Cluster Resources Gollum

Environment Modules

Environment Modules is an open source project that provides a mechanism to dynamically modify a user's environment. More information can be found here. The modules command allows users to easily configure applications or switch application versions in the cluster environment. Please see the man pages below.

Man Pages

Example Usage

  • List available packages

    • module avail

    ---- /export/modules/3.2.8/versions --------------------------------
3.2.8

---- /export/modules/3.2.8/Modules/3.2.8/modulefiles ---------------
dot         module-cvs  module-info modules     null        use.own

---- /export/modules/3.2.8/modulefiles -----------------------------
amber/10                              cuda/7.0                              
amber/11                              cuda/7.5                              
amber/12-13(default)                  cuda/8.0                              
amber/14                              cuda/9.0                              
amber/14tools                         cuda_gbsw/1.0                         
amber/16tools                         cyana/2.1                             
amber/8                               dftb/1.2                              
anaconda/2.2.5.0(default)             dftb/17.1                             
anaconda/2.2.5.0.troy                 dock/6.7(default)                     
anaconda/2.2.5.0a                     dowser/dowser(default)                
autodock/4.2.3(default)               espresso/5.0.2                        
autodock/vina                         espresso/5.0.2-OpenMPI                
autotools/2.69                        fdupes/1.0                            
babel/2.3.2(default)                  fftw/2.1.5                            
babel/2.4.1                           fftw/3.2.2                            
babel/2.4.1a                          fftw/3.3.1(default)                   
blast/2.2.20(default)                 fftw/3.3.4/gnu-4.8.4                  
bonnie/1.03e(default)                 fftw/3.3.4/intel-15.x                 
boost/1.64.0                          fftw/3.3.4/pgi-15.1                   
bzip/1.0.6(default)                   fftw/3.3.7/3.3.7                      
cairo/1.11.4                          gaussian/g03                          
cgenff/1.0.0(default)                 gaussian/g09(default)                 
charmm/c42a2_multiarch                gaussian/g09d                         
charmm/c42a2_multiarch_cuda8          gcc/4.5                               
charmm/c43a1_multiarch                gcc/4.6.1                             
charmm/c43a1_multiarch_cuda8(default) gcc/4.6.3(default)                   
charmm/c43a1_multiarch_cuda9          gcc/4.7.2                             
chimera/1.12                          gcc/4.8.4                             
cluster/0.0.1(default)                gcc/4.9.2                             
cmake/2.2.8                           gcc/4.9.4                             
cmake/2.8.8                           gcc/5.1.0                             
cmake/3.2.2(default)                  gccxml/0.9                            
cmake/3.4.3                           gdb/7.3.1                             
cuda/5.5                              gdb/7.6(default)                      
cuda/6.0                              gdb/8.0.1                            
cuda/6.5                              git/1.7.5.4(default)
  • List loaded packages

    • module list

    Currently Loaded Modulefiles:
  1) modules         2) cluster/0.0.1   3) slurm/1.0       4) cuda/9.0
  • Load packages

    • module load charmm

            This module will set up environment variables
        for CUDA 8.0.
        This module will set up environment variables
        for OpenMM 7.1.0
        This module will set up environment variables
        for the parallel (openmpi) CHARMM version c43a1
        compiled with the GCC compiler.  Should work on 
        both AVX and non-AVX environments.
  • Unload packages

    • module unload charmm

User Modules

Modules allows users to create their own local module files. This is done with the MODULEPATH environment variable.

"The path that the module command searches when looking for modulefiles. Typically, it is set to a default value by the bootstrap procedure. MODULEPATH can be set using 'module use' or by the module initialization script to search group or personal modulefile directories before or after the master modulefile directory."[1]

Please seee the modulefile man page above.