HPC:Environment Modules

From HPC wiki

Environment Modules

The PMACS cluster utilizes modules to enable users to alter their environment. These modules alter your execution path ($PATH) and add or modify the user's environment variables. User loadable modules are available if the system default packages don't meet your requirements. Environment modules are used in place of hard-coding paths in your $HOME/.bashrc file.

To know what modules are available, you'll need to run the "module avail" command from an interactive session:

[asrini@consign ~]$ bsub -Is bash
Job <9990024> is submitted to default queue <interactive>.
<<Waiting for dispatch ...>>
<<Starting on node063.hpc.local>>
    
[asrini@node063 ~]$ module avail

------------------------------------------------------------------- /usr/share/Modules/modulefiles -------------------------------------------------------------------
NAMD-2.9-Linux-x86_64-multicore dot                             module-info                     picard-1.96                     rum-2.0.5_05
STAR-2.3.0e                     java-sdk-1.6.0                  modules                         pkg-config-path                 samtools-0.1.19
STAR-hg19                       java-sdk-1.7.0                  mpich2-x86_64                   python-2.7.5                    use.own
STAR-mm9                        ld-library-path                 null                            r-libs-user
bowtie2-2.1.0                   manpath                         openmpi-1.5.4-x86_64            ruby-1.8.7-p374
devtoolset-2                    module-cvs                      perl5lib                        ruby-1.9.3-p448 


The module names should be pretty self-explainatory, but some are not. To see information about a module you can issue a module show [module name]:

[asrini@node063 ~]$ module show null
-------------------------------------------------------------------
/usr/share/Modules/modulefiles/null:

module-whatis	 does absolutely nothing
-------------------------------------------------------------------

[asrini@node063 ~]$ module show r-libs-user
-------------------------------------------------------------------
/usr/share/Modules/modulefiles/r-libs-user:

module-whatis	 Sets R_LIBS_USER=$HOME/R/library
setenv		 R_LIBS_USER ~/R/library
-------------------------------------------------------------------

[asrini@node063 ~]$ module show devtoolset-2
-------------------------------------------------------------------
/usr/share/Modules/modulefiles/devtoolset-2:

module-whatis	 Devtoolset-2 packages include the newer versions of gcc
prepend-path	 PATH /opt/rh/devtoolset-2/root/usr/bin
prepend-path	 MANPATH /opt/rh/devtoolset-2/root/usr/share/man
prepend-path	 INFOPATH /opt/rh/devtoolset-2/root/usr/share/info
-------------------------------------------------------------------

Example use of modules:

[asrini@node063 ~]$ python -V
Python 2.6.6

[asrini@node063 ~]$ which python
/usr/bin/python

[asrini@node063 ~]$ module load python-2.7.5

[asrini@node063 ~]$ python -V
Python 2.7.5

[asrini@node063 ~]$ which python
/opt/software/python/python-2.7.5/bin/python

After running the above commands, you will be able to use python v2.7.5 till you exit out of the interactive session or till you unload the module:

[asrini@node063 ~]$ module unload python-2.7.5

[asrini@node063 ~]$ which python
/usr/bin/python

Modules may also be included in your job scripts and submitted as a batch job.

Using Modules at Login

In order to have modules automatically load into your environment, you would add the module commands to your $HOME/.bashrc file. Note that modules are not available on the PMACS head node, hence, you'll need to ensure that your login script attempts to load a module only if you are on a compute node:

[asrini@consign ~]$ more .bashrc
# .bashrc

# Source global definitions
if [ -f /etc/bashrc ]; then
	. /etc/bashrc
fi
#
#
# Modules to load
if [ $HOSTNAME != "consign.hpc.local" ] && [ $HOSTNAME != "mercury.pmacs.upenn.edu" ]; then
	module load python-2.7.5
fi

# more stuff below .....

[asrini@consign ~]$ which python
/usr/bin/python
[asrini@consign ~]$ bsub -Is bash
Job <172129> is submitted to default queue <interactive>.
<<Waiting for dispatch ...>>
<<Starting on node063.hpc.local>>
[asrini@node063 ~]$ which python
/opt/software/python/python-2.7.5/bin/python