Skip to content

Software On The Cluster

Modules

  • A tool that simplifies shell initialization and lets users easily modify their environment during the session with modulefiles
  • Each modulefile contains the information needed to configure the shell for an application. (PATH, LD_LIBRARY_PATH, CPATH, etc.)
  • Modules are useful in managing different versions of applications.
  • Modules can also be bundled into metamodules that will load an entire set of different applications (dependencies).

Module Commands

  • module av : to check all available modules
  • module load : to load a particular module
  • module list : to list modules that are loaded
  • module purge : purge any loaded modules

Check All Available Modules

  • To check ALL available modules installed on the cluster:
module av
  • Upon login, environment PATH is set for the system to search executables:
echo $PATH

output

/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/cluster/home/your_utln/bin:/cluster/home/your_utln/.local/bin
  • For example, I would like to use blast, to check what versions of blast are available:
module av blast

output

---------------------- /opt/shared/Modules/modulefiles-rhel6 ----------------------
blast/2.2.24 blast/2.2.31 blast/2.3.0  blast/2.8.1

---------------------- /cluster/tufts/hpc/tools/module ----------------------------
blast-plus/2.11.0

Load Desired Module

  • To load the version I would like to use, and use it:
module load blast-plus/2.11.0

Check Which Modules Are Loaded

  • To check which modules are loaded:
module list

output

Currently Loaded Modulefiles:
    1) use.own     2) blast-plus/2.11.0

Check The Tool Version

  • To determine the tool version:
blastp -version

output

blastp: 2.11.0+
 Package: blast 2.11.0, build Aug 17 2021 06:29:22

Check Module Paths

  • To determine the module paths:
which blastp

output

/cluster/tufts/hpc/tools/spack/linux-rhel7-ivybridge/gcc-9.3.0/blast-plus-2.11.0-ip4jcqabi3a2jscgusnkipvib6goy5mv/bin/blastp

echo $PATH

output

/cluster/tufts/bio/tools/edirect:/cluster/tufts/hpc/tools/spack/linux-rhel7-ivybridge/gcc-9.3.0/blast-plus-2.11.0-ip4jcqabi3a2jscgusnkipvib6goy5mv/bin:/cluster/home/your_utln/.iraf/bin:/cluster/home/your_utln/.iraf/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/cluster/home/your_utln/bin:/cluster/home/your_utln/.local/bin

To Unload Modules

  • To unload a loaded module:
module unload blast-plus/2.11.0

echo $PATH

output

/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/cluster/home/your_utln/bin:/cluster/home/your_utln/.local/bin
  • To unload ALL of the loaded modules:
module purge

module list

output

No Modulefiles Currently Loaded.