From 26f2d41e00bdac57ac1cfab4354811975b02a1e9 Mon Sep 17 00:00:00 2001 From: Lubomir Prda Date: Fri, 3 Feb 2017 13:45:00 +0100 Subject: [PATCH] Some files with good spelling merged with master --- .spelling | 402 ++++++++++++++++++ docs.it4i/anselm/environment-and-modules.md | 2 +- .../anselm/job-submission-and-execution.md | 4 +- docs.it4i/anselm/software/ansys/ansys-cfx.md | 2 +- .../anselm/software/debuggers/allinea-ddt.md | 2 +- .../debuggers/allinea-performance-reports.md | 2 +- docs.it4i/anselm/software/debuggers/cube.md | 2 +- docs.it4i/anselm/software/debuggers/papi.md | 4 +- .../anselm/software/debuggers/scalasca.md | 6 +- .../anselm/software/debuggers/valgrind.md | 2 +- docs.it4i/anselm/software/gpi2.md | 2 +- .../software/intel-suite/intel-compilers.md | 4 +- .../software/intel-suite/intel-debugger.md | 2 +- docs.it4i/anselm/software/isv_licenses.md | 12 +- docs.it4i/anselm/software/mpi/mpi.md | 2 +- .../software/numerical-languages/matlab.md | 4 +- .../numerical-languages/matlab_1314.md | 2 +- .../software/numerical-libraries/fftw.md | 2 +- .../software/numerical-libraries/hdf5.md | 2 +- .../software/numerical-libraries/petsc.md | 4 +- .../software/numerical-libraries/trilinos.md | 4 +- .../omics-master/diagnostic-component-team.md | 2 +- docs.it4i/anselm/software/virtualization.md | 18 +- docs.it4i/anselm/storage.md | 17 +- .../x-window-system.md | 2 +- .../ssh-keys.md | 2 +- docs.it4i/salomon/environment-and-modules.md | 2 +- docs.it4i/salomon/introduction.md | 2 +- .../salomon/job-submission-and-execution.md | 4 +- docs.it4i/salomon/software/ansys/ansys-cfx.md | 2 +- .../salomon/software/ansys/ansys-fluent.md | 2 +- .../salomon/software/ansys/ansys-ls-dyna.md | 6 +- .../software/ansys/ansys-mechanical-apdl.md | 4 +- docs.it4i/salomon/software/ansys/ansys.md | 2 +- docs.it4i/salomon/software/ansys/licensing.md | 2 +- .../ansys/setting-license-preferences.md | 2 +- docs.it4i/salomon/software/ansys/workbench.md | 4 +- .../salomon/software/chemistry/nwchem.md | 2 +- .../salomon/software/chemistry/phono3py.md | 2 +- docs.it4i/salomon/software/compilers.md | 16 +- .../software/comsol/comsol-multiphysics.md | 2 +- .../licensing-and-available-versions.md | 2 +- .../debuggers/allinea-performance-reports.md | 2 +- .../debuggers/intel-vtune-amplifier.md | 4 +- .../salomon/software/debuggers/valgrind.md | 2 +- .../salomon/software/debuggers/vampir.md | 2 +- .../software/intel-suite/intel-compilers.md | 4 +- .../software/intel-suite/intel-debugger.md | 4 +- 48 files changed, 498 insertions(+), 85 deletions(-) diff --git a/.spelling b/.spelling index 1cb0368c..64de0b40 100644 --- a/.spelling +++ b/.spelling @@ -33,6 +33,7 @@ TotalView Valgrind ParaView OpenFOAM +MAX_FAIRSHARE MPI4Py MPICH2 PETSc @@ -86,6 +87,173 @@ AnyConnect X11 backfilling backfilled +SCP +Lustre +QDR +TFLOP +ncpus +myjob +pernode +mpiprocs +ompthreads +qprace +runtime +SVS +ppn +Multiphysics +aeroacoustics +turbomachinery +CFD +LS-DYNA +APDL +MAPDL +multiphysics +AUTODYN +RSM +Molpro +initio +parallelization +NWChem +SCF +ISV +profiler +Pthreads +profilers +OTF +PAPI +PCM +uncore +pre-processing +prepend +CXX +prepended +POMP2 +Memcheck +unaddressable +OTF2 +GPI-2 +GASPI +GPI +MKL +IPP +TBB +GSL +Omics +VNC +Scalasca +IFORT +interprocedural +IDB +cloop +qcow +qcow2 +vmdk +vdi +virtio +paravirtualized +Gbit +tap0 +UDP +TCP +preload +qfat +Rmpi +DCT +datasets +dataset +preconditioners +partitioners +PARDISO +PaStiX +SuiteSparse +SuperLU +ExodusII +NetCDF +ParMETIS +multigrid +HYPRE +SPAI +Epetra +EpetraExt +Tpetra +64-bit +Belos +GMRES +Amesos +IFPACK +preconditioner +Teuchos +Makefiles +SAXPY +NVCC +VCF +HGMD +HUMSAVAR +ClinVar +indels +CIBERER +exomes +tmp +SSHFS +RSYNC +unmount +Cygwin +CygwinX +RFB +TightVNC +TigerVNC +GUIs +XLaunch +UTF-8 +numpad +PuTTYgen +OpenSSH +IE11 +x86 +r21u01n577 +7120P +interprocessor +IPN +toolchains +toolchain +APIs +easyblocks +GM200 +GeForce +GTX +IRUs +ASIC +backplane +ICEX +IRU +PFLOP +T950B +ifconfig +inet +addr +checkbox +appfile +programmatically +http +https +filesystem +phono3py +HDF +splitted +automize +llvm +PGI +GUPC +BUPC +IBV +Aislinn +nondeterminism +stdout +stderr +i.e. +pthreads +uninitialised +broadcasted - docs.it4i/anselm-cluster-documentation/environment-and-modules.md MODULEPATH bashrc @@ -119,6 +287,7 @@ Rmax E5-2665 E5-2470 P5110 +isw - docs.it4i/anselm-cluster-documentation/introduction.md RedHat - docs.it4i/anselm-cluster-documentation/job-priority.md @@ -126,6 +295,8 @@ walltime qexp _List.fairshare _time +_FAIRSHARE +1E6 - docs.it4i/anselm-cluster-documentation/job-submission-and-execution.md 15209.srv11 qsub @@ -146,6 +317,15 @@ jobscript cn108 cn109 cn110 +Name0 +cn17 +_NODEFILE +_O +_WORKDIR +mympiprog.x +_JOBID +myprog.x +openmpi - docs.it4i/anselm-cluster-documentation/network.md ib0 - docs.it4i/anselm-cluster-documentation/prace.md @@ -153,14 +333,19 @@ PRACE qfree it4ifree it4i.portal.clients +prace +1h - docs.it4i/anselm-cluster-documentation/shell-and-data-access.md VPN - docs.it4i/anselm-cluster-documentation/software/ansys/ansys-cfx.md ANSYS CFX cfx.pbs +_r +ane3fl - docs.it4i/anselm-cluster-documentation/software/ansys/ansys-mechanical-apdl.md mapdl.pbs +_dy - docs.it4i/anselm-cluster-documentation/software/ansys/ls-dyna.md HPC lsdyna.pbs @@ -175,9 +360,25 @@ Makefile - docs.it4i/anselm-cluster-documentation/software/gpi2.md gcc cn79 +helloworld +_gpi.c +ibverbs +gaspi +_logger - docs.it4i/anselm-cluster-documentation/software/intel-suite/intel-compilers.md Haswell CPUs +ipo +O3 +vec +xAVX +omp +simd +ivdep +pragmas +openmp +xCORE-AVX2 +axCORE-AVX2 - docs.it4i/anselm-cluster-documentation/software/kvirtualization.md rc.local runlevel @@ -189,6 +390,8 @@ VDE smb.conf TMPDIR run.bat. +slirp +NATs - docs.it4i/anselm-cluster-documentation/software/mpi/mpi4py-mpi-for-python.md NumPy - docs.it4i/anselm-cluster-documentation/software/numerical-languages/matlab_1314.md @@ -197,33 +400,73 @@ matlabcode.m output.out matlabcodefile sched +_feature - docs.it4i/anselm-cluster-documentation/software/numerical-languages/matlab.md UV2000 +maxNumCompThreads +SalomonPBSPro - docs.it4i/anselm-cluster-documentation/software/numerical-languages/octave.md _THREADS +_NUM - docs.it4i/anselm-cluster-documentation/software/numerical-libraries/trilinos.md CMake-aware Makefile.export +_PACKAGE +_CXX +_COMPILER +_INCLUDE +_DIRS +_LIBRARY - docs.it4i/anselm-cluster-documentation/software/ansys/ansys-ls-dyna.md ansysdyna.pbs - docs.it4i/anselm-cluster-documentation/software/ansys/ansys.md svsfem.cz +_ - docs.it4i/anselm-cluster-documentation/software/debuggers/valgrind.md libmpiwrap-amd64-linux +O0 +valgrind +malloc +_PRELOAD - docs.it4i/anselm-cluster-documentation/software/numerical-libraries/magma-for-intel-xeon-phi.md cn204 +_LIBS +MAGMAROOT +_magma +_server +_anselm +_from +_mic.sh +_dgetrf +_mic +_03.pdf - docs.it4i/anselm-cluster-documentation/software/paraview.md cn77 localhost +v4.0.1 - docs.it4i/anselm-cluster-documentation/storage.md ssh.du1.cesnet.cz Plzen ssh.du2.cesnet.cz ssh.du3.cesnet.cz +tier1 +_home +_cache +_tape - docs.it4i/salomon/environment-and-modules.md icc +ictce +ifort +imkl +intel +gompi +goolf +BLACS +iompi +iccifort - docs.it4i/salomon/hardware-overview.md HW +E5-4627v2 - docs.it4i/salomon/job-submission-and-execution.md 15209.isrv5 r21u01n577 @@ -248,6 +491,7 @@ mkdir mympiprog.x mpiexec myprog.x +r4i7n0.ib0.smc.salomon.it4i.cz - docs.it4i/salomon/7d-enhanced-hypercube.md cns1 cns576 @@ -256,7 +500,165 @@ r4i7n17 cns577 cns1008 r37u31n1008 +7D - docs.it4i/anselm-cluster-documentation/resources-allocation-policy.md qsub it4ifree it4i.portal.clients + - docs.it4i/anselm-cluster-documentation/software/ansys/ansys-fluent.md +anslic +_admin + - docs.it4i/anselm-cluster-documentation/software/chemistry/nwchem.md +_DIR + - docs.it4i/anselm-cluster-documentation/software/comsol-multiphysics.md +EDU +comsol +_matlab.pbs +_job.m +mphstart + - docs.it4i/anselm-cluster-documentation/software/debuggers/allinea-performance-reports.md +perf-report +perf +txt +html +mympiprog +_32p + - docs.it4i/anselm-cluster-documentation/software/debuggers/intel-vtune-amplifier.md +Hotspots + - docs.it4i/anselm-cluster-documentation/software/debuggers/scalasca.md +scorep + - docs.it4i/anselm-cluster-documentation/software/isv_licenses.md +edu +ansys +_features +_state.txt +f1 +matlab +acfd +_ansys +_acfd +_aa +_comsol +HEATTRANSFER +_HEATTRANSFER +COMSOLBATCH +_COMSOLBATCH +STRUCTURALMECHANICS +_STRUCTURALMECHANICS +_matlab +_Toolbox +_Image +_Distrib +_Comp +_Engine +_Acquisition +pmode +matlabpool + - docs.it4i/anselm-cluster-documentation/software/mpi/mpi.md +mpirun +BLAS1 +FFT +KMP +_AFFINITY +GOMP +_CPU +bullxmpi-1 +mpich2 + - docs.it4i/anselm-cluster-documentation/software/mpi/Running_OpenMPI.md +bysocket +bycore + - docs.it4i/anselm-cluster-documentation/software/numerical-libraries/fftw.md +gcc3.3.3 +pthread +fftw3 +lfftw3 +_threads-lfftw3 +_omp +icc3.3.3 +FFTW2 +gcc2.1.5 +fftw2 +lfftw +_threads +icc2.1.5 +fftw-mpi3 +_mpi +fftw3-mpi +fftw2-mpi +IntelMPI + - docs.it4i/anselm-cluster-documentation/software/numerical-libraries/gsl.md +dwt.c +mkl +lgsl + - docs.it4i/anselm-cluster-documentation/software/numerical-libraries/hdf5.md +icc +hdf5 +_INC +_SHLIB +_CPP +_LIB +_F90 +gcc49 + - docs.it4i/anselm-cluster-documentation/software/numerical-libraries/petsc.md +_Dist + - docs.it4i/anselm-cluster-documentation/software/nvidia-cuda.md +lcublas + - docs.it4i/anselm-cluster-documentation/software/operating-system.md +6.x + - docs.it4i/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/cygwin-and-x11-forwarding.md +startxwin +cygwin64binXWin.exe +tcp + - docs.it4i/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system.md +Xming +XWin.exe. + - docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/pageant.md +_rsa.ppk + - docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/puttygen.md +_keys +organization.example.com +_rsa + - docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/vpn-connection-fail-in-win-8.1.md +vpnui.exe + - docs.it4i/salomon/ib-single-plane-topology.md +36-port +Mcell.pdf +r21-r38 +nodes.pdf + - docs.it4i/salomon/introduction.md +E5-2680v3 + - docs.it4i/salomon/network.md +r4i1n0 +r4i1n1 +r4i1n2 +r4i1n3 +ip + - docs.it4i/salomon/software/ansys/setting-license-preferences.md +ansys161 + - docs.it4i/salomon/software/ansys/workbench.md +mpifile.txt +solvehandlers.xml + - docs.it4i/salomon/software/chemistry/phono3py.md +vasprun.xml +disp-XXXXX +disp +_fc3.yaml +ir +_grid +_points.yaml +gofree-cond1 + - docs.it4i/salomon/software/compilers.md +HPF + - docs.it4i/salomon/software/comsol/licensing-and-available-versions.md +ver + - docs.it4i/salomon/software/debuggers/aislinn.md +test.cpp + - docs.it4i/salomon/software/debuggers/intel-vtune-amplifier.md +vtune +_update1 + - docs.it4i/salomon/software/debuggers/valgrind.md +EBROOTVALGRIND + - docs.it4i/salomon/software/intel-suite/intel-advisor.md +O2 + - docs.it4i/salomon/software/intel-suite/intel-compilers.md +UV1 diff --git a/docs.it4i/anselm/environment-and-modules.md b/docs.it4i/anselm/environment-and-modules.md index 21230e9e..a0aa6d0b 100644 --- a/docs.it4i/anselm/environment-and-modules.md +++ b/docs.it4i/anselm/environment-and-modules.md @@ -24,7 +24,7 @@ fi ``` !!! note - Do not run commands outputting to standard output (echo, module list, etc) in .bashrc for non-interactive SSH sessions. It breaks fundamental functionality (scp, PBS) of your account! Conside utilization of SSH session interactivity for such commands as stated in the previous example. + Do not run commands outputting to standard output (echo, module list, etc) in .bashrc for non-interactive SSH sessions. It breaks fundamental functionality (SCP, PBS) of your account! Consider utilization of SSH session interactivity for such commands as stated in the previous example. ## Application Modules diff --git a/docs.it4i/anselm/job-submission-and-execution.md b/docs.it4i/anselm/job-submission-and-execution.md index b0ea19bd..f0b88f59 100644 --- a/docs.it4i/anselm/job-submission-and-execution.md +++ b/docs.it4i/anselm/job-submission-and-execution.md @@ -322,7 +322,7 @@ cd $SCRDIR || exit cp $PBS_O_WORKDIR/input . cp $PBS_O_WORKDIR/mympiprog.x . -# load the mpi module +# load the MPI module module load openmpi # execute the calculation @@ -360,7 +360,7 @@ Example jobscript for an MPI job with preloaded inputs and executables, options SCRDIR=/scratch/$USER/myjob cd $SCRDIR || exit -# load the mpi module +# load the MPI module module load openmpi # execute the calculation diff --git a/docs.it4i/anselm/software/ansys/ansys-cfx.md b/docs.it4i/anselm/software/ansys/ansys-cfx.md index b816f026..343bb267 100644 --- a/docs.it4i/anselm/software/ansys/ansys-cfx.md +++ b/docs.it4i/anselm/software/ansys/ansys-cfx.md @@ -49,7 +49,7 @@ echo Machines: $hl Header of the PBS file (above) is common and description can be find on [this site](../../job-submission-and-execution/). SVS FEM recommends to utilize sources by keywords: nodes, ppn. These keywords allows to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources. -Working directory has to be created before sending PBS job into the queue. Input file should be in working directory or full path to input file has to be specified. >Input file has to be defined by common CFX def file which is attached to the cfx solver via parameter -def +Working directory has to be created before sending PBS job into the queue. Input file should be in working directory or full path to input file has to be specified. >Input file has to be defined by common CFX def file which is attached to the CFX solver via parameter -def **License** should be selected by parameter -P (Big letter **P**). Licensed products are the following: aa_r (ANSYS **Academic** Research), ane3fl (ANSYS Multiphysics)-**Commercial**. [More about licensing here](licensing/) diff --git a/docs.it4i/anselm/software/debuggers/allinea-ddt.md b/docs.it4i/anselm/software/debuggers/allinea-ddt.md index 6c1c664f..a5dd069b 100644 --- a/docs.it4i/anselm/software/debuggers/allinea-ddt.md +++ b/docs.it4i/anselm/software/debuggers/allinea-ddt.md @@ -4,7 +4,7 @@ Allinea Forge consist of two tools - debugger DDT and profiler MAP. Allinea DDT, is a commercial debugger primarily for debugging parallel MPI or OpenMP programs. It also has a support for GPU (CUDA) and Intel Xeon Phi accelerators. DDT provides all the standard debugging features (stack trace, breakpoints, watches, view variables, threads etc.) for every thread running as part of your program, or for every process - even if these processes are distributed across a cluster using an MPI implementation. -Allinea MAP is a profiler for C/C++/Fortran HPC codes. It is designed for profiling parallel code, which uses pthreads, OpenMP or MPI. +Allinea MAP is a profiler for C/C++/Fortran HPC codes. It is designed for profiling parallel code, which uses Pthreads, OpenMP or MPI. ## License and Limitations for Anselm Users diff --git a/docs.it4i/anselm/software/debuggers/allinea-performance-reports.md b/docs.it4i/anselm/software/debuggers/allinea-performance-reports.md index 614e6277..7b519b85 100644 --- a/docs.it4i/anselm/software/debuggers/allinea-performance-reports.md +++ b/docs.it4i/anselm/software/debuggers/allinea-performance-reports.md @@ -29,7 +29,7 @@ Instead of [running your MPI program the usual way](../mpi/), use the the perf r $ perf-report mpirun ./mympiprog.x ``` -The mpi program will run as usual. The perf-report creates two additional files, in \*.txt and \*.html format, containing the performance report. Note that [demanding MPI codes should be run within the queue system](../../job-submission-and-execution/). +The MPI program will run as usual. The perf-report creates two additional files, in \*.txt and \*.html format, containing the performance report. Note that [demanding MPI codes should be run within the queue system](../../job-submission-and-execution/). ## Example diff --git a/docs.it4i/anselm/software/debuggers/cube.md b/docs.it4i/anselm/software/debuggers/cube.md index a7f88955..29bd3862 100644 --- a/docs.it4i/anselm/software/debuggers/cube.md +++ b/docs.it4i/anselm/software/debuggers/cube.md @@ -30,7 +30,7 @@ CUBE is a graphical application. Refer to Graphical User Interface documentation !!! note Analyzing large data sets can consume large amount of CPU and RAM. Do not perform large analysis on login nodes. -After loading the appropriate module, simply launch cube command, or alternatively you can use scalasca -examine command to launch the GUI. Note that for Scalasca datasets, if you do not analyze the data with scalasca -examine before to opening them with CUBE, not all performance data will be available. +After loading the appropriate module, simply launch cube command, or alternatively you can use Scalasca -examine command to launch the GUI. Note that for Scalasca data sets, if you do not analyze the data with `scalasca -examine` before to opening them with CUBE, not all performance data will be available. References 1\. diff --git a/docs.it4i/anselm/software/debuggers/papi.md b/docs.it4i/anselm/software/debuggers/papi.md index bc36923e..2ea15593 100644 --- a/docs.it4i/anselm/software/debuggers/papi.md +++ b/docs.it4i/anselm/software/debuggers/papi.md @@ -10,13 +10,13 @@ PAPI can be used with parallel as well as serial programs. ## Usage -To use PAPI, load [module](../../environment-and-modules/) papi: +To use PAPI, load [module](../../environment-and-modules/) PAPI: ```bash $ module load papi ``` -This will load the default version. Execute module avail papi for a list of installed versions. +This will load the default version. Execute module avail pap for a list of installed versions. ## Utilities diff --git a/docs.it4i/anselm/software/debuggers/scalasca.md b/docs.it4i/anselm/software/debuggers/scalasca.md index 19daec04..c01271a5 100644 --- a/docs.it4i/anselm/software/debuggers/scalasca.md +++ b/docs.it4i/anselm/software/debuggers/scalasca.md @@ -23,13 +23,13 @@ Profiling a parallel application with Scalasca consists of three steps: ### Instrumentation -Instrumentation via " scalasca -instrument" is discouraged. Use [Score-P instrumentation](score-p/). +Instrumentation via `scalasca -instrument` is discouraged. Use [Score-P instrumentation](score-p/). ### Runtime Measurement After the application is instrumented, runtime measurement can be performed with the `scalasca -analyze` command. The syntax is: -`scalasca -analyze [scalasca options][launcher] [launcher options][program] [program options]` +`scalasca -analyze [scalasca options] [launcher] [launcher options] [program] [program options]` An example : @@ -61,7 +61,7 @@ If you do not wish to launch the GUI tool, use the "-s" option : scalasca -examine -s ``` -Alternatively you can open CUBE and load the data directly from here. Keep in mind that in that case the preprocessing is not done and not all metrics will be shown in the viewer. +Alternatively you can open CUBE and load the data directly from here. Keep in mind that in that case the pre-processing is not done and not all metrics will be shown in the viewer. Refer to [CUBE documentation](cube/) on usage of the GUI viewer. diff --git a/docs.it4i/anselm/software/debuggers/valgrind.md b/docs.it4i/anselm/software/debuggers/valgrind.md index 2602fdbf..0f704ebc 100644 --- a/docs.it4i/anselm/software/debuggers/valgrind.md +++ b/docs.it4i/anselm/software/debuggers/valgrind.md @@ -259,4 +259,4 @@ Prints this output : (note that there is output printed for every launched MPI p ==31319== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 4 from 4) ``` -We can see that Valgrind has reported use of unitialised memory on the master process (which reads the array to be broadcast) and use of unaddresable memory on both processes. +We can see that Valgrind has reported use of uninitialized memory on the master process (which reads the array to be broadcast) and use of unaddressable memory on both processes. diff --git a/docs.it4i/anselm/software/gpi2.md b/docs.it4i/anselm/software/gpi2.md index ec96e265..2bf86969 100644 --- a/docs.it4i/anselm/software/gpi2.md +++ b/docs.it4i/anselm/software/gpi2.md @@ -155,7 +155,7 @@ Submit the job and run the GPI-2 application Hello from rank 0 of 2 ``` -At the same time, in another session, you may start the gaspi logger: +At the same time, in another session, you may start the GASPI logger: ```bash $ ssh cn79 diff --git a/docs.it4i/anselm/software/intel-suite/intel-compilers.md b/docs.it4i/anselm/software/intel-suite/intel-compilers.md index 66de3b77..9cc1f1e0 100644 --- a/docs.it4i/anselm/software/intel-suite/intel-compilers.md +++ b/docs.it4i/anselm/software/intel-suite/intel-compilers.md @@ -1,6 +1,6 @@ # Intel Compilers -The Intel compilers version 13.1.1 are available, via module intel. The compilers include the icc C and C++ compiler and the ifort fortran 77/90/95 compiler. +The Intel compilers version 13.1.1 are available, via module Intel. The compilers include the ICC C and C++ compiler and the IFORT Fortran 77/90/95 compiler. ```bash $ module load intel @@ -8,7 +8,7 @@ The Intel compilers version 13.1.1 are available, via module intel. The compiler $ ifort -v ``` -The intel compilers provide for vectorization of the code, via the AVX instructions and support threading parallelization via OpenMP +The Intel compilers provide for vectorization of the code, via the AVX instructions and support threading parallelization via OpenMP For maximum performance on the Anselm cluster, compile your programs using the AVX instructions, with reporting where the vectorization was used. We recommend following compilation options for high performance diff --git a/docs.it4i/anselm/software/intel-suite/intel-debugger.md b/docs.it4i/anselm/software/intel-suite/intel-debugger.md index f13086df..d3acd2c5 100644 --- a/docs.it4i/anselm/software/intel-suite/intel-debugger.md +++ b/docs.it4i/anselm/software/intel-suite/intel-debugger.md @@ -70,4 +70,4 @@ Run the idb debugger in GUI mode. The menu Parallel contains number of tools for ## Further Information -Exhaustive manual on idb features and usage is published at [Intel website](http://software.intel.com/sites/products/documentation/doclib/stdxe/2013/composerxe/debugger/user_guide/index.htm) +Exhaustive manual on IDB features and usage is published at [Intel website](http://software.intel.com/sites/products/documentation/doclib/stdxe/2013/composerxe/debugger/user_guide/index.htm) diff --git a/docs.it4i/anselm/software/isv_licenses.md b/docs.it4i/anselm/software/isv_licenses.md index 56270b51..1baf941d 100644 --- a/docs.it4i/anselm/software/isv_licenses.md +++ b/docs.it4i/anselm/software/isv_licenses.md @@ -61,11 +61,13 @@ The general format of the name is `feature__APP__FEATURE`. Names of applications (APP): -* ansys -* comsol -* comsol-edu -* matlab -* matlab-edu +```bash + ansys + comsol + comsol-edu + matlab + matlab-edu +``` To get the FEATUREs of a license take a look into the corresponding state file ([see above](isv_licenses/#Licence)), or use: diff --git a/docs.it4i/anselm/software/mpi/mpi.md b/docs.it4i/anselm/software/mpi/mpi.md index bc60afb1..08be4bce 100644 --- a/docs.it4i/anselm/software/mpi/mpi.md +++ b/docs.it4i/anselm/software/mpi/mpi.md @@ -111,7 +111,7 @@ Compile the above example with The MPI program executable must be compatible with the loaded MPI module. Always compile and execute using the very same MPI module. -It is strongly discouraged to mix mpi implementations. Linking an application with one MPI implementation and running mpirun/mpiexec form other implementation may result in unexpected errors. +It is strongly discouraged to mix MPI implementations. Linking an application with one MPI implementation and running mpirun/mpiexec form other implementation may result in unexpected errors. The MPI program executable must be available within the same path on all nodes. This is automatically fulfilled on the /home and /scratch file system. You need to preload the executable, if running on the local scratch /lscratch file system. diff --git a/docs.it4i/anselm/software/numerical-languages/matlab.md b/docs.it4i/anselm/software/numerical-languages/matlab.md index d7c3d907..cfc958b7 100644 --- a/docs.it4i/anselm/software/numerical-languages/matlab.md +++ b/docs.it4i/anselm/software/numerical-languages/matlab.md @@ -274,8 +274,8 @@ You can use MATLAB on UV2000 in two parallel modes: ### Threaded Mode -Since this is a SMP machine, you can completely avoid using Parallel Toolbox and use only MATLAB's threading. MATLAB will automatically detect the number of cores you have allocated and will set maxNumCompThreads accordingly and certain operations, such as fft, , eig, svd, etc. will be automatically run in threads. The advantage of this mode is that you don't need to modify your existing sequential codes. +Since this is a SMP machine, you can completely avoid using Parallel Toolbox and use only MATLAB's threading. MATLAB will automatically detect the number of cores you have allocated and will set maxNumCompThreads accordingly and certain operations, such as `fft`, `eig`, `svd` etc. will be automatically run in threads. The advantage of this mode is that you don't need to modify your existing sequential codes. ### Local Cluster Mode -You can also use Parallel Toolbox on UV2000. Use l[ocal cluster mode](matlab/#parallel-matlab-batch-job-in-local-mode), "SalomonPBSPro" profile will not work. +You can also use Parallel Toolbox on UV2000. Use [local cluster mode](matlab/#parallel-matlab-batch-job-in-local-mode), "SalomonPBSPro" profile will not work. diff --git a/docs.it4i/anselm/software/numerical-languages/matlab_1314.md b/docs.it4i/anselm/software/numerical-languages/matlab_1314.md index 8c101253..ca2a6261 100644 --- a/docs.it4i/anselm/software/numerical-languages/matlab_1314.md +++ b/docs.it4i/anselm/software/numerical-languages/matlab_1314.md @@ -84,7 +84,7 @@ Once this file is in place, user can request resources from PBS. Following examp -l feature__matlab__MATLAB=1 ``` -This qsub command example shows how to run Matlab with 32 workers in following configuration: 2 nodes (use all 16 cores per node) and 16 workers = mpirocs per node (-l select=2:ncpus=16:mpiprocs=16). If user requires to run smaller number of workers per node then the "mpiprocs" parameter has to be changed. +This qsub command example shows how to run Matlab with 32 workers in following configuration: 2 nodes (use all 16 cores per node) and 16 workers = mpiprocs per node (-l select=2:ncpus=16:mpiprocs=16). If user requires to run smaller number of workers per node then the "mpiprocs" parameter has to be changed. The second part of the command shows how to request all necessary licenses. In this case 1 Matlab-EDU license and 32 Distributed Computing Engines licenses. diff --git a/docs.it4i/anselm/software/numerical-libraries/fftw.md b/docs.it4i/anselm/software/numerical-libraries/fftw.md index 038e1223..ed14410d 100644 --- a/docs.it4i/anselm/software/numerical-libraries/fftw.md +++ b/docs.it4i/anselm/software/numerical-libraries/fftw.md @@ -4,7 +4,7 @@ The discrete Fourier transform in one or more dimensions, MPI parallel FFTW is a C subroutine library for computing the discrete Fourier transform in one or more dimensions, of arbitrary input size, and of both real and complex data (as well as of even/odd data, e.g. the discrete cosine/sine transforms or DCT/DST). The FFTW library allows for MPI parallel, in-place discrete Fourier transform, with data distributed over number of nodes. -Two versions, **3.3.3** and **2.1.5** of FFTW are available on Anselm, each compiled for **Intel MPI** and **OpenMPI** using **intel** and **gnu** compilers. These are available via modules: +Two versions, **3.3.3** and **2.1.5** of FFTW are available on Anselm, each compiled for **Intel MPI** and **OpenMPI** using **Intel** and **gnu** compilers. These are available via modules: | Version | Parallelization | module | linker options | | -------------- | --------------- | ------------------- | ----------------------------------- | diff --git a/docs.it4i/anselm/software/numerical-libraries/hdf5.md b/docs.it4i/anselm/software/numerical-libraries/hdf5.md index d9abd72c..5551864b 100644 --- a/docs.it4i/anselm/software/numerical-libraries/hdf5.md +++ b/docs.it4i/anselm/software/numerical-libraries/hdf5.md @@ -4,7 +4,7 @@ Hierarchical Data Format library. Serial and MPI parallel version. [HDF5 (Hierarchical Data Format)](http://www.hdfgroup.org/HDF5/) is a general purpose library and file format for storing scientific data. HDF5 can store two primary objects: datasets and groups. A dataset is essentially a multidimensional array of data elements, and a group is a structure for organizing objects in an HDF5 file. Using these two basic objects, one can create and store almost any kind of scientific data structure, such as images, arrays of vectors, and structured and unstructured grids. You can also mix and match them in HDF5 files according to your needs. -Versions **1.8.11** and **1.8.13** of HDF5 library are available on Anselm, compiled for **Intel MPI** and **OpenMPI** using **intel** and **gnu** compilers. These are available via modules: +Versions **1.8.11** and **1.8.13** of HDF5 library are available on Anselm, compiled for **Intel MPI** and **OpenMPI** using **Intel** and **gnu** compilers. These are available via modules: | Version | Parallelization | module | C linker options | C++ linker options | Fortran linker options | | --------------------- | --------------------------------- | -------------------------- | --------------------- | ----------------------- | ----------------------- | diff --git a/docs.it4i/anselm/software/numerical-libraries/petsc.md b/docs.it4i/anselm/software/numerical-libraries/petsc.md index 528d13dd..beb0715c 100644 --- a/docs.it4i/anselm/software/numerical-libraries/petsc.md +++ b/docs.it4i/anselm/software/numerical-libraries/petsc.md @@ -32,9 +32,7 @@ PETSc needs at least MPI, BLAS and LAPACK. These dependencies are currently sati PETSc can be linked with a plethora of [external numerical libraries](http://www.mcs.anl.gov/petsc/miscellaneous/external.html), extending PETSc functionality, e.g. direct linear system solvers, preconditioners or partitioners. See below a list of libraries currently included in Anselm `petsc` modules. All these libraries can be used also alone, without PETSc. Their static or shared program libraries are available in -`$PETSC_DIR/$PETSC_ARCH/lib` and header files in `$PETSC_DIR/$PETSC_ARCH/include`. `PETSC_DIR` and `PETSC_ARCH` are environment variables pointing to a specific PETSc instance based on the petsc module loaded. - -### Libraries Linked to PETSc on Anselm (As of 11 April 2015) +`$PETSC_DIR/$PETSC_ARCH/lib` and header files in `$PETSC_DIR/$PETSC_ARCH/include`. `PETSC_DIR` and `PETSC_ARCH` are environment variables pointing to a specific PETSc instance based on the PETSc module loaded. * dense linear algebra * [Elemental](http://libelemental.org/) diff --git a/docs.it4i/anselm/software/numerical-libraries/trilinos.md b/docs.it4i/anselm/software/numerical-libraries/trilinos.md index 42f8bc0d..67486ad6 100644 --- a/docs.it4i/anselm/software/numerical-libraries/trilinos.md +++ b/docs.it4i/anselm/software/numerical-libraries/trilinos.md @@ -34,7 +34,7 @@ First, load the appropriate module: For the compilation of CMake-aware project, Trilinos provides the FIND_PACKAGE( Trilinos ) capability, which makes it easy to build against Trilinos, including linking against the correct list of libraries. For details, see -For compiling using simple makefiles, Trilinos provides Makefile.export system, which allows users to include important Trilinos variables directly into their makefiles. This can be done simply by inserting the following line into the makefile: +For compiling using simple Makefiles, Trilinos provides Makefile.export system, which allows users to include important Trilinos variables directly into their Makefiles. This can be done simply by inserting the following line into the Makefile: ```bash include Makefile.export.Trilinos @@ -46,4 +46,4 @@ or include Makefile.export. ``` -if you are interested only in a specific Trilinos package. This will give you access to the variables such as Trilinos_CXX_COMPILER, Trilinos_INCLUDE_DIRS, Trilinos_LIBRARY_DIRS etc. For the detailed description and example makefile see . +if you are interested only in a specific Trilinos package. This will give you access to the variables such as Trilinos_CXX_COMPILER, Trilinos_INCLUDE_DIRS, Trilinos_LIBRARY_DIRS etc. For the detailed description and example Makefile see . diff --git a/docs.it4i/anselm/software/omics-master/diagnostic-component-team.md b/docs.it4i/anselm/software/omics-master/diagnostic-component-team.md index d8d0c4fc..6dc3cb95 100644 --- a/docs.it4i/anselm/software/omics-master/diagnostic-component-team.md +++ b/docs.it4i/anselm/software/omics-master/diagnostic-component-team.md @@ -11,7 +11,7 @@ TEAM is available at the [following address](http://omics.it4i.cz/team/) VCF files are scanned by this diagnostic tool for known diagnostic disease-associated variants. When no diagnostic mutation is found, the file can be sent to the disease-causing gene discovery tool to see whether new disease associated variants can be found. -TEAM (27) is an intuitive and easy-to-use web tool that fills the gap between the predicted mutations and the final diagnostic in targeted enrichment sequencing analysis. The tool searches for known diagnostic mutations, corresponding to a disease panel, among the predicted patient’s variants. Diagnostic variants for the disease are taken from four databases of disease-related variants (HGMD-public, HUMSAVAR , ClinVar and COSMIC) If no primary diagnostic variant is found, then a list of secondary findings that can help to establish a diagnostic is produced. TEAM also provides with an interface for the definition of and customization of panels, by means of which, genes and mutations can be added or discarded to adjust panel definitions. +TEAM (27) is an intuitive and easy-to-use web tool that fills the gap between the predicted mutations and the final diagnostic in targeted enrichment sequencing analysis. The tool searches for known diagnostic mutations, corresponding to a disease panel, among the predicted patient’s variants. Diagnostic variants for the disease are taken from four databases of disease-related variants (HGMD, HUMSAVAR , ClinVar and COSMIC) If no primary diagnostic variant is found, then a list of secondary findings that can help to establish a diagnostic is produced. TEAM also provides with an interface for the definition of and customization of panels, by means of which, genes and mutations can be added or discarded to adjust panel definitions. ![Interface of the application. Panels for defining targeted regions of interest can be set up by just drag and drop known disease genes or disease definitions from the lists. Thus, virtual panels can be interactively improved as the knowledge of the disease increases.](../../../img/fig5.png) diff --git a/docs.it4i/anselm/software/virtualization.md b/docs.it4i/anselm/software/virtualization.md index a5c7c95a..2133f6b9 100644 --- a/docs.it4i/anselm/software/virtualization.md +++ b/docs.it4i/anselm/software/virtualization.md @@ -73,7 +73,7 @@ QEMU currently supports these image types or formats: * vmdk - VMware 3 & 4, or 6 image format, for exchanging images with that product * vdi - VirtualBox 1.1 compatible image format, for exchanging images with VirtualBox. -You can convert your existing image using qemu-img convert command. Supported formats of this command are: blkdebug blkverify bochs cloop cow dmg file ftp ftps host_cdrom host_device host_floppy http https nbd parallels qcow qcow2 qed raw sheepdog tftp vdi vhdx vmdk vpc vvfat. +You can convert your existing image using `qemu-img convert` command. Supported formats of this command are: `blkdebug blkverify bochs cloop cow dmg file ftp ftps host_cdrom host_device host_floppy http https nbd parallels qcow qcow2 qed raw sheepdog tftp vdi vhdx vmdk vpc vvfat`. We recommend using advanced QEMU native image format qcow2. @@ -89,7 +89,7 @@ Remove all unnecessary software and files. Remove all paging space, swap files, partitions, etc. -Shrink your image. (It is recommended to zero all free space and reconvert image using qemu-img.) +Shrink your image. (It is recommended to zero all free space and reconvert image using `qemu-img`.) ### Modify Your Image for Running Jobs @@ -228,7 +228,7 @@ Run virtual machine (simple) $ qemu-system-x86_64 -hda win.img -enable-kvm -cpu host -smp 16 -m 32768 -vga std -localtime -usb -usbdevice tablet -vnc :0 ``` -You can access virtual machine by VNC viewer (option -vnc) connecting to IP address of compute node. For VNC you must use VPN network. +You can access virtual machine by VNC viewer (option `-vnc`) connecting to IP address of compute node. For VNC you must use VPN network. Install virtual machine from ISO file @@ -301,7 +301,7 @@ Run SLIRP daemon over SSH tunnel on login node and connect it to virtual network $ dpipe vde_plug /tmp/sw0 = ssh login1 $VDE2_DIR/bin/slirpvde -s - --dhcp & ``` -Run qemu using vde network back-end, connect to created virtual switch. +Run QEMU using VDE network back-end, connect to created virtual switch. Basic setup (obsolete syntax) @@ -323,11 +323,11 @@ Optimized setup #### TAP Interconnect -Both user and vde network back-end have low performance. For fast interconnect (10 Gbit/s and more) of compute node (host) and virtual machine (guest) we suggest using Linux kernel TAP device. +Both user and VDE network back-end have low performance. For fast interconnect (10 Gbit/s and more) of compute node (host) and virtual machine (guest) we suggest using Linux kernel TAP device. Cluster Anselm provides TAP device tap0 for your job. TAP interconnect does not provide any services (like NAT, DHCP, DNS, SMB, etc.) just raw networking, so you should provide your services if you need them. -Run qemu with TAP network back-end: +Run QEMU with TAP network back-end: ```bash $ qemu-system-x86_64 ... -device virtio-net-pci,netdev=net1 @@ -338,9 +338,9 @@ Interface tap0 has IP address 192.168.1.1 and network mask 255.255.255.0 (/24). Redirected ports: -* DNS udp/53->udp/3053, tcp/53->tcp3053 -* DHCP udp/67->udp3067 -* SMB tcp/139->tcp3139, tcp/445->tcp3445). +* DNS UDP/53->UDP/3053, TCP/53->TCP/3053 +* DHCP UDP/67->UDP/3067 +* SMB TCP/139->TCP/3139, TCP/445->TCP/3445). You can configure IP address of virtual machine statically or dynamically. For dynamic addressing provide your DHCP server on port 3067 of tap0 interface, you can also provide your DNS server on port 3053 of tap0 interface for example: diff --git a/docs.it4i/anselm/storage.md b/docs.it4i/anselm/storage.md index 7beb9678..fa99fef0 100644 --- a/docs.it4i/anselm/storage.md +++ b/docs.it4i/anselm/storage.md @@ -1,6 +1,6 @@ # Storage -There are two main shared file systems on Anselm cluster, the [HOME](#home) and [SCRATCH](#scratch). All login and compute nodes may access same data on shared file systems. Compute nodes are also equipped with local (non-shared) scratch, ramdisk and tmp file systems. +There are two main shared file systems on Anselm cluster, the [HOME](#home) and [SCRATCH](#scratch). All login and compute nodes may access same data on shared file systems. Compute nodes are also equipped with local (non-shared) scratch, RAM disk and tmp file systems. ## Archiving @@ -357,7 +357,7 @@ First, create the mount point $ mkdir cesnet ``` -Mount the storage. Note that you can choose among the ssh.du1.cesnet.cz (Plzen), ssh.du2.cesnet.cz (Jihlava), ssh.du3.cesnet.cz (Brno) Mount tier1_home **(only 5120M !)**: +Mount the storage. Note that you can choose among the ssh.du1.cesnet.cz (Plzen), ssh.du2.cesnet.cz (Jihlava), ssh.du3.cesnet.cz (Brno) Mount tier1_home **(only 5120 MB !)**: ```bash $ sshfs username@ssh.du1.cesnet.cz:. cesnet/ @@ -389,16 +389,23 @@ Once done, please remember to unmount the storage $ fusermount -u cesnet ``` +<<<<<<< HEAD:docs.it4i/anselm/storage.md ### Rsync Access !!! note Rsync provides delta transfer for best performance, can resume interrupted transfers +======= +### RSYNC access -Rsync is a fast and extraordinarily versatile file copying tool. It is famous for its delta-transfer algorithm, which reduces the amount of data sent over the network by sending only the differences between the source files and the existing files in the destination. Rsync is widely used for backups and mirroring and as an improved copy command for everyday use. +!!! Note "Note" + RSYNC provides delta transfer for best performance, can resume interrupted transfers +>>>>>>> Spelling corrections:docs.it4i/anselm-cluster-documentation/storage.md -Rsync finds files that need to be transferred using a "quick check" algorithm (by default) that looks for files that have changed in size or in last-modified time. Any changes in the other preserved attributes (as requested by options) are made on the destination file directly when the quick check indicates that the file's data does not need to be updated. +RSYNC is a fast and extraordinarily versatile file copying tool. It is famous for its delta-transfer algorithm, which reduces the amount of data sent over the network by sending only the differences between the source files and the existing files in the destination. RSYNC is widely used for backups and mirroring and as an improved copy command for everyday use. -[More about Rsync](https://du.cesnet.cz/en/navody/rsync/start#pro_bezne_uzivatele) +RSYNC finds files that need to be transferred using a "quick check" algorithm (by default) that looks for files that have changed in size or in last-modified time. Any changes in the other preserved attributes (as requested by options) are made on the destination file directly when the quick check indicates that the file's data does not need to be updated. + +[More about RSYNC](https://du.cesnet.cz/en/navody/rsync/start#pro_bezne_uzivatele) Transfer large files to/from CESNET storage, assuming membership in the Storage VO diff --git a/docs.it4i/general/accessing-the-clusters/graphical-user-interface/x-window-system.md b/docs.it4i/general/accessing-the-clusters/graphical-user-interface/x-window-system.md index b9c69512..ccaae883 100644 --- a/docs.it4i/general/accessing-the-clusters/graphical-user-interface/x-window-system.md +++ b/docs.it4i/general/accessing-the-clusters/graphical-user-interface/x-window-system.md @@ -118,7 +118,7 @@ However this method does not seem to work with recent Linux distributions and yo ## Gnome on Windows -Use Xlaunch to start the Xming server or run the XWin.exe. Select the "One window" mode. +Use XLaunch to start the Xming server or run the XWin.exe. Select the "One window" mode. Log in to the cluster, using PuTTY. On the cluster, run the gnome-session command. diff --git a/docs.it4i/general/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.md b/docs.it4i/general/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.md index a2a4d429..36dd1323 100644 --- a/docs.it4i/general/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.md +++ b/docs.it4i/general/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.md @@ -107,4 +107,4 @@ In this example, we add an additional public key, stored in file additional_key. ## How to Remove Your Own Key -Removing your key from authorized_keys can be done simply by deleting the corresponding public key which can be identified by a comment at the end of line (eg. _username@organization.example.com_). +Removing your key from authorized_keys can be done simply by deleting the corresponding public key which can be identified by a comment at the end of line (e.g. _username@organization.example.com_). diff --git a/docs.it4i/salomon/environment-and-modules.md b/docs.it4i/salomon/environment-and-modules.md index 96710135..1da5d4e3 100644 --- a/docs.it4i/salomon/environment-and-modules.md +++ b/docs.it4i/salomon/environment-and-modules.md @@ -24,7 +24,7 @@ fi ``` !!! note - Do not run commands outputting to standard output (echo, module list, etc) in .bashrc for non-interactive SSH sessions. It breaks fundamental functionality (scp, PBS) of your account! Take care for SSH session interactivity for such commands as stated in the previous example. + Do not run commands outputting to standard output (echo, module list, etc) in .bashrc for non-interactive SSH sessions. It breaks fundamental functionality (SCP, PBS) of your account! Take care for SSH session interactivity for such commands as stated in the previous example. ### Application Modules diff --git a/docs.it4i/salomon/introduction.md b/docs.it4i/salomon/introduction.md index 83ff7922..bc466a8d 100644 --- a/docs.it4i/salomon/introduction.md +++ b/docs.it4i/salomon/introduction.md @@ -1,6 +1,6 @@ # Introduction -Welcome to Salomon supercomputer cluster. The Salomon cluster consists of 1008 compute nodes, totaling 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, at least 128 GB RAM. Nodes are interconnected by 7D Enhanced hypercube InfiniBand network and 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](hardware-overview/). +Welcome to Salomon supercomputer cluster. The Salomon cluster consists of 1008 compute nodes, totaling 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, at least 128 GB RAM. Nodes are interconnected by 7D Enhanced hypercube InfiniBand network and 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](hardware-overview/). The cluster runs [CentOS Linux](http://www.bull.com/bullx-logiciels/systeme-exploitation.html) operating system, which is compatible with the RedHat [Linux family.](http://upload.wikimedia.org/wikipedia/commons/1/1b/Linux_Distribution_Timeline.svg) diff --git a/docs.it4i/salomon/job-submission-and-execution.md b/docs.it4i/salomon/job-submission-and-execution.md index e7a4c4ff..db8080a2 100644 --- a/docs.it4i/salomon/job-submission-and-execution.md +++ b/docs.it4i/salomon/job-submission-and-execution.md @@ -422,7 +422,7 @@ cd $SCRDIR || exit cp $PBS_O_WORKDIR/input . cp $PBS_O_WORKDIR/mympiprog.x . -# load the mpi module +# load the MPI module module load OpenMPI # execute the calculation @@ -460,7 +460,7 @@ Example jobscript for an MPI job with preloaded inputs and executables, options SCRDIR=/scratch/work/user/$USER/myjob cd $SCRDIR || exit -# load the mpi module +# load the MPI module module load OpenMPI # execute the calculation diff --git a/docs.it4i/salomon/software/ansys/ansys-cfx.md b/docs.it4i/salomon/software/ansys/ansys-cfx.md index 21ce8f93..2cf29101 100644 --- a/docs.it4i/salomon/software/ansys/ansys-cfx.md +++ b/docs.it4i/salomon/software/ansys/ansys-cfx.md @@ -49,7 +49,7 @@ echo Machines: $hl Header of the pbs file (above) is common and description can be find on [this site](../../job-submission-and-execution/). SVS FEM recommends to utilize sources by keywords: nodes, ppn. These keywords allows to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources. -Working directory has to be created before sending pbs job into the queue. Input file should be in working directory or full path to input file has to be specified. >Input file has to be defined by common CFX def file which is attached to the cfx solver via parameter -def +Working directory has to be created before sending PBS job into the queue. Input file should be in working directory or full path to input file has to be specified. >Input file has to be defined by common CFX def file which is attached to the CFX solver via parameter -def **License** should be selected by parameter -P (Big letter **P**). Licensed products are the following: aa_r (ANSYS **Academic** Research), ane3fl (ANSYS Multiphysics)-**Commercial**. [More about licensing here](licensing/) diff --git a/docs.it4i/salomon/software/ansys/ansys-fluent.md b/docs.it4i/salomon/software/ansys/ansys-fluent.md index 33e711b2..f4867b5c 100644 --- a/docs.it4i/salomon/software/ansys/ansys-fluent.md +++ b/docs.it4i/salomon/software/ansys/ansys-fluent.md @@ -3,7 +3,7 @@ [ANSYS Fluent](http://www.ansys.com/products/fluids/ansys-fluent) software contains the broad physical modeling capabilities needed to model flow, turbulence, heat transfer, and reactions for industrial applications ranging from air flow over an aircraft wing to combustion in a furnace, from bubble columns to oil platforms, from blood flow to semiconductor manufacturing, and from clean room design to wastewater treatment plants. Special models that give the software the ability to model in-cylinder combustion, aeroacoustics, turbomachinery, and multiphase systems have served to broaden its reach. -1. Common way to run Fluent over pbs file +1. Common way to run Fluent over PBS file To run ANSYS Fluent in batch mode you can utilize/modify the default fluent.pbs script and execute it via the qsub command. diff --git a/docs.it4i/salomon/software/ansys/ansys-ls-dyna.md b/docs.it4i/salomon/software/ansys/ansys-ls-dyna.md index 8646c266..89f53c98 100644 --- a/docs.it4i/salomon/software/ansys/ansys-ls-dyna.md +++ b/docs.it4i/salomon/software/ansys/ansys-ls-dyna.md @@ -50,6 +50,10 @@ echo Machines: $hl /ansys_inc/v145/ansys/bin/ansys145 -dis -lsdynampp i=input.k -machines $hl ``` +<<<<<<< HEAD Header of the pbs file (above) is common and description can be find on [this site](../../job-submission-and-execution/). [SVS FEM](http://www.svsfem.cz) recommends to utilize sources by keywords: nodes, ppn. These keywords allows to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources. +======= +Header of the PBS file (above) is common and description can be find on [this site](../../resource-allocation-and-job-execution/job-submission-and-execution/). [SVS FEM](http://www.svsfem.cz) recommends to utilize sources by keywords: nodes, ppn. These keywords allows to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources. +>>>>>>> Spelling corrections -Working directory has to be created before sending pbs job into the queue. Input file should be in working directory or full path to input file has to be specified. Input file has to be defined by common LS-DYNA .**k** file which is attached to the ansys solver via parameter i= +Working directory has to be created before sending PBS job into the queue. Input file should be in working directory or full path to input file has to be specified. Input file has to be defined by common LS-DYNA .**k** file which is attached to the ansys solver via parameter i= diff --git a/docs.it4i/salomon/software/ansys/ansys-mechanical-apdl.md b/docs.it4i/salomon/software/ansys/ansys-mechanical-apdl.md index c1562c1c..0bde6f3a 100644 --- a/docs.it4i/salomon/software/ansys/ansys-mechanical-apdl.md +++ b/docs.it4i/salomon/software/ansys/ansys-mechanical-apdl.md @@ -49,8 +49,8 @@ echo Machines: $hl /ansys_inc/v145/ansys/bin/ansys145 -b -dis -p aa_r -i input.dat -o file.out -machines $hl -dir $WORK_DIR ``` -Header of the pbs file (above) is common and description can be find on [this site](../../resources-allocation-policy/). [SVS FEM](http://www.svsfem.cz) recommends to utilize sources by keywords: nodes, ppn. These keywords allows to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources. +Header of the PBS file (above) is common and description can be find on [this site](../../resources-allocation-policy/). [SVS FEM](http://www.svsfem.cz) recommends to utilize sources by keywords: nodes, ppn. These keywords allows to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources. -Working directory has to be created before sending pbs job into the queue. Input file should be in working directory or full path to input file has to be specified. Input file has to be defined by common APDL file which is attached to the ansys solver via parameter -i +Working directory has to be created before sending PBS job into the queue. Input file should be in working directory or full path to input file has to be specified. Input file has to be defined by common APDL file which is attached to the ansys solver via parameter -i **License** should be selected by parameter -p. Licensed products are the following: aa_r (ANSYS **Academic** Research), ane3fl (ANSYS Multiphysics)-**Commercial**, aa_r_dy (ANSYS **Academic** AUTODYN) [More about licensing here](licensing/) diff --git a/docs.it4i/salomon/software/ansys/ansys.md b/docs.it4i/salomon/software/ansys/ansys.md index f93524a3..a5cac322 100644 --- a/docs.it4i/salomon/software/ansys/ansys.md +++ b/docs.it4i/salomon/software/ansys/ansys.md @@ -2,7 +2,7 @@ **[SVS FEM](http://www.svsfem.cz/)** as **[ANSYS Channel partner](http://www.ansys.com/)** for Czech Republic provided all ANSYS licenses for ANSELM cluster and supports of all ANSYS Products (Multiphysics, Mechanical, MAPDL, CFX, Fluent, Maxwell, LS-DYNA...) to IT staff and ANSYS users. If you are challenging to problem of ANSYS functionality contact please [hotline@svsfem.cz](mailto:hotline@svsfem.cz?subject=Ostrava%20-%20ANSELM) -Anselm provides as commercial as academic variants. Academic variants are distinguished by "**Academic...**" word in the name of license or by two letter preposition "**aa\_**" in the license feature name. Change of license is realized on command line respectively directly in user's pbs file (see individual products). [More about licensing here](licensing/) +Anselm provides as commercial as academic variants. Academic variants are distinguished by "**Academic...**" word in the name of license or by two letter preposition "**aa\_**" in the license feature name. Change of license is realized on command line respectively directly in user's PBS file (see individual products). [More about licensing here](licensing/) To load the latest version of any ANSYS product (Mechanical, Fluent, CFX, MAPDL,...) load the module: diff --git a/docs.it4i/salomon/software/ansys/licensing.md b/docs.it4i/salomon/software/ansys/licensing.md index 04ff6513..1dec4471 100644 --- a/docs.it4i/salomon/software/ansys/licensing.md +++ b/docs.it4i/salomon/software/ansys/licensing.md @@ -1,6 +1,6 @@ # Licensing and Available Versions -## ANSYS Licence Can Be Used By: +## ANSYS license can be used by: * all persons in the carrying out of the CE IT4Innovations Project (In addition to the primary licensee, which is VSB - Technical University of Ostrava, users are CE IT4Innovations third parties - CE IT4Innovations project partners, particularly the University of Ostrava, the Brno University of Technology - Faculty of Informatics, the Silesian University in Opava, Institute of Geonics AS CR.) * all persons who have a valid license diff --git a/docs.it4i/salomon/software/ansys/setting-license-preferences.md b/docs.it4i/salomon/software/ansys/setting-license-preferences.md index fe14541d..b0739a90 100644 --- a/docs.it4i/salomon/software/ansys/setting-license-preferences.md +++ b/docs.it4i/salomon/software/ansys/setting-license-preferences.md @@ -1,6 +1,6 @@ # Setting license preferences -Some ANSYS tools allow you to explicitly specify usage of academic or commercial licenses in the command line (eg. ansys161 -p aa_r to select Academic Research license). However, we have observed that not all tools obey this option and choose commercial license. +Some ANSYS tools allow you to explicitly specify usage of academic or commercial licenses in the command line (e.g. ansys161 -p aa_r to select Academic Research license). However, we have observed that not all tools obey this option and choose commercial license. Thus you need to configure preferred license order with ANSLIC_ADMIN. Please follow these steps and move Academic Research license to the top or bottom of the list accordingly. diff --git a/docs.it4i/salomon/software/ansys/workbench.md b/docs.it4i/salomon/software/ansys/workbench.md index 8ed07d78..fb37e6a7 100644 --- a/docs.it4i/salomon/software/ansys/workbench.md +++ b/docs.it4i/salomon/software/ansys/workbench.md @@ -6,13 +6,13 @@ It is possible to run Workbench scripts in batch mode. You need to configure sol ![](../../../img/AMsetPar1.png) -Enable Distribute Solution checkbox and enter number of cores (eg. 48 to run on two Salomon nodes). If you want the job to run on more then 1 node, you must also provide a so called MPI appfile. In the Additional Command Line Arguments input field, enter: +Enable Distribute Solution checkbox and enter number of cores (e.g. 48 to run on two Salomon nodes). If you want the job to run on more then 1 node, you must also provide a so called MPI appfile. In the Additional Command Line Arguments input field, enter: ```bash -mpifile /path/to/my/job/mpifile.txt ``` -Where /path/to/my/job is the directory where your project is saved. We will create the file mpifile.txt programatically later in the batch script. For more information, refer to \*ANSYS Mechanical APDL Parallel Processing\* \*Guide\*. +Where /path/to/my/job is the directory where your project is saved. We will create the file mpifile.txt programmatically later in the batch script. For more information, refer to \*ANSYS Mechanical APDL Parallel Processing\* \*Guide\*. Now, save the project and close Workbench. We will use this script to launch the job: diff --git a/docs.it4i/salomon/software/chemistry/nwchem.md b/docs.it4i/salomon/software/chemistry/nwchem.md index a26fc701..465adf20 100644 --- a/docs.it4i/salomon/software/chemistry/nwchem.md +++ b/docs.it4i/salomon/software/chemistry/nwchem.md @@ -40,4 +40,4 @@ The recommend to use version 6.5. Version 6.3 fails on Salomon nodes with accele Please refer to [the documentation](http://www.nwchem-sw.org/index.php/Release62:Top-level) and in the input file set the following directives : * MEMORY : controls the amount of memory NWChem will use -* SCRATCH_DIR : set this to a directory in [SCRATCH filesystem](../../storage/storage/) (or run the calculation completely in a scratch directory). For certain calculations, it might be advisable to reduce I/O by forcing "direct" mode, eg. "scf direct" +* SCRATCH_DIR : set this to a directory in [SCRATCH filesystem](../../storage/storage/) (or run the calculation completely in a scratch directory). For certain calculations, it might be advisable to reduce I/O by forcing "direct" mode, e.g. `scf direct` diff --git a/docs.it4i/salomon/software/chemistry/phono3py.md b/docs.it4i/salomon/software/chemistry/phono3py.md index 3f747d23..275c23a3 100644 --- a/docs.it4i/salomon/software/chemistry/phono3py.md +++ b/docs.it4i/salomon/software/chemistry/phono3py.md @@ -87,7 +87,7 @@ Once all jobs are finished and vasprun.xml is created in each disp-XXXXX directo $ phono3py --cf3 disp-{00001..00111}/vasprun.xml ``` -and `disp_fc2.yaml, FORCES_FC2`, `FORCES_FC3` and disp_fc3.yaml should appear and put into the hdf format by +and `disp_fc2.yaml, FORCES_FC2`, `FORCES_FC3` and disp_fc3.yaml should appear and put into the HDF format by ```bash $ phono3py --dim="2 2 2" -c POSCAR diff --git a/docs.it4i/salomon/software/compilers.md b/docs.it4i/salomon/software/compilers.md index 8e62965f..f629a339 100644 --- a/docs.it4i/salomon/software/compilers.md +++ b/docs.it4i/salomon/software/compilers.md @@ -11,7 +11,7 @@ There are several compilers for different programming languages available on the The C/C++ and Fortran compilers are provided by: -Opensource: +Open source: * GNU GCC * Clang/LLVM @@ -82,11 +82,11 @@ For more information about the possibilities of the compilers, please see the ma UPC is supported by two compiler/runtime implementations: * GNU - SMP/multi-threading support only -* Berkley - multi-node support as well as SMP/multi-threading support +* Berkeley - multi-node support as well as SMP/multi-threading support ### GNU UPC Compiler -To use the GNU UPC compiler and run the compiled binaries use the module gupc +To use the GNU UPC compiler and run the compiled binaries use the module GUPC ```bash $ module add gupc @@ -127,18 +127,18 @@ To run the example with 5 threads issue For more information see the man pages. -### Berkley UPC Compiler +### Berkeley UPC Compiler -To use the Berkley UPC compiler and runtime environment to run the binaries use the module bupc +To use the Berkeley UPC compiler and runtime environment to run the binaries use the module BUPC ```bash $ module add BerkeleyUPC/2.16.2-gompi-2015b $ upcc -version ``` -As default UPC network the "smp" is used. This is very quick and easy way for testing/debugging, but limited to one node only. +As default UPC network the "SMP" is used. This is very quick and easy way for testing/debugging, but limited to one node only. -For production runs, it is recommended to use the native InfiniBand implementation of UPC network "ibv". For testing/debugging using multiple nodes, the "mpi" UPC network is recommended. +For production runs, it is recommended to use the native InfiniBand implementation of UPC network "IBV". For testing/debugging using multiple nodes, the "MPI" UPC network is recommended. !!! warning Selection of the network is done at the compile time and not at runtime (as expected)! @@ -162,7 +162,7 @@ Example UPC code: } ``` -To compile the example with the "ibv" UPC network use +To compile the example with the "IBV" UPC network use ```bash $ upcc -network=ibv -o hello.upc.x hello.upc diff --git a/docs.it4i/salomon/software/comsol/comsol-multiphysics.md b/docs.it4i/salomon/software/comsol/comsol-multiphysics.md index 05a6d294..febf0887 100644 --- a/docs.it4i/salomon/software/comsol/comsol-multiphysics.md +++ b/docs.it4i/salomon/software/comsol/comsol-multiphysics.md @@ -115,4 +115,4 @@ cd /apps/cae/COMSOL/51/mli matlab -nodesktop -nosplash -r "mphstart; addpath /scratch/work/user/$USER/work; test_job" ``` -This example shows how to run Livelink for MATLAB with following configuration: 3 nodes and 16 cores per node. Working directory has to be created before submitting (comsol_matlab.pbs) job script into the queue. Input file (test_job.m) has to be in working directory or full path to input file has to be specified. The Matlab command option (-r ”mphstart”) created a connection with a COMSOL server using the default port number. +This example shows how to run LiveLink for MATLAB with following configuration: 3 nodes and 16 cores per node. Working directory has to be created before submitting (comsol_matlab.pbs) job script into the queue. Input file (test_job.m) has to be in working directory or full path to input file has to be specified. The Matlab command option (-r ”mphstart”) created a connection with a COMSOL server using the default port number. diff --git a/docs.it4i/salomon/software/comsol/licensing-and-available-versions.md b/docs.it4i/salomon/software/comsol/licensing-and-available-versions.md index 4358b930..be5a15f2 100644 --- a/docs.it4i/salomon/software/comsol/licensing-and-available-versions.md +++ b/docs.it4i/salomon/software/comsol/licensing-and-available-versions.md @@ -1,6 +1,6 @@ # Licensing and Available Versions -## Comsol Licence Can Be Used By: +## Comsol License Can Be Used By: * all persons in the carrying out of the CE IT4Innovations Project (In addition to the primary licensee, which is VSB - Technical University of Ostrava, users are CE IT4Innovations third parties - CE IT4Innovations project partners, particularly the University of Ostrava, the Brno University of Technology - Faculty of Informatics, the Silesian University in Opava, Institute of Geonics AS CR.) * all persons who have a valid license diff --git a/docs.it4i/salomon/software/debuggers/allinea-performance-reports.md b/docs.it4i/salomon/software/debuggers/allinea-performance-reports.md index 3d0826e9..52b48484 100644 --- a/docs.it4i/salomon/software/debuggers/allinea-performance-reports.md +++ b/docs.it4i/salomon/software/debuggers/allinea-performance-reports.md @@ -28,7 +28,7 @@ Instead of [running your MPI program the usual way](../mpi/mpi/), use the the pe $ perf-report mpirun ./mympiprog.x ``` -The mpi program will run as usual. The perf-report creates two additional files, in \*.txt and \*.html format, containing the performance report. Note that demanding MPI codes should be run within [the queue system](../../job-submission-and-execution/). +The MPI program will run as usual. The perf-report creates two additional files, in \*.txt and \*.html format, containing the performance report. Note that demanding MPI codes should be run within [the queue system](../../job-submission-and-execution/). ## Example diff --git a/docs.it4i/salomon/software/debuggers/intel-vtune-amplifier.md b/docs.it4i/salomon/software/debuggers/intel-vtune-amplifier.md index 2fdbd18e..09a57296 100644 --- a/docs.it4i/salomon/software/debuggers/intel-vtune-amplifier.md +++ b/docs.it4i/salomon/software/debuggers/intel-vtune-amplifier.md @@ -19,7 +19,7 @@ To profile an application with VTune Amplifier, special kernel modules need to b $ qsub -q qexp -A OPEN-0-0 -I -l select=1,vtune=2016_update1 ``` -After that, you can verify the modules sep\*, pax and vtsspp are present in the kernel : +After that, you can verify the modules `sep*`, `pax` and `vtsspp` are present in the kernel : ```bash $ lsmod | grep -e sep -e pax -e vtsspp @@ -42,7 +42,7 @@ and launch the GUI : The GUI will open in new window. Click on "New Project..." to create a new project. After clicking OK, a new window with project properties will appear. At "Application:", select the bath to your binary you want to profile (the binary should be compiled with -g flag). Some additional options such as command line arguments can be selected. At "Managed code profiling mode:" select "Native" (unless you want to profile managed mode .NET/Mono applications). After clicking OK, your project is created. -To run a new analysis, click "New analysis...". You will see a list of possible analysis. Some of them will not be possible on the current CPU (eg. Intel Atom analysis is not possible on Sandy bridge CPU), the GUI will show an error box if you select the wrong analysis. For example, select "Advanced Hotspots". Clicking on Start will start profiling of the application. +To run a new analysis, click "New analysis...". You will see a list of possible analysis. Some of them will not be possible on the current CPU (e.g. Intel Atom analysis is not possible on Sandy bridge CPU), the GUI will show an error box if you select the wrong analysis. For example, select "Advanced Hotspots". Clicking on Start will start profiling of the application. ## Remote Analysis diff --git a/docs.it4i/salomon/software/debuggers/valgrind.md b/docs.it4i/salomon/software/debuggers/valgrind.md index 43011878..5e6a2c8e 100644 --- a/docs.it4i/salomon/software/debuggers/valgrind.md +++ b/docs.it4i/salomon/software/debuggers/valgrind.md @@ -262,4 +262,4 @@ Prints this output : (note that there is output printed for every launched MPI p ==31319== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 4 from 4) ``` -We can see that Valgrind has reported use of unitialised memory on the master process (which reads the array to be broadcasted) and use of unaddresable memory on both processes. +We can see that Valgrind has reported use of uninitialised memory on the master process (which reads the array to be broadcasted) and use of unaddressable memory on both processes. diff --git a/docs.it4i/salomon/software/debuggers/vampir.md b/docs.it4i/salomon/software/debuggers/vampir.md index 99053546..f93680b5 100644 --- a/docs.it4i/salomon/software/debuggers/vampir.md +++ b/docs.it4i/salomon/software/debuggers/vampir.md @@ -1,6 +1,6 @@ # Vampir -Vampir is a commercial trace analysis and visualisation tool. It can work with traces in OTF and OTF2 formats. It does not have the functionality to collect traces, you need to use a trace collection tool (such as [Score-P](score-p/)) first to collect the traces. +Vampir is a commercial trace analysis and visualization tool. It can work with traces in OTF and OTF2 formats. It does not have the functionality to collect traces, you need to use a trace collection tool (such as [Score-P](score-p/)) first to collect the traces. ![](../../../img/Snmekobrazovky20160708v12.33.35.png) diff --git a/docs.it4i/salomon/software/intel-suite/intel-compilers.md b/docs.it4i/salomon/software/intel-suite/intel-compilers.md index 63a05bd9..29b1f394 100644 --- a/docs.it4i/salomon/software/intel-suite/intel-compilers.md +++ b/docs.it4i/salomon/software/intel-suite/intel-compilers.md @@ -1,6 +1,6 @@ # Intel Compilers -The Intel compilers in multiple versions are available, via module intel. The compilers include the icc C and C++ compiler and the ifort fortran 77/90/95 compiler. +The Intel compilers in multiple versions are available, via module intel. The compilers include the icc C and C++ compiler and the ifort Fortran 77/90/95 compiler. ```bash $ module load intel @@ -17,7 +17,7 @@ For maximum performance on the Salomon cluster compute nodes, compile your progr $ ifort -ipo -O3 -xCORE-AVX2 -qopt-report1 -qopt-report-phase=vec myprog.f mysubroutines.f -o myprog.x ``` -In this example, we compile the program enabling interprocedural optimizations between source files (-ipo), aggresive loop optimizations (-O3) and vectorization (-xCORE-AVX2) +In this example, we compile the program enabling interprocedural optimizations between source files (-ipo), aggressive loop optimizations (-O3) and vectorization (-xCORE-AVX2) The compiler recognizes the omp, simd, vector and ivdep pragmas for OpenMP parallelization and AVX2 vectorization. Enable the OpenMP parallelization by the **-openmp** compiler switch. diff --git a/docs.it4i/salomon/software/intel-suite/intel-debugger.md b/docs.it4i/salomon/software/intel-suite/intel-debugger.md index d0fef6ab..a1c2af52 100644 --- a/docs.it4i/salomon/software/intel-suite/intel-debugger.md +++ b/docs.it4i/salomon/software/intel-suite/intel-debugger.md @@ -71,6 +71,6 @@ Run the idb debugger from within the MPI debug option. This will cause the debug Run the idb debugger in GUI mode. The menu Parallel contains number of tools for debugging multiple threads. One of the most useful tools is the **Serialize Execution** tool, which serializes execution of concurrent threads for easy orientation and identification of concurrency related bugs. -## Further Information +## Further information -Exhaustive manual on idb features and usage is published at Intel website, +Exhaustive manual on IDB features and usage is published at Intel website, -- 2.24.1