Software

Modules

The cluster uses modules to control which versions of software are used. Modules must be "loaded" in order to use the software that they represent. By default, several modules are loaded. You can view your loaded modules by running 'module list' on the login node.

danbarke@idran:~$ module list

Currently Loaded Modules:
1) PrivateModules 2) biostat/1.0 3) slurm/18.08.6 4) R/3.6.2-gcc8.3.0 5) jags/4.3.0 6) gsl/2.5 7) StdEnv

As you can see, by default, R 3.6.2 is loaded.

You can view all of the versions available for a particular title with 'module spider <package>'.
danbarke@idran:~$ module spider R

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R:
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Description:
R is a language and environment for statistical computing and graphics.

Versions:

R/3.5.1-gcc8.3

R/3.5.1

R/3.6.1-gcc8.3.0

R/3.6.1

R/3.6.2-gcc8.3.0

R/4.0.1-gcc8.3.0

 

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To find other possible module matches do:
module -r spider '.*R.*'

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To find detailed information about R please enter the full name.
For example:

$ module spider R/3.6.2-gcc8.3.0
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We can see that there are 6 versions of R available on the cluster, some compiled with the system gcc and others with the newer gcc 8.3.0.

If you want to switch to a different version of R, all you have to do is load the module with 'module load <package>/<version>'

[danbarke@idran ~]$ module load R/4.0.1-gcc8.3.0 

The following have been reloaded with a version change:

  1) R/3.6.2-gcc8.3.0 => R/4.0.1-gcc8.3.0

Now when I do a `module list` I see that R/4.0.1-gcc8.3.0 is loaded.
danbarke@idran:~$ module list

Currently Loaded Modules:
1) PrivateModules 2) biostat/1.0 3) slurm/18.08.6 4) R/4.0.1-gcc8.3.0 5) jags/4.3.0 6) gsl/2.5 7) StdEnv

 

Example Usage

$ module load R
$ which R
$ module unload R
$ module load openbugs

Module Subcommands

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

To load a list of modules different then the default you have the ~/privatemodules/ directory at your disposal. To load specific modules at login that are not in the site defaults put the module commands into the file default file in ~/privatemodules/default. You can put any module command in this default file. So 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.

Available Modules

The following list of software is available on the cluster.

If there is software missing that you need please email sph-biostat-help@umich.edu to have it added to the repository. As always you are free to install software in your home directory.

Module Versions (D)efault  Description Licenses Available Notes
admixture

1.3.0

ADMIXTURE is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets N/A Vendor
bcftools

1.9

1.10.2

BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF N/A Vendor
biostat

1.0

Biostatistics local repository N/A Vendor
gcc

8.3.0

9.3.0

GCC is the GNU C/C++/Fortran compiler suite. N/A Vendor
gcta

1.92.2

GCTA a tool for Genome-wide Complex Trait Analysis N/A Vendor

gmp

6.1.2

GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating-point numbers. N/A Vendor

gsl

2.5

GNU Scientific Library   Vendor
gurobi

8.1.0

The Gurobi Optimizer is a state-of-the-art solver for linear programming (LP), quadratic programming (QP) and mixed-integer programming (MILP and MIQP). It was designed from the ground up to exploit modern multi-core processors. N/A Vendor
jags

4.3.0

JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation not wholly unlike BUGS. N/A Vendor
KING

2.2.2

KING is a toolset to explore genotype data from a genome-wide association study (GWAS) or a sequencing project N/A Vendor
lapack

3.7.1

LAPACK is written in Fortran 90 and provides routines for solving systems of simultaneous linear equations, least-squares solutions of linear systems of equations, eigenvalue problems, and singular value problems.  N/A Vendor
matlab

R2019a

R2020b

Matlab is an interactive package for numerical analysis, matrix computation, control system design, and linear system analysis and design. unlimited Vendor
mpc 1.1.0 GNU MPC is a C library for the arithmetic of complex numbers with arbitrarily high precision and correct rounding of the result N/A Vendor
mpfr 4.0.2 The MPFR library is a C library for multiple-precision floating-point computations with correct rounding N/A Vendor
openbugs 3.2.3 BUGS is a software package for performing Bayesian inference Using Gibbs Sampling. N/A Vendor
plink 1.90 PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. N/A Vendor
python-anaconda 2020.01 (3.7)
2021.05 (3.8)
 The Anaconda distribution packages python with many frequently used packages like numpy, scipy, and pandas    
R

R/3.5.1-gcc8.3

R/3.6.1-gcc8.3.0

R/3.6.2-gcc8.3.0 (D)

R/4.0.2-gcc8.3.0

R/4.1.0-gcc8.3.0

R/4.1.2-gcc8.3.0

R is a language and environment for statistical computing and graphics. N/A Vendor
slurm

21.08.5

Slurm Resource Manager and Job Scheduler N/A Vendor