Merge branch 'add_soft' into 'master'

Add soft

See merge request !167

docs.it4i/software/lang/python.md

+# Python
+
+Python is a widely used high-level programming language for general-purpose programming, created by Guido van Rossum and first released in 1991. An interpreted language, Python has a design philosophy that emphasizes code readability (notably using whitespace indentation to delimit code blocks rather than curly brackets or keywords), and a syntax that allows programmers to express concepts in fewer lines of code than might be used in languages such as C++ or Java.The language provides constructs intended to enable writing clear programs on both a small and large scale.
+
+Python features a dynamic type system and automatic memory management and supports multiple programming paradigms, including object-oriented, imperative, functional programming, and procedural styles. It has a large and comprehensive standard library.
+
+* [Documentation for Python 3.X](http://docs.python.org/3/)
+* [Documentation for Python 2.X](http://docs.python.org/2/)
+
+## Python on the IT4Innovations Clusters
+
+On the clusters we have the Python 2.X and Python 3.X software installed. How to use these modules is shown below.
+
+!!! note
+    Use the command `ml av python/` to get up-to-date versions of the modules.
+
+```console
+$ ml av python/
+
+-------------------------- /apps/modules/lang --------------------------
+   Python/2.7.8-intel-2015b       Python/2.7.9-gompi-2015e      Python/2.7.10-GCC-4.9.3-2.25-bare    Python/2.7.11-intel-2016a      Python/3.4.3-intel-2015b      Python/3.5.2-intel-2017.00
+   Python/2.7.8-intel-2016.01     Python/2.7.9-ictce-7.3.5      Python/2.7.10-GNU-4.9.3-2.25-bare    Python/2.7.11-intel-2017a      Python/3.5.1-intel-2016.01    Python/3.5.2
+   Python/2.7.9-foss-2015b        Python/2.7.9-intel-2015b      Python/2.7.11-foss-2016a             Python/2.7.11-intel-2017.00    Python/3.5.1-intel-2017.00    Python/3.6.1
+   Python/2.7.9-foss-2015g        Python/2.7.9-intel-2016.01    Python/2.7.11-GCC-4.9.3-2.25-bare    Python/2.7.13-base             Python/3.5.1                  Python/3.6.2-base          (D)
+   Python/2.7.9-GNU-5.1.0-2.25    Python/2.7.9                  Python/2.7.11-intel-2015b            Python/2.7.13                  Python/3.5.2-foss-2016a
+
+-------------------------- /apps/modules/math ---------------------------
+   ScientificPython/2.9.4-intel-2015b-Python-2.7.9    ScientificPython/2.9.4-intel-2015b-Python-2.7.11    ScientificPython/2.9.4-intel-2016.01-Python-2.7.9 (D)
+
+  Where:
+   D:  Default Module
+
+  If you need software that is not listed, request it at support@it4i.cz.
+```
+
+## Python 2.X
+
+Python 2.7 is scheduled to be the last major version in the 2.x series before it moves into an extended maintenance period. This release contains many of the features that were first released in Python 3.1.
+
+```console
+$ ml av python/2
+
+----------------------------------------------------------------------------------------------- /apps/modules/lang ------------------------------------------------------------------------------------------------
+   Python/2.7.8-intel-2015b      Python/2.7.9-GNU-5.1.0-2.25    Python/2.7.9-intel-2016.01           Python/2.7.11-foss-2016a             Python/2.7.11-intel-2017a
+   Python/2.7.8-intel-2016.01    Python/2.7.9-gompi-2015e       Python/2.7.9                         Python/2.7.11-GCC-4.9.3-2.25-bare    Python/2.7.11-intel-2017.00
+   Python/2.7.9-foss-2015b       Python/2.7.9-ictce-7.3.5       Python/2.7.10-GCC-4.9.3-2.25-bare    Python/2.7.11-intel-2015b            Python/2.7.13-base
+   Python/2.7.9-foss-2015g       Python/2.7.9-intel-2015b       Python/2.7.10-GNU-4.9.3-2.25-bare    Python/2.7.11-intel-2016a            Python/2.7.13
+
+----------------------------------------------------------------------------------------------- /apps/modules/math ------------------------------------------------------------------------------------------------
+   ScientificPython/2.9.4-intel-2015b-Python-2.7.9    ScientificPython/2.9.4-intel-2015b-Python-2.7.11    ScientificPython/2.9.4-intel-2016.01-Python-2.7.9 (D)
+
+  Where:
+   D:  Default Module
+
+  If you need software that is not listed, request it at support@it4i.cz.
+```
+
+### Used Module Python/2.X
+
+```console
+$ python --version
+Python 2.6.6
+$ ml Python/2.7.13
+$ python --version
+Python 2.7.1
+```
+
+### Packages in Python/2.X
+
+```console
+$ pip list
+appdirs (1.4.3)
+asn1crypto (0.22.0)
+backports-abc (0.5)
+backports.shutil-get-terminal-size (1.0.0)
+backports.ssl-match-hostname (3.5.0.1)
+BeautifulSoup (3.2.1)
+beautifulsoup4 (4.5.3)
+...
+```
+
+### How to Install New Package to Python/2.X?
+
+```console
+$ ml Python/2.7.13
+$ python --version
+$ pip install wheel --user
+Collecting wheel
+  Downloading wheel-0.30.0-py2.py3-none-any.whl (49kB)
+    100% |████████████████████████████████| 51kB 835kB/s
+Installing collected packages: wheel
+Successfully installed wheel-0.30.0
+```
+
+### How to Update Package in Python/2.X?
+
+```console
+$ ml Python/2.7.13
+$ python --version
+$ pip install scipy --upgrade --user
+Collecting scipy
+  Downloading scipy-0.19.1-cp27-cp27mu-manylinux1_x86_64.whl (45.0MB)
+    100% |████████████████████████████████| 45.0MB 5.8kB/s
+Requirement already up-to-date: numpy>=1.8.2 in /apps/all/Python/2.7.13/lib/python2.7/site-packages (from scipy)
+Installing collected packages: scipy
+Successfully installed scipy-0.19.1
+```
+
+## Python 3.X
+
+Python 3.0 (a.k.a. "Python 3000" or "Py3k") is a new version of the language that is incompatible with the 2.x line of releases. The language is mostly the same, but many details, especially how built-in objects like dictionaries and strings work, have changed considerably, and a lot of deprecated features have finally been removed. Also, the standard library has been reorganized in a few prominent places.
+
+```console
+$ ml av python/3
+
+---------------------- /apps/modules/lang ----------------------
+   Python/3.4.3-intel-2015b      Python/3.5.1-intel-2017.00    Python/3.5.2-foss-2016a       Python/3.5.2    Python/3.6.2-base (D)
+   Python/3.5.1-intel-2016.01    Python/3.5.1                  Python/3.5.2-intel-2017.00    Python/3.6.1
+
+  Where:
+   D:  Default Module
+
+  If you need software that is not listed, request it at support@it4i.cz.
+
+```
+
+### Used Module Python/3.X
+
+```console
+$ python --version
+Python 2.6.6
+$ ml Python/3.6.2-base
+$ python --version
+Python 3.6.2
+```
+
+### Packages in Python/3.X
+
+```console
+$ pip3 list
+nose (1.3.7)
+pip (8.0.2)
+setuptools (20.1.1)
+```
+
+### How to Install New Package to Python/3.X
+
+```console
+$ ml Python/3.6.2-base
+$ python --version
+Python 3.6.2
+$ pip3 install pandas --user
+Collecting pandas
+  Downloading pandas-0.20.3.tar.gz (10.4MB)
+    100% |████████████████████████████████| 10.4MB 42kB/s
+Collecting python-dateutil>=2 (from pandas)
+  Downloading python_dateutil-2.6.1-py2.py3-none-any.whl (194kB)
+    100% |████████████████████████████████| 196kB 1.3MB/s
+Collecting pytz>=2011k (from pandas)
+  Downloading pytz-2017.2-py2.py3-none-any.whl (484kB)
+    100% |████████████████████████████████| 487kB 757kB/s
+Collecting numpy>=1.7.0 (from pandas)
+  Using cached numpy-1.13.1.zip
+Collecting six>=1.5 (from python-dateutil>=2->pandas)
+  Downloading six-1.11.0-py2.py3-none-any.whl
+Building wheels for collected packages: pandas, numpy
+  Running setup.py bdist_wheel for pandas ... done
+  Stored in directory: /home/kru0052/.cache/pip/wheels/dd/17/6c/a1c7e8d855f3a700b21256329fd396d105b533c5ed3e20c5e9
+  Running setup.py bdist_wheel for numpy ... done
+  Stored in directory: /home/kru0052/.cache/pip/wheels/94/44/90/4ce81547e3e5f4398b1601d0051e828b8160f8d3f3dd5a0c8c
+Successfully built pandas numpy
+Installing collected packages: six, python-dateutil, pytz, numpy, pandas
+Successfully installed numpy-1.13.1 pandas-0.20.3 python-dateutil-2.6.1 pytz-2017.2 six-1.11.0
+```
+
+### How to Update Package in Python/3.X?
+
+```console
+$ pip3 install scipy --upgrade --user
+Collecting scipy
+  Downloading scipy-0.19.1-cp27-cp27mu-manylinux1_x86_64.whl (45.0MB)
+    100% |████████████████████████████████| 45.0MB 5.8kB/s
+Requirement already up-to-date: numpy>=1.8.2 in /apps/all/Python/3.6.2/lib/python3.6/site-packages (from scipy)
+Installing collected packages: scipy
+Successfully installed scipy-0.19.1
+```

docs.it4i/software/lmod.md → docs.it4i/software/modules/lmod.md

@@ -4,9 +4,6 @@ Lmod is a modules tool, a modern alternative to the oudated & no longer actively
 
 Detailed documentation on Lmod is available [here](http://lmod.readthedocs.io).
 
-!!! warning
-    All the new modules will be availabe in Lmod environment only.
-
 ## Benefits
 
 * significantly more responsive module commands, in particular module avail (ml av)

docs.it4i/software/operating-system.md

-# Anselm
-
-The operating system on Anselm is Linux - [**Red Hat Enterprise Linux release 6.x**](https://en.wikipedia.org/wiki/Red_Hat_Enterprise_Linux).
-
-# Salomon
-
-The operating system on Salomon is Linux - [**CentOS 6.x**](https://en.wikipedia.org/wiki/CentOS)
-
-The CentOS Linux distribution is a stable, predictable, manageable and reproducible platform derived from the sources of Red Hat Enterprise Linux (RHEL).

mkdocs.yml

@@ -60,22 +60,22 @@ pages:
     - PRACE User Support: anselm/prace.md
   - 'Software':
     - 'Modules':
-      - Lmod Environment: software/lmod.md
+      - Lmod Environment: software/modules/lmod.md
       - Modules Matrix: modules-matrix.md
       - Available Salomon Modules: modules-salomon.md
       - Available Salomon Modules on UV: modules-salomon-uv.md
       - Available Anselm Modules: modules-anselm.md
     - ISV Licenses: software/isv_licenses.md
     - 'Bioinformatics':
-      - Bioinformatics Applications: software/bioinformatics.md
+      - Bioinformatics Applications: software/bio/bioinformatics.md
       - 'Omics Master':
-        - Overview: software/omics-master/overview.md
-        - Diagnostic Component (TEAM): software/omics-master/diagnostic-component-team.md
-        - Priorization Component (BiERApp): software/omics-master/priorization-component-bierapp.md
+        - Overview: software/bio/omics-master/overview.md
+        - Diagnostic Component (TEAM): software/bio/omics-master/diagnostic-component-team.md
+        - Priorization Component (BiERApp): software/bio/omics-master/priorization-component-bierapp.md
     - 'CAE':
       - 'COMSOL':
-        - COMSOL: software/comsol/comsol-multiphysics.md
-        - Licensing and Available Versions: software/comsol/licensing-and-available-versions.md
+        - COMSOL: software/cae/comsol/comsol-multiphysics.md
+        - Licensing and Available Versions: software/cae/comsol/licensing-and-available-versions.md
     - 'Chemistry':
       - Molpro: software/chemistry/molpro.md
       - Orca: software/chemistry/orca.md
@@ -100,18 +100,18 @@ pages:
       - NVIDIA CUDA: anselm/software/nvidia-cuda.md
     - 'Intel':
       - 'Intel Suite':
-        - Introduction: software/intel-suite/intel-parallel-studio-introduction.md
-        - Intel Advisor: software/intel-suite/intel-advisor.md
-        - Intel Compilers: software/intel-suite/intel-compilers.md
-        - Intel Debugger: software/intel-suite/intel-debugger.md
-        - Intel IPP: software/intel-suite/intel-integrated-performance-primitives.md
-        - Intel Inspector: software/intel-suite/intel-inspector.md
-        - Intel MKL: software/intel-suite/intel-mkl.md
-        - Intel TBB: software/intel-suite/intel-tbb.md
-        - Intel Trace Analyzer and Collector: software/intel-suite/intel-trace-analyzer-and-collector.md
+        - Introduction: software/intel/intel-suite/intel-parallel-studio-introduction.md
+        - Intel Advisor: software/intel/intel-suite/intel-advisor.md
+        - Intel Compilers: software/intel/intel-suite/intel-compilers.md
+        - Intel Debugger: software/intel/intel-suite/intel-debugger.md
+        - Intel IPP: software/intel/intel-suite/intel-integrated-performance-primitives.md
+        - Intel Inspector: software/intel/intel-suite/intel-inspector.md
+        - Intel MKL: software/intel/intel-suite/intel-mkl.md
+        - Intel TBB: software/intel/intel-suite/intel-tbb.md
+        - Intel Trace Analyzer and Collector: software/intel/intel-suite/intel-trace-analyzer-and-collector.md
       - 'Intel Xeon Phi':
-        - Intel Xeon Phi Salomon: software/intel-xeon-phi.md
-        - Intel Xeon Phi Anselm: software/intel-xeon-phi.anselm.md
+        - Intel Xeon Phi Salomon: software/intel/intel-xeon-phi.md
+        - Intel Xeon Phi Anselm: software/intel/intel-xeon-phi.anselm.md
     - 'Machine Learning':
       - Introduction: software/machine-learning/introduction.md
       - TensorFlow: software/machine-learning/tensorflow.md
@@ -136,30 +136,32 @@ pages:
       - MAGMA for Intel Xeon Phi: software/numerical-libraries/magma-for-intel-xeon-phi.md
       - PETSc: software/numerical-libraries/petsc.md
       - Trilinos: software/numerical-libraries/trilinos.md
-    - 'Programming Languages':
-      - Java: software/java.md
-      - C#: software/csc.md
+    - 'Languages':
+      - Java: software/lang/java.md
+      - C#: software/lang/csc.md
+      - Python: software/lang/python.md
+      - Python-Conda: software/lang/conda.md
     - 'Phys':
       - LMGC90: salomon/software/phys/LMGC90.md
     - 'Tools':
       - 'ANSYS':
-        - Introduction: software/ansys/ansys.md
-        - ANSYS CFX: software/ansys/ansys-cfx.md
-        - ANSYS Fluent: software/ansys/ansys-fluent.md
-        - ANSYS LS-DYNA: software/ansys/ansys-ls-dyna.md
-        - ANSYS MAPDL: software/ansys/ansys-mechanical-apdl.md
-        - LS-DYNA: software/ansys/ls-dyna.md
-        - Workbench: software/ansys/workbench.md
-        - Setting License Preferences: software/ansys/licensing.md
-        - Licensing and Available Versions: software/ansys/setting-license-preferences.md
-      - EasyBuild: software/easybuild.md
-      - Singularity Container: software/singularity.md
-      - Spack: software/spack.md
-      - Virtualization: software/virtualization.md
+        - Introduction: software/tools/ansys/ansys.md
+        - ANSYS CFX: software/tools/ansys/ansys-cfx.md
+        - ANSYS Fluent: software/tools/ansys/ansys-fluent.md
+        - ANSYS LS-DYNA: software/tools/ansys/ansys-ls-dyna.md
+        - ANSYS MAPDL: software/tools/ansys/ansys-mechanical-apdl.md
+        - LS-DYNA: software/tools/ansys/ls-dyna.md
+        - Workbench: software/tools/ansys/workbench.md
+        - Setting License Preferences: software/tools/ansys/licensing.md
+        - Licensing and Available Versions: software/tools/ansys/setting-license-preferences.md
+      - EasyBuild: software/tools/easybuild.md
+      - Singularity Container: software/tools/singularity.md
+      - Spack: software/tools/spack.md
+      - Virtualization: software/tools/virtualization.md
     - 'Visualisation':
-      - GPI-2: software/gpi2.md
-      - OpenFOAM: software/openfoam.md
-      - ParaView: software/paraview.md
+      - GPI-2: software/viz/gpi2.md
+      - OpenFOAM: software/viz/openfoam.md
+      - ParaView: software/viz/paraview.md
   - PBS Pro Documentation: pbspro.md
 
 extra: