Environment modules
The physics softwares and common libraries such as GNU Scientific Library and Boost are provided through the Environment Modules system, or modules for short. The modules are regularly updated and maintained by the system administrator.
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| xkcd, Compiling |
The command module avail shows all the available modules.
$ module avail
----------------------- /opt/ohpc/pub/moduledeps/gnu7-openmpi -----------------------
boost/1.63.0 fftw/3.3.6 herwig/7.1.2 scipy/0.19.1 whizard/2.6.3
--------------------------- /opt/ohpc/pub/moduledeps/gnu7 ---------------------------
ExRootAnalysis/1.1.4 lhapdf/6.2.1 pdtoolkit/3.24
MG5aMC_PY8_interface/1.0 looptools/2.14 pythia/8.2.35
ccfits/2.5 metis/5.1.0 python/2.7.14 (D)
cfitsio/3.430 mpich/3.2 python/3.4.6
collier/1.2 mvapich2/2.2 python/3.5.4
delphes/3.4.1 numpy/1.13.1 python/3.6.4
fastjet/3.3.0 ocaml/4.06.0 rivet/2.6.0
golem/1.3.3 ocr/1.0.1 root/6.12.06
gsl/2.4 openblas/0.2.20 sherpa/2.2.4
hdf5/1.10.1 openmpi/1.10.7 (L) superlu/5.2.1
hepmc/2.06.09 openmpi3/3.0.0 yoda/1.7.0b1
----------------------------- /opt/ohpc/pub/modulefiles -----------------------------
autotools (L) gnu7/7.2.0 (L) ohpc (L) prun/1.2 (L)
cmake/3.9.2 hwloc/1.11.8 papi/5.5.1 singularity/2.4
gnu/5.4.0 llvm5/5.0.0 pmix/1.2.3 valgrind/3.13.0
Where:
L: Module is loaded
D: Default Module
Use "module spider" to find all possible modules.
Use "module keyword key1 key2 ..." to search for all possible modules matching any
of the "keys".
For example, if you want to use ROOT, run
module load root/6.12.06
The version number could be omitted if only one version is available or the default module is good enough to use. The list of loaded modules can be seen by
$ module list
Currently Loaded Modules:
1) autotools 3) gnu7/7.2.0 5) ohpc 7) root/6.12.06
2) prun/1.2 4) openmpi/1.10.7 6) python/2.7.14
The list in the above tells you that ROOT 6.12.06 and Python 2.7.14 are loaded in the current environment. Indeed, they are added to your $PATH.
$ which root
/opt/ohpc/pub/libs/gnu7/root/6.12.06/bin/root
$ which python
/opt/ohpc/pub/libs/gnu7/python-2.7.14/bin/python
module show prints out the commands in the module file. For example,
$ module show root
---------------------------------------------------------------------------------
/opt/ohpc/pub/moduledeps/gnu7/root/6.12.06:
---------------------------------------------------------------------------------
whatis("Name: ROOT built with gnu7 toolchain ")
whatis("Version: 6.12.06 ")
whatis("Category: runtime library ")
whatis("Description: ROOT is a modular scientific software framework. ")
whatis("URL https://root.cern.ch ")
depends_on("python/2.7.14")
prepend_path("PATH","/opt/ohpc/pub/libs/gnu7/root/6.12.06/bin")
prepend_path("MANPATH","/opt/ohpc/pub/libs/gnu7/root/6.12.06/man")
prepend_path("INCLUDE","/opt/ohpc/pub/libs/gnu7/root/6.12.06/include")
prepend_path("LD_LIBRARY_PATH","/opt/ohpc/pub/libs/gnu7/root/6.12.06/lib")
prepend_path("PYTHONPATH","/opt/ohpc/pub/libs/gnu7/root/6.12.06/lib")
setenv("ROOTSYS","/opt/ohpc/pub/libs/gnu7/root/6.12.06")
help([[
This module loads the ROOT program and library
built with the gnu7 compiler toolchain.
Version 6.12.06
]])
This shows that ROOTSYS environment variable has been added. For a script to use ROOT given as below,
#! /bin/bash -l
#
#SBATCH --job-name=test
#SBATCH --output=root_output.txt
#
#SBATCH --partition=espresso
#SBATCH --ntasks=1
#SBATCH --nodes=1
#SBATCH --mem-per-cpu=100
#SBATCH --time=10:00
module load root
root -b -q $ROOTSYS/tutorials/math/binomial.C
running sbatch run.sh (run.sh is the name of the script given above) gives us
$ cat root_output.txt
------------------------------------------------------------
| Welcome to ROOT 6.12/06 http://root.cern.ch |
| (c) 1995-2017, The ROOT Team |
| Built for linuxx8664gcc |
| From tag v6-12-06, 9 February 2018 |
| Try '.help', '.demo', '.license', '.credits', '.quit'/'.q' |
------------------------------------------------------------
Processing /opt/ohpc/pub/libs/gnu7/root/6.12.06/tutorials/math/binomial.C...
TMath::Binomial simple test
Build the Tartaglia triangle
============================
n= 0 1
n= 1 1 1
n= 2 1 2 1
n= 3 1 3 3 1
n= 4 1 4 6 4 1
n= 5 1 5 10 10 5 1
n= 6 1 6 15 20 15 6 1
n= 7 1 7 21 35 35 21 7 1
n= 8 1 8 28 56 70 56 28 8 1
n= 9 1 9 36 84 126 126 84 36 9 1
n=10 1 10 45 120 210 252 210 120 45 10 1
n=11 1 11 55 165 330 462 462 330 165 55 11 1
n=12 1 12 66 220 495 792 924 792 495 220 66 12 1
TMath::Binomial fancy test
Verify Newton formula for (x+y)^n
x,y in [-2,2] and n from 0 to 9
=================================
Average Error = 1.064988e-13
Users of another shell like Zsh must initialize the module function before running module. See files in $MODULESHOME/init. For example, if you're using Z shell, the script in the above should be
#! /bin/zsh -l
#
#SBATCH --job-name=test
#SBATCH --output=root_output.txt
#
#SBATCH --partition=espresso
#SBATCH --ntasks=1
#SBATCH --nodes=1
#SBATCH --mem-per-cpu=100
#SBATCH --time=10:00
. $MODULESHOME/init/zsh
module load root
root -b -q $ROOTSYS/tutorials/math/binomial.C
Notice /bin/zsh in the first line and . $MODULESHOME/init/zsh.
module unload will unload the module.
$ module unload root
$ module list
Currently Loaded Modules:
1) autotools 2) prun/1.2 3) gnu7/7.2.0 4) openmpi/1.10.7 5) ohpc
Note that Python 2.7.14 has been unloaded as well since it was loaded as a requirement to load ROOT. If what you want is just Python 2.7.14,
$ module load python/2.7.14
$ module list
Currently Loaded Modules:
1) autotools 3) gnu7/7.2.0 5) ohpc
2) prun/1.2 4) openmpi/1.10.7 6) python/2.7.14
$ which python
/opt/ohpc/pub/libs/gnu7/python-2.7.14/bin/python
module avail shows that you could use GCC 5.4.0 (gnu/5.4.0), while GCC 7.2.0 (gnu7/7.2.0) is currently loaded.
$ gcc --version
gcc (GCC) 7.2.0
Copyright (C) 2017 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
Since GCC 7.2.0 conflicts with GCC 5.4.0 (they cannot coexist in an environment), you cannot load directly GCC 5, but switch to it by running
$ module switch gnu7 gnu/5.4.0
Due to MODULEPATH changes, the following have been reloaded:
1) python/2.7.14
The following have been reloaded with a version change:
1) openmpi/1.10.7 => openmpi/1.10.6
$ module list
Currently Loaded Modules:
1) autotools 3) ohpc 5) openmpi/1.10.6
2) prun/1.2 4) gnu/5.4.0 6) python/2.7.14
$ gcc --version
gcc (GCC) 5.4.0
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
The list of loaded modules will be reset once you re-login the master server. All the modules can be removed from your environment by purging them.
$ module purge
$ module list
No modules loaded
Sometimes, it's necessary to remove .lmod.d in your home directory to refresh the list of available modules.
rm -rf ~/.lmod.d
module avail
module --help will show other useful commands.