Environment Modules

Access to many applications and libraries is controlled by the modules utility. The module command allows you to easily manipulate your Linux environment to use various applications and programming libraries, sometimes including older or newer versions than the default. When you need to change your environment you simply add or rm modules. Here are some of the commands you’ll need.

List Available Software

[username@bisonnet-hpc ~]$ module avail
--------------------------------- /software/etc/modulefiles ----------------------------------
DRAP/1.91(default)         gaussian/16.B.01-avx2       python/2.7           
gaussian/16.B.01(default)  matlab/R2018a(default)      python/3.6(default)  
gaussian/16.B.01-avx       ncbi-blast/2.7.1+(default)  R/3.5.0(default)     

----------------------------------- /cm/local/modulefiles ------------------------------------
cluster-tools-ext/8.1  cm-scale/8.1  cmsub           gcc/7.2.0        module-git   openldap  
cluster-tools/8.1      cmd           dot             ipmitool/1.8.18  module-info  shared    
cm-cloud-copy/8.1      cmsh          freeipmi/1.5.7  lua/5.3.4        null         

----------------------------------- /cm/shared/modulefiles -----------------------------------
acml/gcc-int64/64/5.3.1          cuda91/profiler/9.1.85                  iozone/3_471                    
acml/gcc-int64/fma4/5.3.1        cuda91/toolkit/9.1.85                   lapack/gcc/64/3.8.0             
acml/gcc-int64/mp/64/5.3.1       default-environment                     mpich/ge/gcc/64/3.2.1           
acml/gcc-int64/mp/fma4/5.3.1     fftw2/openmpi/gcc/64/double/2.1.5       mpiexec/0.84_432                
acml/gcc/64/5.3.1                fftw2/openmpi/gcc/64/float/2.1.5        mvapich2/gcc/64/2.3b            
acml/gcc/fma4/5.3.1              fftw3/openmpi/gcc/64/3.3.7              netcdf/gcc/64/4.5.0             
acml/gcc/mp/64/5.3.1             gdb/8.0.1                               netperf/2.7.0                   
acml/gcc/mp/fma4/5.3.1           globalarrays/openmpi/gcc/64/5.6.1       openblas/dynamic(default)       
blacs/openmpi/gcc/64/1.1patch03  hdf5/1.10.1                             openblas/dynamic/0.2.20         
blas/gcc/64/3.8.0                hdf5_18/1.8.20                          openmpi/gcc/64/1.10.7           
bonnie++/1.97.3                  hpl/2.2                                 scalapack/openmpi/gcc/64/2.0.2  
cuda91/blas/9.1.85               hwloc/1.11.8                            sge/2011.11p1                   
cuda91/fft/9.1.85                intel-tbb-oss/ia32/2018_20170919oss     slurm/17.11.2                   
cuda91/nsight/9.1.85             intel-tbb-oss/intel64/2018_20170919oss  torque/6.1.1

List Software In Your Environment

[username@bisonnet-hpc ~]$ module list
Currently Loaded Modulefiles:
 1) gcc/7.2.0   2) slurm/17.11.2   3) python/3.6(default)

Add Software to Your Environment

[username@bisonnet-hpc ~]$ module load python/3.6

You can also load the default version of a software package by dropping the version:

[username@bisonnet-hpc ~]$ module load python

Remove Software from Your Environment

[username@bisonnet-hpc ~]$ module unload python/3.6

Module Conflicts

Modules will prevent you from adding conflicting packages. For example, you’ll receive an error if you try to add two versions of Python to your environment. To change to a new version, either unload one version and load another or use the switch command:

[username@bisonnet-hpc ~]$ module list 
Currently Loaded Modulefiles:
   1) python/3.6 
[username@linuxremote1 ~]$ module switch python/2.7

Add Modules at Login

To add modules to your Linux environment that will load every time you login, use:
(NOTE: only run the echo command once; then just use initadd to add additional modules):

[username@bisonnet-hpc ~]$ echo "module add null" >> ~/.bashrc
[username@bisonnet-hpc ~]$ module initadd python/3.6

Likewise, you can remove commands from your initial environment using:

[username@bisonnet-hpc ~]$ module initrm python/3.6

Additional Help

[username@bisonnet-hpc ~]$ module help