Commit ed8f7827 authored by David Hrbáč's avatar David Hrbáč

Merge branch 'add_soft' into 'master'

Add soft

See merge request sccs/docs.it4i.cz!167
parents 813fc816 dd5439c9
# 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) ~]$
```
# 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
......
# 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
```
......@@ -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)
......
# 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).
......@@ -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:
......
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