S-`</br>`-S-`</br>`-S-`</br>`-SA` |
| S4MPLE | 1.0.0 | `-S-` |
| samtools | 0.1.19 | `--A` |
| SAMtools | 1.3-foss-2015g</br>1.6-intel-2017a</br>1.8-intel-2017a | `-S-`</br>`-S-`</br>`-S-` |
| ScaLAPACK | 2.0.2-gompi-2015b-OpenBLAS-0.2.14-LAPACK-3.5.0</br>2.0.2-gompi-2015e-OpenBLAS-0.2.14-LAPACK-3.5.0</br>2.0.2-gompi-2015g-OpenBLAS-0.2.14-LAPACK-3.5.0</br>2.0.2-gompi-2016.04-OpenBLAS-0.2.18-LAPACK-3.6.0</br>2.0.2-gompi-2016a-OpenBLAS-0.2.15-LAPACK-3.6.0</br>2.0.2-gompi-2017a-OpenBLAS-0.2.19-LAPACK-3.7.0</br>2.0.2-gompi-2017b-OpenBLAS-0.2.20</br>2.0.2-gompi-2018a-OpenBLAS-0.2.20</br>2.0.2-OpenBLAS-0.2.14-LAPACK-3.5.0 | `US-`</br>`US-`</br>`USA`</br>`-SA`</br>`-SA`</br>`USA`</br>`-SA`</br>`-SA`</br>`-S-` |
| Scalasca | 2.3.1-foss-2016a</br>2.3.1-intel-2015b</br>2.4-GCC-6.3.0-2.27-MPICH | `--A`</br>`-S-`</br>`-S-` |
| ScientificPython | 2.9.4-foss-2015g-Python-2.7.9</br>2.9.4-intel-2015b-Python-2.7.9</br>2.9.4-intel-2015b-Python-2.7.11</br>2.9.4-intel-2016.01-Python-2.7.9 | `--A`</br>`-SA`</br>`-SA`</br>`-SA` |
| scikit-image | 0.12.3-Python-2.7.13</br>0.13.1-Py-3.6 | `-SA`</br>`-SA` |
| scikit-learn | 0.18.2-Python-3.6.1</br>0.19.1-Py-3.6 | `-SA`</br>`-SA` |
| Scipion | 1.0.1-Java-1.8.0_112-OpenMPI-1.10.2-GCC-5.3.0-2.26 | `-S-` |
| scipy | 0.19.1-Python-2.7.13-base</br>1.0.0-Py-2.7</br>1.0.0-Py-3.6 | `-SA`</br>`-SA`</br>`-SA` |
| scite | 3.4.3 | `--A` |
| SCons | 2.3.6-foss-2015g-Python-2.7.9</br>2.3.6-Py-2.7</br>2.3.6-Python-2.7.9</br>2.5.1-intel-2015b-Python-2.7.11</br>2.5.1-intel-2017a-Python-2.7.13</br>2.5.1-Python-2.7.13</br>3.0.0</br>3.0.0-intel-2017a-Python-2.7.13</br>3.0.1-Py-2.7 | `-SA`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-` |
| Score-P | 2.0.1-foss-2016a</br>3.0-intel-2015b</br>3.1-intel-2017a</br>4.1-GCC-6.3.0-2.27-MPICH | `--A`</br>`-S-`</br>`-S-`</br>`-S-` |
| SCOTCH | 5.1.12b_esmumps-foss-2015b</br>6.0.0_esmumps-intel-2015b</br>6.0.3-intel-2015b</br>6.0.3-intel-2016.01</br>6.0.4-intel-2015b</br>6.0.4-intel-2016.01</br>6.0.4-intel-2017a</br>6.0.5a-intel-2017a | `-S-`</br>`US-`</br>`US-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`USA`</br>`-SA` |
| SDE | 7.41.0 | `-S-` |
| seaborn | 0.8.1-Py-3.6 | `-SA` |
| seekpath | 1.5.0-Python-2.7.13-base | `-SA` |
| Sen2Cor | 2.3.1-Python-2.7.13 | `-S-` |
| SentinelToolboxes | 5.0.0 | `-S-` |
| Serf | 1.3.8</br>1.3.8-foss-2015g | `-S-`</br>`-SA` |
| Siesta | 4.1-b2-intel-2017a | `-SA` |
| singledispatch | 3.4.0.3-Py-2.7 | `-S-` |
| Singularity | 2.2.1-GCC-6.3.0-2.27</br>2.2.99-GCC-6.3.0-2.27-develop</br>2.3.1</br>2.3.2</br>2.4.2</br>2.4.4</br>2.5.1</br>2.6.0</br>3.0.0-GCC-6.3.0-2.27 | `USA`</br>`-S-`</br>`-SA`</br>`-SA`</br>`-SA`</br>`-SA`</br>`-SA`</br>`-S-`</br>`-S-` |
| Singularity-wrappers | master | `-S-` |
| SIONlib | 1.6.1-intel-2015b-tools</br>1.6.1-tools</br>1.7.1-foss-2017a | `-S-`</br>`-SA`</br>`-SA` |
| SIP | 4.19.6-Py-3.6 | `-SA` |
| six | 1.11.0-Py-2.7</br>1.11.0-Py-3.6 | `-SA`</br>`-SA` |
| SLEPc | 3.7.4-intel-2017a | `-SA` |
| snappy | 1.1.3 | `--A` |
| snpEff | 3.6 | `--A` |
| SnpEff | 4.1_G | `US-` |
| SnuCL | 1.3.3-gompi-2015e | `-S-` |
| Spack | default | `-SA` |
| Spark | 1.5.2</br>2.1.0</br>2.3.0 | `-S-`</br>`-S-`</br>`-SA` |
| sparsehash | 2.0.3-foss-2018a</br>2.0.3-GCCcore-6.4.0 | `-SA`</br>`-S-` |
| spatialindex | 1.8.5-foss-2015g | `-S-` |
| SpatiaLite | 4.3.0a | `--A` |
| spglib-python | 1.10.2.4-Py-3.6 | `-SA` |
| spGPU | master-GCC-4.9.3-2.25 | `--A` |
| SQLite | 3.8.8.1</br>3.8.8.1-foss-2015b</br>3.8.8.1-foss-2015g</br>3.8.8.1-foss-2016a</br>3.8.8.1-gompi-2015e</br>3.8.8.1-ictce-7.3.5</br>3.8.8.1-intel-2015b</br>3.8.8.1-intel-2016.01</br>3.8.8.1-GNU-5.1.0-2.25</br>3.9.2-foss-2016a</br>3.9.2-intel-2015b</br>3.9.2-intel-2017.00</br>3.13.0</br>3.13.0-intel-2017a</br>3.17.0</br>3.18.2-GCC-6.3.0-2.27</br>3.21.0</br>3.24.0</br>3.25.2-GCC-6.3.0-2.27 | `-SA`</br>`US-`</br>`USA`</br>`--A`</br>`-S-`</br>`-S-`</br>`USA`</br>`-SA`</br>`-S-`</br>`--A`</br>`-SA`</br>`--A`</br>`USA`</br>`-SA`</br>`USA`</br>`--A`</br>`USA`</br>`-SA`</br>`-S-` |
| sqsgenerator | 20180226-Py-3.6</br>20180823-Py-3.6 | `-SA`</br>`-S-` |
| squashfs-tools | 4.3 | `-SA` |
| Subversion | 1.8.16-foss-2015g</br>1.9.3 | `-SA`</br>`-S-` |
| SuiteSparse | 4.4.3-intel-2015b-ParMETIS-4.0.3</br>4.4.3-intel-2016.01-ParMETIS-4.0.3</br>4.4.5-intel-2015b-METIS-5.1.0</br>4.4.6-intel-2015b-ParMETIS-4.0.3</br>4.5.3-intel-2017.00-METIS-5.1.0</br>4.5.3-intel-2017a-ParMETIS-4.0.3</br>4.5.5-intel-2017a-METIS-5.1.0 | `-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-SA`</br>`-SA` |
| SUMO | 0.25.0-foss-2015g</br>0.26.0-foss-2015g</br>0.27.1-foss-2015g | `-S-`</br>`-S-`</br>`-S-` |
| SWIG | 2.0.12-intel-2015b-Python-2.7.9</br>2.0.12-Python-2.7.9</br>3.0.7-Python-2.7.9</br>3.0.12-GCC-6.3.0-2.27-Py-2.7</br>3.0.12-Python-2.7.13</br>3.0.12-Python-3.6.1 | `-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`USA`</br>`-S-` |
| sympy | 0.7.6.1-intel-2015b-Python-2.7.11</br>0.7.6-intel-2015b-Python-2.7.9</br>0.7.6-intel-2016.01-Python-2.7.9</br>1.1.1-Py-3.6 | `-S-`</br>`-S-`</br>`-S-`</br>`-SA` |
| Szip | 2.1</br>2.1.1-GCC-6.3.0-2.27</br>2.1-foss-2015b</br>2.1-foss-2015g</br>2.1-foss-2016a</br>2.1-ictce-7.3.5</br>2.1-intel-2015b</br>2.1-intel-2016.01</br>2.1-intel-2017.00</br>2.1-intel-2017a | `-SA`</br>`-S-`</br>`US-`</br>`-S-`</br>`-SA`</br>`-S-`</br>`USA`</br>`-SA`</br>`-S-`</br>`USA` |
| szip | 2.1 | `--A` |
| tabulate | 0.8.2-Py-3.6 | `-SA` |
| Tar | 1.29 | `-S-` |
| tbb | 4.3.5.187</br>4.4.2.152</br>13.5.192</br>14.0.1</br>15.2.164</br>15.3.187</br>2017.6.196 | `-S-`</br>`USA`</br>`--A`</br>`--A`</br>`--A`</br>`--A`</br>`-SA` |
| Tcl | 8.5.12</br>8.5.12-intel-2015b</br>8.6.3</br>8.6.3-foss-2015g</br>8.6.3-foss-2016a</br>8.6.3-gompi-2015e</br>8.6.3-ictce-7.3.5</br>8.6.3-intel-2015b</br>8.6.3-intel-2016.01</br>8.6.4</br>8.6.4-foss-2015b</br>8.6.4-foss-2016a</br>8.6.4-intel-2015b</br>8.6.4-intel-2017.00</br>8.6.5</br>8.6.5-intel-2017a</br>8.6.6</br>8.6.6-GCCcore-6.3.0</br>8.6.7-GCC-6.3.0-2.27 | `--A`</br>`US-`</br>`-SA`</br>`USA`</br>`--A`</br>`-S-`</br>`-S-`</br>`USA`</br>`-SA`</br>`--A`</br>`US-`</br>`--A`</br>`-SA`</br>`--A`</br>`--A`</br>`-SA`</br>`USA`</br>`-SA`</br>`--A` |
| tcl | 8.5.15 | `--A` |
| tcsh | 6.18.01-intel-2015b</br>6.19.00 | `US-`</br>`-SA` |
| tensorboard | 1.6.0-Py-3.6 | `-S-` |
| Tensorflow | 1.1.0</br>1.1.0-CUDA-7.5.18-Python-3.6.1</br>1.1.0-CUDA-8.0.44-Python-3.6.1</br>1.2.0-intel-2017b-mkl</br>1.2.0-GCC-7.1.0-2.28</br>1.2.1</br>1.3.0</br>1.3.0-intel-2017b-mkl</br>1.6.0rc0</br>1.6.0rc0-CUDA-9.0.176-Python-3.6.1</br>1.6.0rc0-Py-3.6</br>1.6.0rc0-Py-3.6-CUDA-9.0.176 | `-SA`</br>`--A`</br>`--A`</br>`-S-`</br>`-S-`</br>`--A`</br>`-S-`</br>`-S-`</br>`-S-`</br>`--A`</br>`-S-`</br>`--A` |
| tensorflow-tensorboard | 1.5.1-Py-3.6 | `-S-` |
| termcolor | 1.1.0-Py-3.6 | `-S-` |
| Theano | 0.9.0-Python-3.6.1</br>1.0.1-Py-3.6 | `-SA`</br>`-S-` |
| Tix | 8.1.4-intel-2017a | `-S-` |
| tk | 8.5.15 | `--A` |
| Tk | 8.5.12</br>8.5.12-intel-2015b</br>8.6.3</br>8.6.4-foss-2015b-no-X11</br>8.6.4-foss-2016a-no-X11</br>8.6.4-intel-2015b-no-X11</br>8.6.4-intel-2017.00-no-X11</br>8.6.4-no-X11</br>8.6.5</br>8.6.5-intel-2017a</br>8.6.6</br>8.6.7-GCC-6.3.0-2.27 | `--A`</br>`US-`</br>`-SA`</br>`US-`</br>`--A`</br>`-SA`</br>`--A`</br>`--A`</br>`--A`</br>`-SA`</br>`USA`</br>`--A` |
| tmux | 2.3 | `-SA` |
| Togl | 1.7-intel-2017a | `-S-` |
| toolz | 0.9.0-Py-3.6 | `-SA` |
| tornado | 4.5.3-Py-2.7 | `-S-` |
| totalview | 8.12</br>8.13 | `--A`</br>`--A` |
| TotalView | 8.15.4-6-linux-x86-64</br>2018.1.12</br>2018.2.6 | `-S-`</br>`-S-`</br>`-S-` |
| trilinos | 11.2.3-gcc-openmpi-mkl-dbg</br>11.2.3-gcc-openmpi-mkl-opt</br>11.2.3-icc | `--A`</br>`--A`</br>`--A` |
| Trilinos | 12.10.1-intel-2017a-Python-2.7.11</br>12.10.1-intel-2017a-Python-2.7.11-test | `-SA`</br>`-S-` |
| Trimmomatic | 0.35-Java-1.7.0_79 | `-S-` |
| TRIQS | 1.4.1-foss-2017a | `-S-` |
| turbovnc | 1.2.2</br>1.2.3 | `--A`</br>`-S-` |
| Ubuntu | 16.04</br>16.04-GPU</br>16.04-OpenFOAM | `-SA`</br>`--A`</br>`-S-` |
| urllib3 | 1.22-Py-3.6 | `-SA` |
| util-linux | 2.26.1</br>2.26.1-foss-2015g</br>2.28-intel-2016a</br>2.29</br>2.29.2</br>2.32 | `-SA`</br>`-S-`</br>`--A`</br>`--A`</br>`USA`</br>`-SA` |
| Valgrind | 3.11.0-foss-2015b</br>3.11.0-intel-2015b</br>3.13.0-intel-2017b | `-S-`</br>`-S-`</br>`-S-` |
| valgrind | 3.9.0-impi | `--A` |
| Vampir | 8.5.0</br>9.0.0 | `-SA`</br>`-S-` |
| vampir | 8.2 | `--A` |
| VampirServer | 8.5.0-intel-2015b</br>9.0.0-intel-2015b | `-S-`</br>`-S-` |
| VASP | 5.4.1-intel-2015b-24Jun15</br>5.4.4-intel-2016a-CUDA-8.0.44-mkl=sequential</br>5.4.4-intel-2017a-mkl=cluster</br>5.4.4-intel-2017a-mkl=paralel</br>5.4.4-intel-2017a-mkl=sequential</br>5.4.4-intel-2017b-mkl=cluster</br>5.4.4-intel-2017c-CUDA-9.1.85-mkl=sequential | `USA`</br>`--A`</br>`USA`</br>`USA`</br>`USA`</br>`-SA`</br>`--A` |
| vde2 | 2.3.2 | `--A` |
| VDE2 | 2.3.2-GCC-4.4.7-system | `US-` |
| virtualenv | 15.1.0-Py-2.7 | `-S-` |
| virtualgl | 2.4 | `--A` |
| VirtualGL | 2.4.1 | `-S-` |
| VisIt | 2.10.0 | `US-` |
| VTK | 6.3.0-intel-2017a-Python-2.7.13</br>7.1.1-intel-2017a-Python-2.7.13 | `-SA`</br>`-SA` |
| VTune | 2017_update5</br>2018_update3 | `-S-`</br>`-SA` |
| webencodings | 0.5.1-Py-3.6 | `-S-` |
| Werkzeug | 0.14.1-Py-3.6 | `-S-` |
| wheel | 0.30.0-Py-3.6 | `-S-` |
| wien2k | 13.1</br>14.2 | `--A`</br>`--A` |
| wine | 1.7.29 | `--A` |
| Wine | 1.7.29-GCC-4.4.7-system</br>1.7.29-GNU-5.1.0-2.25 | `-S-`</br>`-S-` |
| X11 | 20160819</br>20170314 | `USA`</br>`USA` |
| x264 | 20160430</br>20160430-intel-2017a | `--A`</br>`-S-` |
| x86_adapt | github | `-S-` |
| xbitmaps | 1.1.1</br>1.1.1-foss-2015g</br>1.1.1-intel-2015b | `--A`</br>`-S-`</br>`-S-` |
| xcb-proto | 1.10-Python-2.7.8</br>1.11</br>1.11-foss-2015g-Python-2.7.9</br>1.11-intel-2015b-Python-2.7.9</br>1.11-Python-2.7.9 | `-S-`</br>`-SA`</br>`-S-`</br>`-S-`</br>`-SA` |
| xcb-util | 0.4.0 | `--A` |
| xcb-util-image | 0.4.0 | `--A` |
| xcb-util-keysyms | 0.4.0 | `--A` |
| xcb-util-renderutil | 0.3.9 | `--A` |
| xcb-util-wm | 0.4.1 | `--A` |
| xdrfile | 1.1.4-foss-2015g</br>1.1.4-foss-2016a</br>1.1.4-intel-2015b | `-SA`</br>`-SA`</br>`--A` |
| xextproto | 7.3.0</br>7.3.0-foss-2015g</br>7.3.0-foss-2016a</br>7.3.0-intel-2015b</br>7.3.0-intel-2016a | `-SA`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-` |
| xineramaproto | 1.2.1</br>1.2.1-intel-2015b | `-SA`</br>`-S-` |
| XKeyboardConfig | 2.21 | `-S-` |
| XML-Parser | 2.44 | `-S-` |
| xorg-macros | 1.17</br>1.17-foss-2015g</br>1.19.0-foss-2016a</br>1.19.0-intel-2016a</br>1.19.1 | `-SA`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-` |
| xproto | 7.0.26</br>7.0.26-foss-2015g</br>7.0.26-intel-2015b</br>7.0.28</br>7.0.28-foss-2016a</br>7.0.28-intel-2016a | `-SA`</br>`-S-`</br>`-S-`</br>`-SA`</br>`-S-`</br>`-S-` |
| xtrans | 1.3.4</br>1.3.4-intel-2015b</br>1.3.5</br>1.3.5-foss-2015g</br>1.3.5-foss-2016a</br>1.3.5-intel-2015b</br>1.3.5-intel-2016a | `--A`</br>`-S-`</br>`-SA`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-` |
| Xvfb | 1.17.4 | `-S-` |
| XZ | 5.2.2</br>5.2.2-foss-2016a</br>5.2.2-intel-2017.00</br>5.2.3 | `-SA`</br>`-SA`</br>`--A`</br>`USA` |
| Yasm | 1.3.0</br>1.3.0-intel-2017a | `--A`</br>`-S-` |
| zlib | 1.2.7-intel-2015b</br>1.2.8</br>1.2.8-foss-2015b</br>1.2.8-foss-2015g</br>1.2.8-foss-2016a</br>1.2.8-gompi-2015e</br>1.2.8-ictce-7.3.5</br>1.2.8-intel-2015b</br>1.2.8-intel-2016.01</br>1.2.8-intel-2016a</br>1.2.8-intel-2017.00</br>1.2.8-GCCcore-5.3.0</br>1.2.8-GCCcore-5.3.1-snapshot-20160419</br>1.2.8-GCCcore-6.3.0</br>1.2.8-GNU-5.1.0-2.25-intel-2015b</br>1.2.11</br>1.2.11-foss-2017a</br>1.2.11-GCCcore-6.3.0 | `US-`</br>`USA`</br>`US-`</br>`USA`</br>`-SA`</br>`-S-`</br>`-S-`</br>`USA`</br>`-SA`</br>`--A`</br>`-SA`</br>`-S-`</br>`-S-`</br>`--A`</br>`-S-`</br>`USA`</br>`-S-`</br>`-SA` |
| zsh | 5.2-foss-2018a | `-S-` |
---8<--- "modules_matrix_search.md"
# Available Modules
## Compiler
| Module | Description |
| ------ | ----------- |
| [icc](http://software.intel.com/en-us/intel-compilers/) | Intel C and C++ compilers |
## Data
| Module | Description |
| ------ | ----------- |
| [HDF5](http://www.hdfgroup.org/HDF5/) | HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections. |
## Devel
| Module | Description |
| ------ | ----------- |
| [devel_environment](https://docs.it4i.cz/software/mic/mic_environment) | Devel environment for intel xeon phi GCC 5.1.1 Python 2.7.12 Perl 5.14.2 CMake 2.8.7 Make 3.82 ncurses 5.9 ... |
| [M4](http://www.gnu.org/software/m4/m4.html) | GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible although it has some extensions (for example, handling more than 9 positional parameters to macros). GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc. |
| [ncurses](http://www.gnu.org/software/ncurses/) | The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses. |
## Lang
| Module | Description |
| ------ | ----------- |
| [Bison](http://www.gnu.org/software/bison) | Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables. |
| [flex](http://flex.sourceforge.net/) | Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, sometimes called a tokenizer, is a program which recognizes lexical patterns in text. |
| [Tcl](http://www.tcl.tk/) | Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more. |
## Lib
| Module | Description |
| ------ | ----------- |
| [libreadline](http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html) | The GNU Readline library provides a set of functions for use by applications that allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. The Readline library includes additional functions to maintain a list of previously-entered command lines, to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands. |
| [zlib](http://www.zlib.net/) | zlib is designed to be a free, general-purpose, legally unencumbered -- that is, not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system. |
## Math
| Module | Description |
| ------ | ----------- |
| GMP | &nbsp; |
| [Octave](http://www.gnu.org/software/octave/) | GNU Octave is a high-level interpreted language, primarily intended for numerical computations. |
## Mpi
| Module | Description |
| ------ | ----------- |
| [impi](http://software.intel.com/en-us/intel-mpi-library/) | Intel MPI Library, compatible with MPICH ABI |
## Numlib
| Module | Description |
| ------ | ----------- |
| [imkl](http://software.intel.com/en-us/intel-mkl/) | Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more. |
## Toolchain
| Module | Description |
| ------ | ----------- |
| [iccifort](http://software.intel.com/en-us/intel-cluster-toolkit-compiler/) | Intel C, C++ & Fortran compilers |
| [ifort](http://software.intel.com/en-us/intel-compilers/) | Intel Fortran compiler |
| [iimpi](http://software.intel.com/en-us/intel-cluster-toolkit-compiler/) | Intel C/C++ and Fortran compilers, alongside Intel MPI. |
| [intel](http://software.intel.com/en-us/intel-cluster-toolkit-compiler/) | Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL). |
## Tools
| Module | Description |
| ------ | ----------- |
| [bzip2](http://www.bzip.org/) | bzip2 is a freely available, patent free, high-quality data compressor. It typically compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical compressors), whilst being around twice as fast at compression and six times faster at decompression. |
| [cURL](http://curl.haxx.se) | libcurl is a free and easy-to-use client-side URL transfer library |
| [expat](http://expat.sourceforge.net/) | Expat is an XML parser library written in C. It is a stream-oriented parser in which an application registers handlers for things the parser might find in the XML document (like start tags) |
| OpenSSL | &nbsp; |
## Vis
| Module | Description |
| ------ | ----------- |
| [gettext](http://www.gnu.org/software/gettext/) | GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation |
# Available Modules
## Bio
| Module | Description |
| ------ | ----------- |
| [FastQC](http://www.bioinformatics.babraham.ac.uk/projects/download.html) | A quality control application for high throughput sequence data |
| [GATK](http://www.broadinstitute.org/gatk/) | The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size. |
| [SnpEff](http://snpeff.sourceforge.net/) | Genetic variant annotation and effect prediction toolbox. |
## Cae
| Module | Description |
| ------ | ----------- |
| COMSOL | &nbsp; |
| [OpenFOAM](http://www.openfoam.com/) | OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics. |
## Chem
| Module | Description |
| ------ | ----------- |
| [ABINIT](http://www.abinit.org/) | Abinit is a plane wave pseudopotential code for doing condensed phase electronic structure calculations using DFT. |
| [Libint](https://sourceforge.net/p/libint/) | Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory. |
| [libxc](http://www.tddft.org/programs/octopus/wiki/index.php/Libxc) | Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals. |
## Compiler
| Module | Description |
| ------ | ----------- |
| [GCC](http://gcc.gnu.org/) | The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...). |
| GCCcore | &nbsp; |
| icc | &nbsp; |
| [ifort](http://software.intel.com/en-us/intel-compilers/) | Fortran compiler from Intel |
| [LLVM](http://llvm.org/) | The LLVM Core libraries provide a modern source- and target-independent optimizer, along with code generation support for many popular CPUs (as well as some less common ones!) These libraries are built around a well specified code representation known as the LLVM intermediate representation ("LLVM IR"). The LLVM Core libraries are well documented, and it is particularly easy to invent your own language (or port an existing compiler) to use LLVM as an optimizer and code generator. |
## Data
| Module | Description |
| ------ | ----------- |
| [GDAL](http://www.gdal.org/) | GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for data translation and processing. |
| [HDF5](http://www.hdfgroup.org/HDF5/) | HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections. |
| [netCDF](http://www.unidata.ucar.edu/software/netcdf/) | NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. |
| [netCDF-Fortran](http://www.unidata.ucar.edu/software/netcdf/) | NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. |
## Devel
| Module | Description |
| ------ | ----------- |
| [Autoconf](http://www.gnu.org/software/autoconf/) | Autoconf is an extensible package of M4 macros that produce shell scripts to automatically configure software source code packages. These scripts can adapt the packages to many kinds of UNIX-like systems without manual user intervention. Autoconf creates a configuration script for a package from a template file that lists the operating system features that the package can use, in the form of M4 macro calls. |
| [Automake](http://www.gnu.org/software/automake/automake.html) | Automake: GNU Standards-compliant Makefile generator |
| [Autotools](http://autotools.io) | This bundle collect the standard GNU build tools: Autoconf, Automake and libtool |
| [Boost](http://www.boost.org/) | Boost provides free peer-reviewed portable C++ source libraries. |
| [CMake](http://www.cmake.org) | CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software. |
| [Doxygen](http://www.doxygen.org) | Doxygen is a documentation system for C++, C, Java, Objective-C, Python, IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D. |
| [M4](http://www.gnu.org/software/m4/m4.html) | GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible although it has some extensions (for example, handling more than 9 positional parameters to macros). GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc. |
| [make](http://www.gnu.org/software/make/make.html) | make-3.82: GNU version of make utility |
| [Mako](http://www.makotemplates.org) | A super-fast templating language that borrows the best ideas from the existing templating languages |
| [Maven](http://maven.apache.org/index.html) | Binary maven install, Apache Maven is a software project management and comprehension tool. Based on the concept of a project object model (POM), Maven can manage a project's build, reporting and documentation from a central piece of information. |
| [ncurses](http://www.gnu.org/software/ncurses/) | The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses. |
| [PCRE](http://www.pcre.org/) | The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5. |
| [pkg-config](http://www.freedesktop.org/wiki/Software/pkg-config/) | pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the correct compiler options on the command line so an application can use gcc -o test test.c `pkg-config --libs --cflags glib-2.0` for instance, rather than hard-coding values on where to find glib (or other libraries). |
| [Qt](http://qt-project.org/) | Qt is a comprehensive cross-platform C++ application framework. |
| [Qt5](http://qt.io/) | Qt is a comprehensive cross-platform C++ application framework. |
| [sparsehash](https://github.com/sparsehash/sparsehash) | An extremely memory-efficient hash_map implementation. 2 bits/entry overhead! The SparseHash library contains several hash-map implementations, including implementations that optimize for space or speed. |
| [SQLite](http://www.sqlite.org/) | SQLite: SQL Database Engine in a C Library |
| [SWIG](http://www.swig.org/) | SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages. |
| [xorg-macros](http://cgit.freedesktop.org/xorg/util/macros) | X.org macros utilities. |
## Lang
| Module | Description |
| ------ | ----------- |
| [Bison](http://www.gnu.org/software/bison) | Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables. |
| flex | &nbsp; |
| [Java](http://java.com/) | Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers. |
| [Lua](http://www.lua.org/) | Lua is a powerful, fast, lightweight, embeddable scripting language. Lua combines simple procedural syntax with powerful data description constructs based on associative arrays and extensible semantics. Lua is dynamically typed, runs by interpreting bytecode for a register-based virtual machine, and has automatic memory management with incremental garbage collection, making it ideal for configuration, scripting, and rapid prototyping. |
| [Mono](http://mono-framework.com) | An open source, cross-platform, implementation of C# and the CLR that is binary compatible with Microsoft.NET. |
| [NASM](http://www.nasm.us/) | NASM: General-purpose x86 assembler |
| [OpenCL-runtime](https://software.intel.com/en-us/intel-opencl) | OpenCL™ is the first open, royalty-free standard for cross-platform, parallel programming of modern processors found in personal computers, servers and handheld/embedded devices. OpenCL (Open Computing Language) greatly improves speed and responsiveness for a wide spectrum of applications in numerous market categories from gaming and entertainment to scientific and medical software. |
| [Perl](http://www.perl.org/) | Larry Wall's Practical Extraction and Report Language |
| [Python](http://python.org/) | Python is a programming language that lets you work more quickly and integrate your systems more effectively. |
| [R](http://www.r-project.org/) | R is a free software environment for statistical computing and graphics. |
| [Tcl](http://www.tcl.tk/) | Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more. |
## Lib
| Module | Description |
| ------ | ----------- |
| [libdrm](http://dri.freedesktop.org) | Direct Rendering Manager runtime library. |
| [libffi](http://sourceware.org/libffi/) | The libffi library provides a portable, high level programming interface to various calling conventions. This allows a programmer to call any function specified by a call interface description at run-time. |
| [libjpeg-turbo](http://sourceforge.net/libjpeg-turbo/) | libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG compression and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding. |
| [libpng](http://www.libpng.org/pub/png/libpng.html) | libpng is the official PNG reference library |
| [libpthread-stubs](http://xcb.freedesktop.org/) | The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility. |
| [libreadline](http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html) | The GNU Readline library provides a set of functions for use by applications that allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. The Readline library includes additional functions to maintain a list of previously-entered command lines, to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands. |
| [libsndfile](http://www.mega-nerd.com/libsndfile) | Libsndfile is a C library for reading and writing files containing sampled sound (such as MS Windows WAV and the Apple/SGI AIFF format) through one standard library interface. |
| [LibTIFF](http://www.remotesensing.org/libtiff/) | tiff: Library and tools for reading and writing TIFF data files |
| libtool | &nbsp; |
| [libxml2](http://xmlsoft.org/) | Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform). |
| [nettle](http://www.lysator.liu.se/~nisse/nettle/) | Nettle is a cryptographic library that is designed to fit easily in more or less any context: In crypto toolkits for object-oriented languages (C++, Python, Pike, ...), in applications like LSH or GNUPG, or even in kernel space. |
| [PROJ](http://trac.osgeo.org/proj/) | Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates |
| [tbb](http://software.intel.com/en-us/articles/intel-tbb/) | Intel Threading Building Blocks 4.0 (Intel TBB) is a widely used, award-winning C++ template library for creating reliable, portable, and scalable parallel applications. Use Intel TBB for a simple and rapid way of developing robust task-based parallel applications that scale to available processor cores, are compatible with multiple environments, and are easier to maintain. Intel TBB is the most proficient way to implement future-proof parallel applications that tap into the power and performance of multicore and manycore hardware platforms. |
| [zlib](http://www.zlib.net/) | zlib is designed to be a free, general-purpose, legally unencumbered -- that is, not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system. |
## Math
| Module | Description |
| ------ | ----------- |
| [Eigen](http://eigen.tuxfamily.org/index.php?title=Main_Page) | Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms. |
| [GEOS](http://trac.osgeo.org/geos) | GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS) |
| GMP | &nbsp; |
| [METIS](http://glaros.dtc.umn.edu/gkhome/metis/metis/overview) | METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes. |
| [MPFR](http://www.mpfr.org) | The MPFR library is a C library for multiple-precision floating-point computations with correct rounding. |
| [SCOTCH](http://gforge.inria.fr/projects/scotch/) | Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning. |
## Mpi
| Module | Description |
| ------ | ----------- |
| [impi](http://software.intel.com/en-us/intel-mpi-library/) | The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification. |
| [OpenMPI](http://www.open-mpi.org/) | The Open MPI Project is an open source MPI-2 implementation. |
## Numlib
| Module | Description |
| ------ | ----------- |
| [CGAL](http://www.cgal.org/) | The goal of the CGAL Open Source Project is to provide easy access to efficient and reliable geometric algorithms in the form of a C++ library. |
| [cuDNN](https://developer.nvidia.com/cudnn) | The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks. |
| [FFTW](http://www.fftw.org) | FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data. |
| [imkl](http://software.intel.com/en-us/intel-mkl/) | Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more. |
| [NLopt](http://ab-initio.mit.edu/wiki/index.php/NLopt) | NLopt is a free/open-source library for nonlinear optimization, providing a common interface for a number of different free optimization routines available online as well as original implementations of various other algorithms. |
| [OpenBLAS](http://xianyi.github.com/OpenBLAS/) | OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version. |
| [ScaLAPACK](http://www.netlib.org/scalapack/) | The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers. |
## Phys
| Module | Description |
| ------ | ----------- |
| [VASP](http://www.vasp.at) | The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles. |
## System
| Module | Description |
| ------ | ----------- |
| [CUDA](https://developer.nvidia.com/cuda-toolkit) | CUDA (formerly Compute Unified Device Architecture) is a parallel computing platform and programming model created by NVIDIA and implemented by the graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs. |
| [hwloc](http://www.open-mpi.org/projects/hwloc/) | The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various system attributes such as cache and memory information as well as the locality of I/O devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering information about modern computing hardware so as to exploit it accordingly and efficiently. |
| [libpciaccess](http://cgit.freedesktop.org/xorg/lib/libpciaccess/) | Generic PCI access library. |
## Toolchain
| Module | Description |
| ------ | ----------- |
| foss | GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK. |
| [GNU](http://www.gnu.org/software/) | Compiler-only toolchain with GCC and binutils. |
| gompi | GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support. |
| [iccifort](http://software.intel.com/en-us/intel-cluster-toolkit-compiler/) | Intel C, C++ and Fortran compilers |
| [iimpi](http://software.intel.com/en-us/intel-cluster-toolkit-compiler/) | Intel C/C++ and Fortran compilers, alongside Intel MPI. |
| [intel](http://software.intel.com/en-us/intel-cluster-toolkit-compiler/) | Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL. |
| [PRACE](http://www.prace-ri.eu/PRACE-Common-Production) | The PRACE Common Production Environment (PCPE) is a set of software tools and libraries that are planned to be available on all PRACE execution sites. The PCPE also defines a set of environment variables that try to make compilation on all sites as homogeneous and simple as possible. |
| [Py](https://www.python.org) | Python 2.7 toolchain |
## Tools
| Module | Description |
| ------ | ----------- |
| [Bash](http://www.gnu.org/software/bash) | Bash is an sh-compatible command language interpreter that executes commands read from the standard input or from a file. Bash also incorporates useful features from the Korn and C shells (ksh and csh). |
| [binutils](http://directory.fsf.org/project/binutils/) | binutils: GNU binary utilities |
| [BLCR](http://crd.lbl.gov/departments/computer-science/CLaSS/research/BLCR/) | Future Technologies Group researchers are developing a hybrid kernel/user implementation of checkpoint/restart. Their goal is to provide a robust, production quality implementation that checkpoints a wide range of applications, without requiring changes to be made to application code. This work focuses on checkpointing parallel applications that communicate through MPI, and on compatibility with the software suite produced by the SciDAC Scalable Systems Software ISIC. |
| [bzip2](http://www.bzip.org/) | bzip2 is a freely available, patent free, high-quality data compressor. It typically compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical compressors), whilst being around twice as fast at compression and six times faster at decompression. |
| [cURL](http://curl.haxx.se) | libcurl is a free and easy-to-use client-side URL transfer library, supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling and more. |
| [DMTCP](http://dmtcp.sourceforge.net/index.html) | DMTCP (Distributed MultiThreaded Checkpointing) transparently checkpoints a single-host or distributed computation in user-space -- with no modifications to user code or to the O/S. |
| EasyBuild | &nbsp; |
| [expat](http://expat.sourceforge.net/) | Expat is an XML parser library written in C. It is a stream-oriented parser in which an application registers handlers for things the parser might find in the XML document (like start tags) |
| [git](http://git-scm.com/) | Git is a free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency. |
| [gzip](http://www.gnu.org/software/gzip/) | gzip (GNU zip) is a popular data compression program as a replacement for compress |
| MATLAB | &nbsp; |
| [Mercurial](http://mercurial.selenic.com/) | Mercurial is a free, distributed source control management tool. It efficiently handles projects of any size and offers an easy and intuitive interface. |
| [moreutils](https://joeyh.name/code/moreutils/) | Moreutils is a growing collection of the unix tools that nobody thought to write long ago when unix was young. |
| [numactl](http://oss.sgi.com/projects/libnuma/) | The numactl program allows you to run your application program on specific cpu's and memory nodes. It does this by supplying a NUMA memory policy to the operating system before running your program. The libnuma library provides convenient ways for you to add NUMA memory policies into your own program. |
| pigz | &nbsp; |
| [QEMU](http://wiki.qemu.org/Main_Page) | QEMU is a generic and open source machine emulator and virtualizer. |
| [RStudio](https://www.rstudio.com) | RStudio is a set of integrated tools designed to help you be more productive with R. It includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management. |
| Singularity | &nbsp; |
| [Szip](http://www.hdfgroup.org/doc_resource/SZIP/) | Szip compression software, providing lossless compression of scientific data |
| [tcsh](http://www.tcsh.org) | Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). It is a command language interpreter usable both as an interactive login shell and a shell script command processor. It includes a command-line editor, programmable word completion, spelling correction, a history mechanism, job control and a C-like syntax. |
| [util-linux](http://www.kernel.org/pub/linux/utils/util-linux) | Set of Linux utilities |
| [VDE2](http://vde.sourceforge.net) | VDE is an ethernet compliant virtual network that can be spawned over a set of physical computer over the Internet. VDE is part of virtualsquare project. |
| [VTune](http://software.intel.com/en-us/intel-vtune-amplifier-xe) | Intel VTune Amplifier XE 2016 is the premier performance profiler for C, C++, C#, Fortran, Assembly and Java. |
| [XZ](http://tukaani.org/xz/) | xz: XZ utilities |
## Vis
| Module | Description |
| ------ | ----------- |
| [cairo](http://cairographics.org) | Cairo is a 2D graphics library with support for multiple output devices. Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB |
| [fontconfig](http://www.freedesktop.org/software/fontconfig) | Fontconfig is a library designed to provide system-wide font configuration, customization and application access. |
| [freetype](http://freetype.org) | FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display servers, font conversion tools, text image generation tools, and many other products as well. |
| [gettext](http://www.gnu.org/software/gettext/) | GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation |
| [GLib](http://www.gtk.org/) | GLib is one of the base libraries of the GTK+ project |
| [JasPer](http://www.ece.uvic.ca/~frodo/jasper/) | The JasPer Project is an open-source initiative to provide a free software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard. |
| [libGLU](ftp://ftp.freedesktop.org/pub/mesa/glu/) | The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. |
| [Mesa](http://www.mesa3d.org/) | Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics. |
| [ParaView](http://www.paraview.org) | ParaView is a scientific parallel visualizer. |
| [pixman](http://www.pixman.org/) | Pixman is a low-level software library for pixel manipulation, providing features such as image compositing and trapezoid rasterization. Important users of pixman are the cairo graphics library and the X server. |
| [Tk](http://www.tcl.tk/) | Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building a graphical user interface (GUI) in many different programming languages. |
| [VisIt](https://wci.llnl.gov/simulation/computer-codes/visit) | VisIt is an Open Source, interactive, scalable, visualization, animation and analysis tool |
| [X11](https://www.x.org) | The X Window System (X11) is a windowing system for bitmap displays |
# Available Modules
## Os
| Module | Description |
| ------ | ----------- |
| [CentOS](https://www.centos.org/) | The CentOS Project is a community-driven free software effort focused on delivering a robust open source ecosystem. For users, we offer a consistent manageable platform that suits a wide variety of deployments. For open source communities, we offer a solid, predictable base to build upon, along with extensive resources to build, test, release, and maintain their code. We’re also expanding the availability of CentOS images across a number of vendors, providing official images for Amazon, Google, and more. For self-hosted cloud, we also provide a generic cloud-init enabled image. For more information about updates and improvements in CentOS 7, please check out the release notes or the release announcement in the mailing list archive. |
| [Debian](https://www.debian.org/) | Debian is a Unix-like operating system composed entirely of free software packaged by a team of volunteers. The Debian Project was started by Ian Murdock on August 16, 1993, Debian 0.01 was released on September 15, 1993, and the first stable version, 1.1, was released on June 17, 1996. The Debian stable branch is the most popular edition for personal computers and network servers, and is used as a base for many other distributions. The project's work is carried out over the Internet, guided by the Debian Project Leader and three foundational documents: the Debian Social Contract, the Debian Constitution, and the Debian Free Software Guidelines. New distributions are updated continually, and the next candidate is released after a time-based freeze. One of the earliest operating systems based on the Linux kernel, Debian has been developed openly and distributed freely in the spirit of the GNU Project. This decision drew the support of the Free Software Foundation, which sponsored the project for one year from November 1994 to November 1995. When the sponsorship ended, the Debian Project formed Software in the Public Interest to continue supporting development. While all Debian releases are based on the GNU userland and GNU C Library (glibc), kernels other than Linux are also available, including FreeBSD and the GNU Hurd microkernel. |
| [Singularity-wrappers](https://docs.it4i.cz) | Wrappers for Singularity containers (mailto:easybuild@vsb.cz). |
| [Ubuntu](https://www.ubuntu.com/) | Ubuntu is a Debian-based Linux operating system for personal computers, tablets and smartphones, where Ubuntu Touch edition is used. It also runs network servers. That is usually with the Ubuntu Server edition, either on physical or virtual servers (such as on mainframes) or with containers, that is with enterprise-class features. It runs on the most popular architectures, including server-class ARM-based. Ubuntu is published by Canonical Ltd, who offer commercial support. It is based on free software and named after the Southern African philosophy of ubuntu (literally, 'human-ness'), which Canonical Ltd. suggests can be loosely translated as "humanity to others" or "I am what I am because of who we all are". Since Ubuntu 11.04 Natty Narwhal Ubuntu has used Unity as its default user interface for the desktop, but following the release of Ubuntu 17.10 it will move to the GNOME 3 desktop instead, as work on Unity ends. Ubuntu is the most popular operating system running in hosted environments, so–called "clouds", as it is the most popular server Linux distribution. Development of Ubuntu is led by UK-based Canonical Ltd., a company of South African entrepreneur Mark Shuttleworth. Canonical generates revenue through the sale of technical support and other services related to Ubuntu. The Ubuntu project is publicly committed to the principles of open-source software development; people are encouraged to use free software, study how it works, improve upon it, and distribute it. |
## Bio
| Module | Description |
| ------ | ----------- |
| [ABySS](http://www.bcgsc.ca/platform/bioinfo/software/abyss) | Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler |
| [almost](http://www-almost.ch.cam.ac.uk/site) | all atom molecular simulation toolkit - is a fast and flexible molecular modeling environment that provides powerful and efficient algorithms for molecular simulation, homology modeling, de novo design and ab-initio calculations. |
| [BCFtools](http://www.htslib.org/) | Samtools is a suite of programs for interacting with high-throughput sequencing data. BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants |
| [bcl2fastq2](https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html) | bcl2fastq Conversion Software both demultiplexes data and converts BCL files generated by Illumina sequencing systems to standard FASTQ file formats for downstream analysis. |
| [BWA](http://bio-bwa.sourceforge.net/) | Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. |
| [FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) | FastQC is a quality control application for high throughput sequence data. It reads in sequence data in a variety of formats and can either provide an interactive application to review the results of several different QC checks, or create an HTML based report which can be integrated into a pipeline. |
| [GATK](http://www.broadinstitute.org/gatk/) | The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size. |
| [GROMACS](http://www.gromacs.org) | GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. |
| [HTSlib](http://www.htslib.org/) | A C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix |
| [picard](http://sourceforge.net/projects/picard) | A set of tools (in Java) for working with next generation sequencing data in the BAM format. |
| [PLUMED](http://www.plumed-code.org) | PLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines. Free energy calculations can be performed as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. |
| [RELION](http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page) | RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM). |
| [Rosetta](https://www.rosettacommons.org) | Rosetta is the premier software suite for modeling macromolecular structures. As a flexible, multi-purpose application, it includes tools for structure prediction, design, and remodeling of proteins and nucleic acids. |
| [SAMtools](http://www.htslib.org/) | SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. |
| [SnpEff](http://snpeff.sourceforge.net/) | Genetic variant annotation and effect prediction toolbox. |
| [Trimmomatic](http://www.usadellab.org/cms/?page=trimmomatic) | Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.The selection of trimming steps and their associated parameters are supplied on the command line. |
## Cae
| Module | Description |
| ------ | ----------- |
| [COMSOL](https://www.comsol.com/) | The COMSOL Multiphysics simulation environment facilitates the steps in the modeling process – defining your geometry, meshing, specifying your physics, solving, and then visualizing your results. It also serves as a platform for the application specific modules. |
| [deMonNano](http://www.demon-software.com) | deMonNano is a software package for density functional theory based tight binding calculations. It is part of the deMon (density of Montréal) suite of programs. The present version of the code of deMon for DFT is now known as deMon2k. This code and general information about deMon are available at http://www.demon-software.com |
| [Digimat](http://www.mscsoftware.com/product/digimat) | The Nonlinear Multi-scale Material and Structure Modeling Platform - Todays' major challenge is the shift from metal to composite in order to bring significant weight saving in the design. This paradigm however requires a dedicated tool for composite design in order to take into account the specific composite behavior. Classical design tools are not able to describe accurately the local composite material behavior, leading to introduction of safety factors and lack of confidence in the design. |
| [FreeFem++](http://www.freefem.org) | FreeFem++ is a partial differential equation solver. It has its own language. freefem scripts can solve multiphysics non linear systems in 2D and 3D. Problems involving PDE (2d, 3d) from several branches of physics such as fluid-structure interactions require interpolations of data on several meshes and their manipulation within one program. FreeFem++ includes a fast 2^d-tree-based interpolation algorithm and a language for the manipulation of data on multiple meshes (as a follow up of bamg (now a part of FreeFem++ ). FreeFem++ is written in C++ and the FreeFem++ language is a C++ idiom. It runs on Macs, Windows, Unix machines. FreeFem++ replaces the older freefem and freefem+. |
| [HyperWorks](https://altairhyperworks.com/) | Altair HyperMesh is a high-performance finite element pre-processor to prepare even the largest models, starting from import of CAD geometry to exporting an analysis run for various disciplines. This module is licensed for specified users only. For more informations please contact Pavel Marsalek mailto:pavel.marsalek@vsb.cz. |
| [Marc](http://www.mscsoftware.com/product/marc) | Advanced Nonlinear Simulation Solution. Simulate products more accurately with the industry’s leading nonlinear FEA solver technology. |
| [OpenFOAM](http://www.openfoam.com/) | OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics. |
## Chem
| Module | Description |
| ------ | ----------- |
| [ABINIT](http://www.abinit.org/) | Abinit is a plane wave pseudopotential code for doing condensed phase electronic structure calculations using DFT. |
| [Amber](http://ambermd.org) | A set of molecular mechanical force fields for the simulation of biomolecules |
| [ASE](https://wiki.fysik.dtu.dk/ase/) | ASE is a python package providing an open source Atomic Simulation Environment in the Python scripting language. |
| [ChronusQ](https://github.com/liresearchgroup/chronusq_public) | ChronusQ is a high-performance computational chemistry software package with a strong emphasis on explicitly time-dependent and post-SCF quantum mechanical methods. |
| [CP2K](http://www.cp2k.org/) | CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials. |
| [LAMMPS](http://lammps.sandia.gov) | LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. Has potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. |
| [libctl](http://ab-initio.mit.edu/libctl) | libctl is a free Guile-based library implementing flexible control files for scientific simulations. |
| [Libint](https://sourceforge.net/p/libint/) | Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory. |
| [libxc](http://www.tddft.org/programs/octopus/wiki/index.php/Libxc) | Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals. |
| [Molden](http://www.cmbi.ru.nl/molden/) | Molden is a package for displaying Molecular Density from the Ab Initio packages GAMESS-UK, GAMESS-US and GAUSSIAN and the Semi-Empirical packages Mopac/Ampac |
| [Molpro](http://www.molpro.net) | Molpro quantum chemistry package |
| [NAMD](http://www.ks.uiuc.edu/Research/namd/) | NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. |
| [NWChem](http://www.nwchem-sw.org) | NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters. NWChem software can handle: biomolecules, nanostructures, and solid-state; from quantum to classical, and all combinations; Gaussian basis functions or plane-waves; scaling from one to thousands of processors; properties and relativity. |
| [Octopus](http://www.tddft.org/programs/octopus/wiki/index.php/Main_Page) | Octopus is a scientific program aimed at the ab initio virtual experimentation on a hopefully ever-increasing range of system types. Electrons are described quantum-mechanically within density-functional theory (DFT), in its time-dependent form (TDDFT) when doing simulations in time. Nuclei are described classically as point particles. Electron-nucleus interaction is described within the pseudopotential approximation. |
| [OpenBabel](http://openbabel.org) | Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas. |
| [ORCA](http://cec.mpg.de/forum/) | ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- and multireference correlated ab initio methods. It can also treat environmental and relativistic effects. |
| [PLUMED](http://www.plumed-code.org) | PLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines. Free energy calculations can be performed as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. |
| [pWord2Vec](https://github.com/IntelLabs/pWord2Vec) | This tool provides an efficient implementation of the continuous bag-of-words and skip-gram architectures for computing vector representations of words. These representations can be subsequently used in many natural language processing applications and for further research. |
| [QuantumESPRESSO](http://www.pwscf.org/) | Quantum ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft). |
| [S4MPLE](http://infochim.u-strasbg.fr/spip.php?rubrique152) | S4MPLE (Sampler For Multiple Protein-Ligand Entities) is a flexible molecular modeling tool, supporting empirical force field-driven conformational sampling and geometry optimization heuristics using a hybrid genetic algorithm (GA). |
| [Scipion](https://github.com/I2PC/scipion/wiki) | Scipion is an image processing framework for obtaining 3D models of macromolecular complexes using Electron Microscopy (3DEM). It integrates several software packages and presents a unified interface for both biologists and developers. Scipion allows you to execute workflows combining different software tools, while taking care of formats and conversions. Additionally, all steps are tracked and can be reproduced later on. |
| [xdrfile](http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library) | XTC library |
## Compiler
| Module | Description |
| ------ | ----------- |
| [BerkeleyUPC](http://upc.lbl.gov) | The goal of the Berkeley UPC compiler group is to develop a portable, high performance implementation of UPC for large-scale multiprocessors, PC clusters, and clusters of shared memory multiprocessors. |
| [Clang](http://clang.llvm.org/) | C, C++, Objective-C compiler, based on LLVM. Does not include C++ standard library -- use libstdc++ from GCC. |
| [GCC](http://gcc.gnu.org/) | The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...). |
| [GCCcore](http://gcc.gnu.org/) | The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...). |
| [Go](http://www.golang.org) | Go is an open source programming language that makes it easy to build simple, reliable, and efficient software. |
| [icc](http://software.intel.com/en-us/intel-compilers/) | C and C++ compiler from Intel |
| [ifort](http://software.intel.com/en-us/intel-compilers/) | Fortran compiler from Intel |
| [ispc](http://ispc.github.io/) | Intel SPMD Program Compilers; An open-source compiler for high-performance SIMD programming on the CPU. ispc is a compiler for a variant of the C programming language, with extensions for 'single program, multiple data' (SPMD) programming. Under the SPMD model, the programmer writes a program that generally appears to be a regular serial program, though the execution model is actually that a number of program instances execute in parallel on the hardware. |
| [LLVM](http://llvm.org/) | The LLVM Core libraries provide a modern source- and target-independent optimizer, along with code generation support for many popular CPUs (as well as some less common ones!) These libraries are built around a well specified code representation known as the LLVM intermediate representation ("LLVM IR"). The LLVM Core libraries are well documented, and it is particularly easy to invent your own language (or port an existing compiler) to use LLVM as an optimizer and code generator. |
| [OpenCoarrays](http://www.opencoarrays.org) | OpenCoarrays is an open-source software project for developing, porting and tuning transport layers that support coarray Fortran compilers. |
| [PGI](http://www.pgroup.com/) | C, C++ and Fortran compilers from The Portland Group - PGI |
## Data
| Module | Description |
| ------ | ----------- |
| [GDAL](http://www.gdal.org/) | GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for data translation and processing. |
| [h5py](http://www.h5py.org/) | HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data. |
| [HDF5](http://www.hdfgroup.org/HDF5/) | HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections. |
| [netCDF](http://www.unidata.ucar.edu/software/netcdf/) | NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. |
| [netCDF-Fortran](http://www.unidata.ucar.edu/software/netcdf/) | NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. |
| [PostgreSQL](http://www.mysql.com/) | PostgreSQL is a powerful, open source object-relational database system. It is fully ACID compliant, has full support for foreign keys, joins, views, triggers, and stored procedures (in multiple languages). It includes most SQL:2008 data types, including INTEGER, NUMERIC, BOOLEAN, CHAR, VARCHAR, DATE, INTERVAL, and TIMESTAMP. It also supports storage of binary large objects, including pictures, sounds, or video. It has native programming interfaces for C/C++, Java, .Net, Perl, Python, Ruby, Tcl, ODBC, among others, and exceptional documentation. |
| [redis](https://redis.io) | Redis is an open source (BSD licensed), in-memory data structure store, used as a database, cache and message broker. |
| [scikit-learn](http://scikit-learn.org/stable/index.html) | Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. It strives to be simple and efficient, accessible to everybody, and reusable in various contexts. |
| [XML-Parser](http://search.cpan.org/~toddr/XML-Parser-2.41/) | This is a Perl extension interface to James Clark's XML parser, expat. |
## Debugger
| Module | Description |
| ------ | ----------- |
| [aislinn](https://github.com/spirali/aislinn) | Aislinn is a dynamic verifier for MPI programs; it can check all possible runs with respect to nondeterminism introduced by MPI. |
| [DDT](http://www.allinea.com/) | Debugger for scalar, multi-threaded and large-scale parallel applications. |
| [Forge](http://www.allinea.com/products/develop-allinea-forge) | Allinea Forge is the complete toolsuite for software development - with everything needed to debug, profile, optimize, edit and build C, C++ and FORTRAN applications on Linux for high performance - from single threads through to complex parallel HPC codes with MPI, OpenMP, threads or CUDA. |
| [PerformanceReports](http://www.allinea.com/products/allinea-performance-reports) | Allinea Performance Reports are the most effective way to characterize and understand the performance of HPC application runs. One single-page HTML report elegantly answers a range of vital questions for any HPC site. - Is this application well-optimized for the system and the processors it is running on? - Does it benefit from running at this scale? - Are there I/O, networking or threading bottlenecks affecting performance? - Which hardware, software or configuration changes can we make to improve performance further. - How much energy did this application use? |
| [TotalView](http://www.roguewave.com/products/totalview.aspx) | Dynamic source code and memory debugging for C, C++ and Fortran applications. |
| [Valgrind](http://valgrind.org/downloads/) | Valgrind: Debugging and profiling tools |
## Devel
| Module | Description |
| ------ | ----------- |
| [ant](http://ant.apache.org/) | Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications. |
| [Autoconf](http://www.gnu.org/software/autoconf/) | Autoconf is an extensible package of M4 macros that produce shell scripts to automatically configure software source code packages. These scripts can adapt the packages to many kinds of UNIX-like systems without manual user intervention. Autoconf creates a configuration script for a package from a template file that lists the operating system features that the package can use, in the form of M4 macro calls. |
| [Automake](http://www.gnu.org/software/automake/automake.html) | Automake: GNU Standards-compliant Makefile generator |
| [Autotools](http://autotools.io) | This bundle collect the standard GNU build tools: Autoconf, Automake and libtool |
| [Bazel](http://bazel.io/) | Bazel is a build tool that builds code quickly and reliably. It is used to build the majority of Google's software. |
| [Boost](http://www.boost.org/) | Boost provides free peer-reviewed portable C++ source libraries. |
| [CMake](http://www.cmake.org) | CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software. |
| [Doxygen](http://www.doxygen.org) | Doxygen is a documentation system for C++, C, Java, Objective-C, Python, IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D. |
| [fontsproto](http://www.freedesktop.org/wiki/Software/xlibs) | X11 font extension wire protocol |
| [glproto](http://www.freedesktop.org/wiki/Software/xlibs) | X protocol and ancillary headers |
| [GObject-Introspection](https://wiki.gnome.org/GObjectIntrospection/) | GObject introspection is a middleware layer between C libraries (using GObject) and language bindings. The C library can be scanned at compile time and generate a metadata file, in addition to the actual native C library. Then at runtime, language bindings can read this metadata and automatically provide bindings to call into the C library. |
| [gperf](http://www.gnu.org/software/gperf/) | GNU gperf is a perfect hash function generator. For a given list of strings, it produces a hash function and hash table, in form of C or C++ code, for looking up a value depending on the input string. The hash function is perfect, which means that the hash table has no collisions, and the hash table lookup needs a single string comparison only. |
| [guile](http://www.gnu.org/software/guile) | Guile is the GNU Ubiquitous Intelligent Language for Extensions, the official extension language for the GNU operating system. |
| [intltool](http://freedesktop.org/wiki/Software/intltool/) | intltool is a set of tools to centralize translation of many different file formats using GNU gettext-compatible PO files. |
| [Jansson](http://www.digip.org/jansson/) | Jansson is a C library for encoding, decoding and manipulating JSON data. Its main features and design principles are: * Simple and intuitive API and data model * Comprehensive documentation * No dependencies on other libraries * Full Unicode support (UTF-8) * Extensive test suite |
| [JUnit](http://sourceforge.net/projects/junit) | A programmer-oriented testing framework for Java. |
| [libICU](http://maven.apache.org/index.html) | Binary maven install, Apache Maven is a software project management and comprehension tool. Based on the concept of a project object model (POM), Maven can manage a project's build, reporting and documentation from a central piece of information. |
| [libSM](http://www.freedesktop.org/wiki/Software/xlibs) | X11 Session Management library, which allows for applications to both manage sessions, and make use of session managers to save and restore their state for later use. |
| [M4](http://www.gnu.org/software/m4/m4.html) | GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible although it has some extensions (for example, handling more than 9 positional parameters to macros). GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc. |
| [make](http://www.gnu.org/software/make/make.html) | make-3.82: GNU version of make utility |
| [makedepend](http://www.linuxfromscratch.org/blfs/view/svn/x/makedepend.html) | The makedepend package contains a C-preprocessor like utility to determine build-time dependencies. |
| [Mako](http://www.makotemplates.org) | A super-fast templating language that borrows the best ideas from the existing templating languages |
| [Maven](http://maven.apache.org/index.html) | Binary maven install, Apache Maven is a software project management and comprehension tool. Based on the concept of a project object model (POM), Maven can manage a project's build, reporting and documentation from a central piece of information. |
| [ncurses](http://www.gnu.org/software/ncurses/) | The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses. |
| [PCRE](http://www.pcre.org/) | The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5. |
| [PCRE2](http://www.pcre.org/) | The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5. |
| [pkg-config](http://www.freedesktop.org/wiki/Software/pkg-config/) | pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the correct compiler options on the command line so an application can use gcc -o test test.c `pkg-config --libs --cflags glib-2.0` for instance, rather than hard-coding values on where to find glib (or other libraries). |
| [protobuf](http://python.org/) | Python is a programming language that lets you work more quickly and integrate your systems more effectively. |
| [protobuf-python](https://github.com/google/protobuf/) | Python Protocol Buffers runtime library. |
| [python-meep](https://code.launchpad.net/python-meep) | Python wrapper for the Meep FDTD solver. |
| [Qt](http://qt-project.org/) | Qt is a comprehensive cross-platform C++ application framework. |
| [Qt5](http://qt.io/) | Qt is a comprehensive cross-platform C++ application framework. |
| [renderproto](http://www.freedesktop.org/wiki/Software/xlibs) | Xrender protocol and ancillary headers |
| [SCons](http://www.scons.org/) | SCons is a software construction tool. |
| [Spack](https://spack.io/) | Spack is a package manager for supercomputers, Linux, and macOS. It makes installing scientific software easy. With Spack, you can build a package with multiple versions, configurations, platforms, and compilers, and all of these builds can coexist on the same machine. |
| [Spark](http://spark.apache.org) | Spark is Hadoop MapReduce done in memory |
| [sparsehash](https://github.com/sparsehash/sparsehash) | An extremely memory-efficient hash_map implementation. 2 bits/entry overhead! The SparseHash library contains several hash-map implementations, including implementations that optimize for space or speed. |
| [SQLite](http://www.sqlite.org/) | SQLite: SQL Database Engine in a C Library |
| [squashfs-tools](http://squashfs.sourceforge.net/) | Squashfs is a compressed read-only filesystem for Linux. |
| [SWIG](http://www.swig.org/) | SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages. |
| [xbitmaps](http://www.freedesktop.org/wiki/Software/xlibs) | provides bitmaps for x |
| [xcb-proto](http://xcb.freedesktop.org/) | The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility. |
| [xextproto](http://www.freedesktop.org/wiki/Software/xlibs) | XExtProto protocol headers. |
| [xineramaproto](http://www.freedesktop.org/wiki/Software/xlibs) | X protocol and ancillary headers for xinerama |
| [XKeyboardConfig](http://www.freedesktop.org/wiki/Software/XKeyboardConfig/) | The non-arch keyboard configuration database for X Window. The goal is to provide the consistent, well-structured, frequently released open source of X keyboard configuration data for X Window System implementations (free, open source and commercial). The project is targeted to XKB-based systems. |
| [xorg-macros](http://cgit.freedesktop.org/xorg/util/macros) | X.org macros utilities. |
| [xproto](http://www.freedesktop.org/wiki/Software/xlibs) | X protocol and ancillary headers |
| [xtrans](http://www.freedesktop.org/wiki/Software/xlibs) | xtrans includes a number of routines to make X implementations transport-independent; at time of writing, it includes support for UNIX sockets, IPv4, IPv6, and DECnet. |
## Geo
| Module | Description |
| ------ | ----------- |
| [DCW](http://gmt.soest.hawaii.edu/projects/gmt) | country polygons for GMT |
| [Doris](http://doris.tudelft.nl/) | Delft object-oriented radar interferometric software |
| [FEFLOW](https://www.mikepoweredbydhi.com/products/feflow) | FEFLOW provides best-in-class technology for groundwater flow, contaminant, groundwater age and heat transport simulations. With its efficient user interface and its yet unmatched range of functionality and flexibility, FEFLOW has become a standard in premium groundwater modelling over the last 35 years. |
| [PHREEQC](https://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc/) | A Computer Program for Speciation, Batch-Reaction, One-Dimensional Transport, and Inverse Geochemical Calculations |
| [PROJ_4](http://proj.osgeo.org) | PROJ.4 - Cartographic Projections Library originally written by Gerald Evenden then of the USGS. |
## Lang
| Module | Description |
| ------ | ----------- |
| [Anaconda2](https://www.continuum.io/anaconda-overview) | Built to complement the rich, open source Python community, the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture. |
| [Anaconda3](https://www.continuum.io/anaconda-overview) | Built to complement the rich, open source Python community, the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture. |
| [Bison](http://www.gnu.org/software/bison) | Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables. |
| [byacc](http://invisible-island.net/byacc/byacc.html) | Berkeley Yacc (byacc) is generally conceded to be the best yacc variant available. In contrast to bison, it is written to avoid dependencies upon a particular compiler. |
| [Cython](https://pypi.python.org/pypi/Cython/) | The Cython language makes writing C extensions for the Python language as easy as Python itself. Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and optimizations. |
| [dotNET-Core-Runtime](https://www.microsoft.com/net/) | .NET is a free, cross-platform, open source developer platform for building many different types of applications. |
| [dotNET-Core-SDK](https://www.microsoft.com/net/) | .NET is a free, cross-platform, open source developer platform for building many different types of applications. |
| [flex](http://flex.sourceforge.net/) | Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, sometimes called a tokenizer, is a program which recognizes lexical patterns in text. |
| [FriBidi](https://github.com/fribidi/fribidi) | The Free Implementation of the Unicode Bidirectional Algorithm. |
| [Java](http://java.com/) | Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers. |
| [libgdiplus](https://github.com/mono/libgdiplus) | An Open Source implementation of the GDI+ API. |
| [Lua](http://www.lua.org/) | Lua is a powerful, fast, lightweight, embeddable scripting language. Lua combines simple procedural syntax with powerful data description constructs based on associative arrays and extensible semantics. Lua is dynamically typed, runs by interpreting bytecode for a register-based virtual machine, and has automatic memory management with incremental garbage collection, making it ideal for configuration, scripting, and rapid prototyping. |
| [Mono](http://www.mono-project.com) | Mono is an open source implementation of Microsoft's .NET Framework based on the ECMA standards for C# and the Common Language Runtime. |
| [NASM](http://www.nasm.us/) | NASM: General-purpose x86 assembler |
| [NodeJS](http://nodejs.org) | Node.js is a platform built on Chrome's JavaScript runtime for easily building fast, scalable network applications. Node.js uses an event-driven, non-blocking I/O model that makes it lightweight and efficient, perfect for data-intensive real-time applications that run across distributed devices. |
| [OpenCL-builder](https://software.intel.com/en-us/intel-opencl) | OpenCL™ is the first open, royalty-free standard for cross-platform, parallel programming of modern processors found in personal computers, servers and handheld/embedded devices. OpenCL (Open Computing Language) greatly improves speed and responsiveness for a wide spectrum of applications in numerous market categories from gaming and entertainment to scientific and medical software. This is builder (formerly runtime) package. |
| [OpenCL-runtime](https://software.intel.com/en-us/intel-opencl) | OpenCL™ is the first open, royalty-free standard for cross-platform, parallel programming of modern processors found in personal computers, servers and handheld/embedded devices. OpenCL (Open Computing Language) greatly improves speed and responsiveness for a wide spectrum of applications in numerous market categories from gaming and entertainment to scientific and medical software. |
| [OpenCL-sdk](https://software.intel.com/en-us/intel-opencl) | OpenCL™ is the first open, royalty-free standard for cross-platform, parallel programming of modern processors found in personal computers, servers and handheld/embedded devices. OpenCL (Open Computing Language) greatly improves speed and responsiveness for a wide spectrum of applications in numerous market categories from gaming and entertainment to scientific and medical software. |
| [Perl](http://www.perl.org/) | Larry Wall's Practical Extraction and Report Language |
| [Python](http://python.org/) | Python is a programming language that lets you work more quickly and integrate your systems more effectively. |
| [R](http://www.r-project.org/) | R is a free software environment for statistical computing and graphics. |
| [Racket](http://racket-lang.org) | Racket is a full-spectrum programming language. It goes beyond Lisp and Scheme with dialects that support objects, types, laziness, and more. |
| [RapidJSON](http://rapidjson.org/) | A fast JSON parser/generator for C++ with both SAX/DOM style API Tencent is pleased to support the open source community by making RapidJSON available. Copyright (C) 2015 THL A29 Limited, a Tencent company, and Milo Yip. All rights reserved. |
| [Ruby](https://www.ruby-lang.org) | Ruby is a dynamic, open source programming language with a focus on simplicity and productivity. It has an elegant syntax that is natural to read and easy to write. |
| [SnuCL](http://snucl.snu.ac.kr) | An OpenCL Framework for Heterogeneous Clusters |
| [sqsgenerator](https://github.com/dnoeger/sqsgenerator) | This package is a Special Quasirandom Structure generator written in Python3/Cython. Please note that the programm currently only works with Python 3. |
| [Tcl](http://www.tcl.tk/) | Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more. |
| [Yasm](http://www.tortall.net/projects/yasm/) | Yasm: Complete rewrite of the NASM assembler with BSD license |
## Lib
| Module | Description |
| ------ | ----------- |
| [ACE](http://www.dre.vanderbilt.edu/~schmidt/ACE-overview.html) | The ADAPTIVE Communication Environment (ACE) is a freely available, open-source object-oriented (OO) framework that implements many core patterns for concurrent communication software. ACE provides a rich set of reusable C++ wrapper facades and framework components that perform common communication software tasks across a range of OS platforms. The communication software tasks provided by ACE include event demultiplexing and event handler dispatching, signal handling, service initialization, interprocess communication, shared memory management, message routing, dynamic (re)configuration of distributed services, concurrent execution and synchronization. ACE is targeted for developers of high-performance and real-time communication services and applications. It simplifies the development of OO network applications and services that utilize interprocess communication, event demultiplexing, explicit dynamic linking, and concurrency. In addition, ACE automates system configuration and reconfiguration by dynamically linking services into applications at run-time and executing these services in one or more processes or threads. |
| [ACTC](https://sourceforge.net/projects/actc) | ACTC converts independent triangles into triangle strips or fans. |
| [astroid](https://github.com/PyCQA/astroid) | The aim of this module is to provide a common base representation of python source code for projects such as pychecker, pyreverse, pylint… Well, actually the development of this library is essentially governed by pylint’s needs. It used to be called logilab-astng. |
| [cereal](http://uscilab.github.io/cereal/) | cereal is a header-only C++11 serialization library. |
| [darshan-runtime](http://www.mcs.anl.gov/research/projects/darshan/) | Darshan is designed to capture an accurate picture of application I/O behavior, including properties such as patterns of access within files, with minimum overhead. The name is taken from a Sanskrit word for “sight” or “vision”. Darshan can be used to investigate and tune the I/O behavior of complex HPC applications. In addition, Darshan’s lightweight design makes it suitable for full time deployment for workload characterization of large systems. We hope that such studies will help the storage research community to better serve the needs of scientific computing. Darshan was originally developed on the IBM Blue Gene series of computers deployed at the Argonne Leadership Computing Facility, but it is portable across a wide variety of platforms include the Cray XE6, Cray XC30, and Linux clusters. Darshan routinely instruments jobs using up to 786,432 compute cores on the Mira system at ALCF. |
| [darshan-util](http://www.mcs.anl.gov/research/projects/darshan/) | Darshan is designed to capture an accurate picture of application I/O behavior, including properties such as patterns of access within files, with minimum overhead. The name is taken from a Sanskrit word for “sight” or “vision”. Darshan can be used to investigate and tune the I/O behavior of complex HPC applications. In addition, Darshan’s lightweight design makes it suitable for full time deployment for workload characterization of large systems. We hope that such studies will help the storage research community to better serve the needs of scientific computing. Darshan was originally developed on the IBM Blue Gene series of computers deployed at the Argonne Leadership Computing Facility, but it is portable across a wide variety of platforms include the Cray XE6, Cray XC30, and Linux clusters. Darshan routinely instruments jobs using up to 786,432 compute cores on the Mira system at ALCF. |
| [Embree](https://embree.github.io/index.html) | Embree is a collection of high-performance ray tracing kernels, developed at Intel. |
| [ETSF_IO](http://www.etsf.eu/resources/software/libraries_and_tools) | A library of F90 routines to read/write the ETSF file format has been written. It is called ETSF_IO and available under LGPL. |
| [FOX](http://fox-toolkit.org) | FOX is a C++ based Toolkit for developing Graphical User Interfaces easily and effectively. It offers a wide, and growing, collection of Controls, and provides state of the art facilities such as drag and drop, selection, as well as OpenGL widgets for 3D graphical manipulation. |
| [freeglut](http://freeglut.sourceforge.net/) | freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library. |
| [glibc](https://www.gnu.org/software/libc/) | The Glibc package contains the main C library. This library provides the basic routines for allocating memory, searching directories, opening and closing files, reading and writing files, string handling, pattern matching, arithmetic, and so on. |
| [GLM](https://github.com/g-truc/glm) | OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphics software based on the OpenGL Shading Language (GLSL) specifications. |
| [HyperLoom](https://code.it4i.cz/ADAS/loom) | Framework for distributed task execution |
| [isort](https://github.com/timothycrosley/isort) | isort is a Python utility / library to sort imports alphabetically, and automatically separated into sections. It provides a command line utility, Python library and plugins for various editors to quickly sort all your imports. |
| [libarchive](https://www.libarchive.org/) | Multi-format archive and compression library |
| [libdrm](http://dri.freedesktop.org) | Direct Rendering Manager runtime library. |
| [libevent](http://libevent.org/) | The libevent API provides a mechanism to execute a callback function when a specific event occurs on a file descriptor or after a timeout has been reached. Furthermore, libevent also support callbacks due to signals or regular timeouts. |
| [libffi](http://sourceware.org/libffi/) | The libffi library provides a portable, high level programming interface to various calling conventions. This allows a programmer to call any function specified by a call interface description at run-time. |
| [libfontenc](http://www.freedesktop.org/wiki/Software/xlibs/) | X11 font encoding library |
| [libgd](http://libgd.bitbucket.org/) | GD is an open source code library for the dynamic creation of images by programmers. |
| [libglade](https://developer.gnome.org/libglade/) | Libglade is a library for constructing user interfaces dynamically from XML descriptions. |
| [libjpeg-turbo](http://sourceforge.net/libjpeg-turbo/) | libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG compression and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding. |
| [libmatheval](http://www.gnu.org/software/libmatheval/) | GNU libmatheval is a library (callable from C and Fortran) to parse and evaluate symbolic expressions input as text. |
| [libMesh](http://libmesh.github.io/) | The libMesh library provides a framework for the numerical simulation of partial differential equations using arbitrary unstructured discretizations on serial and parallel platforms. A major goal of the library is to provide support for adaptive mesh refinement (AMR) computations in parallel while allowing a research scientist to focus on the physics they are modeling. |
| [libpng](http://www.libpng.org/pub/png/libpng.html) | libpng is the official PNG reference library |
| [libpthread-stubs](http://xcb.freedesktop.org/) | The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility. |
| [libreadline](http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html) | The GNU Readline library provides a set of functions for use by applications that allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. The Readline library includes additional functions to maintain a list of previously-entered command lines, to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands. |
| [librsync](http://git-scm.com/) | librsync is a library for calculating and applying network deltas, with an interface designed to ease integration into diverse network applications. |
| [libsndfile](http://www.mega-nerd.com/libsndfile) | Libsndfile is a C library for reading and writing files containing sampled sound (such as MS Windows WAV and the Apple/SGI AIFF format) through one standard library interface. |
| [LIBSVM](http://www.csie.ntu.edu.tw/~cjlin/libsvm/) | LIBSVM is an integrated software for support vector classification, (C-SVC, nu-SVC), regression (epsilon-SVR, nu-SVR) and distribution estimation (one-class SVM). It supports multi-class classification. |
| [LibTIFF](http://www.remotesensing.org/libtiff/) | tiff: Library and tools for reading and writing TIFF data files |
| [libtool](http://www.gnu.org/software/libtool) | GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface. |
| [libunistring](http://www.gnu.org/software/libunistring/) | This library provides functions for manipulating Unicode strings and for manipulating C strings according to the Unicode standard. |
| [libunwind](http://www.nongnu.org/libunwind/) | The primary goal of libunwind is to define a portable and efficient C programming interface (API) to determine the call-chain of a program. The API additionally provides the means to manipulate the preserved (callee-saved) state of each call-frame and to resume execution at any point in the call-chain (non-local goto). The API supports both local (same-process) and remote (across-process) operation. As such, the API is useful in a number of applications |
| [LibUUID](http://sourceforge.net/projects/libuuid/) | Portable uuid C library |
| [libuv](https://github.com/libuv) | libuv is a multi-platform support library with a focus on asynchronous I/O. It was primarily developed for use by Node.js, but it's also used by Luvit, Julia, pyuv, and others. |
| [libxcb](http://xcb.freedesktop.org/) | The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility. |
| [libxml2](http://xmlsoft.org/) | Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform). |
| [libxslt](http://xmlsoft.org/) | Libxslt is the XSLT C library developed for the GNOME project (but usable outside of the Gnome platform). |
| [libyaml](http://pyyaml.org/wiki/LibYAML) | LibYAML is a YAML 1.1 parser and emitter written in C. |
| [libzip](https://nih.at/libzip/) | libzip is a C library for reading, creating, and modifying zip archives. Files can be added from data buffers, files, or compressed data copied directly from other zip archives. Changes made without closing the archive can be reverted. The API is documented by man pages. |
| [lxml](http://lxml.de/) | The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt. |
| [MATIO](http://sourceforge.net/projects/matio/) | matio is an C library for reading and writing Matlab MAT files. |
| [mpi4py](http://mpi4py.scipy.org/docs) | MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for the Python programming language, allowing any Python program to exploit multiple processors. |
| [nettle](http://www.lysator.liu.se/~nisse/nettle/) | Nettle is a cryptographic library that is designed to fit easily in more or less any context: In crypto toolkits for object-oriented languages (C++, Python, Pike, ...), in applications like LSH or GNUPG, or even in kernel space. |
| [OpenCoarrays](http://www.opencoarrays.org) | OpenCoarrays is an open-source software project for developing, porting and tuning transport layers that support coarray Fortran compilers. |
| [PROJ](http://trac.osgeo.org/proj/) | Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates |
| [psycopg2](http://initd.org/psycopg/) | Psycopg is the most popular PostgreSQL adapter for the Python programming language. |
| [pylint](https://github.com/PyCQA/pylint) | Pylint is a Python source code analyzer which looks for programming errors, helps enforcing a coding standard and sniffs for some code smells (as defined in Martin Fowler's Refactoring book). |
| [PyYAML](https://pypi.python.org/pypi/PyYAML/) | PyYAML is a YAML parser and emitter for the Python programming language. |
| [QCA](http://delta.affinix.com/qca/) | QCA aims to provide a straightforward and cross-platform crypto API, using Qt datatypes and conventions. QCA separates the API from the implementation, using plugins known as Providers |
| [Qwt](http://qwt.sourceforge.net/index.html) | The Qwt library contains GUI Components and utility classes which are primarily useful for programs with a technical background. Beside a framework for 2D plots it provides scales, sliders, dials, compasses, thermometers, wheels and knobs to control or display values, arrays, or ranges of type double. |
| [scipy](https://github.com/jupyter/testpath) | Test utilities for code working with files and commands |
| [SIONlib](http://www.fz-juelich.de/ias/jsc/EN/Expertise/Support/Software/SIONlib/_node.html) | SIONlib is a scalable I/O library for parallel access to task-local files. The library not only supports writing and reading binary data to or from several thousands of processors into a single or a small number of physical files, but also provides global open and close functions to access SIONlib files in parallel. This package provides a stripped-down installation of SIONlib for use with performance tools (e.g., Score-P), with renamed symbols to avoid conflicts when an application using SIONlib itself is linked against a tool requiring a different SIONlib version. |
| [spatialindex](https://libspatialindex.github.io/index.html) | The purpose of this library is to provide: * An extensible framework that will support robust spatial indexing methods. * Support for sophisticated spatial queries. Range, point location, nearest neighbor and k-nearest neighbor as well as parametric queries (defined by spatial constraints) should be easy to deploy and run. * Easy to use interfaces for inserting, deleting and updating information. |
| [tbb](http://software.intel.com/en-us/articles/intel-tbb/) | Intel Threading Building Blocks 4.0 (Intel TBB) is a widely used, award-winning C++ template library for creating reliable, portable, and scalable parallel applications. Use Intel TBB for a simple and rapid way of developing robust task-based parallel applications that scale to available processor cores, are compatible with multiple environments, and are easier to maintain. Intel TBB is the most proficient way to implement future-proof parallel applications that tap into the power and performance of multicore and manycore hardware platforms. |
| [Tensorflow](https://www.tensorflow.org/) | An open-source software library for Machine Intelligence |
| [TRIQS](https://triqs.ipht.cnrs.fr) | TRIQS (Toolbox for Research on Interacting Quantum Systems) is a scientific project providing a set of C++ and Python libraries to develop new tools for the study of interacting quantum systems. |
| [zlib](http://www.zlib.net/) | zlib is designed to be a free, general-purpose, legally unencumbered -- that is, not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system. |
## Math
| Module | Description |
| ------ | ----------- |
| [Eigen](http://eigen.tuxfamily.org/index.php?title=Main_Page) | Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms. |
| [FIAT](https://bitbucket.org/fenics-project/fiat) | The FInite element Automatic Tabulator FIAT supports generation of arbitrary order instances of the Lagrange elements on lines, triangles, and tetrahedra. It is also capable of generating arbitrary order instances of Jacobi-type quadrature rules on the same element shapes. |
| [GEOS](http://trac.osgeo.org/geos) | GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS) |
| [GMP](http://gmplib.org/) | GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers. |
| [h5py](http://www.h5py.org/) | HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data. |
| [Harminv](http://ab-initio.mit.edu/wiki/index.php/Harminv) | Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion - given a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially decaying) in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those sinusoids. |
| [ISL](http://isl.gforge.inria.fr/) | isl is a library for manipulating sets and relations of integer points bounded by linear constraints. |
| [Keras](https://keras.io/) | Keras is a minimalist, highly modular neural networks library, written in Python and capable of running on top of either TensorFlow or Theano. |
| [libcerf](http://gnuplot.sourceforge.net/) | libcerf is a self-contained numeric library that provides an efficient and accurate implementation of complex error functions, along with Dawson, Faddeeva, and Voigt functions. |
| [libsmm](https://www.cp2k.org/) | Library for small matrix multiplies. |
| [libxsmm](https://github.com/hfp/libxsmm) | LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications targeting Intel Architecture (x86). |
| [MATLAB](http://www.mathworks.com/products/matlab) | MATLAB is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran. |
| [METIS](http://glaros.dtc.umn.edu/gkhome/metis/metis/overview) | METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes. |
| [MPC](http://www.multiprecision.org/) | Gnu Mpc is a C library for the arithmetic of complex numbers with arbitrarily high precision and correct rounding of the result. It extends the principles of the IEEE-754 standard for fixed precision real floating point numbers to complex numbers, providing well-defined semantics for every operation. At the same time, speed of operation at high precision is a major design goal. |
| [MPFR](http://www.mpfr.org) | The MPFR library is a C library for multiple-precision floating-point computations with correct rounding. |
| [MUMPS](http://graal.ens-lyon.fr/MUMPS/) | [A parallel sparse direct solver |
| [numpy](http://www.numpy.org) | NumPy is the fundamental package for scientific computing with Python. It contains among other things: a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases. |
| [Octave](http://www.gnu.org/software/octave/) | GNU Octave is a high-level interpreted language, primarily intended for numerical computations. |
| [ParMETIS](http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview) | ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes. |
| [Qhull](http://www.qhull.org) | Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, furthest-site Delaunay triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, and higher dimensions. Qhull implements the Quickhull algorithm for computing the convex hull. |
| [ScientificPython](https://sourcesup.cru.fr/projects/scientific-py/) | ScientificPython is a collection of Python modules for scientific computing. It contains support for geometry, mathematical functions, statistics, physical units, IO, visualization, and parallelization. |
| [scipy](https://github.com/jupyter/testpath) | Test utilities for code working with files and commands |
| [SCOTCH](http://gforge.inria.fr/projects/scotch/) | Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning. |
| [sympy](http://sympy.org/) | SymPy is a Python library for symbolic mathematics. It aims to become a full-featured computer algebra system (CAS) while keeping the code as simple as possible in order to be comprehensible and easily extensible. SymPy is written entirely in Python and does not require any external libraries. |
| [Theano](http://deeplearning.net/software/theano) | Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently. |
## Mpi
| Module | Description |
| ------ | ----------- |
| [impi](http://software.intel.com/en-us/intel-mpi-library/) | The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification. |
| [MPI_NET](http://www.osl.iu.edu/research/mpi.net/) | MPI.NET is a high-performance, easy-to-use implementation of the Message Passing Interface (MPI) for Microsoft's .NET environment |
| [MPICH](http://www.mpich.org/) | MPICH v3.x is an open source high-performance MPI 3.0 implementation. It does not support InfiniBand (use MVAPICH2 with InfiniBand devices). |
| [MPT](https://www.nas.nasa.gov/hecc/support/kb/sgi-mpt_89.html) | [The modulefile defines paths and environment variables needed to use MPT in a non-default location. |
| [MVAPICH2](http://mvapich.cse.ohio-state.edu/overview/mvapich2/) | This is an MPI 3.0 implementation. It is based on MPICH2 and MVICH. |
| [OpenMPI](http://www.open-mpi.org/) | The Open MPI Project is an open source MPI-2 implementation. |
## Numlib
| Module | Description |
| ------ | ----------- |
| [Armadillo](http://arma.sourceforge.net/) | Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions. |
| [arpack-ng](http://forge.scilab.org/index.php/p/arpack-ng/) | ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. |
| [ATLAS](http://math-atlas.sourceforge.net) | ATLAS (Automatically Tuned Linear Algebra Software) is the application of the AEOS (Automated Empirical Optimization of Software) paradigm, with the present emphasis on the Basic Linear Algebra Subprograms (BLAS), a widely used, performance-critical, linear algebra kernel library. |
| [CGAL](http://www.cgal.org/) | [The goal of the CGAL Open Source Project is to provide easy access to efficient and reliable geometric algorithms in the form of a C++ library. |
| [Clp](https://projects.coin-or.org/Clp) | [Clp (COIN-OR linear programming) is an open-source linear programming solver written in C++. It is primarily meant to be used as a callable library, but a basic stand-alone executable version is also available. It is a part of the COIN-OR project (https://www.coin-or.org). |
| [CNTKCustomMKL](https://www.microsoft.com/en-us/cognitive-toolkit/) | The default CNTK math library is the Intel Math Kernel Library (Intel MKL). CNTK supports using the Intel MKL via a custom library version (CNTK custom MKL). |
| [FFTW](http://www.fftw.org) | FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data. |
| [GSL](http://www.gnu.org/software/gsl/) | The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting. |
| [Hypre](https://computation.llnl.gov/casc/linear_solvers/sls_hypre.html) | Hypre is a library for solving large, sparse linear systems of equations on massively parallel computers. The problems of interest arise in the simulation codes being developed at LLNL and elsewhere to study physical phenomena in the defense, environmental, energy, and biological sciences. |
| [imkl](http://software.intel.com/en-us/intel-mkl/) | Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more. |
| [LAPACK](http://www.netlib.org/lapack/) | LAPACK is written in Fortran90 and provides routines for solving systems of simultaneous linear equations, least-squares solutions of linear systems of equations, eigenvalue problems, and singular value problems. |
| [LAPACKE](http://www.netlib.org/lapack/lapacke.html) | LAPACKE C Interface to LAPACK header files and library |
| [LIBLINEAR](http://www.csie.ntu.edu.tw/~cjlin/liblinear/) | LIBLINEAR is a simple package for solving large-scale regularized linear classification and regression. It supports L2-regularized logistic regression, L2-loss support vector classification L1-loss support vector classification, L1-regularized L2-loss support vector classification, L1-regularized logistic regression L2-regularized L2-loss support vector regression, L1-loss support vector regression. |
| [mkl](http://software.intel.com/en-us/intel-mkl/) | Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more. |
| [MPI-LIBLINEAR](https://www.csie.ntu.edu.tw/~cjlin/libsvmtools/distributed-liblinear/mpi/) | MPI LIBLINEAR is an extension of LIBLINEAR on distributed environments. The usage and the data format are the same as LIBLINEAR. It supports L2-regularized logistic regression, L2-regularized logistic regression, L2-regularized L2-loss linear SVM (primal trust-region Newton), L2-regularized L1-loss linear SVM (dual), L2-regularized logistic regression (primal limited common directions), L2-regularized L2-loss linear SVM (primal limited common directions). Module created by the PERMON Team (http://permon.it4i.cz). |
| [NLopt](http://ab-initio.mit.edu/wiki/index.php/NLopt) | NLopt is a free/open-source library for nonlinear optimization, providing a common interface for a number of different free optimization routines available online as well as original implementations of various other algorithms. |
| [OpenBLAS](http://xianyi.github.com/OpenBLAS/) | OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version. |
| [PETSc](http://www.mcs.anl.gov/petsc) | PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. |
| [PFFT](https://www-user.tu-chemnitz.de/~mpip/software.php?lang=en) | PFFT is a software library for computing massively parallel, fast Fourier transformations on distributed memory architectures. PFFT can be understood as a generalization of FFTW-MPI to multidimensional data decomposition. |
| [qrupdate](https://sourceforge.net/projects/qrupdate/) | qrupdate is a Fortran library for fast updates of QR and Cholesky decompositions. |
| [ScaLAPACK](http://www.netlib.org/scalapack/) | The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers. |
| [SLEPc](http://www.grycap.upv.es/slepc/) | SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution of large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for either standard or generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a partial SVD of a large, sparse, rectangular matrix, and to solve quadratic eigenvalue problems. |
| [SuiteSparse](http://www.cise.ufl.edu/research/sparse/SuiteSparse/) | SuiteSparse is a collection of libraries manipulate sparse matrices. |
| [Trilinos](http://trilinos.sandia.gov/) | The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems. A unique design feature of Trilinos is its focus on packages. |
## Perf
| Module | Description |
| ------ | ----------- |
| [Advisor](https://software.intel.com/intel-advisor-xe) | Vectorization Optimization and Thread Prototyping - Vectorize & thread code or performance “dies” - Easy workflow + data + tips = faster code faster - Prioritize, Prototype & Predict performance gain |
| [Cube](http://www.scalasca.org/software/cube-4.x/download.html) | Cube, which is used as performance report explorer for Scalasca and Score-P, is a generic tool for displaying a multi-dimensional performance space consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree can be collapsed or expanded to achieve the desired level of granularity. |
| [ipp](http://software.intel.com/en-us/articles/intel-ipp/) | Intel Integrated Performance Primitives (Intel IPP) is an extensive library of multicore-ready, highly optimized software functions for multimedia, data processing, and communications applications. Intel IPP offers thousands of optimized functions covering frequently used fundamental algorithms. |
| [MAP](http://www.allinea.com/) | C, C++ and F90 profiler for high performance and multithreaded Linux applications |
| [OPARI2](http://www.score-p.org) | OPARI2, the successor of Forschungszentrum Juelich's OPARI, is a source-to-source instrumentation tool for OpenMP and hybrid codes. It surrounds OpenMP directives and runtime library calls with calls to the POMP2 measurement interface. |
| [OTF2](http://www.score-p.org) | The Open Trace Format 2 is a highly scalable, memory efficient event trace data format plus support library. It will become the new standard trace format for Scalasca, Vampir, and Tau and is open for other tools. |
| [PAPI](http://icl.cs.utk.edu/projects/papi/) | PAPI provides the tool designer and application engineer with a consistent interface and methodology for use of the performance counter hardware found in most major microprocessors. PAPI enables software engineers to see, in near real time, the relation between software performance and processor events. In addition Component PAPI provides access to a collection of components that expose performance measurement opportunites across the hardware and software stack. |
| [PDT](http://www.cs.uoregon.edu/research/pdt/) | Program Database Toolkit (PDT) is a framework for analyzing source code written in several programming languages and for making rich program knowledge accessible to developers of static and dynamic analysis tools. PDT implements a standard program representation, the program database (PDB), that can be accessed in a uniform way through a class library supporting common PDB operations. |
| [perfboost](http://www.sgi.com/) | Use applications compiled with other MPIs with SGI MPI |
| [perfcatcher](http://www.sgi.com/) | Light-weight application profiler for SGI MPI |
| [PerfReports](http://www.allinea.com/") | helps you address the question of quality of utilization. It provides a one page HTML report - collecting, analyzing and reporting the key metrics that impact performance. It can be used without changing either the source code or the application - removing the barriers and opening access to everyon |
| [PerfSuite](http://perfsuite.ncsa.illinois.edu/") | PerfSuite is a collection of tools, utilities, and libraries for software performance analysis where the primary design goals are ease of use, comprehensibility, interoperability, and simplicity. This software can provide a good "entry point" for more detailed performance analysis and can help point the way towards selecting other tools and/or techniques using more specialized software if necessary (for example, tools/libraries from academic research groups or third-party commercial software |
| [Scalasca](http://www.scalasca.org/) | Scalasca is a software tool that supports the performance optimization of parallel programs by measuring and analyzing their runtime behavior. The analysis identifies potential performance bottlenecks – in particular those concerning communication and synchronization – and offers guidance in exploring their causes. |
| [Score-P](http://www.vi-hps.org/projects/score-p//) | Score-P offers the user a maximum of convenience by supporting a number of analysis tools. Currently, it works with Periscope, Scalasca, Vampir, and Tau and is open for other tools. Score-P comes together with the new Open Trace Format Version 2, the Cube4 profiling format and the Opari2 instrumenter (see below). Score-P is available under the New BSD Open Source license. |
| [Vampir](http://www.vampir.eu) | The Vampir software tool provides an easy-to-use framework that enables developers to quickly display and analyze arbitrary program behavior at any level of detail. The tool suite implements optimized event analysis algorithms and customizable displays that enable fast and interactive rendering of very complex performance monitoring data. |
| [VampirServer](http://www.vampir.eu) | The Vampir software tool provides an easy-to-use framework that enables developers to quickly display and analyze arbitrary program behavior at any level of detail. The tool suite implements optimized event analysis algorithms and customizable displays that enable fast and interactive rendering of very complex performance monitoring data. |
## Phys
| Module | Description |
| ------ | ----------- |
| [ALAMODE](http://alamode.readthedocs.io/) | ALAMODE is an open source software designed for analyzing lattice anharmonicity and lattice thermal conductivity of solids. By using an external DFT package such as VASP and Quantum ESPRESSO, you can extract harmonic and anharmonic force constants straightforwardly with ALAMODE. Using the calculated anharmonic force constants, you can also estimate lattice thermal conductivity, phonon linewidth, and other anharmonic phonon properties from first principles. |
| [CASMcode](CASMcode) | CASM (https://github.com/prisms-center/CASMcode) is an open source software package designed to perform first-principles statistical mechanical studies of multi-component crystalline solids. CASM interfaces with first-principles electronic structure codes, automates the construction and parameterization of effective Hamiltonians and subsequently builds highly optimized (kinetic) Monte Carlo codes to predict finite-temperature thermodynamic and kinetic properties. CASM uses group theoretic techniques that take full advantage of crystal symmetry in order to rigorously construct effective Hamiltonians for almost arbitrary degrees of freedom in crystalline solids. This includes cluster expansions for configurational disorder in multi-component solids and lattice-dynamical effective Hamiltonians for vibrational degrees of freedom involved in structural phase transitions. |
| [DynaPhoPy](https://github.com/abelcarreras/DynaPhoPy) | Software to calculate crystal microscopic anharmonic properties from molecular dynamics (MD) using the normal-mode-decomposition technique. These properties include the phonon frequency shifts and linewidths, as well as the renormalized force constanst and thermal properties by using quasiparticle theory. This code includes interfaces for MD outputs from VASP and LAMMPS .PHONOPY code is used to obtain harmonic phonon modes. |
| [Elk](http://elk.sourceforge.net/) | An all-electron full-potential linearised augmented-plane wave (FP-LAPW) code with many advanced features. Written originally at Karl-Franzens-Universität Graz as a milestone of the EXCITING EU Research and Training Network, the code is designed to be as simple as possible so that new developments in the field of density functional theory (DFT) can be added quickly and reliably. |
| [LMGC90](https://git-xen.lmgc.univ-montp2.fr/lmgc90/) | LMGC90 is a free and open source software dedicated to multiple physics simulation of discrete material and structures. Module created by Jiri Tomcala from the PERMON Team (http://permon.it4i.cz) and Josef Hrabal from IT4I Supercomputing Services |
| [Meep](http://ab-initio.mit.edu/wiki/index.php/Meep) | Meep (or MEEP) is a free finite-difference time-domain (FDTD) simulation software package developed at MIT to model electromagnetic systems. |
| [Netgen](https://ngsolve.org/) | Netgen/NGSolve is a high performance multiphysics finite element software. It is widely used to analyze models from solid mechanics, fluid dynamics and electromagnetics. Due to its flexible Python interface new physical equations and solution algorithms can be implemented easily. |
| [phono3py](http://phonopy.sourceforge.net/phono3py/index.html) | This software calculates phonon-phonon interaction related properties |
| [phonopy](http://python.org/) | Python is a programming language that lets you work more quickly and integrate your systems more effectively. |
| [PLUTO](https://github.com/JohannesBuchner/PLUTO) | PLUTO is Godunov-type code for astrophysical fluid dynamics supporting several modules and algorithms. This is the v 4.2 (August 2015) version of the code (http://plutocode.ph.unito.it). This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. |
| [PragTic](http://permon.it4i.cz/pragtic) | PragTic is a module for massively parallel runs of the PragTic library. Homepage: http://permon.it4i.cz/pragtic. Module created by Jiri Tomcala from the PERMON Team (http://permon.it4i.cz) |
| [Sen2Cor](http://step.esa.int/main/third-party-plugins-2/sen2cor/) | Sen2Cor is a processor for Sentinel-2 Level 2A product generation and formatting; it performs the atmospheric-, terrain and cirrus correction of Top-Of- Atmosphere Level 1C input data. Sen2Cor creates Bottom-Of-Atmosphere, optionally terrain- and cirrus corrected reflectance images; additional, Aerosol Optical Thickness-, Water Vapor-, Scene Classification Maps and Quality Indicators for cloud and snow probabilities. Its output product format is equivalent to the Level 1C User Product: JPEG 2000 images, three different resolutions, 60, 20 and 10 m. |
| [Siesta](http://departments.icmab.es/leem/siesta) | SIESTA is both a method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids. This version si compiled with OpenMP and MPI support. |
| [VASP](http://www.vasp.at) | The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles. To use VASP, You need academic licenses from University of Wiena. Follow the instructions https://www.vasp.at/index.php/faqs. Then send us please a list of authorized users and their ID for which you need this access. Please use only http://support.it4i.cz/rt. We are responsible to verify your licenses. After succesfull verification You will be granted to use VASP in our enviroment. |
## Python
| Module | Description |
| ------ | ----------- |
| [absl-py](https://pypi.python.org/pypi/absl-py) | Abseil Python Common Libraries, see https://github.com/abseil/abseil-py. |
| [ASE](https://wiki.fysik.dtu.dk/ase/) | ASE is a python package providing an open source Atomic Simulation Environment in the Python scripting language. |
| [asn1crypto](https://pypi.python.org/pypi/asn1crypto) | A fast, pure Python library for parsing and serializing ASN.1 structures. |
| [astor](https://pypi.python.org/pypi/astor) | Read/rewrite/write Python ASTs |
| [asv](https://github.com/airspeed-velocity/asv) | Airspeed velocity (asv) is a tool for benchmarking Python packages over their lifetime. |
| [attrs](http://www.attrs.org/) | Classes Without Boilerplate |
| [backports_abc](https://pypi.python.org/pypi/backports_abc) | A backport of recent additions to the "collections.abc" module. |
| [bcrypt](https://pypi.python.org/pypi/bcrypt) | Modern password hashing for your software and your servers |
| [bleach](https://pypi.python.org/pypi/bleach) | An easy safelist-based HTML-sanitizing tool. |
| [BoltzTraP2](https://www.imc.tuwien.ac.at/index.php?id=21094) | BoltzTraP2 is a modern implementation of the smoothed Fourier interpolation algorithm for electronic bands that formed the base of the original and widely used BoltzTraP code. |
| [certifi](https://pypi.python.org/pypi/certifi) | Python package for providing Mozillas CA Bundle. |
| [cffi](https://pypi.python.org/pypi/cffi) | Foreign Function Interface for Python calling C code. |
| [click](https://pypi.python.org/pypi/click) | A simple wrapper around optparse for powerful command line utilities. |
| [cryptography](https://pypi.python.org/pypi/cryptography) | Cryptography is a package which provides cryptographic recipes and primitives to Python developers. |
| [cycler](https://matplotlib.org/cycler) | Composable style cycles. |
| [dask](https://pypi.python.org/pypi/dask) | Parallel PyData with Task Scheduling. |
| [decorator](https://pypi.python.org/pypi/decorator) | Better living through Python with decorators. |
| [dist-keras](https://pypi.python.org/pypi/dist-keras) | Distributed Deep learning with Apache Spark with Keras. |
| [DynaPhoPy](https://github.com/abelcarreras/DynaPhoPy) | Software to calculate crystal microscopic anharmonic properties from molecular dynamics (MD) using the normal-mode-decomposition technique. These properties include the phonon frequency shifts and linewidths, as well as the renormalized force constanst and thermal properties by using quasiparticle theory. This code includes interfaces for MD outputs from VASP and LAMMPS .PHONOPY code is used to obtain harmonic phonon modes. |
| [enum34](https://pypi.python.org/pypi/enum34) | An enumeration is a set of symbolic names (members) bound to unique, constant values. |
| [fasteners](https://pypi.python.org/pypi/fasteners) | A python package that provides useful locks. |
| [Flask](https://pypi.python.org/pypi/flask) | A microframework based on Werkzeug, Jinja2 and good intentions. |
| [gast](https://pypi.python.org/pypi/gast) | Python AST that abstracts the underlying Python version |
| [grpcio](https://pypi.python.org/pypi/grpcio) | HTTP/2-based RPC framework |
| [h5py](http://www.h5py.org/) | HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data. |
| [html5lib](https://pypi.python.org/pypi/html5lib) | HTML parser based on the WHATWG HTML specification. |
| [idna](https://pypi.python.org/pypi/idna) | Support for the Internationalised Domain Names in Applications (IDNA) protocol as specified in RFC 5891. |
| [ipaddress](https://pypi.python.org/pypi/ipaddress) | IPv4/IPv6 manipulation library. |
| [itsdangerous](https://pypi.python.org/pypi/itsdangerous) | Various helpers to pass trusted data to untrusted environments and back. |
| [Jinja2](https://pypi.python.org/pypi/jinja) | A small but fast and easy to use stand-alone template engine written in pure python. |
| [Keras](https://keras.io/) | Keras is a minimalist, highly modular neural networks library, written in Python and capable of running on top of either TensorFlow or Theano. |
| [latexcodec](https://pypi.python.org/pypi/latexcodec) | A lexer and codec to work with LaTeX code in Python. |
| [loom](https://code.it4i.cz/ADAS/loom) | Framework for distributed task execution |
| [lxml](http://lxml.de/) | The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt. |
| [Mako](http://www.makotemplates.org) | A super-fast templating language that borrows the best ideas from the existing templating languages |
| [Markdown](https://pypi.python.org/pypi/Markdown) | Python implementation of Markdown. |
| [MarkupSafe](https://pypi.python.org/pypi/markupsafe) | Implements a XML/HTML/XHTML Markup safe string for Python. |
| [matplotlib](http://matplotlib.org) | matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits. |
| [Mercurial](http://mercurial.selenic.com/) | Mercurial is a free, distributed source control management tool. It efficiently handles projects of any size and offers an easy and intuitive interface. |
| [monotonic](https://pypi.python.org/pypi/monotonic) | This module provides a monotonic() function which returns the value (in fractional seconds) of a clock which never goes backwards. |
| [monty](https://pypi.python.org/pypi/monty) | Monty is the missing complement to Python. |
| [mpi4py](http://mpi4py.scipy.org/docs) | MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for the Python programming language, allowing any Python program to exploit multiple processors. |
| [mpmath](https://pypi.python.org/pypi/mpmath) | Python library for arbitrary-precision floating-point arithmetic. |
| [networkx](https://pypi.python.org/pypi/networkx) | NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks. |
| [numpy](http://www.numpy.org) | NumPy is the fundamental package for scientific computing with Python. It contains among other things: a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases. |
| [packaging](https://pypi.python.org/pypi/packaging) | Core utilities for Python packages. |
| [palettable](https://pypi.python.org/pypi/palettable) | Color palettes for Python. |
| [pandas](https://pypi.python.org/pypi/pandas) | Powerful data structures for data analysis, time series,and statistics. |
| [paramiko](https://pypi.python.org/pypi/paramiko) | This is a library for making SSH2 connections (client or server). |
| [phonopy](http://python.org/) | Python is a programming language that lets you work more quickly and integrate your systems more effectively. |
| [Pillow](http://pillow.readthedocs.org/) | Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors. |
| [Platypus](https://github.com/andyrimmer/Platypus) | The Platypus variant caller. |
| [pluggy](https://github.com/pytest-dev/pluggy) | Plugin and hook calling mechanisms for python. |
| [pudb](https://pypi.python.org/pypi/pudb) | PuDB is a full-screen, console-based visual debugger for Python. |
| [py4j](https://pypi.python.org/pypi/py4j) | Enables Python programs to dynamically access arbitrary Java objects. |
| [pyasn1](https://pypi.python.org/pypi/pyasn1) | Pure-Python implementation of ASN.1 types and DER/BER/CER codecs (X.208) |
| [pybtex](https://pypi.python.org/pypi/pybtex) | A BibTeX-compatible bibliography processor in Python. |
| [pycparser](https://pypi.python.org/pypi/pycparser) | Pycparser is a complete parser of the C language, written in pure Python using the PLY parsing library. It parses C code into an AST and can serve as a front-end for C compilers or analysis tools. |
| [PyDispatcher](https://pypi.python.org/pypi/PyDispatcher) | Multi-producer-multi-consumer signal dispatching mechanism. |
| [pydot](https://pypi.python.org/pypi/pydot) | A Python interface to GraphViz and the DOT language. |
| [pyFFTW](https://pypi.python.org/pypi/pyFFTW) | A pythonic wrapper around FFTW, the FFT library, presenting a unified interface for all the supported transforms. |
| [pymatgen](https://pypi.python.org/pypi/pymatgen) | Python Materials Genomics is a robust materials analysis code that defines core object representations for structures and molecules with support for many electronic structure codes. It is currently the core analysis code powering the Materials Project (https://www.materialsproject.org). |
| [PyNaCl](https://pypi.python.org/pypi/PyNaCl) | Python binding to the Networking and Cryptography (NaCl) library |
| [pyparsing](http://pyparsing.wikispaces.com) | The pyparsing module provides a library of classes that client code uses to construct the grammar directly in Python code. |
| [PyQt](http://www.riverbankcomputing.co.uk/software/pyqt) | PyQt is a set of Python v2 and v3 bindings for Digia's Qt application framework. |
| [PyQt5](http://www.riverbankcomputing.co.uk/software/pyqt) | PyQt5 is a set of Python bindings for v5 of the Qt application framework from The Qt Company. |
| [pyspark](https://pypi.python.org/pypi/pyspark) | Apache Spark Python API |
| [pytest](http://pytest.org) | Simple powerful testing with Python |
| [python-dateutil](https://github.com/dateutil/dateutil) | Useful extensions to the standard Python datetime features. |
| [pytz](http://pytz.sourceforge.net/) | pytz brings the Olson tz database into Python. This library allows accurate and cross platform timezone calculations using Python 2.4 or higher. |
| [PyWavelets](https://pypi.python.org/pypi/PyWavelets) | PyWavelets, wavelet transform module. |
| [PyYAML](https://pypi.python.org/pypi/PyYAML/) | PyYAML is a YAML parser and emitter for the Python programming language. |
| [pyzmq](https://pypi.python.org/pypi/pyzmq) | Python bindings for 0MQ. |
| [ranger](https://github.com/ranger/ranger) | ranger is a console file manager with VI key bindings. It provides a minimalistic and nice curses interface with a view on the directory hierarchy. It ships with rifle, a file launcher that is good at automatically finding out which program to use for what file type. |
| [requests](https://pypi.python.org/pypi/requests) | Python HTTP for Humans. |
| [ruamel.yaml](https://pypi.python.org/pypi/ruamel.yaml) | ruamel.yaml is a YAML parser/emitter that supports roundtrip preservation of comments, seq/map flow style, and map key order |
| [scikit-image](http://scikit-learn.org/stable/index.html) | Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. It strives to be simple and efficient, accessible to everybody, and reusable in various contexts. |
| [scikit-learn](http://scikit-learn.org/stable/index.html) | Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. It strives to be simple and efficient, accessible to everybody, and reusable in various contexts. |
| [scipy](https://github.com/jupyter/testpath) | Test utilities for code working with files and commands |
| [SCons](http://www.scons.org/) | SCons is a software construction tool. |
| [seaborn](https://pypi.python.org/pypi/seaborn) | Seaborn: statistical data visualization |
| [singledispatch](https://pypi.python.org/pypi/singledispatch) | A small but fast and easy to use stand-alone template engine written in pure python. |
| [SIP](http://www.riverbankcomputing.com/software/sip/) | SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries. |
| [six](https://github.com/benjaminp/six) | Python 2 and 3 compatibility library. |
| [spglib-python](https://pypi.python.org/pypi/spglib) | Spglib for Python. Spglib is a library for finding and handling crystal symmetries written in C. |
| [sympy](http://sympy.org/) | SymPy is a Python library for symbolic mathematics. It aims to become a full-featured computer algebra system (CAS) while keeping the code as simple as possible in order to be comprehensible and easily extensible. SymPy is written entirely in Python and does not require any external libraries. |
| [tabulate](https://pypi.python.org/pypi/tabulate) | Pretty-print tabular data. |
| [tensorboard](https://github.com/tensorflow/tensorboard) | TensorBoard lets you watch Tensors Flow. |
| [Tensorflow](https://www.tensorflow.org/) | An open-source software library for Machine Intelligence |
| [tensorflow-tensorboard](https://github.com/tensorflow/tensorboard) | TensorBoard lets you watch Tensors Flow. |
| [termcolor](https://pypi.python.org/pypi/termcolor) | ANSII Color formatting for output in terminal. |
| [Theano](http://deeplearning.net/software/theano) | Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently. |
| [toolz](https://pypi.python.org/pypi/toolz) | List processing tools and functional utilities. |
| [tornado](https://pypi.python.org/pypi/tornado) | Tornado is a Python web framework and asynchronous networking library, originally developed at FriendFeed. |
| [urllib3](https://pypi.python.org/pypi/urllib3) | HTTP library with thread-safe connection pooling, file post, and more. |
| [virtualenv](https://pypi.python.org/pypi/virtualenv) | Virtual Python Environment builder. |
| [webencodings](https://pypi.python.org/pypi/webencodings) | Character encoding aliases for legacy web content. |
| [Werkzeug](https://pypi.python.org/pypi/Werkzeug) | The comprehensive WSGI web application library. |
| [wheel](https://pypi.python.org/pypi/wheel) | A built-package format for Python. |
## System
| Module | Description |
| ------ | ----------- |
| [eudev](https://wiki.gentoo.org/wiki/Project:Eudev) | eudev is a fork of systemd-udev with the goal of obtaining better compatibility with existing software such as OpenRC and Upstart, older kernels, various toolchains and anything else required by users and various distributions. |
| [hwloc](http://www.open-mpi.org/projects/hwloc/) | The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various system attributes such as cache and memory information as well as the locality of I/O devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering information about modern computing hardware so as to exploit it accordingly and efficiently. |
| [libpciaccess](http://cgit.freedesktop.org/xorg/lib/libpciaccess/) | Generic PCI access library. |
| [LibreSSL](http://www.libressl.org/) | LibreSSL is a version of the TLS/crypto stack forked from OpenSSL in 2014, with goals of modernizing the codebase, improving security, and applying best practice development processes. Primary development occurs inside the OpenBSD source tree with the usual care the project is known for. On a regular basis the code is re-packaged for portable use by other operating systems (Linux, FreeBSD, Windows, etc). |
| [OpenSSL](http://www.openssl.org/) | The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) protocols as well as a full-strength general purpose cryptography library. |
## Toolchain
| Module | Description |
| ------ | ----------- |
| foss | GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK. |
| [GNU](http://www.gnu.org/software/) | Compiler-only toolchain with GCC and binutils. |
| gompi | GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support. |
| [iccifort](http://software.intel.com/en-us/intel-cluster-toolkit-compiler/) | Intel C, C++ and Fortran compilers |
| [ictce](http://software.intel.com/en-us/intel-cluster-toolkit-compiler/) | Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL. |
| [iimpi](http://software.intel.com/en-us/intel-cluster-toolkit-compiler/) | Intel C/C++ and Fortran compilers, alongside Intel MPI. |
| [intel](http://software.intel.com/en-us/intel-cluster-toolkit-compiler/) | Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL. |
| [iomkl](http://software.intel.com/en-us/intel-cluster-toolkit-compiler/) | Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & OpenMPI. |
| [iompi](http://software.intel.com/en-us/intel-cluster-toolkit-compiler/) | Intel C/C++ and Fortran compilers, alongside Open MPI. |
| [libc](https://www.gnu.org/software/libc/) | The Glibc package contains the main C library. This library provides the basic routines for allocating memory, searching directories, opening and closing files, reading and writing files, string handling, pattern matching, arithmetic, and so on. |
| [PRACE](http://www.prace-ri.eu/PRACE-Common-Production) | The PRACE Common Production Environment (PCPE) is a set of software tools and libraries that are planned to be available on all PRACE execution sites. The PCPE also defines a set of environment variables that try to make compilation on all sites as homogeneous and simple as possible. |
| [prace](http://www.prace-ri.eu/PRACE-Common-Production) | PRACE Common Production Environment (PCPE) Initialisation of the PRACE common production environment. This allows you to assume that the following tools/libraries are available by default in your PATH/environment. * Fortran, C, C++ Compilers * MPI * BLAS, LAPACK, BLACS, ScaLAPACK * FFTW * HDF5, NetCDF The compiler commands on are: * mpif90 - Fortran compiler * mpicc - C compiler * mpicxx - C++ compiler For more information on the PCPE please see the documentation at: http://www.prace-ri.eu/PRACE-Common-Production For help using this system, please see Local User Guide available at: http://prace-ri.eu/Best-Practice-Guide-Anselm-HTML |
| [Py](https://www.python.org) | Python 2.7 toolchain |
## Tools
| Module | Description |
| ------ | ----------- |
| [ANSYS](http://www.ansys.com) | ANSYS simulation software enables organizations to confidently predict how their products will operate in the real world. We believe that every product is a promise of something greater. |
| [APR](http://apr.apache.org/) | Apache Portable Runtime (APR) libraries. |
| [APR-util](http://apr.apache.org/) | Apache Portable Runtime (APR) util libraries. |
| [Bash](http://www.gnu.org/software/bash) | Bash is an sh-compatible command language interpreter that executes commands read from the standard input or from a file. Bash also incorporates useful features from the Korn and C shells (ksh and csh). |
| [BeoPEST](http://www.prinmath.com/pest/) | BeoPEST is a special version of John Doherty's PEST adapted for Beowulf clusters. BeoPEST is identical in operation to Parallel PEST, except that it instead of a master and slaves that communicate through the file system, BeoPEST uses a master and smart slaves that communicate via TCP/IP or MPI. BeoPEST also uses smart slaves which offloads much of the effort to the slaves which is important for BeoPEST to scale to hundreds or thousands of slaves. More detail is provided in the BeoPEST Documentation. |
| [binutils](http://directory.fsf.org/project/binutils/) | binutils: GNU binary utilities |
| [bzip2](http://www.bzip.org/) | bzip2 is a freely available, patent free, high-quality data compressor. It typically compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical compressors), whilst being around twice as fast at compression and six times faster at decompression. |
| [CORALbenchmark](https://asc.llnl.gov/CORAL-benchmarks) | Benchmark Codes |
| [Coreutils](http://www.gnu.org/software/coreutils/) | The GNU Core Utilities are the basic file, shell and text manipulation utilities of the GNU operating system. These are the core utilities which are expected to exist on every operating system. |
| [cURL](http://curl.haxx.se) | libcurl is a free and easy-to-use client-side URL transfer library, supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling and more. |
| [DMTCP](http://dmtcp.sourceforge.net/index.html) | DMTCP (Distributed MultiThreaded Checkpointing) transparently checkpoints a single-host or distributed computation in user-space -- with no modifications to user code or to the O/S. |
| [duplicity](http://duplicity.nongnu.org/index.html) | Encrypted bandwidth-efficient backup using the rsync algorithm. |
| [EasyBuild](https://easybuilders.github.io/easybuild) | EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way. |
| [expat](http://expat.sourceforge.net/) | Expat is an XML parser library written in C. It is a stream-oriented parser in which an application registers handlers for things the parser might find in the XML document (like start tags) |
| [Ghostscript](http://ghostscript.com) | Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to different targets. It used to be part of the cups printing stack, but is no longer used for that. |
| [git](http://git-scm.com/) | Git is a free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency. |
| [globus](http://toolkit.globus.org/toolkit/") | Set environment variables to enable usage of Globus |
| [GLPK](https://www.gnu.org/software/glpk/) | The GLPK (GNU Linear Programming Kit) package is intended for solving large-scale linear programming (LP), mixed integer programming (MIP), and other related problems. It is a set of routines written in ANSI C and organized in the form of a callable library. |
| [gperftools](http://github.com/gperftools/gperftools) | gperftools are for use by developers so that they can create more robust applications. Especially of use to those developing multi-threaded applications in C++ with templates. Includes TCMalloc, heap-checker, heap-profiler and cpu-profiler. |
| [Graph500](http://graph500.org/) | Reference code of the Graph500 benchmark. |
| [gzip](http://www.gnu.org/software/gzip/) | gzip (GNU zip) is a popular data compression program as a replacement for compress |
| [Hadoop](http://archive.cloudera.com/cdh5/cdh/5/) | Hadoop MapReduce by Cloudera |
| [help2man](https://www.gnu.org/software/help2man/) | help2man produces simple manual pages from the '--help' and '--version' output of other commands. |
| [HPL](http://www.netlib.org/benchmark/hpl/) | HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the High Performance Computing Linpack Benchmark. |
| [Inspector](http://software.intel.com/en-us/intel-inspector-xe) | Intel Inspector XE 2013 is an easy to use memory error checker and thread checker for serial and parallel applications |
| [IOR](https://github.com/chaos/ior) | The IOR software is used for benchmarking parallel file systems using POSIX, MPIIO, or HDF5 interfaces. |
| [itac](http://software.intel.com/en-us/intel-trace-analyzer/) | The Intel Trace Collector is a low-overhead tracing library that performs event-based tracing in applications. The Intel Trace Analyzer provides a convenient way to monitor application activities gathered by the Intel Trace Collector through graphical displays. |
| [JOE](http://joe-editor.sourceforge.net) | JOE is a full featured terminal-based screen editor which is distributed under the GNU General Public License (GPL) |
| [LicenseChecker](http://www.it4i.cz) | Tools for Dr. Sevcik (mailto:dr.sevcik@vsb.cz)- checking license files |
| [likwid](https://github.com/RRZE-HPC/likwid) | Toolsuite of command line applications for performance oriented programmers |
| [Lmod](http://sourceforge.net/projects/lmod/) | Lmod is a Lua based module system. Modules allow for dynamic modification of a user's environment under Unix systems. See www.tacc.utexas.edu/tacc-projects/lmod for a complete description. Lmod is a new implementation that easily handles the MODULEPATH Hierarchical problem. It is drop-in replacement for TCL/C modules and reads TCL modulefiles directly. |
| [LSMS](https://asc.llnl.gov/CORAL-benchmarks/#lsms) | LSMS benchmark, part of CORAL suite |
| [mdtest](http://sourceforge.net/projects/mdtest/) | mdtest is an MPI-coordinated metadata benchmark test that performs open/stat/close operations on files and directories and then reports the performance. |
| [Mercurial](http://mercurial.selenic.com/) | Mercurial is a free, distributed source control management tool. It efficiently handles projects of any size and offers an easy and intuitive interface. |
| [MIKE](http://www.mikepoweredbydhi.com) | MIKE Powered by DHI is a part of DHI, the global organisation dedicated to solving challenges in water environments worldwide. |
| [moreutils](https://joeyh.name/code/moreutils/) | Moreutils is a growing collection of the unix tools that nobody thought to write long ago when unix was young. |
| [networkx](https://pypi.python.org/pypi/networkx) | NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks. |
| [numactl](http://oss.sgi.com/projects/libnuma/) | The numactl program allows you to run your application program on specific cpu's and memory nodes. It does this by supplying a NUMA memory policy to the operating system before running your program. The libnuma library provides convenient ways for you to add NUMA memory policies into your own program. |
| [osm2pgsql](http://wiki.openstreetmap.org/wiki/Osm2pgsql) | osm2pgsql is a command-line based program that converts OpenStreetMap data to postGIS-enabled PostgreSQL databases |
| [PAPI](http://icl.cs.utk.edu/projects/papi/) | PAPI provides the tool designer and application engineer with a consistent interface and methodology for use of the performance counter hardware found in most major microprocessors. PAPI enables software engineers to see, in near real time, the relation between software performance and processor events. In addition Component PAPI provides access to a collection of components that expose performance measurement opportunites across the hardware and software stack. |
| [parallel](http://savannah.gnu.org/projects/parallel/) | parallel: Build and execute shell commands in parallel |
| [PatchELF](https://nixos.org/patchelf.html) | PatchELF is a small utility to modify the dynamic linker and RPATH of ELF executables. |
| [pigz](http://zlib.net/pigz/) | pigz, which stands for parallel implementation of gzip, is a fully functional replacement for gzip that exploits multiple processors and multiple cores to the hilt when compressing data. pigz was written by Mark Adler, and uses the zlib and pthread libraries. |
| [QBOX](https://asc.llnl.gov/CORAL-benchmarks/#qbox) | QBOX benchmark, part of CORAL suite |
| [QEMU](http://wiki.qemu.org/Main_Page) | QEMU is a generic and open source machine emulator and virtualizer. |
| [RStudio](https://www.rstudio.com) | RStudio is a set of integrated tools designed to help you be more productive with R. It includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management. |
| [Scalasca](http://www.scalasca.org/) | Scalasca is a software tool that supports the performance optimization of parallel programs by measuring and analyzing their runtime behavior. The analysis identifies potential performance bottlenecks – in particular those concerning communication and synchronization – and offers guidance in exploring their causes. |
| [Score-P](http://www.vi-hps.org/projects/score-p//) | Score-P offers the user a maximum of convenience by supporting a number of analysis tools. Currently, it works with Periscope, Scalasca, Vampir, and Tau and is open for other tools. Score-P comes together with the new Open Trace Format Version 2, the Cube4 profiling format and the Opari2 instrumenter (see below). Score-P is available under the New BSD Open Source license. |
| [SDE](https://software.intel.com/en-us/articles/intel-software-development-emulator) | Intel Software Development Emulator is a pintool that enables the development of applications using instruction set extensions that are not currently implemented in hardware. |
| [SentinelToolboxes](https://sentinel.esa.int/web/sentinel/toolboxes) | A common architecture for all Sentinel Toolboxes is being jointly developed by Brockmann Consult, Array Systems Computing and C-S called the Sentinel Application Platform (SNAP). The SNAP architecture is ideal for Earth Observation processing and analysis due the following technological innovations: Extensibility, Portability, Modular Rich Client Platform, Generic EO Data Abstraction, Tiled Memory Management, and a Graph Processing Framework. |
| [Serf](http://serf.apache.org/) | The serf library is a high performance C-based HTTP client library built upon the Apache Portable Runtime (APR) library |
| [Singularity](http://gmkurtzer.github.io/singularity) | Singularity is a portable application stack packaging and runtime utility. |
| [Subversion](http://subversion.apache.org/) | Subversion is an open source version control system. |
| [Szip](http://www.hdfgroup.org/doc_resource/SZIP/) | Szip compression software, providing lossless compression of scientific data |
| [Tar](http://www.gnu.org/software/tar/tar.html) | tar: The GNU tape archiver |
| [tcsh](http://www.tcsh.org) | Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). It is a command language interpreter usable both as an interactive login shell and a shell script command processor. It includes a command-line editor, programmable word completion, spelling correction, a history mechanism, job control and a C-like syntax. |
| [tmux](https://github.com/tmux/tmux/wiki) | It lets you switch easily between several programs in one terminal, detach them (they keep running in the background) and reattach them to a different terminal |
| [turbovnc](http://www.turbovnc.org) | TurboVNC is a derivative of VNC (Virtual Network Computing) that is tuned to provide peak performance for 3D and video workloads. |
| [util-linux](http://www.kernel.org/pub/linux/utils/util-linux) | Set of Linux utilities |
| [VDE2](http://vde.sourceforge.net) | VDE is an ethernet compliant virtual network that can be spawned over a set of physical computer over the Internet. VDE is part of virtualsquare project. |
| [VirtualGL](http://www.virtualgl.org) | VirtualGL is an open source toolkit that gives any Unix or Linux remote display software the ability to run OpenGL applications with full 3D hardware acceleration. |
| [VTune](http://software.intel.com/en-us/intel-vtune-amplifier-xe) | Intel VTune Amplifier XE 2016 is the premier performance profiler for C, C++, C#, Fortran, Assembly and Java. |
| [Wine](https://www.winehq.org) | Wine (originally an acronym for "Wine Is Not an Emulator") is a compatibility layer capable of running Windows applications on several POSIX-compliant operating systems, such as Linux, Mac OSX, & BSD. |
| [x86_adapt](https://github.com/tud-zih-energy/x86_adapt) | http://dx.doi.org/10.1007/s00450-013-0243-7 |
| [XZ](http://tukaani.org/xz/) | xz: XZ utilities |
| [zsh](http://www.zsh.org/) | Zsh is a shell designed for interactive use, although it is also a powerful scripting language. |
## Vis
| Module | Description |
| ------ | ----------- |
| [ATK](https://developer.gnome.org/ATK/stable/) | ATK provides the set of accessibility interfaces that are implemented by other toolkits and applications. Using the ATK interfaces, accessibility tools have full access to view and control running applications. |
| [cairo](http://cairographics.org) | Cairo is a 2D graphics library with support for multiple output devices. Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB |
| [ffmpeg](https://www.ffmpeg.org/) | A complete, cross-platform solution to record, convert and stream audio and video. |
| [FFmpeg](https://www.ffmpeg.org/) | A complete, cross-platform solution to record, convert and stream audio and video. |
| [fixesproto](http://www.freedesktop.org/wiki/Software/xlibs) | X.org FixesProto protocol headers. |
| [FLTK](http://www.fltk.org) | FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL and its built-in GLUT emulation. |
| [fontconfig](http://www.freedesktop.org/software/fontconfig) | Fontconfig is a library designed to provide system-wide font configuration, customization and application access. |
| [freetype](http://freetype.org) | FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display servers, font conversion tools, text image generation tools, and many other products as well. |
| [Gdk-Pixbuf](https://developer.gnome.org/gdk-pixbuf/stable/) | The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it was distributed as part of GTK+ 2 but it was split off into a separate package in preparation for the change to GTK+ 3. |
| [gettext](http://www.gnu.org/software/gettext/) | GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation |
| [GL2PS](http://www.geuz.org/gl2ps/) | GL2PS: an OpenGL to PostScript printing library |
| [GLib](http://www.gtk.org/) | GLib is one of the base libraries of the GTK+ project |
| [gnuplot](http://gnuplot.sourceforge.net/) | Portable interactive, function plotting utility |
| [GPI-2](http://www.gpi-site.com/gpi2/) | GPI-2 is an API for the development of scalable, asynchronous and fault tolerant parallel applications. |
| [grace](http://freecode.com/projects/grace) | Grace is a WYSIWYG 2D plotting tool for X Windows System and Motif. |
| [GraphicsMagick](http://www.graphicsmagick.org/) | GraphicsMagick is the swiss army knife of image processing. |
| [GTK+](https://developer.gnome.org/gtk+/stable/) | The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications. |
| [HarfBuzz](http://www.freedesktop.org/wiki/Software/HarfBuzz) | HarfBuzz is an OpenType text shaping engine. |
| [inputproto](http://www.freedesktop.org/wiki/Software/xlibs) | X.org InputProto protocol headers. |
| [JasPer](http://www.ece.uvic.ca/~frodo/jasper/) | The JasPer Project is an open-source initiative to provide a free software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard. |
| [kbproto](http://www.freedesktop.org/wiki/Software/xlibs) | X.org KBProto protocol headers. |
| [libepoxy](https://github.com/anholt/libepoxy) | Epoxy is a library for handling OpenGL function pointer management for you |
| [libGLU](ftp://ftp.freedesktop.org/pub/mesa/glu/) | The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. |
| [libICE](http://www.freedesktop.org/wiki/Software/xlibs) | X Inter-Client Exchange library for freedesktop.org |
| [libX11](http://www.freedesktop.org/wiki/Software/xlibs) | X11 client-side library |
| [libXau](http://www.freedesktop.org/wiki/Software/xlibs) | The libXau package contains a library implementing the X11 Authorization Protocol. This is useful for restricting client access to the display. |
| [libXdamage](http://www.freedesktop.org/wiki/Software/xlibs) | X Damage extension library |
| [libXdmcp](http://www.freedesktop.org/wiki/Software/xlibs) | The libXdmcp package contains a library implementing the X Display Manager Control Protocol. This is useful for allowing clients to interact with the X Display Manager. |
| [libXext](http://www.freedesktop.org/wiki/Software/xlibs) | Common X Extensions library |
| [libXfixes](http://www.freedesktop.org/wiki/Software/xlibs) | X Fixes extension library |
| [libXfont](http://www.freedesktop.org/wiki/Software/xlibs) | X font libary |
| [libXft](http://www.freedesktop.org/wiki/Software/xlibs) | X11 client-side library |
| [libXinerama](http://www.freedesktop.org/wiki/Software/xlibs) | Xinerama multiple monitor library |
| [libXrender](http://www.freedesktop.org/wiki/Software/xlibs) | X11 client-side library |
| [libXt](http://www.freedesktop.org/wiki/Software/xlibs) | libXt provides the X Toolkit Intrinsics, an abstract widget library upon which other toolkits are based. Xt is the basis for many toolkits, including the Athena widgets (Xaw), and LessTif (a Motif implementation). |
| [matplotlib](http://matplotlib.org) | matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits. |
| [Mesa](http://www.mesa3d.org/) | Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics. |
| [motif](http://motif.ics.com/) | Motif refers to both a graphical user interface (GUI) specification and the widget toolkit for building applications that follow that specification under the X Window System on Unix and other POSIX-compliant systems. It was the standard toolkit for the Common Desktop Environment and thus for Unix. |
| [OpenCV](http://opencv.org/) | OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library. OpenCV was built to provide a common infrastructure for computer vision applications and to accelerate the use of machine perception in the commercial products. |
| [opencv-python](http://deeplearning.net/software/theano) | Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently. |
| [OpenDX](http://www.opendx.org) | Open source visualization software package based on IBM's Visualization Data Explorer. |
| [OpenJPEG](http://www.openjpeg.org/) | OpenJPEG is an open-source JPEG 2000 codec written in C language. |
| [OSPRay](http://www.ospray.org) | A Ray Tracing Based Rendering Engine for High-Fidelity Visualization |
| [p4vasp](http://www.p4vasp.at) | p4vasp is a visualization suite for the Vienna Ab-initio Simulation Package (VASP). It contains an extensible GUI framework, that can be used to view material structure, density of states, band-structure and more. |
| [Pango](http://www.pango.org/) | Pango is a library for laying out and rendering of text, with an emphasis on internationalization. Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x. |
| [ParaView](http://www.paraview.org) | ParaView is a scientific parallel visualizer. |
| [Pillow](http://pillow.readthedocs.org/) | Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors. |
| [pixman](http://www.pixman.org/) | Pixman is a low-level software library for pixel manipulation, providing features such as image compositing and trapezoid rasterization. Important users of pixman are the cairo graphics library and the X server. |
| [PyCairo](http://cairographics.org/pycairo/) | Python bindings for the cairo library |
| [PyGObject](http://www.pygtk.org/) | Python Bindings for GLib/GObject/GIO/GTK+ |
| [PyGTK](http://www.pygtk.org/) | PyGTK lets you to easily create programs with a graphical user interface using the Python programming language. |
| [python-dateutil](https://github.com/dateutil/dateutil) | Useful extensions to the standard Python datetime features. |
| [scikit-image](http://scikit-learn.org/stable/index.html) | Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. It strives to be simple and efficient, accessible to everybody, and reusable in various contexts. |
| [seekpath](https://github.com/giovannipizzi/seekpath) | SeeK-path is a python module to obtain and visualize band paths in the Brillouin zone of crystal structures. The definition of k-point labels follows crystallographic convention, as defined and discussed in the HPKOT paper. Moreover, the Bravais lattice is detected properly using the spacegroup symmetry. Also the suggested band path provided in the HPKOT paper is returned. Systems without time-reversal and inversion-symmetry are also properly taken into account. |
| [SUMO](http://www.sumo.dlr.de/wiki/Main_Page) | Simulation of Urban MObility (SUMO) is an open source, highly portable, microscopic and continuous road traffic simulation package designed to handle large road networks. |
| [Tix](http://tix.sourceforge.net/) | Tix, the Tk Interface eXtension, is a powerful set of user interface components that expands the capabilities of your Tcl/Tk and Python applications. Using Tix together with Tk will greatly enhance the appearance and functionality of your application. |
| [Tk](http://www.tcl.tk/) | Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building a graphical user interface (GUI) in many different programming languages. |
| [Togl](https://sourceforge.net/projects/togl/) | A Tcl/Tk widget for OpenGL rendering. |
| [VisIt](https://wci.llnl.gov/simulation/computer-codes/visit) | VisIt is an Open Source, interactive, scalable, visualization, animation and analysis tool |
| [VTK](http://www.vtk.org) | The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation. |
| [X11](https://www.x.org) | The X Window System (X11) is a windowing system for bitmap displays |
| [x264](http://www.videolan.org/developers/x264.html) | x264 is a free software library and application for encoding video streams into the H.264/MPEG-4 AVC compression format, and is released under the terms of the GNU GPL. |
| [Xvfb](http://www.x.org) | Xvfb is an X server that can run on machines with no display hardware and no physical input devices. It emulates a dumb framebuffer using virtual memory. |
## Vizserv
| Module | Description |
| ------ | ----------- |
| [CUDA](https://developer.nvidia.com/cuda-toolkit) | CUDA (formerly Compute Unified Device Architecture) is a parallel computing platform and programming model created by NVIDIA and implemented by the graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs. |
* ![pdf](img/pdf.png)[PBS Pro Programmer's Guide][1]
* ![pdf](img/pdf.png)[PBS Pro Quick Start Guide][2]
* ![pdf](img/pdf.png)[PBS Pro Reference Guide][3]
* ![pdf](img/pdf.png)[PBS Pro User's Guide][4]
[1]: http://www.pbsworks.com/pdfs/PBSProgramGuide13.0.pdf
[2]: http://www.pbsworks.com/pdfs/PBSQuickStartGuide13.0.pdf
[3]: http://www.pbsworks.com/pdfs/PBSReferenceGuide13.0.pdf
[4]: http://www.pbsworks.com/pdfs/PBSUserGuide13.0.pdf
# PRACE User Support
## Introduction
PRACE users coming to the TIER-1 systems offered through the DECI calls are in general treated as standard users and so most of the general documentation applies to them as well. This section shows the main differences for quicker orientation, but often uses references to the original documentation. PRACE users who don't undergo the full procedure (including signing the IT4I AuP on top of the PRACE AuP) will not have a password and thus access to some services intended for regular users. This can lower their comfort, but otherwise they should be able to use the TIER-1 system as intended. Please see the [Obtaining Login Credentials section][1], if the same level of access is required.
All general [PRACE User Documentation][a] should be read before continuing reading the local documentation here.
## Help and Support
If you have any troubles, need information, request support or want to install additional software, use [PRACE Helpdesk][b].
Information about the local services are provided in the [introduction of general user documentation Salomon][2] and [introduction of general user documentation Anselm][3]. Please keep in mind, that standard PRACE accounts don't have a password to access the web interface of the local (IT4Innovations) request tracker and thus a new ticket should be created by sending an e-mail to support[at]it4i.cz.
## Obtaining Login Credentials
In general PRACE users already have a PRACE account setup through their HOMESITE (institution from their country) as a result of rewarded PRACE project proposal. This includes signed PRACE AuP, generated and registered certificates, etc.
If there's a special need a PRACE user can get a standard (local) account at IT4Innovations. To get an account on a cluster, the user needs to obtain the login credentials. The procedure is the same as for general users of the cluster, so see the corresponding [section of the general documentation here][1].
## Accessing the Cluster
### Access With GSI-SSH
For all PRACE users the method for interactive access (login) and data transfer based on grid services from Globus Toolkit (GSI SSH and GridFTP) is supported.
The user will need a valid certificate and to be present in the PRACE LDAP (contact your HOME SITE or the primary investigator of your project for LDAP account creation).
Most of the information needed by PRACE users accessing the TIER-1 systems can be found here:
* [General user's FAQ][c]
* [Certificates FAQ][d]
* [Interactive access using GSISSH][e]
* [Data transfer with GridFTP][f]
* [Data transfer with gtransfer][g]
Before you start to use any of the services don't forget to create a proxy certificate from your certificate:
```console
$ grid-proxy-init
```
To check whether your proxy certificate is still valid (by default it's valid 12 hours), use:
```console
$ grid-proxy-info
```
To access the cluster, several login nodes running GSI SSH service are available. The service is available from public Internet as well as from the internal PRACE network (accessible only from other PRACE partners).
#### Access From PRACE Network:
It is recommended to use the single DNS name **name-cluster**-prace.it4i.cz which is distributed between the four login nodes. If needed, user can login directly to one of the login nodes. The addresses are:
For Salomon cluster:
| Login address | Port | Protocol | Login node |
| ---------------------------- | ---- | -------- | -------------------------------- |
| salomon-prace.it4i.cz | 2222 | gsissh | login1, login2, login3 or login4 |
| login1-prace.salomon.it4i.cz | 2222 | gsissh | login1 |
| login2-prace.salomon.it4i.cz | 2222 | gsissh | login2 |
| login3-prace.salomon.it4i.cz | 2222 | gsissh | login3 |
| login4-prace.salomon.it4i.cz | 2222 | gsissh | login4 |
```console
$ gsissh -p 2222 salomon-prace.it4i.cz
```
For Anselm cluster:
| Login address | Port | Protocol | Login node |
| --------------------------- | ---- | -------- | ---------------- |
| anselm-prace.it4i.cz | 2222 | gsissh | login1 or login2 |
| login1-prace.anselm.it4i.cz | 2222 | gsissh | login1 |
| login2-prace.anselm.it4i.cz | 2222 | gsissh | login2 |
```console
$ gsissh -p 2222 anselm-prace.it4i.cz
```
When logging from other PRACE system, the prace_service script can be used:
```console
$ gsissh `prace_service -i -s salomon`
```
```console
$ gsissh `prace_service -i -s anselm`
```
#### Access From Public Internet:
It is recommended to use the single DNS name **name-cluster**.it4i.cz which is distributed between the four login nodes. If needed, user can login directly to one of the login nodes. The addresses are:
For Salomon cluster:
| Login address | Port | Protocol | Login node |
| ---------------------------- | ---- | -------- | -------------------------------- |
| salomon.it4i.cz | 2222 | gsissh | login1, login2, login3 or login4 |
| login1.salomon.it4i.cz | 2222 | gsissh | login1 |
| login2-prace.salomon.it4i.cz | 2222 | gsissh | login2 |
| login3-prace.salomon.it4i.cz | 2222 | gsissh | login3 |
| login4-prace.salomon.it4i.cz | 2222 | gsissh | login4 |
```console
$ gsissh -p 2222 salomon.it4i.cz
```
For Anselm cluster:
| Login address | Port | Protocol | Login node |
| --------------------- | ---- | -------- | ---------------- |
| anselm.it4i.cz | 2222 | gsissh | login1 or login2 |
| login1.anselm.it4i.cz | 2222 | gsissh | login1 |
| login2.anselm.it4i.cz | 2222 | gsissh | login2 |
```console
$ gsissh -p 2222 anselm.it4i.cz
```
When logging from other PRACE system, the prace_service script can be used:
```console
$ gsissh `prace_service -e -s salomon`
```
```console
$ gsissh `prace_service -e -s anselm`
```
Although the preferred and recommended file transfer mechanism is [using GridFTP][5], the GSI SSH
implementation supports also SCP, so for small files transfer gsiscp can be used:
```console
$ gsiscp -P 2222 _LOCAL_PATH_TO_YOUR_FILE_ salomon.it4i.cz:_SALOMON_PATH_TO_YOUR_FILE_
$ gsiscp -P 2222 salomon.it4i.cz:_SALOMON_PATH_TO_YOUR_FILE_ _LOCAL_PATH_TO_YOUR_FILE_
$ gsiscp -P 2222 _LOCAL_PATH_TO_YOUR_FILE_ salomon-prace.it4i.cz:_SALOMON_PATH_TO_YOUR_FILE_
$ gsiscp -P 2222 salomon-prace.it4i.cz:_SALOMON_PATH_TO_YOUR_FILE_ _LOCAL_PATH_TO_YOUR_FILE_
```
```console
$ gsiscp -P 2222 _LOCAL_PATH_TO_YOUR_FILE_ anselm.it4i.cz:_ANSELM_PATH_TO_YOUR_FILE_
$ gsiscp -P 2222 anselm.it4i.cz:_ANSELM_PATH_TO_YOUR_FILE_ _LOCAL_PATH_TO_YOUR_FILE_
$ gsiscp -P 2222 _LOCAL_PATH_TO_YOUR_FILE_ anselm-prace.it4i.cz:_ANSELM_PATH_TO_YOUR_FILE_
$ gsiscp -P 2222 anselm-prace.it4i.cz:_ANSELM_PATH_TO_YOUR_FILE_ _LOCAL_PATH_TO_YOUR_FILE_
```
### Access to X11 Applications (VNC)
If the user needs to run X11 based graphical application and does not have a X11 server, the applications can be run using VNC service. If the user is using regular SSH based access, see the [section in general documentation][6].
If the user uses GSI SSH based access, then the procedure is similar to the [SSH based access][6], only the port forwarding must be done using GSI SSH:
```console
$ gsissh -p 2222 salomon.it4i.cz -L 5961:localhost:5961
```
### Access With SSH
After successful obtainment of login credentials for the local IT4Innovations account, the PRACE users can access the cluster as regular users using SSH. For more information see [the section in general documentation for Salomon][9] and [the section in general documentation for Anselm][9].
## File Transfers
PRACE users can use the same transfer mechanisms as regular users (if they've undergone the full registration procedure). For information about this, see [the section in the general documentation for Salomon][8] and [the section in general documentation for Anselm][9].
Apart from the standard mechanisms, for PRACE users to transfer data to/from Salomon cluster, a GridFTP server running Globus Toolkit GridFTP service is available. The service is available from public Internet as well as from the internal PRACE network (accessible only from other PRACE partners).
There's one control server and three backend servers for striping and/or backup in case one of them would fail.
### Access From PRACE Network
For Salomon cluster:
| Login address | Port | Node role |
| ----------------------------- | ---- | --------------------------- |
| gridftp-prace.salomon.it4i.cz | 2812 | Front end /control server |
| lgw1-prace.salomon.it4i.cz | 2813 | Backend / data mover server |
| lgw2-prace.salomon.it4i.cz | 2813 | Backend / data mover server |
| lgw3-prace.salomon.it4i.cz | 2813 | Backend / data mover server |
Copy files **to** Salomon by running the following commands on your local machine:
```console
$ globus-url-copy file://_LOCAL_PATH_TO_YOUR_FILE_ gsiftp://gridftp-prace.salomon.it4i.cz:2812/home/prace/_YOUR_ACCOUNT_ON_SALOMON_/_PATH_TO_YOUR_FILE_
```
For Anselm cluster:
| Login address | Port | Node role |
| ---------------------------- | ---- | --------------------------- |
| gridftp-prace.anselm.it4i.cz | 2812 | Front end /control server |
| login1-prace.anselm.it4i.cz | 2813 | Backend / data mover server |
| login2-prace.anselm.it4i.cz | 2813 | Backend / data mover server |
| dm1-prace.anselm.it4i.cz | 2813 | Backend / data mover server |
Copy files **to** Anselm by running the following commands on your local machine:
```console
$ globus-url-copy file://_LOCAL_PATH_TO_YOUR_FILE_ gsiftp://gridftp-prace.anselm.it4i.cz:2812/home/prace/_YOUR_ACCOUNT_ON_ANSELM_/_PATH_TO_YOUR_FILE_
```
Or by using prace_service script:
```console
$ globus-url-copy file://_LOCAL_PATH_TO_YOUR_FILE_ gsiftp://`prace_service -i -f salomon`/home/prace/_YOUR_ACCOUNT_ON_SALOMON_/_PATH_TO_YOUR_FILE_
```
```console
$ globus-url-copy file://_LOCAL_PATH_TO_YOUR_FILE_ gsiftp://`prace_service -i -f anselm`/home/prace/_YOUR_ACCOUNT_ON_ANSELM_/_PATH_TO_YOUR_FILE_
```
Copy files **from** Salomon:
```console
$ globus-url-copy gsiftp://gridftp-prace.salomon.it4i.cz:2812/home/prace/_YOUR_ACCOUNT_ON_SALOMON_/_PATH_TO_YOUR_FILE_ file://_LOCAL_PATH_TO_YOUR_FILE_
```
Copy files **from** Anselm:
```console
$ globus-url-copy gsiftp://gridftp-prace.anselm.it4i.cz:2812/home/prace/_YOUR_ACCOUNT_ON_ANSELM_/_PATH_TO_YOUR_FILE_ file://_LOCAL_PATH_TO_YOUR_FILE_
```
Or by using prace_service script:
```console
$ globus-url-copy gsiftp://`prace_service -i -f salomon`/home/prace/_YOUR_ACCOUNT_ON_SALOMON_/_PATH_TO_YOUR_FILE_ file://_LOCAL_PATH_TO_YOUR_FILE_
```
```console
$ globus-url-copy gsiftp://`prace_service -i -f anselm`/home/prace/_YOUR_ACCOUNT_ON_ANSELM_/_PATH_TO_YOUR_FILE_ file://_LOCAL_PATH_TO_YOUR_FILE_
```
### Access From Public Internet
For Salomon cluster:
| Login address | Port | Node role |
| ----------------------- | ---- | --------------------------- |
| gridftp.salomon.it4i.cz | 2812 | Front end /control server |
| lgw1.salomon.it4i.cz | 2813 | Backend / data mover server |
| lgw2.salomon.it4i.cz | 2813 | Backend / data mover server |
| lgw3.salomon.it4i.cz | 2813 | Backend / data mover server |
Copy files **to** Salomon by running the following commands on your local machine:
```console
$ globus-url-copy file://_LOCAL_PATH_TO_YOUR_FILE_ gsiftp://gridftp.salomon.it4i.cz:2812/home/prace/_YOUR_ACCOUNT_ON_SALOMON_/_PATH_TO_YOUR_FILE_
```
For Anselm cluster:
| Login address | Port | Node role |
| ---------------------- | ---- | --------------------------- |
| gridftp.anselm.it4i.cz | 2812 | Front end /control server |
| login1.anselm.it4i.cz | 2813 | Backend / data mover server |
| login2.anselm.it4i.cz | 2813 | Backend / data mover server |
| dm1.anselm.it4i.cz | 2813 | Backend / data mover server |
Copy files **to** Anselm by running the following commands on your local machine:
```console
$ globus-url-copy file://_LOCAL_PATH_TO_YOUR_FILE_ gsiftp://gridftp.anselm.it4i.cz:2812/home/prace/_YOUR_ACCOUNT_ON_ANSELM_/_PATH_TO_YOUR_FILE_
```
Or by using prace_service script:
```console
$ globus-url-copy file://_LOCAL_PATH_TO_YOUR_FILE_ gsiftp://`prace_service -e -f salomon`/home/prace/_YOUR_ACCOUNT_ON_SALOMON_/_PATH_TO_YOUR_FILE_
```
```console
$ globus-url-copy file://_LOCAL_PATH_TO_YOUR_FILE_ gsiftp://`prace_service -e -f anselm`/home/prace/_YOUR_ACCOUNT_ON_ANSELM_/_PATH_TO_YOUR_FILE_
```
Copy files **from** Salomon:
```console
$ globus-url-copy gsiftp://gridftp.salomon.it4i.cz:2812/home/prace/_YOUR_ACCOUNT_ON_SALOMON_/_PATH_TO_YOUR_FILE_ file://_LOCAL_PATH_TO_YOUR_FILE_
```
Copy files **from** Anselm:
```console
$ globus-url-copy gsiftp://gridftp.anselm.it4i.cz:2812/home/prace/_YOUR_ACCOUNT_ON_ANSELM_/_PATH_TO_YOUR_FILE_ file://_LOCAL_PATH_TO_YOUR_FILE_
```
Or by using prace_service script:
```console
$ globus-url-copy gsiftp://`prace_service -e -f salomon`/home/prace/_YOUR_ACCOUNT_ON_SALOMON_/_PATH_TO_YOUR_FILE_ file://_LOCAL_PATH_TO_YOUR_FILE_
```
```console
$ globus-url-copy gsiftp://`prace_service -e -f anselm`/home/prace/_YOUR_ACCOUNT_ON_ANSELM_/_PATH_TO_YOUR_FILE_ file://_LOCAL_PATH_TO_YOUR_FILE_
```
Generally both shared file systems are available through GridFTP:
| File system mount point | Filesystem | Comment |
| ----------------------- | ---------- | -------------------------------------------------------------- |
| /home | Lustre | Default HOME directories of users in format /home/prace/login/ |
| /scratch | Lustre | Shared SCRATCH mounted on the whole cluster |
More information about the shared file systems is available [for Salomon here][10] and [for Anselm here][11].
!!! hint
`prace` directory is used for PRACE users on the SCRATCH file system.
Only Salomon cluster /scratch:
| Data type | Default path |
| ---------------------------- | ------------------------------- |
| large project files | /scratch/work/user/prace/login/ |
| large scratch/temporary data | /scratch/temp/ |
## Usage of the Cluster
There are some limitations for PRACE user when using the cluster. By default PRACE users aren't allowed to access special queues in the PBS Pro to have high priority or exclusive access to some special equipment like accelerated nodes and high memory (fat) nodes. There may be also restrictions obtaining a working license for the commercial software installed on the cluster, mostly because of the license agreement or because of insufficient amount of licenses.
For production runs always use scratch file systems. The available file systems are described [for Salomon here][10] and [for Anselm here][11].
### Software, Modules and PRACE Common Production Environment
All system wide installed software on the cluster is made available to the users via the modules. The information about the environment and modules usage is in this [section of general documentation][12].
PRACE users can use the "prace" module to use the [PRACE Common Production Environment][h].
```console
$ ml prace
```
### Resource Allocation and Job Execution
General information about the resource allocation, job queuing and job execution is in this [section of general documentation for Salomon][13] and [section of general documentation for Anselm][14].
For PRACE users, the default production run queue is "qprace". PRACE users can also use two other queues "qexp" and "qfree".
For Salomon:
| queue | Active project | Project resources | Nodes | priority | authorization | walltime |
| ----------------------------- | -------------- | ----------------- | -------------------------- | -------- | ------------- | --------- |
| **qexp** Express queue | no | none required | 32 nodes, max 8 per user | 150 | no | 1 / 1 h |
| **qprace** Production queue | yes | >0 | 1006 nodes, max 86 per job | 0 | no | 24 / 48 h |
| **qfree** Free resource queue | yes | none required | 752 nodes, max 86 per job | -1024 | no | 12 / 12 h |
For Anselm:
| queue | Active project | Project resources | Nodes | priority | authorization | walltime |
| ----------------------------- | -------------- | ----------------- | ------------------- | -------- | ------------- | --------- |
| **qexp** Express queue | no | none required | 2 reserved, 8 total | high | no | 1 / 1h |
| **qprace** Production queue | yes | > 0 | 178 w/o accelerator | medium | no | 24 / 48 h |
| **qfree** Free resource queue | yes | none required | 178 w/o accelerator | very low | no | 12 / 12 h |
**qprace**, the PRACE This queue is intended for normal production runs. It is required that active project with nonzero remaining resources is specified to enter the qprace. The queue runs with medium priority and no special authorization is required to use it. The maximum runtime in qprace is 48 hours. If the job needs longer time, it must use checkpoint/restart functionality.
### Accounting & Quota
The resources that are currently subject to accounting are the core hours. The core hours are accounted on the wall clock basis. The accounting runs whenever the computational cores are allocated or blocked via the PBS Pro workload manager (the qsub command), regardless of whether the cores are actually used for any calculation. See [example in the general documentation for Salomon][13] and [example in the general documentation for Anselm][14].
PRACE users should check their project accounting using the [PRACE Accounting Tool (DART)][i].
Users who have undergone the full local registration procedure (including signing the IT4Innovations Acceptable Use Policy) and who have received local password may check at any time, how many core-hours have been consumed by themselves and their projects using the command "it4ifree". You need to know your user password to use the command and that the displayed core hours are "system core hours" which differ from PRACE "standardized core hours".
!!! note
The **it4ifree** command is a part of it4i.portal.clients package, [located here][j].
```console
$ it4ifree
Password:
PID Total Used ...by me Free
-------- ------- ------ -------- -------
OPEN-0-0 1500000 400644 225265 1099356
DD-13-1 10000 2606 2606 7394
```
By default file system quota is applied. To check the current status of the quota (separate for HOME and SCRATCH) use
```console
$ quota
$ lfs quota -u USER_LOGIN /scratch
```
If the quota is insufficient, contact the [support][15] and request an increase.
[1]: general/obtaining-login-credentials/obtaining-login-credentials.md
[2]: salomon/introduction.md
[3]: anselm/introduction.md
[5]: #file-transfers
[6]: general/accessing-the-clusters/graphical-user-interface/x-window-system.md
[8]: salomon/shell-and-data-access.md
[9]: anselm/shell-and-data-access.md
[10]: salomon/storage.md
[11]: anselm/storage.md
[12]: environment-and-modules.md
[13]: salomon/resources-allocation-policy.md
[14]: anselm/resources-allocation-policy.md
[15]: #help-and-support
[a]: http://www.prace-ri.eu/user-documentation/
[b]: http://www.prace-ri.eu/helpdesk-guide264/
[c]: http://www.prace-ri.eu/Users-General-FAQs
[d]: http://www.prace-ri.eu/Certificates-FAQ
[e]: http://www.prace-ri.eu/Interactive-Access-Using-gsissh
[f]: http://www.prace-ri.eu/Data-Transfer-with-GridFTP-Details
[g]: http://www.prace-ri.eu/Data-Transfer-with-gtransfer
[h]: http://www.prace-ri.eu/prace-common-production-environment/
[i]: http://www.prace-ri.eu/accounting-report-tool/
[j]: https://pypi.python.org/pypi/it4i.portal.clients
Sitemap: https://docs.it4i.cz/sitemap.xml.gz
User-agent: *
Disallow:
# 7D Enhanced Hypercube
![](../img/7D_Enhanced_hypercube.png)
| Node type | Count | Short name | Long name | Rack |
| ------------------------------------ | ----- | ---------------- | ------------------------ | ----- |
| M-Cell compute nodes w/o accelerator | 576 | cns1 -cns576 | r1i0n0 - r4i7n17 | 1-4 |
| compute nodes MIC accelerated | 432 | cns577 - cns1008 | r21u01n577 - r37u31n1008 | 21-38 |
## IB Topology
![](../img/Salomon_IB_topology.png)
# Capacity Computing
## Introduction
In many cases, it is useful to submit huge (100+) number of computational jobs into the PBS queue system. Huge number of (small) jobs is one of the most effective ways to execute embarrassingly parallel calculations, achieving best runtime, throughput and computer utilization.
However, executing huge number of jobs via the PBS queue may strain the system. This strain may result in slow response to commands, inefficient scheduling and overall degradation of performance and user experience, for all users. For this reason, the number of jobs is **limited to 100 per user, 1500 per job array**
!!! note
Please follow one of the procedures below, in case you wish to schedule more than 100 jobs at a time.
* Use [Job arrays][1] when running huge number of [multithread][2] (bound to one node only) or multinode (multithread across several nodes) jobs
* Use [GNU parallel][3] when running single core jobs
* Combine [GNU parallel with Job arrays][4] when running huge number of single core jobs
## Policy
1. A user is allowed to submit at most 100 jobs. Each job may be [a job array][1].
1. The array size is at most 1500 subjobs.
## Job Arrays
!!! note
Huge number of jobs may be easily submitted and managed as a job array.
A job array is a compact representation of many jobs, called subjobs. The subjobs share the same job script, and have the same values for all attributes and resources, with the following exceptions:
* each subjob has a unique index, $PBS_ARRAY_INDEX
* job Identifiers of subjobs only differ by their indices
* the state of subjobs can differ (R,Q,...etc.)
All subjobs within a job array have the same scheduling priority and schedule as independent jobs. Entire job array is submitted through a single qsub command and may be managed by qdel, qalter, qhold, qrls and qsig commands as a single job.
### Shared jobscript
All subjobs in job array use the very same, single jobscript. Each subjob runs its own instance of the jobscript. The instances execute different work controlled by $PBS_ARRAY_INDEX variable.
Example:
Assume we have 900 input files with name beginning with "file" (e. g. file001, ..., file900). Assume we would like to use each of these input files with program executable myprog.x, each as a separate job.
First, we create a tasklist file (or subjobs list), listing all tasks (subjobs) - all input files in our example:
```console
$ find . -name 'file*' > tasklist
```
Then we create jobscript:
```bash
#!/bin/bash
#PBS -A PROJECT_ID
#PBS -q qprod
#PBS -l select=1:ncpus=24,walltime=02:00:00
# change to scratch directory
SCR=/scratch/work/user/$USER/$PBS_JOBID
mkdir -p $SCR ; cd $SCR || exit
# get individual tasks from tasklist with index from PBS JOB ARRAY
TASK=$(sed -n "${PBS_ARRAY_INDEX}p" $PBS_O_WORKDIR/tasklist)
# copy input file and executable to scratch
cp $PBS_O_WORKDIR/$TASK input ; cp $PBS_O_WORKDIR/myprog.x .
# execute the calculation
./myprog.x < input > output
# copy output file to submit directory
cp output $PBS_O_WORKDIR/$TASK.out
```
In this example, the submit directory holds the 900 input files, executable myprog.x and the jobscript file. As input for each run, we take the filename of input file from created tasklist file. We copy the input file to scratch (/scratch/work/user/$USER/$PBS_JOBID), execute the myprog.x and copy the output file back to the submit directory, under the $TASK.out name. The myprog.x runs on one node only and must use threads to run in parallel. Be aware, that if the myprog.x **is not multithreaded**, then all the **jobs are run as single thread programs in sequential** manner. Due to allocation of the whole node, the **accounted time is equal to the usage of whole node**, while using only 1/24 of the node!
If huge number of parallel multicore (in means of multinode multithread, e. g. MPI enabled) jobs is needed to run, then a job array approach should also be used. The main difference compared to previous example using one node is that the local scratch should not be used (as it's not shared between nodes) and MPI or other technique for parallel multinode run has to be used properly.
### Submit the Job Array
To submit the job array, use the qsub -J command. The 900 jobs of the [example above][5] may be submitted like this:
```console
$ qsub -N JOBNAME -J 1-900 jobscript
506493[].isrv5
```
In this example, we submit a job array of 900 subjobs. Each subjob will run on full node and is assumed to take less than 2 hours (note the #PBS directives in the beginning of the jobscript file, dont' forget to set your valid PROJECT_ID and desired queue).
Sometimes for testing purposes, you may need to submit only one-element array. This is not allowed by PBSPro, but there's a workaround:
```console
$ qsub -N JOBNAME -J 9-10:2 jobscript
```
This will only choose the lower index (9 in this example) for submitting/running your job.
### Manage the Job Array
Check status of the job array by the qstat command.
```console
$ qstat -a 506493[].isrv5
isrv5:
Req'd Req'd Elap
Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time
--------------- -------- -- |---|---| ------ --- --- ------ ----- - -----
12345[].dm2 user2 qprod xx 13516 1 24 -- 00:50 B 00:02
```
The status B means that some subjobs are already running.
Check status of the first 100 subjobs by the qstat command.
```console
$ qstat -a 12345[1-100].isrv5
isrv5:
Req'd Req'd Elap
Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time
--------------- -------- -- |---|---| ------ --- --- ------ ----- - -----
12345[1].isrv5 user2 qprod xx 13516 1 24 -- 00:50 R 00:02
12345[2].isrv5 user2 qprod xx 13516 1 24 -- 00:50 R 00:02
12345[3].isrv5 user2 qprod xx 13516 1 24 -- 00:50 R 00:01
12345[4].isrv5 user2 qprod xx 13516 1 24 -- 00:50 Q --
. . . . . . . . . . .
, . . . . . . . . . .
12345[100].isrv5 user2 qprod xx 13516 1 24 -- 00:50 Q --
```
Delete the entire job array. Running subjobs will be killed, queueing subjobs will be deleted.
```console
$ qdel 12345[].isrv5
```
Deleting large job arrays may take a while.
Display status information for all user's jobs, job arrays, and subjobs.
```console
$ qstat -u $USER -t
```
Display status information for all user's subjobs.
```console
$ qstat -u $USER -tJ
```
Read more on job arrays in the [PBSPro Users guide][6].
## GNU Parallel
!!! note
Use GNU parallel to run many single core tasks on one node.
GNU parallel is a shell tool for executing jobs in parallel using one or more computers. A job can be a single command or a small script that has to be run for each of the lines in the input. GNU parallel is most useful in running single core jobs via the queue system on the cluster.
For more information and examples see the parallel man page:
```console
$ ml parallel
$ man parallel
```
### GNU Parallel jobscript
The GNU parallel shell executes multiple instances of the jobscript using all cores on the node. The instances execute different work, controlled by the $PARALLEL_SEQ variable.
Example:
Assume we have 101 input files with name beginning with "file" (e. g. file001, ..., file101). Assume we would like to use each of these input files with program executable myprog.x, each as a separate single core job. We call these single core jobs tasks.
First, we create a tasklist file, listing all tasks - all input files in our example:
```console
$ find . -name 'file*' > tasklist
```
Then we create jobscript:
```bash
#!/bin/bash
#PBS -A PROJECT_ID
#PBS -q qprod
#PBS -l select=1:ncpus=24,walltime=02:00:00
[ -z "$PARALLEL_SEQ" ] &&
{ ml parallel ; exec parallel -a $PBS_O_WORKDIR/tasklist $0 ; }
# change to scratch directory
SCR=/scratch/work/user/$USER/$PBS_JOBID/$PARALLEL_SEQ
mkdir -p $SCR ; cd $SCR || exit
# get individual task from tasklist
TASK=$1
# copy input file and executable to scratch
cp $PBS_O_WORKDIR/$TASK input
# execute the calculation
cat input > output
# copy output file to submit directory
cp output $PBS_O_WORKDIR/$TASK.out
```
In this example, tasks from tasklist are executed via the GNU parallel. The jobscript executes multiple instances of itself in parallel, on all cores of the node. Once an instace of jobscript is finished, new instance starts until all entries in tasklist are processed. Currently processed entry of the joblist may be retrieved via $1 variable. Variable $TASK expands to one of the input filenames from tasklist. We copy the input file to the scratch, execute the myprog.x and copy the output file back to the submit directory, under the $TASK.out name.
### Submit the Job
To submit the job, use the qsub command. The 101 tasks' job of the [example above][7] may be submitted like this:
```console
$ qsub -N JOBNAME jobscript
12345.dm2
```
In this example, we submit a job of 101 tasks. 24 input files will be processed in parallel. The 101 tasks on 24 cores are assumed to complete in less than 2 hours.
!!! note
Use #PBS directives in the beginning of the jobscript file, dont' forget to set your valid PROJECT_ID and desired queue.
## Job Arrays and GNU Parallel
!!! note
Combine the Job arrays and GNU parallel for best throughput of single core jobs
While job arrays are able to utilize all available computational nodes, the GNU parallel can be used to efficiently run multiple single-core jobs on single node. The two approaches may be combined to utilize all available (current and future) resources to execute single core jobs.
!!! note
Every subjob in an array runs GNU parallel to utilize all cores on the node
### GNU Parallel, Shared jobscript
Combined approach, very similar to job arrays, can be taken. Job array is submitted to the queuing system. The subjobs run GNU parallel. The GNU parallel shell executes multiple instances of the jobscript using all cores on the node. The instances execute different work, controlled by the $PBS_JOB_ARRAY and $PARALLEL_SEQ variables.
Example:
Assume we have 960 input files with name beginning with "file" (e. g. file001, ..., file960). Assume we would like to use each of these input files with program executable myprog.x, each as a separate single core job. We call these single core jobs tasks.
First, we create a tasklist file, listing all tasks - all input files in our example:
```console
$ find . -name 'file*' > tasklist
```
Next we create a file, controlling how many tasks will be executed in one subjob
```console
$ seq 48 > numtasks
```
Then we create jobscript:
```bash
#!/bin/bash
#PBS -A PROJECT_ID
#PBS -q qprod
#PBS -l select=1:ncpus=24,walltime=02:00:00
[ -z "$PARALLEL_SEQ" ] &&
{ ml parallel ; exec parallel -a $PBS_O_WORKDIR/numtasks $0 ; }
# change to scratch directory
SCR=/scratch/work/user/$USER/$PBS_JOBID/$PARALLEL_SEQ
mkdir -p $SCR ; cd $SCR || exit
# get individual task from tasklist with index from PBS JOB ARRAY and index form Parallel
IDX=$(($PBS_ARRAY_INDEX + $PARALLEL_SEQ - 1))
TASK=$(sed -n "${IDX}p" $PBS_O_WORKDIR/tasklist)
[ -z "$TASK" ] && exit
# copy input file and executable to scratch
cp $PBS_O_WORKDIR/$TASK input
# execute the calculation
cat input > output
# copy output file to submit directory
cp output $PBS_O_WORKDIR/$TASK.out
```
In this example, the jobscript executes in multiple instances in parallel, on all cores of a computing node. Variable $TASK expands to one of the input filenames from tasklist. We copy the input file to the scratch, execute the myprog.x and copy the output file back to the submit directory, under the $TASK.out name. The numtasks file controls how many tasks will be run per subjob. Once an task is finished, new task starts, until the number of tasks in numtasks file is reached.
!!! note
Select subjob walltime and number of tasks per subjob carefully
When deciding this values, think about following guiding rules :
1. Let n = N / 24. Inequality (n + 1) x T < W should hold. The N is number of tasks per subjob, T is expected single task walltime and W is subjob walltime. Short subjob walltime improves scheduling and job throughput.
1. Number of tasks should be modulo 24.
1. These rules are valid only when all tasks have similar task walltimes T.
### Submit the Job Array (-J)
To submit the job array, use the qsub -J command. The 960 tasks' job of the [example above][8] may be submitted like this:
```console
$ qsub -N JOBNAME -J 1-960:48 jobscript
12345[].dm2
```
In this example, we submit a job array of 20 subjobs. Note the -J 1-960:48, this must be the same as the number sent to numtasks file. Each subjob will run on full node and process 24 input files in parallel, 48 in total per subjob. Every subjob is assumed to complete in less than 2 hours.
!!! note
Use #PBS directives in the beginning of the jobscript file, dont' forget to set your valid PROJECT_ID and desired queue.
## Examples
Download the examples in [capacity.zip][9], illustrating the above listed ways to run huge number of jobs. We recommend to try out the examples, before using this for running production jobs.
Unzip the archive in an empty directory on the cluster and follow the instructions in the README file
```console
$ unzip capacity.zip
$ cd capacity
$ cat README
```
[1]: #job-arrays
[2]: #shared-jobscript-on-one-node
[3]: #gnu-parallel
[4]: #job-arrays-and-gnu-parallel
[5]: #array_example
[6]: ../pbspro.md
[7]: #gp_example
[8]: #combined_example
[9]: capacity.zip
File added
# Compute Nodes
## Nodes Configuration
Salomon is cluster of x86-64 Intel based nodes. The cluster contains two types of compute nodes of the same processor type and memory size.
Compute nodes with MIC accelerator **contains two Intel Xeon Phi 7120P accelerators.**
[More about][1] schematic representation of the Salomon cluster compute nodes IB topology.
### Compute Nodes Without Accelerator
* codename "grafton"
* 576 nodes
* 13 824 cores in total
* two Intel Xeon E5-2680v3, 12-core, 2.5 GHz processors per node
* 128 GB of physical memory per node
![cn_m_cell](../img/cn_m_cell.jpg)
### Compute Nodes With MIC Accelerator
* codename "perrin"
* 432 nodes
* 10 368 cores in total
* two Intel Xeon E5-2680v3, 12-core, 2.5 GHz processors per node
* 128 GB of physical memory per node
* MIC accelerator 2 x Intel Xeon Phi 7120P per node, 61-cores, 16 GB per accelerator
![cn_mic](../img/cn_mic-1.jpg)
![(source Silicon Graphics International Corp.)](../img/sgi-c1104-gp1.jpeg)
![cn_mic](../img/cn_mic.jpg)
### Uv 2000
* codename "UV2000"
* 1 node
* 112 cores in total
* 14 x Intel Xeon E5-4627v2, 8-core, 3.3 GHz processors, in 14 NUMA nodes
* 3328 GB of physical memory per node
* 1 x NVIDIA GM200 (GeForce GTX TITAN X), 12 GB RAM
![](../img/uv-2000.jpeg)
### Compute Nodes Summary
| Node type | Count | Memory | Cores |
| -------------------------- | ----- | ----------------- | ----------------------------------- |
| Nodes without accelerator | 576 | 128 GB | 24 @ 2.5GHz |
| Nodes with MIC accelerator | 432 | 128 GB, MIC 32GB | 24 @ 2.5GHz, MIC 61 @ 1.238 GHz |
| UV2000 SMP node | 1 | 3328GB | 112 @ 3.3GHz |
## Processor Architecture
Salomon is equipped with Intel Xeon processors Intel Xeon E5-2680v3. Processors support Advanced Vector Extensions 2.0 (AVX2) 256-bit instruction set.
### Intel Xeon E5-2680v3 Processor
* 12-core
* speed: 2.5 GHz, up to 3.3 GHz using Turbo Boost Technology
* peak performance: 40 GFLOP/s per core @ 2.5 GHz
* caches:
* Intel® Smart Cache: 30 MB
* memory bandwidth at the level of the processor: 68 GB/s
### MIC Accelerator Intel Xeon Phi 7120P Processor
* 61-core
* speed: 1.238
GHz, up to 1.333 GHz using Turbo Boost Technology
* peak performance: 18.4 GFLOP/s per core
* caches:
* L2: 30.5 MB
* memory bandwidth at the level of the processor: 352 GB/s
## Memory Architecture
Memory is equally distributed across all CPUs and cores for optimal performance. Memory is composed of memory modules of the same size and evenly distributed across all memory controllers and memory channels.
### Compute Node Without Accelerator
* 2 sockets
* Memory Controllers are integrated into processors.
* 8 DDR4 DIMMs per node
* 4 DDR4 DIMMs per CPU
* 1 DDR4 DIMMs per channel
* Populated memory: 8 x 16 GB DDR4 DIMM >2133 MHz
### Compute Node With MIC Accelerator
2 sockets
Memory Controllers are integrated into processors.
* 8 DDR4 DIMMs per node
* 4 DDR4 DIMMs per CPU
* 1 DDR4 DIMMs per channel
Populated memory: 8 x 16 GB DDR4 DIMM 2133 MHz
MIC Accelerator Intel Xeon Phi 7120P Processor
* 2 sockets
* Memory Controllers are are connected via an
Interprocessor Network (IPN) ring.
* 16 GDDR5 DIMMs per node
* 8 GDDR5 DIMMs per CPU
* 2 GDDR5 DIMMs per channel
[1]: ib-single-plane-topology.md
# Hardware Overview
## Introduction
The Salomon cluster consists of 1008 computational nodes of which 576 are regular compute nodes and 432 accelerated nodes. Each node is a powerful x86-64 computer, equipped with 24 cores (two twelve-core Intel Xeon processors) and 128 GB RAM. The nodes are interlinked by high speed InfiniBand and Ethernet networks. All nodes share 0.5 PB /home NFS disk storage to store the user files. Users may use a DDN Lustre shared storage with capacity of 1.69 PB which is available for the scratch project data. The user access to the Salomon cluster is provided by four login nodes.
[More about][1] schematic representation of the Salomon cluster compute nodes IB topology.
![Salomon](../img/salomon-2.jpg)
The parameters are summarized in the following tables:
## General Information
| **In general** | |
| ------------------------------------------- | ------------------------------------------- |
| Primary purpose | High Performance Computing |
| Architecture of compute nodes | x86-64 |
| Operating system | CentOS 6.x Linux |
| [**Compute nodes**][2] | |
| Totally | 1008 |
| Processor | 2 x Intel Xeon E5-2680v3, 2.5 GHz, 12 cores |
| RAM | 128GB, 5.3 GB per core, DDR4@2133 MHz |
| Local disk drive | no |
| Compute network / Topology | InfiniBand FDR56 / 7D Enhanced hypercube |
| w/o accelerator | 576 |
| MIC accelerated | 432 |
| **In total** | |
| Total theoretical peak performance (Rpeak) | 2011 TFLOP/s |
| Total amount of RAM | 129.024 TB |
## Compute Nodes
| Node | Count | Processor | Cores | Memory | Accelerator |
| --------------- | ----- | --------------------------------- | ----- | ------ | --------------------------------------------- |
| w/o accelerator | 576 | 2 x Intel Xeon E5-2680v3, 2.5 GHz | 24 | 128 GB | - |
| MIC accelerated | 432 | 2 x Intel Xeon E5-2680v3, 2.5 GHz | 24 | 128 GB | 2 x Intel Xeon Phi 7120P, 61 cores, 16 GB RAM |
For more details refer to the [Compute nodes][2].
## Remote Visualization Nodes
For remote visualization two nodes with NICE DCV software are available each configured:
| Node | Count | Processor | Cores | Memory | GPU Accelerator |
| ------------- | ----- | --------------------------------- | ----- | ------ | ----------------------------- |
| visualization | 2 | 2 x Intel Xeon E5-2695v3, 2.3 GHz | 28 | 512 GB | NVIDIA QUADRO K5000, 4 GB RAM |
## SGI Uv 2000
For large memory computations a special SMP/NUMA SGI UV 2000 server is available:
| Node | Count | Processor | Cores | Memory | Extra HW |
| ------ | ----- | ------------------------------------------- | ----- | --------------------- | ------------------------------------------------------------------------ |
| UV2000 | 1 | 14 x Intel Xeon E5-4627v2, 3.3 GHz, 8 cores | 112 | 3328 GB DDR3@1866 MHz | 2 x 400GB local SSD, 1x NVIDIA GM200 (GeForce GTX TITAN X), 12 GB RAM |
![](../img/uv-2000.jpeg)
[1]: ib-single-plane-topology.md
[2]: compute-nodes.md
# IB Single-Plane Topology
A complete M-Cell assembly consists of four compute racks. Each rack contains 4 x physical IRUs - Independent rack units. Using one dual socket node per one blade slot leads to 8 logical IRUs. Each rack contains 4 x 2 SGI ICE X IB Premium Blades.
The SGI ICE X IB Premium Blade provides the first level of interconnection via dual 36-port Mellanox FDR InfiniBand ASIC switch with connections as follows:
* 9 ports from each switch chip connect to the unified backplane, to connect the 18 compute node slots
* 3 ports on each chip provide connectivity between the chips
* 24 ports from each switch chip connect to the external bulkhead, for a total of 48
## IB Single-Plane Topology - ICEX M-Cell
Each color in each physical IRU represents one dual-switch ASIC switch.
[IB single-plane topology - ICEX Mcell.pdf][1]
![IB single-plane topology - ICEX Mcell.pdf](../img/IBsingleplanetopologyICEXMcellsmall.png)
## IB Single-Plane Topology - Accelerated Nodes
Each of the 3 inter-connected D racks are equivalent to one half of M-Cell rack. 18 x D rack with MIC accelerated nodes [r21-r38] are equivalent to 3 M-Cell racks as shown in a diagram [7D Enhanced Hypercube][2].
As shown in a diagram [IB Topology][3]
* Racks 21, 22, 23, 24, 25, 26 are equivalent to one M-Cell rack.
* Racks 27, 28, 29, 30, 31, 32 are equivalent to one M-Cell rack.
* Racks 33, 34, 35, 36, 37, 38 are equivalent to one M-Cell rack.
[IB single-plane topology - Accelerated nodes.pdf][4]
![IB single-plane topology - Accelerated nodes.pdf](../img/IBsingleplanetopologyAcceleratednodessmall.png)
[1]: ../src/IB_single-plane_topology_-_ICEX_Mcell.pdf
[2]: 7d-enhanced-hypercube.md
[3]: 7d-enhanced-hypercube.md#ib-topology)
[4]: ../src/IB_single-plane_topology_-_Accelerated_nodes.pdf
# Introduction
Welcome to Salomon supercomputer cluster. The Salomon cluster consists of 1008 compute nodes, totalling 24192 compute cores with 129 TB RAM and giving over 2 Pflop/s theoretical peak performance. Each node is a powerful x86-64 computer, equipped with 24 cores, and at least 128 GB RAM. Nodes are interconnected through a 7D Enhanced hypercube InfiniBand network and are equipped with Intel Xeon E5-2680v3 processors. The Salomon cluster consists of 576 nodes without accelerators, and 432 nodes equipped with Intel Xeon Phi MIC accelerators. Read more in [Hardware Overview][1].
The cluster runs with a [CentOS Linux][a] operating system, which is compatible with the RedHat [Linux family][b].
## Water-Cooled Compute Nodes With MIC Accelerators
![](../img/salomon.jpg)
![](../img/salomon-1.jpeg)
## Tape Library T950B
![](../img/salomon-3.jpeg)
![](../img/salomon-4.jpeg)
[1]: hardware-overview.md
[a]: http://www.bull.com/bullx-logiciels/systeme-exploitation.html
[b]: http://upload.wikimedia.org/wikipedia/commons/1/1b/Linux_Distribution_Timeline.svg
# Job Scheduling
## Job Execution Priority
Scheduler gives each job an execution priority and then uses this job execution priority to select which job(s) to run.
Job execution priority is determined by these job properties (in order of importance):
1. queue priority
1. fair-share priority
1. eligible time
### Queue Priority
Queue priority is priority of queue where job is queued before execution.
Queue priority has the biggest impact on job execution priority. Execution priority of jobs in higher priority queues is always greater than execution priority of jobs in lower priority queues. Other properties of job used for determining job execution priority (fair-share priority, eligible time) cannot compete with queue priority.
Queue priorities can be seen [here][a].
### Fair-Share Priority
Fair-share priority is priority calculated on recent usage of resources. Fair-share priority is calculated per project, all members of project share same fair-share priority. Projects with higher recent usage have lower fair-share priority than projects with lower or none recent usage.
Fair-share priority is used for ranking jobs with equal queue priority.
Fair-share priority is calculated as
---8<--- "fairshare_formula.md"
where MAX_FAIRSHARE has value 1E6,
usage<sub>Project</sub> is cumulated usage by all members of selected project,
usage<sub>Total</sub> is total usage by all users, by all projects.
Usage counts allocated core-hours (`ncpus x walltime`). Usage is decayed, or cut in half periodically, at the interval 168 hours (one week).
## Jobs Queued in Queue qexp Are Not Calculated to Project's Usage.
!!! note
Calculated usage and fair-share priority can be seen [here][b].
Calculated fair-share priority can be also seen as Resource_List.fairshare attribute of a job.
### Eligible Time
Eligible time is amount (in seconds) of eligible time job accrued while waiting to run. Jobs with higher eligible time gains higher priority.
Eligible time has the least impact on execution priority. Eligible time is used for sorting jobs with equal queue priority and fair-share priority. It is very, very difficult for eligible time to compete with fair-share priority.
Eligible time can be seen as eligible_time attribute of job.
### Formula
Job execution priority (job sort formula) is calculated as:
---8<--- "job_sort_formula.md"
### Job backfilling
The scheduler uses job backfilling.
Backfilling means fitting smaller jobs around the higher-priority jobs that the scheduler is going to run next, in such a way that the higher-priority jobs are not delayed. Backfilling allows us to keep resources from becoming idle when the top job (job with the highest execution priority) cannot run.
The scheduler makes a list of jobs to run in order of execution priority. Scheduler looks for smaller jobs that can fit into the usage gaps around the highest-priority jobs in the list. The scheduler looks in the prioritized list of jobs and chooses the highest-priority smaller jobs that fit. Filler jobs are run only if they will not delay the start time of top jobs.
It means, that jobs with lower execution priority can be run before jobs with higher execution priority.
!!! note
It is **very beneficial to specify the walltime** when submitting jobs.
Specifying more accurate walltime enables better scheduling, better execution times and better resource usage. Jobs with suitable (small) walltime could be backfilled - and overtake job(s) with higher priority.
### Job Placement
Job [placement can be controlled by flags during submission][1].
---8<--- "mathjax.md"
[1]: job-submission-and-execution.md#job_placement
[a]: https://extranet.it4i.cz/rsweb/salomon/queues
[b]: https://extranet.it4i.cz/rsweb/salomon/projects
# Job Submission and Execution
## Job Submission
When allocating computational resources for the job, specify:
1. suitable queue for your job (default is qprod)
1. number of computational nodes required
1. number of cores per node required
1. maximum wall time allocated to your calculation, note that jobs exceeding maximum wall time will be killed
1. Project ID
1. Jobscript or interactive switch
!!! note
Use the **qsub** command to submit your job to a queue for allocation of the computational resources.
Submit the job using the qsub command:
```console
$ qsub -A Project_ID -q queue -l select=x:ncpus=y,walltime=[[hh:]mm:]ss[.ms] jobscript
```
The qsub submits the job into the queue, in another words the qsub command creates a request to the PBS Job manager for allocation of specified resources. The resources will be allocated when available, subject to above described policies and constraints. **After the resources are allocated the jobscript or interactive shell is executed on first of the allocated nodes.**
!!! note
PBS statement nodes (qsub -l nodes=nodespec) is not supported on Salomon cluster.
### Job Submission Examples
```console
$ qsub -A OPEN-0-0 -q qprod -l select=64:ncpus=24,walltime=03:00:00 ./myjob
```
In this example, we allocate 64 nodes, 24 cores per node, for 3 hours. We allocate these resources via the qprod queue, consumed resources will be accounted to the Project identified by Project ID OPEN-0-0. Jobscript myjob will be executed on the first node in the allocation.
```console
$ qsub -q qexp -l select=4:ncpus=24 -I
```
In this example, we allocate 4 nodes, 24 cores per node, for 1 hour. We allocate these resources via the qexp queue. The resources will be available interactively
```console
$ qsub -A OPEN-0-0 -q qlong -l select=10:ncpus=24 ./myjob
```
In this example, we allocate 10 nodes, 24 cores per node, for 72 hours. We allocate these resources via the qlong queue. Jobscript myjob will be executed on the first node in the allocation.
```console
$ qsub -A OPEN-0-0 -q qfree -l select=10:ncpus=24 ./myjob
```
In this example, we allocate 10 nodes, 24 cores per node, for 12 hours. We allocate these resources via the qfree queue. It is not required that the project OPEN-0-0 has any available resources left. Consumed resources are still accounted for. Jobscript myjob will be executed on the first node in the allocation.
### Intel Xeon Phi Co-Processors
To allocate a node with Xeon Phi co-processor, user needs to specify that in select statement. Currently only allocation of whole nodes with both Phi cards as the smallest chunk is supported. Standard PBSPro approach through attributes "accelerator", "naccelerators" and "accelerator_model" is used. The "accelerator_model" can be omitted, since on Salomon only one type of accelerator type/model is available.
The absence of specialized queue for accessing the nodes with cards means, that the Phi cards can be utilized in any queue, including qexp for testing/experiments, qlong for longer jobs, qfree after the project resources have been spent, etc. The Phi cards are thus also available to PRACE users. There's no need to ask for permission to utilize the Phi cards in project proposals.
```console
$ qsub -A OPEN-0-0 -I -q qprod -l select=1:ncpus=24:accelerator=True:naccelerators=2:accelerator_model=phi7120 ./myjob
```
In this example, we allocate 1 node, with 24 cores, with 2 Xeon Phi 7120p cards, running batch job ./myjob. The default time for qprod is used, e. g. 24 hours.
```console
$ qsub -A OPEN-0-0 -I -q qlong -l select=4:ncpus=24:accelerator=True:naccelerators=2 -l walltime=56:00:00 -I
```
In this example, we allocate 4 nodes, with 24 cores per node (totalling 96 cores), with 2 Xeon Phi 7120p cards per node (totalling 8 Phi cards), running interactive job for 56 hours. The accelerator model name was omitted.
#### Intel Xeon Phi - Queue QMIC
Examples executions
```console
-l select=1
exec_vnode = (r21u05n581-mic0:naccelerators=1:ncpus=0)
-l select=4
(r21u05n581-mic0:naccelerators=1:ncpus=0)+(r21u05n581-mic1:naccelerators=1:ncpus=0)+(r21u06n582-mic0:naccelerators=1:ncpus=0)+(r21u06n582-mic1:naccelerators=1:ncpus=0)
-l select=4:naccelerators=1
(r21u05n581-mic0:naccelerators=1:ncpus=0)+(r21u05n581-mic1:naccelerators=1:ncpus=0)+(r21u06n582-mic0:naccelerators=1:ncpus=0)+(r21u06n582-mic1:naccelerators=1:ncpus=0)
-l select=1:naccelerators=2
(r21u05n581-mic0:naccelerators=1+r21u05n581-mic1:naccelerators=1)
-l select=2:naccelerators=2
(r21u05n581-mic0:naccelerators=1+r21u05n581-mic1:naccelerators=1)+(r21u06n582-mic0:naccelerators=1+r21u06n582-mic1:naccelerators=1)
-l select=1:ncpus=24:naccelerators=2
(r22u32n610:ncpus=24+r22u32n610-mic0:naccelerators=1+r22u32n610-mic1:naccelerators=1)
-l select=1:ncpus=24:naccelerators=0+4
(r33u17n878:ncpus=24:naccelerators=0)+(r33u13n874-mic0:naccelerators=1:ncpus=0)+(r33u13n874-mic1:naccelerators=1:ncpus=0)+(r33u16n877-mic0:naccelerators=1:ncpus=0)+(r33u16n877-mic1:naccelerators=1:ncpus=0)
```
### UV2000 SMP
!!! note
13 NUMA nodes available on UV2000
Per NUMA node allocation.
Jobs are isolated by cpusets.
The UV2000 (node uv1) offers 3TB of RAM and 104 cores, distributed in 13 NUMA nodes. A NUMA node packs 8 cores and approx. 247GB RAM (with exception, node 11 has only 123GB RAM). In the PBS the UV2000 provides 13 chunks, a chunk per NUMA node (see [Resource allocation policy][1]). The jobs on UV2000 are isolated from each other by cpusets, so that a job by one user may not utilize CPU or memory allocated to a job by other user. Always, full chunks are allocated, a job may only use resources of the NUMA nodes allocated to itself.
```console
$ qsub -A OPEN-0-0 -q qfat -l select=13 ./myjob
```
In this example, we allocate all 13 NUMA nodes (corresponds to 13 chunks), 104 cores of the SGI UV2000 node for 24 hours. Jobscript myjob will be executed on the node uv1.
```console
$ qsub -A OPEN-0-0 -q qfat -l select=1:mem=2000GB ./myjob
```
In this example, we allocate 2000GB of memory on the UV2000 for 24 hours. By requesting 2000GB of memory, memory from 10 chunks and 8 cores are allocated. Jobscript myjob will be executed on the node uv1.
```console
$ qsub -A OPEN-0-0 -q qfat -l select=1:mem=3099GB,walltime=48:00:00 ./myjob
```
In this example, we allocate 3099GB of memory on the UV2000 for 48 hours. By requesting 3099GB of memory, memory from all 13 chunks and 8 cores are allocated. Jobscript myjob will be executed on the node uv1.
```console
$ qsub -A OPEN-0-0 -q qfat -l select=2:mem=1000GB,walltime=48:00:00 ./myjob
```
In this example, we allocate 2000GB of memory and 16 cores on the UV2000 for 48 hours. By requesting 1000GB of memory per chunk, 2000GB of memory and 16 cores are allocated. Jobscript myjob will be executed on the node uv1.
### Useful Tricks
All qsub options may be [saved directly into the jobscript][2]. In such a case, no options to qsub are needed.
```console
$ qsub ./myjob
```
By default, the PBS batch system sends an e-mail only when the job is aborted. Disabling mail events completely can be done like this:
```console
$ qsub -m n
```
## Advanced Job Placement
### Placement by Name
!!! note
Not useful for ordinary computing, suitable for node testing/bechmarking and management tasks.
Specific nodes may be selected using PBS resource attribute host (for hostnames):
```console
qsub -A OPEN-0-0 -q qprod -l select=1:ncpus=24:host=r24u35n680+1:ncpus=24:host=r24u36n681 -I
```
Specific nodes may be selected using PBS resource attribute cname (for short names in cns[0-1]+ format):
```console
qsub -A OPEN-0-0 -q qprod -l select=1:ncpus=24:host=cns680+1:ncpus=24:host=cns681 -I
```
In this example, we allocate nodes r24u35n680 and r24u36n681, all 24 cores per node, for 24 hours. Consumed resources will be accounted to the Project identified by Project ID OPEN-0-0. The resources will be available interactively.
### Placement by Network Location
Network location of allocated nodes in the [InifiBand network][3] influences efficiency of network communication between nodes of job. Nodes on the same InifiBand switch communicate faster with lower latency than distant nodes. To improve communication efficiency of jobs, PBS scheduler on Salomon is configured to allocate nodes - from currently available resources - which are as close as possible in the network topology.
For communication intensive jobs it is possible to set stricter requirement - to require nodes directly connected to the same InifiBand switch or to require nodes located in the same dimension group of the InifiBand network.
### Placement by InifiBand Switch
Nodes directly connected to the same InifiBand switch can communicate most efficiently. Using the same switch prevents hops in the network and provides for unbiased, most efficient network communication. There are 9 nodes directly connected to every InifiBand switch.
!!! note
We recommend allocating compute nodes of a single switch when the best possible computational network performance is required to run job efficiently.
Nodes directly connected to the one InifiBand switch can be allocated using node grouping on PBS resource attribute switch.
In this example, we request all 9 nodes directly connected to the same switch using node grouping placement.
```console
$ qsub -A OPEN-0-0 -q qprod -l select=9:ncpus=24 -l place=group=switch ./myjob
```
### Placement by Specific InifiBand Switch
!!! note
Not useful for ordinary computing, suitable for testing and management tasks.
Nodes directly connected to the specific InifiBand switch can be selected using the PBS resource attribute _switch_.
In this example, we request all 9 nodes directly connected to r4i1s0sw1 switch.
```console
$ qsub -A OPEN-0-0 -q qprod -l select=9:ncpus=24:switch=r4i1s0sw1 ./myjob
```
List of all InifiBand switches:
```console
$ qmgr -c 'print node @a' | grep switch | awk '{print $6}' | sort -u
r1i0s0sw0
r1i0s0sw1
r1i1s0sw0
r1i1s0sw1
r1i2s0sw0
...
```
List of all all nodes directly connected to the specific InifiBand switch:
```console
$ qmgr -c 'p n @d' | grep 'switch = r36sw3' | awk '{print $3}' | sort
r36u31n964
r36u32n965
r36u33n966
r36u34n967
r36u35n968
r36u36n969
r37u32n970
r37u33n971
r37u34n972
```
### Placement by Hypercube Dimension
Nodes located in the same dimension group may be allocated using node grouping on PBS resource attribute ehc\_[1-7]d .
| Hypercube dimension | node_group_key | #nodes per group |
| ------------------- | -------------- | ---------------- |
| 1D | ehc_1d | 18 |
| 2D | ehc_2d | 36 |
| 3D | ehc_3d | 72 |
| 4D | ehc_4d | 144 |
| 5D | ehc_5d | 144,288 |
| 6D | ehc_6d | 432,576 |
| 7D | ehc_7d | all |
In this example, we allocate 16 nodes in the same [hypercube dimension][4] 1 group.
```console
$ qsub -A OPEN-0-0 -q qprod -l select=16:ncpus=24 -l place=group=ehc_1d -I
```
For better understanding:
List of all groups in dimension 1:
```console
$ qmgr -c 'p n @d' | grep ehc_1d | awk '{print $6}' | sort |uniq -c
18 r1i0
18 r1i1
18 r1i2
18 r1i3
...
```
List of all all nodes in specific dimension 1 group:
```console
$ $ qmgr -c 'p n @d' | grep 'ehc_1d = r1i0' | awk '{print $3}' | sort
r1i0n0
r1i0n1
r1i0n10
r1i0n11
...
```
## Job Management
!!! note
Check status of your jobs using the **qstat** and **check-pbs-jobs** commands
```console
$ qstat -a
$ qstat -a -u username
$ qstat -an -u username
$ qstat -f 12345.isrv5
```
Example:
```console
$ qstat -a
srv11:
Req'd Req'd Elap
Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time
--------------- -------- -- |---|---| ------ --- --- ------ ----- - -----
16287.isrv5 user1 qlong job1 6183 4 64 -- 144:0 R 38:25
16468.isrv5 user1 qlong job2 8060 4 64 -- 144:0 R 17:44
16547.isrv5 user2 qprod job3x 13516 2 32 -- 48:00 R 00:58
```
In this example user1 and user2 are running jobs named job1, job2 and job3x. The jobs job1 and job2 are using 4 nodes, 16 cores per node each. The job1 already runs for 38 hours and 25 minutes, job2 for 17 hours 44 minutes. The job1 already consumed 64 x 38.41 = 2458.6 core hours. The job3x already consumed 0.96 x 32 = 30.93 core hours. These consumed core hours will be accounted on the respective project accounts, regardless of whether the allocated cores were actually used for computations.
Check status of your jobs using check-pbs-jobs command. Check presence of user's PBS jobs' processes on execution hosts. Display load, processes. Display job standard and error output. Continuously display (tail -f) job standard or error output.
```console
$ check-pbs-jobs --check-all
$ check-pbs-jobs --print-load --print-processes
$ check-pbs-jobs --print-job-out --print-job-err
$ check-pbs-jobs --jobid JOBID --check-all --print-all
$ check-pbs-jobs --jobid JOBID --tailf-job-out
```
Examples:
```console
$ check-pbs-jobs --check-all
JOB 35141.dm2, session_id 71995, user user2, nodes r3i6n2,r3i6n3
Check session id: OK
Check processes
r3i6n2: OK
r3i6n3: No process
```
In this example we see that job 35141.dm2 currently runs no process on allocated node r3i6n2, which may indicate an execution error.
```console
$ check-pbs-jobs --print-load --print-processes
JOB 35141.dm2, session_id 71995, user user2, nodes r3i6n2,r3i6n3
Print load
r3i6n2: LOAD: 16.01, 16.01, 16.00
r3i6n3: LOAD: 0.01, 0.00, 0.01
Print processes
%CPU CMD
r3i6n2: 0.0 -bash
r3i6n2: 0.0 /bin/bash /var/spool/PBS/mom_priv/jobs/35141.dm2.SC
r3i6n2: 99.7 run-task
...
```
In this example we see that job 35141.dm2 currently runs process run-task on node r3i6n2, using one thread only, while node r3i6n3 is empty, which may indicate an execution error.
```console
$ check-pbs-jobs --jobid 35141.dm2 --print-job-out
JOB 35141.dm2, session_id 71995, user user2, nodes r3i6n2,r3i6n3
Print job standard output:
======================== Job start ==========================
Started at : Fri Aug 30 02:47:53 CEST 2013
Script name : script
Run loop 1
Run loop 2
Run loop 3
```
In this example, we see actual output (some iteration loops) of the job 35141.dm2
!!! note
Manage your queued or running jobs, using the **qhold**, **qrls**, **qdel,** **qsig** or **qalter** commands
You may release your allocation at any time, using qdel command
```console
$ qdel 12345.isrv5
```
You may kill a running job by force, using qsig command
```console
$ qsig -s 9 12345.isrv5
```
Learn more by reading the pbs man page
```console
$ man pbs_professional
```
## Job Execution
### Jobscript
!!! note
Prepare the jobscript to run batch jobs in the PBS queue system
The Jobscript is a user made script, controlling sequence of commands for executing the calculation. It is often written in bash, other scripts may be used as well. The jobscript is supplied to PBS **qsub** command as an argument and executed by the PBS Professional workload manager.
!!! note
The jobscript or interactive shell is executed on first of the allocated nodes.
```console
$ qsub -q qexp -l select=4:ncpus=24 -N Name0 ./myjob
$ qstat -n -u username
isrv5:
Req'd Req'd Elap
Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time
--------------- -------- -- |---|---| ------ --- --- ------ ----- - -----
15209.isrv5 username qexp Name0 5530 4 96 -- 01:00 R 00:00
r21u01n577/0*24+r21u02n578/0*24+r21u03n579/0*24+r21u04n580/0*24
```
In this example, the nodes r21u01n577, r21u02n578, r21u03n579, r21u04n580 were allocated for 1 hour via the qexp queue. The jobscript myjob will be executed on the node r21u01n577, while the nodes r21u02n578, r21u03n579, r21u04n580 are available for use as well.
!!! note
The jobscript or interactive shell is by default executed in home directory
```console
$ qsub -q qexp -l select=4:ncpus=24 -I
qsub: waiting for job 15210.isrv5 to start
qsub: job 15210.isrv5 ready
$ pwd
/home/username
```
In this example, 4 nodes were allocated interactively for 1 hour via the qexp queue. The interactive shell is executed in the home directory.
!!! note
All nodes within the allocation may be accessed via ssh. Unallocated nodes are not accessible to user.
The allocated nodes are accessible via ssh from login nodes. The nodes may access each other via ssh as well.
Calculations on allocated nodes may be executed remotely via the MPI, ssh, pdsh or clush. You may find out which nodes belong to the allocation by reading the $PBS_NODEFILE file
```console
qsub -q qexp -l select=2:ncpus=24 -I
qsub: waiting for job 15210.isrv5 to start
qsub: job 15210.isrv5 ready
$ pwd
/home/username
$ sort -u $PBS_NODEFILE
r2i5n6.ib0.smc.salomon.it4i.cz
r4i6n13.ib0.smc.salomon.it4i.cz
r4i7n0.ib0.smc.salomon.it4i.cz
r4i7n2.ib0.smc.salomon.it4i.cz
$ pdsh -w r2i5n6,r4i6n13,r4i7n[0,2] hostname
r4i6n13: r4i6n13
r2i5n6: r2i5n6
r4i7n2: r4i7n2
r4i7n0: r4i7n0
```
In this example, the hostname program is executed via pdsh from the interactive shell. The execution runs on all four allocated nodes. The same result would be achieved if the pdsh is called from any of the allocated nodes or from the login nodes.
### Example Jobscript for MPI Calculation
!!! note
Production jobs must use the /scratch directory for I/O
The recommended way to run production jobs is to change to /scratch directory early in the jobscript, copy all inputs to /scratch, execute the calculations and copy outputs to home directory.
```bash
#!/bin/bash
# change to scratch directory, exit on failure
SCRDIR=/scratch/work/user/$USER/myjob
mkdir -p $SCRDIR
cd $SCRDIR || exit
# copy input file to scratch
cp $PBS_O_WORKDIR/input .
cp $PBS_O_WORKDIR/mympiprog.x .
# load the MPI module
ml OpenMPI
# execute the calculation
mpiexec -pernode ./mympiprog.x
# copy output file to home
cp output $PBS_O_WORKDIR/.
#exit
exit
```
In this example, some directory on the /home holds the input file input and executable mympiprog.x . We create a directory myjob on the /scratch filesystem, copy input and executable files from the /home directory where the qsub was invoked ($PBS_O_WORKDIR) to /scratch, execute the MPI programm mympiprog.x and copy the output file back to the /home directory. The mympiprog.x is executed as one process per node, on all allocated nodes.
!!! note
Consider preloading inputs and executables onto [shared scratch][5] before the calculation starts.
In some cases, it may be impractical to copy the inputs to scratch and outputs to home. This is especially true when very large input and output files are expected, or when the files should be reused by a subsequent calculation. In such a case, it is users responsibility to preload the input files on shared /scratch before the job submission and retrieve the outputs manually, after all calculations are finished.
!!! note
Store the qsub options within the jobscript. Use **mpiprocs** and **ompthreads** qsub options to control the MPI job execution.
### Example Jobscript for MPI Calculation With Preloaded Inputs
Example jobscript for an MPI job with preloaded inputs and executables, options for qsub are stored within the script :
```bash
#!/bin/bash
#PBS -q qprod
#PBS -N MYJOB
#PBS -l select=100:ncpus=24:mpiprocs=1:ompthreads=24
#PBS -A OPEN-0-0
# change to scratch directory, exit on failure
SCRDIR=/scratch/work/user/$USER/myjob
cd $SCRDIR || exit
# load the MPI module
ml OpenMPI
# execute the calculation
mpiexec ./mympiprog.x
#exit
exit
```
In this example, input and executable files are assumed preloaded manually in /scratch/$USER/myjob directory. Note the **mpiprocs** and **ompthreads** qsub options, controlling behavior of the MPI execution. The mympiprog.x is executed as one process per node, on all 100 allocated nodes. If mympiprog.x implements OpenMP threads, it will run 24 threads per node.
HTML commented section #2 (examples need to be reworked)
### Example Jobscript for Single Node Calculation
!!! note
Local scratch directory is often useful for single node jobs. Local scratch will be deleted immediately after the job ends. Be very careful, use of RAM disk filesystem is at the expense of operational memory.
Example jobscript for single node calculation, using [local scratch][5] on the node:
```bash
#!/bin/bash
# change to local scratch directory
cd /lscratch/$PBS_JOBID || exit
# copy input file to scratch
cp $PBS_O_WORKDIR/input .
cp $PBS_O_WORKDIR/myprog.x .
# execute the calculation
./myprog.x
# copy output file to home
cp output $PBS_O_WORKDIR/.
#exit
exit
```
In this example, some directory on the home holds the input file input and executable myprog.x . We copy input and executable files from the home directory where the qsub was invoked ($PBS_O_WORKDIR) to local scratch /lscratch/$PBS_JOBID, execute the myprog.x and copy the output file back to the /home directory. The myprog.x runs on one node only and may use threads.
[1]: resources-allocation-policy.md
[2]: #example-jobscript-for-mpi-calculation-with-preloaded-inputs
[3]: network.md
[4]: 7d-enhanced-hypercube.md
[5]: storage.md
# Network
All compute and login nodes of Salomon are interconnected by 7D Enhanced hypercube [InfiniBand][a] network and by Gigabit [Ethernet][b] network. Only [InfiniBand][c] network may be used to transfer user data.
## InfiniBand Network
All compute and login nodes of Salomon are interconnected by 7D Enhanced hypercube [Infiniband][a] network (56 Gbps). The network topology is a [7D Enhanced hypercube][1].
Read more about schematic representation of the Salomon cluster [IB single-plain topology][2] ([hypercube dimension][1]).
The compute nodes may be accessed via the Infiniband network using ib0 network interface, in address range 10.17.0.0 (mask 255.255.224.0). The MPI may be used to establish native Infiniband connection among the nodes.
The network provides **2170MB/s** transfer rates via the TCP connection (single stream) and up to **3600MB/s** via native Infiniband protocol.
## Example
```console
$ qsub -q qexp -l select=4:ncpus=16 -N Name0 ./myjob
$ qstat -n -u username
Req'd Req'd Elap
Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time
--------------- -------- -- |---|---| ------ --- --- ------ ----- - -----
15209.isrv5 username qexp Name0 5530 4 96 -- 01:00 R 00:00
r4i1n0/0*24+r4i1n1/0*24+r4i1n2/0*24+r4i1n3/0*24
```
In this example, we access the node r4i1n0 by Infiniband network via the ib0 interface.
```console
$ ssh 10.17.35.19
```
In this example, we get
information of the Infiniband network.
```console
$ ifconfig
....
inet addr:10.17.35.19....
....
$ ip addr show ib0
....
inet 10.17.35.19....
....
```
[1]: 7d-enhanced-hypercube.md
[2]: ib-single-plane-topology.md
[a]: http://en.wikipedia.org/wiki/InfiniBand
[b]: http://en.wikipedia.org/wiki/Ethernet
[c]: http://en.wikipedia.org/wiki/InfiniBand
# Resources Allocation Policy
## Job Queue Policies
The resources are allocated to the job in a fair-share fashion, subject to constraints set by the queue and resources available to the Project. The fair-share at Anselm ensures that individual users may consume approximately equal amount of resources per week. Detailed information in the [Job scheduling][1] section. The resources are accessible via several queues for queueing the jobs. The queues provide prioritized and exclusive access to the computational resources. Following table provides the queue partitioning overview:
!!! note
Check the queue status [here][a].
| queue | active project | project resources | nodes | min ncpus | priority | authorization | walltime |
| ------------------------------- | -------------- | -------------------- | ------------------------------------------------------------- | --------- | -------- | ------------- | --------- |
| **qexp** Express queue | no | none required | 32 nodes, max 8 per user | 24 | 150 | no | 1 / 1h |
| **qprod** Production queue | yes | > 0 | 1006 nodes, max 86 per job | 24 | 0 | no | 24 / 48h |
| **qlong** Long queue | yes | > 0 | 256 nodes, max 40 per job, only non-accelerated nodes allowed | 24 | 0 | no | 72 / 144h |
| **qmpp** Massive parallel queue | yes | > 0 | 1006 nodes | 24 | 0 | yes | 2 / 4h |
| **qfat** UV2000 queue | yes | > 0 | 1 (uv1) | 8 | 200 | yes | 24 / 48h |
| **qfree** Free resource queue | yes | < 120% of allocation | 987 nodes, max 86 per job | 24 | -1024 | no | 12 / 12h |
| **qviz** Visualization queue | yes | none required | 2 (with NVIDIA Quadro K5000) | 4 | 150 | no | 1 / 8h |
| **qmic** Intel Xeon Phi cards | yes | > 0 | 864 Intel Xeon Phi cards, max 8 mic per job | 0 | 0 | no | 24 / 48h |
!!! note
**The qfree queue is not free of charge**. [Normal accounting][2] applies. However, it allows for utilization of free resources, once a Project exhausted all its allocated computational resources. This does not apply to Directors Discretion (DD projects) but may be allowed upon request.
* **qexp**, the Express queue: This queue is dedicated for testing and running very small jobs. It is not required to specify a project to enter the qexp. There are 2 nodes always reserved for this queue (w/o accelerator), maximum 8 nodes are available via the qexp for a particular user. The nodes may be allocated on per core basis. No special authorization is required to use it. The maximum runtime in qexp is 1 hour.
* **qprod**, the Production queue: This queue is intended for normal production runs. It is required that active project with nonzero remaining resources is specified to enter the qprod. All nodes may be accessed via the qprod queue, however only 86 per job. Full nodes, 24 cores per node are allocated. The queue runs with medium priority and no special authorization is required to use it. The maximum runtime in qprod is 48 hours.
* **qlong**, the Long queue: This queue is intended for long production runs. It is required that active project with nonzero remaining resources is specified to enter the qlong. Only 336 nodes without acceleration may be accessed via the qlong queue. Full nodes, 24 cores per node are allocated. The queue runs with medium priority and no special authorization is required to use it. The maximum runtime in qlong is 144 hours (three times of the standard qprod time - 3 \* 48 h)
* **qmpp**, the massively parallel queue. This queue is intended for massively parallel runs. It is required that active project with nonzero remaining resources is specified to enter the qmpp. All nodes may be accessed via the qmpp queue. Full nodes, 24 cores per node are allocated. The queue runs with medium priority and no special authorization is required to use it. The maximum runtime in qmpp is 4 hours. An PI needs explicitly ask support for authorization to enter the queue for all users associated to her/his Project.
* **qfat**, the UV2000 queue. This queue is dedicated to access the fat SGI UV2000 SMP machine. The machine (uv1) has 112 Intel IvyBridge cores at 3.3GHz and 3.25TB RAM (8 cores and 128GB RAM are dedicated for system). An PI needs explicitly ask support for authorization to enter the queue for all users associated to her/his Project.
* **qfree**, the Free resource queue: The queue qfree is intended for utilization of free resources, after a Project exhausted all its allocated computational resources (Does not apply to DD projects by default. DD projects have to request for persmission on qfree after exhaustion of computational resources.). It is required that active project is specified to enter the queue. Consumed resources will be accounted to the Project. Access to the qfree queue is automatically removed if consumed resources exceed 120% of the resources allocated to the Project. Only 987 nodes without accelerator may be accessed from this queue. Full nodes, 24 cores per node are allocated. The queue runs with very low priority and no special authorization is required to use it. The maximum runtime in qfree is 12 hours.
* **qviz**, the Visualization queue: Intended for pre-/post-processing using OpenGL accelerated graphics. Currently when accessing the node, each user gets 4 cores of a CPU allocated, thus approximately 73 GB of RAM and 1/7 of the GPU capacity (default "chunk"). If more GPU power or RAM is required, it is recommended to allocate more chunks (with 4 cores each) up to one whole node per user, so that all 28 cores, 512 GB RAM and whole GPU is exclusive. This is currently also the maximum allowed allocation per one user. One hour of work is allocated by default, the user may ask for 2 hours maximum.
* **qmic**, the queue qmic to access MIC nodes. It is required that active project with nonzero remaining resources is specified to enter the qmic. All 864 MICs are included.
!!! note
To access node with Xeon Phi co-processor user needs to specify that in [job submission select statement][3].
## Queue Notes
The job wall-clock time defaults to **half the maximum time**, see table above. Longer wall time limits can be [set manually, see examples][3].
Jobs that exceed the reserved wall-clock time (Req'd Time) get killed automatically. Wall-clock time limit can be changed for queuing jobs (state Q) using the qalter command, however can not be changed for a running job (state R).
Salomon users may check current queue configuration [here][b].
## Queue Status
!!! note
Check the status of jobs, queues and compute nodes [here][a].
![RSWEB Salomon](../img/rswebsalomon.png "RSWEB Salomon")
Display the queue status on Salomon:
```console
$ qstat -q
```
The PBS allocation overview may be obtained also using the rspbs command.
```console
$ rspbs
Usage: rspbs [options]
Options:
--version show program's version number and exit
-h, --help show this help message and exit
--get-server-details Print server
--get-queues Print queues
--get-queues-details Print queues details
--get-reservations Print reservations
--get-reservations-details
Print reservations details
--get-nodes Print nodes of PBS complex
--get-nodeset Print nodeset of PBS complex
--get-nodes-details Print nodes details
--get-jobs Print jobs
--get-jobs-details Print jobs details
--get-jobs-check-params
Print jobid, job state, session_id, user, nodes
--get-users Print users of jobs
--get-allocated-nodes
Print allocated nodes of jobs
--get-allocated-nodeset
Print allocated nodeset of jobs
--get-node-users Print node users
--get-node-jobs Print node jobs
--get-node-ncpus Print number of ncpus per node
--get-node-allocated-ncpus
Print number of allocated ncpus per node
--get-node-qlist Print node qlist
--get-node-ibswitch Print node ibswitch
--get-user-nodes Print user nodes
--get-user-nodeset Print user nodeset
--get-user-jobs Print user jobs
--get-user-jobc Print number of jobs per user
--get-user-nodec Print number of allocated nodes per user
--get-user-ncpus Print number of allocated ncpus per user
--get-qlist-nodes Print qlist nodes
--get-qlist-nodeset Print qlist nodeset
--get-ibswitch-nodes Print ibswitch nodes
--get-ibswitch-nodeset
Print ibswitch nodeset
--summary Print summary
--get-node-ncpu-chart
Obsolete. Print chart of allocated ncpus per node
--server=SERVER Use given PBS server
--state=STATE Only for given job state
--jobid=JOBID Only for given job ID
--user=USER Only for given user
--node=NODE Only for given node
--nodestate=NODESTATE
Only for given node state (affects only --get-node*
--get-qlist-* --get-ibswitch-* actions)
--incl-finished Include finished jobs
```
---8<--- "resource_accounting.md"
---8<--- "mathjax.md"
[1]: job-priority.md
[2]: #resource-accounting-policy
[3]: job-submission-and-execution.md
[a]: https://extranet.it4i.cz/rsweb/salomon/
[b]: https://extranet.it4i.cz/rsweb/salomon/queues
# Accessing the Cluster
## Shell Access
The Salomon cluster is accessed by SSH protocol via login nodes login1, login2, login3 and login4 at address salomon.it4i.cz. The login nodes may be addressed specifically, by prepending the login node name to the address.
!!! note
The alias salomon.it4i.cz is currently not available through VPN connection. Please use loginX.salomon.it4i.cz when connected to VPN.
| Login address | Port | Protocol | Login node |
| ---------------------- | ---- | -------- | ------------------------------------- |
| salomon.it4i.cz | 22 | ssh | round-robin DNS record for login[1-4] |
| login1.salomon.it4i.cz | 22 | ssh | login1 |
| login2.salomon.it4i.cz | 22 | ssh | login2 |
| login3.salomon.it4i.cz | 22 | ssh | login3 |
| login4.salomon.it4i.cz | 22 | ssh | login4 |
The authentication is by the [private key][1] only.
!!! note
Please verify SSH fingerprints during the first logon. They are identical on all login nodes:
md5:
f6:28:98:e4:f9:b2:a6:8f:f2:f4:2d:0a:09:67:69:80 (DSA)
70:01:c9:9a:5d:88:91:c7:1b:c0:84:d1:fa:4e:83:5c (RSA)
sha256:
epkqEU2eFzXnMeMMkpX02CykyWjGyLwFj528Vumpzn4 (DSA)
WNIrR7oeQDYpBYy4N2d5A6cJ2p0837S7gzzTpaDBZrc (RSA)
Private key authentication:
On **Linux** or **Mac**, use
```console
local $ ssh -i /path/to/id_rsa username@salomon.it4i.cz
```
If you see warning message "UNPROTECTED PRIVATE KEY FILE!", use this command to set lower permissions to private key file.
```console
local $ chmod 600 /path/to/id_rsa
```
On **Windows**, use [PuTTY ssh client][2].
After logging in, you will see the command prompt:
```console
_____ _
/ ____| | |
| (___ __ _| | ___ _ __ ___ ___ _ __
\___ \ / _` | |/ _ \| '_ ` _ \ / _ \| '_ \
____) | (_| | | (_) | | | | | | (_) | | | |
|_____/ \__,_|_|\___/|_| |_| |_|\___/|_| |_|
http://www.it4i.cz/?lang=en
Last login: Tue Jul 9 15:57:38 2018 from your-host.example.com
[username@login2.salomon ~]$
```
!!! note
The environment is **not** shared between login nodes, except for [shared filesystems][3].
## Data Transfer
Data in and out of the system may be transferred by the [scp][a] and sftp protocols.
| Address | Port | Protocol |
| ---------------------- | ---- | --------- |
| salomon.it4i.cz | 22 | scp, sftp |
| login1.salomon.it4i.cz | 22 | scp, sftp |
| login2.salomon.it4i.cz | 22 | scp, sftp |
| login3.salomon.it4i.cz | 22 | scp, sftp |
| login4.salomon.it4i.cz | 22 | scp, sftp |
The authentication is by the [private key][1] only.
On linux or Mac, use scp or sftp client to transfer the data to Salomon:
```console
local $ scp -i /path/to/id_rsa my-local-file username@salomon.it4i.cz:directory/file
```
```console
local $ scp -i /path/to/id_rsa -r my-local-dir username@salomon.it4i.cz:directory
```
or
```console
local $ sftp -o IdentityFile=/path/to/id_rsa username@salomon.it4i.cz
```
Very convenient way to transfer files in and out of the Salomon computer is via the fuse filesystem [sshfs][b].
```console
local $ sshfs -o IdentityFile=/path/to/id_rsa username@salomon.it4i.cz:. mountpoint
```
Using sshfs, the users Salomon home directory will be mounted on your local computer, just like an external disk.
Learn more on ssh, scp and sshfs by reading the manpages
```console
$ man ssh
$ man scp
$ man sshfs
```
On Windows, use [WinSCP client][c] to transfer the data. The [win-sshfs client][d] provides a way to mount the Salomon filesystems directly as an external disc.
More information about the shared file systems is available [here][3].
## Connection Restrictions
Outgoing connections, from Salomon Cluster login nodes to the outside world, are restricted to following ports:
| Port | Protocol |
| ---- | -------- |
| 22 | ssh |
| 80 | http |
| 443 | https |
| 9418 | git |
!!! note
Please use **ssh port forwarding** and proxy servers to connect from Salomon to all other remote ports.
Outgoing connections, from Salomon Cluster compute nodes are restricted to the internal network. Direct connections form compute nodes to outside world are cut.
## Port Forwarding
### Port Forwarding From Login Nodes
!!! note
Port forwarding allows an application running on Salomon to connect to arbitrary remote host and port.
It works by tunneling the connection from Salomon back to users workstation and forwarding from the workstation to the remote host.
Pick some unused port on Salomon login node (for example 6000) and establish the port forwarding:
```console
local $ ssh -R 6000:remote.host.com:1234 salomon.it4i.cz
```
In this example, we establish port forwarding between port 6000 on Salomon and port 1234 on the remote.host.com. By accessing localhost:6000 on Salomon, an application will see response of remote.host.com:1234. The traffic will run via users local workstation.
Port forwarding may be done **using PuTTY** as well. On the PuTTY Configuration screen, load your Salomon configuration first. Then go to Connection->SSH->Tunnels to set up the port forwarding. Click Remote radio button. Insert 6000 to Source port textbox. Insert remote.host.com:1234. Click Add button, then Open.
Port forwarding may be established directly to the remote host. However, this requires that user has ssh access to remote.host.com
```console
$ ssh -L 6000:localhost:1234 remote.host.com
```
Note: Port number 6000 is chosen as an example only. Pick any free port.
### Port Forwarding From Compute Nodes
Remote port forwarding from compute nodes allows applications running on the compute nodes to access hosts outside Salomon Cluster.
First, establish the remote port forwarding form the login node, as [described above][4].
Second, invoke port forwarding from the compute node to the login node. Insert following line into your jobscript or interactive shell
```console
$ ssh -TN -f -L 6000:localhost:6000 login1
```
In this example, we assume that port forwarding from login1:6000 to remote.host.com:1234 has been established beforehand. By accessing localhost:6000, an application running on a compute node will see response of remote.host.com:1234
### Using Proxy Servers
Port forwarding is static, each single port is mapped to a particular port on remote host. Connection to other remote host, requires new forward.
!!! note
Applications with inbuilt proxy support, experience unlimited access to remote hosts, via single proxy server.
To establish local proxy server on your workstation, install and run SOCKS proxy server software. On Linux, sshd demon provides the functionality. To establish SOCKS proxy server listening on port 1080 run:
```console
local $ ssh -D 1080 localhost
```
On Windows, install and run the free, open source [Sock Puppet][e] server.
Once the proxy server is running, establish ssh port forwarding from Salomon to the proxy server, port 1080, exactly as [described above][4].
```console
local $ ssh -R 6000:localhost:1080 salomon.it4i.cz
```
Now, configure the applications proxy settings to **localhost:6000**. Use port forwarding to access the [proxy server from compute nodes][4] as well.
## Graphical User Interface
* The [X Window system][5] is a principal way to get GUI access to the clusters.
* The [Virtual Network Computing][6] is a graphical [desktop sharing][f] system that uses the [Remote Frame Buffer protocol][g] to remotely control another [computer][h].
## VPN Access
* Access to IT4Innovations internal resources via [VPN][7].
[1]: ../general/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.md
[2]: ../general/accessing-the-clusters/shell-access-and-data-transfer/putty.md
[3]: storage.md
[4]: #port-forwarding-from-login-nodes
[5]: ../general/accessing-the-clusters/graphical-user-interface/x-window-system.md
[6]: ../general/accessing-the-clusters/graphical-user-interface/vnc.md
[7]: ../general/accessing-the-clusters/vpn-access.md
[a]: http://en.wikipedia.org/wiki/Secure_copy
[b]: http://linux.die.net/man/1/sshfs
[c]: http://winscp.net/eng/download.php
[d]: http://code.google.com/p/win-sshfs/
[e]: http://sockspuppet.com/
[f]: http://en.wikipedia.org/wiki/Desktop_sharing
[g]: http://en.wikipedia.org/wiki/RFB_protocol
[h]: http://en.wikipedia.org/wiki/Computer