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...]
You might want to set up a personal modulefile that loads and unloads a collection of other modules. Below is an example of such a module. The module is called 'myngs' and loads a specific version of Novocraft, Cufflinks and Tophat. You will need to put this module file into /home/user/privatemodules/.
#%Module1.0
# this module is called myngs
module-whatis "Loads novocraft/3.00.02 cufflinks/2.0.1 tophat/2.0.8/bowtie2-2.1.0"
set mode [module-info mode]
#
if { $mode == "whatis" } { exit }
#
foreach modulename { novocraft/3.00.02 cufflinks/2.0.1 tophat/2.0.8/bowtie2-2.1.0 } {
if { [is-loaded $modulename] && $mode == "remove" } { module unload $modulename }
if { ![is-loaded $modulename] && $mode == "load" } { module load $modulename }
#
if { $mode == "load" || $mode == "remove" } {
if { [is-loaded $modulename] } { puts stderr "$modulename is loaded" }
if { ![is-loaded $modulename] } { puts stderr "$modulename is unloaded" }
}
}Here is a sample session using the above module.
[user@helix ~]$ module load use.own [user@helix ~]$ module list Currently Loaded Modulefiles: 1) use.own [user@helix ~]$ module load myngs novocraft/3.00.02 is loaded cufflinks/2.0.1 is loaded tophat/2.0.8/bowtie2-2.1.0 is loaded [user@helix ~]$ module list Currently Loaded Modulefiles: 1) use.own 3) cufflinks/2.0.1 5) myngs 2) novocraft/3.00.02 4) tophat/2.0.8/bowtie2-2.1.0 [user@helix ~]$ module unload myngs novocraft/3.00.02 is unloaded cufflinks/2.0.1 is unloaded tophat/2.0.8/bowtie2-2.1.0 is unloaded [user@helix ~]$ module list Currently Loaded Modulefiles: 1) use.own
To set up modules that will be shared by a group, the easiest way is to create a 'modulefiles' directory in some area that is shared by the group, and put the group modules into that directory. Each user in the group who wants to access these modules can then create a link from the shared area to their own /home/user/privatemodules/ area. For example, suppose the group has a shared area called /data/DBCImaging.
helix% mkdir /data/DBCImaging/modulefilesCreate the desired modulefiles in this directory. If a personal/group module has the same name as a system module, the system module will get lower priority, and your personal module will be loaded first.
Now each user in the group who wants to use these shared modules should create a link from their /home/user/privatemodules area.
helix% ln -s /data/DCBImaging/modulefiles /home/user/privatemodules/shared helix% module load use.own helix% module avail ----------------------- /home/user/privatemodules ------------------------------- blast shared/bowtie/0.12.8 shared/bowtie/2-2.0.6 freesurfer/5.1 shared/bowtie/0.12.9 shared/bowtie/2-2.1.0 myngs shared/bowtie/2-2.0.0-beta7 shared/octave_test/3.2.4 nested shared/bowtie/2-2.0.2 shared/octave_test/3.6.1 shared/bowtie/0.12.5 shared/bowtie/2-2.0.5 susantest ---------------------------- /usr/local/Modules/3.2.9/modulefiles --------------- BEAST/1.5.2 eman2/2.06 openmpi/1.6/gnu/eth BEAST/1.5.4 eman2/2.06_121120 openmpi/1.6/gnu/ib BEAST/1.6.1 eman2/2.06_ib openmpi/1.6/gnu/ipath BEAST/1.6.2 express/1.2.2 openmpi/1.6/intel/eth BEAST/1.7.1 express/1.3.1(default) openmpi/1.6/intel/ib [...] helix% module load shared/octave_test/3.2.4 helix% module list Currently Loaded Modulefiles: 1) use.own 2) shared/octave_test/3.6.1
Users who do not have access to the shared area (in this case /data/DBCImaging) will not be able to see the shared modules.
