UVA ✎ linux_environment_modules [Computing Support]

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==== Software Modules ====

[[http://modules.sourceforge.net|Software Modules]] make it easy for you to use software installed on our Linux systems. We provide a wide range of software across all our servers so that you don't have to install software on your own.  We also offer different versions of software, letting users choose which they want to use. 

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=== Module Requests ===
If a module is needed but not listed, please send an email to cshelpdesk@virginia.edu with the following:\\
1. In the subject line, write "Software Module Request: // software name and the version //"\\
2. In the body of the email, please include information about the software being requested (version and any associated links)

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=== Using Modules ===

Type ''%%module avail%%'' to get a list of available software.

//(this list is just an example, more may be available)//

<code>
[abc1de@portal04 ~]$ module avail
------------------------------- /sw/centos/Modules/systemModfiles -------------------------------------------------------------
slurm-client         slurm-client-testing

--------------------------------- /sw/centos/Modules/modulefiles --------------------------------------------------------------
afl               cmake-3.10        cudnn-7.3.1       gdb-8.1           libav             netdata           php7              ruby
altera_pro        cmake-3.15        cudnn-7.5.0       ghex              libtorch          nios2eds          php7.1.10         ruby2.5.1
anaconda3         cs6620            dmd               git               libtorch-1.3.1    nvtop             python            sbt
anaconda3-2019.10 cuda-toolkit      dmd-2.088.0       gradle            lua               openmpi           python2           scala
antlr             cuda-toolkit-10   doxygen           hashcat           lua-5.3.4         openmpi2.1.5      python2.7.15      sqlite3
atom              cuda-toolkit-10.1 eclipse           java              lxd               openmpi4.0.0      python3           storm
boost             cuda-toolkit-8.0  emacs             java11            modelsim_ae       openmpi4.0.2      python3.6.2       svn
boost-1.67.0      cuda-toolkit-9.0  fio               java8             modelsim_ase      parallel          python3.8.0       torch
clang-llvm        cuda-toolkit-9.2  gcc               java8u161         nano              perl              qsys              verilator
clang-llvm-6.0.0  cudnn             gcc-5.5.0         java9             nccl              perl-5.26         quartus
clang-llvm-7.1.0  cudnn-7.0.5       gcc-6.3.0         java9.0.4         nccl-10.0         perl-6            R
cmake             cudnn-7.1.1       gcc-7.1.0         lammps            nccl-9.2          php               rstudio

------------------------------- /sw/linux-any/Modules/modulefiles -------------------------------------------------------------
ant               cplex             cplex-opl         dmd-2.088.0       ripgrep           scons-3.0.1       vscode
antlr             cplex-concert     cplex-studio-all  go                sbt               tmux
apktool           cplex-cpoptimizer dmd               matlab            scons             tmux-2.7

</code>

Load the software module using''%%module load%%''.  Now the software is ready to use.

<code>
abc1de@portal04 ~ $ module load python3              # Load the module for use in your current session
abc1de@portal04 ~ $ which python
/sw/centos/python/3.6.2/bin/python
abc1de@portal04 ~ $ python                           # When you run `python` you get the version that has been loaded
Python 3.6.2 (default, Oct  6 2017, 13:03:05) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>>
</code>

''%%module list%%'' will show what modules you have loaded.

<code>
abc1de@portal ~ $ module load matlab
abc1de@portal ~ $ module load php
abc1de@portal ~ $ module list
Currently Loaded Modulefiles:
  1) matlab    2) python3   3) php
</code>

''%%module display%%'' will show specific information about the environment variables setup by a module.

<code>
abc1de@portal ~ $ module display python
-------------------------------------------------------------------
/sw/centos/Modules/modulefiles/python:
 
module-whatis	 Python current 
prepend-path	 PATH /sw/centos/python/current/bin 
prepend-path	 LD_LIBRARY_PATH /sw/centos/python/current/lib 
prepend-path	 LD_INCLUDE_PATH /sw/centos/python/current/include 
prepend-path	 MANPATH /sw/centos/python/current/share/man 
-------------------------------------------------------------------
abc1de@portal ~ $ echo $LD_LIBRARY_PATH 
/sw/centos/python/3.6.2/lib
</code>

Use ''%%module switch%%'' to change one version of software for another and ''%%module unload%%'' to unload modules when you are done or no longer want this software.

<code>
abc1de@portal ~ $ module switch python3 python2
abc1de@portal ~ $ module unload php
</code>\\

=== Shell Scripting/Slurm Batch ===

If you write shell scripts or slurm batch files that make use of these software packages, remember that you must still load modules from inside of your script.  For example, your script must contain the line ''%%module load python3%%'' before you can use python from inside of your script. 

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=== Initialize Modules System ===

To make modules work from inside SLURM or scripts, you must including the following line in your script **before** loading any modules:

<code bash>
source /etc/profile.d/modules.sh
</code>\\

=== Virtual Environments ===
For most Python related packages (i.e. pip install ...), it is often more applicable to utilize a virtual environment. This can be done with [[ https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html | Anaconda]]
or [[ https://docs.python.org/3/library/venv.html | venv ]]. The former requires loading an anaconda module, and the latter requires the python3 module.