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 modulesmodule load/unload
: to load or unload a particular modulemodule list
: to list modules that are loadedmodule 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)