This page shows you how to handle your shell environment via the linux module system
Enable modules on cuda01/adagio:
echo -e "\nexport MODULEPATH=/group/ag_cmb/software/modules:\$MODULEPATH" >> ~/.bashrc
Enable modules on cuda02/cuda03/allegro:
echo -e "\nexport MODULEPATH=/import/ag_cmb/software/modules:\$MODULEPATH" >> ~/.bashrc
schiffm@cuda03:~$ module load compiler/4.6.3 openmm/5.1Use the latest (installed) GitHub HEAD of OpenMM:
schiffm@cuda03:~$ module load compiler/4.6.3 openmm/gitUse AceMD:
schiffm@cuda03:~$ module load acemd/dev.3124
List all loaded modules:
schiffm@cuda03:~$ module list
List all available modules:
schiffm@cuda03:~$ module avail
Remove a loaded module:
schiffm@cuda03:~$ module unload openmm/git
Remove all loaded modules:
schiffm@cuda03:~$ module purge
The linux module system …
schiffm@cuda03:~$ module avail ------------------------- /import/ag_cmb/software/modules -------------------------- acemd/dev.3124 compiler/4.6.3 openmm/5.1 openmm/git --------------------------- /usr/share/modules/versions ---------------------------- 3.2.9 -------------------------- /usr/share/modules/modulefiles -------------------------- dot module-cvs module-info modules null use.ownTo see what happens when we load a module, we will use the acemd software as an example. Before we load the acemd module, we look at the PATH, LD_LIBRARY_PATH, and ACEMD_HOME variables and convince ourself that the latter is empty and that the others contain no trace of the acemd installation:
schiffm@cuda03:~$ echo $PATH /home/schiffm/local/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games:/opt/dell/srvadmin/bin schiffm@cuda03:~$ echo $LD_LIBRARY_PATH schiffm@cuda03:~$ echo $ACEMD_HOMENow, we load the module with the module load acemd/dev.3124 command
schiffm@cuda03:~$ module load acemd/dev.3124 Module for acemd dev.3124 loaded.and check again the PATH, LD_LIBRARY_PATH, and ACEMD_HOME variables
schiffm@cuda03:~$ echo $PATH /import/ag_cmb/software/acemd-dev.3124/bin:/home/schiffm/local/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games:/opt/dell/srvadmin/bin schiffm@cuda03:~$ echo $LD_LIBRARY_PATH /import/ag_cmb/software/acemd-dev.3124/lib schiffm@cuda03:~$ echo $ACEMD_HOME /import/ag_cmb/software/acemd-dev.3124
Finally, we remove the acemd module again:
schiffm@cuda03:~$ module unload acemd/dev.3124I won't show it here, but you can trust me that the acemd paths are now completely stripped from the PATH, LD_LIBRARY_PATH, and ACEMD_HOME variables
The modules for our local software installations are in the grouphome (on cuda01/adagio)
schiffm@cuda01:~$ ls -l /group/ag_cmb/software/modules/* /group/ag_cmb/software/modules/compiler: insgesamt 4 -rw-r--r-- 1 schiffm cmb 1032 Okt 30 09:34 4.6.3 /group/ag_cmb/software/modules/openmm: insgesamt 8 -rw-r--r-- 1 schiffm cmb 1203 Okt 30 09:52 5.1 -rw-r--r-- 1 schiffm cmb 1203 Okt 30 09:52 git
and in the directory for local installations (on cuda02/cuda03/allegro)
schiffm@cuda03:~$ ls -l /import/ag_cmb/software/modules/* /import/ag_cmb/software/modules/acemd: insgesamt 2 -rw-r--r-- 1 schiffm biocomps 1107 Okt 30 10:17 dev.3124 /import/ag_cmb/software/modules/compiler: insgesamt 2 -rw-r--r-- 1 schiffm biocomps 1033 Okt 30 10:05 4.6.3 /import/ag_cmb/software/modules/openmm: insgesamt 3 -rw-r--r-- 1 schiffm biocomps 1204 Okt 30 10:06 5.1 -rw-r--r-- 1 schiffm biocomps 1204 Okt 30 10:06 git