Software
Modules
The cluster uses Lmod modules to dynamically load available software into your session on the cluster.
Basic Usage
A comprehensive guide can be found on the Lmod website.
Loading Modules
Modules must be "loaded" in order to use the software that they represent.
$ module load R
If you need a specific version of a package, you must specify it with "module/version.number"
$ module load R/4.4.0
Several modules are loaded by default based on department usage.
$ module list
Currently Loaded Modules:
1) slurm/23.2.7 2) R/4.2.2 3) jags/4.3.1 4) gcc/10.4.0 5) gsl/2.7.1 6) StdEnv
Module Availability
$ module avail
----------------------------------------- Applications compiled with GCC 10.4.0 ------------------------------------------
R/3.6.3 R/4.4.0 fftw3/3.3.10 gurobi/10.0.1 openbugs/3.2.3
R/4.1.2 Ropenblas/4.2.2 gdal/3.6.2 imagemagick/7.1.0 proj/9.1.1
R/4.2.2 (L,D) cmake/3.25.2 gsl/2.7.1 (L) jags/4.3.1 (L)
----------------------------------------- Core applications including compilers ------------------------------------------
StdEnv (L) geos/3.11.1 mosek/10.0.37 nlopt/2.7.1 slurm/23.2.7 (L)
boost/1.81.0 gmp/6.2.1 mpc/1.3.1 python3.10-anaconda/2023.03
gcc/10.4.0 (L) matlab/R2022b mpfr/4.2.0 python3.9-anaconda/2022.10
---------------------------------------- Bioinformatics and genetics applications ----------------------------------------
admixture/1.3.0 bowtie2/2.5.1 gsea/4.3.2 multiqc/1.14 rseqc/5.0.1 trimmomatic/0.39.0
bcftools/1.17 deeptools/3.5.2 htslib/1.17 plink/2.00a4 samtools/1.17 ucsc/393
bedtools/2.30.0 fastqc/0.12.1 king/2.3.0 rsem/1.3.3 star/2.7.10b
Where:
L: Module is loaded
D: Default Module
"module overview" or "ml ov" to display the number of modules for each name.
Use "module spider" to find all possible modules and extensions.
Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys".
Module Sub-Commands
| Command | Description | example |
|---|---|---|
| list | List current loaded modules | module list |
| avail | List all modules available in the system | module avail |
| show | Display details of a module | module show R |
| load | Load a module into your environment | module load R |
| unload | Remove a currently loaded module from your environment | module unload R |
| whatis | Display the module description information | module whatis R |
Private Modules
If you're familiar with the Lmod system, you're free to install user modules for yourself.
The cluster implementation of Lmod will look in your home directory for a "dot folder"
with an Lmod directory in it. Use something like ~/.modules/
To load specific modules at login that are not in the site defaults, put the module
commands into a default file in ~/.modules/default. You can put any module command in this default file; if you would like to run a different version of an existing package you can
unload that module and then load it via the default file.
Requesting Modules
There are many pre-installed modules available for you to use on the Biostat Cluster. If there is software missing that you need please email sph-biostat-help@umich.edu to have it added. If you're familiar with the Lmod system, you're free to install user modules for yourself.