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--- linux_environment_modules [2020/03/09 13:09]
pgh5a
+++ linux_environment_modules [2022/01/31 19:22] (current)
@@ Line 1: / Line 1: @@
-====== Environment Modules ======
+==== Software Modules ====
-[[http://modules.sourceforge.net|Environment Modules]] are designed to manage custom package installations.  Software in our department is all installed to a network filesystem mounted over NFS where each package available is installed to it's own directory.  This allows us to manage a wide range of software across different Linux distributions without users having to deal with any configuration.  We can include different versions of software, letting users choose which they want to use.
+[[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.
-===== Available Modules =====
+\\
-Please see [[linux_modules:start|Available Modules]] for a listing of available software.
+=== Module Requests ===
+If a module is needed but not listed, please send an email to cshelpdesk@virginia.edu with the following:\\
+. In the subject line, write "Software Module Request: // software name and the version //"\\
+. In the body of the email, please include information about the software being requested (version and any associated links)
-===== Using Modules =====
+\\
-On any Linux system in our department, you can run ''%%module avail%%'' from your shell to get a list of available software.
+=== Using Modules ===
+Type ''%%module avail%%'' to get a list of available software.
+//(this list is just an example, more may be available)//
 <code>
-[pgh5a@portal04 ~]$ module avail
+[abc1de@portal04 ~]$ module avail
 ------------------------------- /sw/centos/Modules/systemModfiles -------------------------------------------------------------
 slurm-client         slurm-client-testing
@@ Line 37: / Line 44: @@
 </code>
-After deciding what software you want to use, load the package using''%%module load%%''.  Now the software is ready to use.
+Load the software module using''%%module load%%''.  Now the software is ready to use.
 <code>
-pgh5a@portal04 ~ $ module load python3              # Load the module for use in your current session
+abc1de@portal04 ~ $ module load python3              # Load the module for use in your current session
-pgh5a@portal04 ~ $ which python
+abc1de@portal04 ~ $ which python
 /sw/centos/python/3.6.2/bin/python
-pgh5a@portal04 ~ $ python                           # When you run `python` you get the version that has been loaded
+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
@@ Line 50: / Line 57: @@
 </code>
-After loading several modules in your session, ''%%module list%%'' will show what modules have been loaded.
+''%%module list%%'' will show what modules you have loaded.
 <code>
-pgh5a@portal ~ $ module load matlab
+abc1de@portal ~ $ module load matlab
-pgh5a@portal ~ $ module load php
+abc1de@portal ~ $ module load php
-pgh5a@portal ~ $ module list
+abc1de@portal ~ $ module list
 Currently Loaded Modulefiles:
 ) matlab    2) python3   3) php
 </code>
-''%%module display%%'' will show specific information about the environment variables that will be modified by a module.
+''%%module display%%'' will show specific information about the environment variables setup by a module.
 <code>
-pgh5a@portal ~ $ module display python
+abc1de@portal ~ $ module display python
 -------------------------------------------------------------------
 /sw/centos/Modules/modulefiles/python:
@@ Line 73: / Line 80: @@
 prepend-path	 MANPATH /sw/centos/python/current/share/man
 -------------------------------------------------------------------
-pgh5a@portal ~ $ echo $LD_LIBRARY_PATH
+abc1de@portal ~ $ echo $LD_LIBRARY_PATH
 /sw/centos/python/3.6.2/lib
 </code>
-You can ''%%switch%%'', changing one version of software for another, or ''%%unload%%'' modules when you are done or no longer want this software.
+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>
-pgh5a@portal ~ $ module switch python3 python2
+abc1de@portal ~ $ module switch python3 python2
-pgh5a@portal ~ $ module unload php
+abc1de@portal ~ $ module unload php
-</code>
+</code>\\
-===== Things to keep in mind =====
+=== Shell Scripting/Slurm Batch ===
-==== 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.
-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.
+\\
 === Initialize Modules System ===
@@ Line 96: / Line 103: @@
 <code bash>
 source /etc/profile.d/modules.sh
-</code>
+</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.