Helix and Biowulf now use environment modules to dynamically set up environments for different applications. Users can type commands like:
module load ThisApp module unload ThisApp to set up the environment for a particular application. The 'module load' command will set PATH, LD_LIBRARY_PATH and other environment variables as necessary. Any previous environment setups in your .bashrc or .cshrc files will continue to work, but modules are generally easier to use. The Helix and Biowulf application pages have been updated to describe the modules command for each application. This page contains some general information about modules.
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The command module avail will show all available modules.
[user@helix]$ module avail ---------- /usr/local/Modules/3.2.9/modulefiles ----------- afni/18Oct2012(default) cuda/3.1 modules namd/2.9-ipath afni/18Oct2012-openmp cuda/4.0.17 mpich2-x86_64 null afni/21Dec2011 dot namd/2.7+plumed1.3 perl/5.12.1 amber/10-gige fftw3 namd/2.7-gige perl/5.12.1-threads amber/10-ipath gromacs/4.0.4 namd/2.7-ib perl/5.8.8 amber/11 gromacs/4.0.7 namd/2.7-ipath perl/5.8.9 amber/11-gpu gromacs/4.5.1 namd/2.8+plumed1.3 python/2.5.1 amber/12(default) gromacs/4.5.3 namd/2.8-gige python/2.6.4 blast gromacs/4.5.5(default) namd/2.8-gpu python/2.7.1 chromopainter gromacs/4.6-dev namd/2.8-ib qiime cmake/2.8.0 hmmer namd/2.8-ipath use.own cuda/2.3 module-cvs namd/2.9-gige velvet/1.2.03 cuda/3.0 module-info namd/2.9-ib velvet/1.2.07 [...etc...]
To see the versions available for a particular application, use module avail appname. e.g.
[user@helix]$ module avail gromacs ---------- /usr/local/Modules/3.2.9/modulefiles ----------- gromacs/4.0.4 gromacs/4.5.1 gromacs/4.5.5(default) gromacs/4.0.7 gromacs/4.5.3 gromacs/4.6-dev
To load a module, use the command module load appname. The default version will get loaded. If you want a particular version, use module load appname/version e.g
[user@helix]$ module list No Modulefiles Currently Loaded. [user@helix]$ module load gromacs [user@helix]$ module list Currently Loaded Modulefiles: 1) gromacs/4.5.5
[user@helix]$ module load gromacs/4.5.3 [user@helix]$ module list Currently Loaded Modulefiles: 1) gromacs/4.5.3
Multiple modules can be loaded in a single command. e.g.
[user@helix]$ module load plinkseq macs bowtie [user@helix]$ module list Currently Loaded Modulefiles: 1) plinkseq/0.08 2) macs/2.0.10 3) bowtie/2-2.0.2
To unload a module, use the command module unload Appname. e.g.
[user@helix]$ module list Currently Loaded Modulefiles: 1) gromacs/4.5.3 [user@helix]$ module unload gromacs/4.5.3
[user@helix]$ module list Currently Loaded Modulefiles: 1) qiime 2) perl/5.8.9
[user@helix]$ module list Currently Loaded Modulefiles: 1) perl/5.8.9 [user@helix]$ module switch perl perl/5.12.1 [user@helix]$ module list Currently Loaded Modulefiles: 1) perl/5.12.1
If you want to see what changes a module will make to your environment without loading it, use the 'module display' command. e.g.
[user@helix]$ module display blast ------------------------------------------------------------------- /usr/local/Modules/3.2.9/modulefiles/blast: module-whatis Sets up NCBI Blast prepend-path PATH /usr/local/blast/ncbi/bin prepend-path PATH /usr/local/blast/bin -------------------------------------------------------------------
If you prefer to set paths directly instead of using modules, you can use the information from 'module display' to do so.
Create a directory called privatemodules in your home directory. Then type the command: module load use.own and any personal module files in this directory will become available for you to list, load or unload. You can make copies of the system modulefiles in /usr/local/Modules/default/modulefiles to use as templates.
[user@helix ~]$ module load use.own [user@helix ~]$ module avail ---------- /home/user/privatemodules ---------- hmmer/2.3 ---------- /usr/local/Modules/3.2.9/modulefiles ----------- afni/18Oct2012(default) cuda/3.1 modules namd/2.9-ipath afni/18Oct2012-openmp cuda/4.0.17 mpich2-x86_64 null afni/21Dec2011 dot namd/2.7+plumed1.3 perl/5.12.1 [...etc...]
