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
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
R:
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
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
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
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
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
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 |
