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diff --git a/docs.it4i/software/lang/conda.md b/docs.it4i/software/lang/conda.md
new file mode 100644
index 0000000000000000000000000000000000000000..a4a4e97b3cdb20b811e881e2f695658afec6ff0e
--- /dev/null
+++ b/docs.it4i/software/lang/conda.md
@@ -0,0 +1,144 @@
+# Conda (Anaconda)
+
+Conda is an open source package management system and environment management system that runs on Windows, macOS and Linux. Conda quickly installs, runs and updates packages and their dependencies. Conda easily creates, saves, loads and switches between environments on your local computer. It was created for Python programs, but it can package and distribute software for any language.
+
+Conda as a package manager helps you find and install packages. If you need a package that requires a different version of Python, you do not need to switch to a different environment manager, because conda is also an environment manager. With just a few commands, you can set up a totally separate environment to run that different version of Python, while continuing to run your usual version of Python in your normal environment.
+
+Conda treats Python the same as any other package, so it is easy to manage and update multiple installations.
+Anaconda supports Python 2.7, 3.4, 3.5 and 3.6. The default is Python 2.7 or 3.6, depending on which installer you used:
+
+ * For the installers “Anaconda” and “Miniconda,” the default is 2.7.
+ * For the installers “Anaconda3” or “Miniconda3,” the default is 3.6.
+
+## Conda on the IT4Innovations Clusters
+
+On the clusters we have the Anaconda2 and Anaconda3 software installed. How to use these modules is shown below.
+
+!!! note
+ Use the command `ml av conda` to get up-to-date versions of the modules.
+
+```console
+$ ml av conda
+
+------------- /apps/modules/lang ---------------------------------
+Anaconda2/4.4.0 Anaconda3/4.4.0
+```
+
+## Anaconda2
+
+The default is Python 2.7
+
+### First Usage Module Anaconda2
+
+```console
+$ ml Anaconda2/4.4.0
+$ python --version
+Python 2.7.13 :: Anaconda 4.4.0 (64-bit)
+$ conda install numpy
+Fetching package metadata .........
+Solving package specifications: .
+
+Package plan for installation in environment /apps/all/Anaconda2/4.4.0:
+
+The following packages will be UPDATED:
+
+anaconda: 4.4.0-np112py27_0 --> custom-py27_0
+...
+...
+...
+CondaIOError: Missing write permissions in: /apps/all/Anaconda2/4.4.0
+#
+# You don't appear to have the necessary permissions to install packages
+# into the install area '/apps/all/Anaconda2/4.4.0'.
+# However you can clone this environment into your home directory and
+# then make changes to it.
+# This may be done using the command:
+#
+# $ conda create -n my_root --clone="/apps/all/Anaconda2/4.4.0"
+$
+$ conda create -n anaconda2 --clone="/apps/all/Anaconda2/4.4.0"
+Source: /apps/all/Anaconda2/4.4.0
+Destination: /home/svi47/.conda/envs/anaconda2
+The following packages cannot be cloned out of the root environment:
+- conda-4.3.21-py27_0
+- conda-env-2.6.0-0
+Packages: 213
+...
+...
+...
+#
+# To activate this environment, use:
+# > source activate anaconda2
+#
+# To deactivate this en
+```
+
+### Usage Module Anaconda2
+
+```console
+$ ml Anaconda2/4.4.0
+$ source activate anaconda2
+(anaconda2) ~]$
+```
+
+## Anaconda3
+
+The default is Python 3.6
+
+### First usage Module Anaconda3
+
+```console
+$ ml Anaconda3/4.4.0
+$ python --version
+Python 3.6.1 :: Anaconda 4.4.0 (64-bit)
+$ conda install numpy
+Fetching package metadata .........
+Solving package specifications: .
+
+Package plan for installation in environment /apps/all/Anaconda3/4.4.0:
+
+The following packages will be UPDATED:
+
+anaconda: 4.4.0-np112py36_0 --> custom-py36_0
+...
+...
+...
+CondaIOError: Missing write permissions in: /apps/all/Anaconda3/4.4.0
+#
+# You don't appear to have the necessary permissions to install packages
+# into the install area '/apps/all/Anaconda3/4.4.0'.
+# However you can clone this environment into your home directory and
+# then make changes to it.
+# This may be done using the command:
+#
+# $ conda create -n my_root --clone="/apps/all/Anaconda3/4.4.0"
+$
+$ conda create -n anaconda3 --clone="/apps/all/Anaconda3/4.4.0"
+Source: /apps/all/Anaconda3/4.4.0
+Destination: /home/svi47/.conda/envs/anaconda3
+The following packages cannot be cloned out of the root environment:
+- conda-4.3.21-py36_0
+- conda-env-2.6.0-0
+Packages: 200
+Files: 6
+...
+...
+...
+#
+# To activate this environment, use:
+# > source activate anaconda3
+#
+# To deactivate this environment, use:
+# > source deactivate anaconda3
+#
+$ source activate anaconda3
+(anaconda3) ~]$
+```
+
+### Usage Module Anaconda3
+
+```console
+$ ml Anaconda3/4.4.0
+$ source activate anaconda3
+(anaconda3) ~]$
+```
diff --git a/docs.it4i/software/csc.md b/docs.it4i/software/lang/csc.md
similarity index 88%
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index 0ec91fb1de21248fe723b610e931b80e8c418f0e..0f61cb8c4c3b9eae5579289d3d905a3ffd9480ce 100644
--- a/docs.it4i/software/csc.md
+++ b/docs.it4i/software/lang/csc.md
@@ -1,6 +1,18 @@
# CSharp
-C# is available on the cluster. Activate C# by loading the Mono module:
+C# is available on the cluster.
+
+```console
+$ ml av mono
+
+-------------------- /apps/modules/lang ---------------
+ Mono/5.0.0.100
+```
+
+!!! note
+ Use the command `ml av mono` to get up-to-date versions of the modules.
+
+Activate C# by loading the Mono module:
```console
$ ml Mono
diff --git a/docs.it4i/software/java.md b/docs.it4i/software/lang/java.md
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diff --git a/docs.it4i/software/lang/python.md b/docs.it4i/software/lang/python.md
new file mode 100644
index 0000000000000000000000000000000000000000..200802952fa37916b865a214dfbcbca8b492373d
--- /dev/null
+++ b/docs.it4i/software/lang/python.md
@@ -0,0 +1,186 @@
+# 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% |â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–| 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% |â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–| 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% |â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–| 10.4MB 42kB/s
+Collecting python-dateutil>=2 (from pandas)
+ Downloading python_dateutil-2.6.1-py2.py3-none-any.whl (194kB)
+ 100% |â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–| 196kB 1.3MB/s
+Collecting pytz>=2011k (from pandas)
+ Downloading pytz-2017.2-py2.py3-none-any.whl (484kB)
+ 100% |â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–| 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% |â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–â–| 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
+```
diff --git a/docs.it4i/software/lmod.md b/docs.it4i/software/modules/lmod.md
similarity index 99%
rename from docs.it4i/software/lmod.md
rename to docs.it4i/software/modules/lmod.md
index 24a93cbc8873a822a74950b720973bec6783284e..4aad91ce85aff13e59594cc1efaeee4ce6465d78 100644
--- a/docs.it4i/software/lmod.md
+++ b/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)
diff --git a/docs.it4i/software/operating-system.md b/docs.it4i/software/operating-system.md
deleted file mode 100644
index 5f022fdff9bc624befd9f0082ae38f675c52e5ff..0000000000000000000000000000000000000000
--- a/docs.it4i/software/operating-system.md
+++ /dev/null
@@ -1,9 +0,0 @@
-# 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).
diff --git a/docs.it4i/software/ansys/ansys-cfx.md b/docs.it4i/software/tools/ansys/ansys-cfx.md
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diff --git a/mkdocs.yml b/mkdocs.yml
index c60b9a2fc4bcb77766da059648009d91ca8e8363..ddd69f1dd80e39b5498e0665cc09e636562c7807 100644
--- a/mkdocs.yml
+++ b/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: