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).

Useful Module Commands

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

To check ALL available modules installed on the cluster:

[your_utln@login-prod-01 ~]$ module av

Upon login, environment PATH is set for the system to search executables:

[your_utln@login-prod-01 ~]$ echo $PATH

/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, load the version I would like to use, and use it:

[your_utln@login-prod-01 ~]$ module av blast

---------------------- /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

[your_utln@login-prod-01 ~]$ module load blast-plus/2.11.0

[your_utln@login-prod-01 ~]$ module list

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

[your_utln@login-prod-01 ~]$ which blastp

/cluster/tufts/hpc/tools/spack/linux-rhel7-ivybridge/gcc-9.3.0/blast-plus-2.11.0-ip4jcqabi3a2jscgusnkipvib6goy5mv/bin/blastp
[your_utln@login-prod-01 ~]$ echo $PATH

/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

[your_utln@login-prod-01 ~]$ blastp -version

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

I can also unload a loaded modules:

[your_utln@login-prod-01 ~]$ module unload blast-plus/2.11.0

[your_utln@login-prod-01 ~]$ echo $PATH

/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/cluster/home/your_utln/bin:/cluster/home/your_utln/.local/bin

I can unload ALL of the loaded modules:

[your_utln@login-prod-01 ~]$ module purge

[your_utln@login-prod-01 ~]$ module list

No Modulefiles Currently Loaded.

Install Software/Packages

  • R (R command line recommanded)
    • R/4.0.0
    • gcc
    • gdal
    • curl
  • Python (Conda env recommanded)
    • anaconda/3 (older version, source activate)
    • anaconda/2021.05 (newer version, source activate)
    • Use the same version of conda on one conda env every time
  • Other software compiled from source
    • gcc
    • cmake
    • ... any dependencies, load if available, install if not.
    • Follow instructions (read it through)
    • Use "--prefix=" to install in non-standard locations
    • Modify the environment variables !!! (such as PATH, LD_LIBRARY_PATH, CPATH, .etc)