Environment variables
By default user common variables printed out by the env command:
test@node009:~$ env MANPATH=/sNow/easybuild/lmod/lmod/share/man:: EASYBUILD_MODULES_TOOL=Lmod TERM=xterm SHELL=/bin/bash MODULEPATH_ROOT=/sNow/easybuild/modulefiles SSH_CLIENT=10.80.60.5 58918 22 LMOD_PKG=/sNow/easybuild/lmod/lmod EASYBUILD_INSTALLPATH=/sNow/easybuild/debian/8.8/Broadwell LMOD_VERSION=7.4.20 EASYBUILD_PREFIX=/sNow/easybuild/debian/8.8/Broadwell OS=debian SSH_TTY=/dev/pts/0 USER=test LMOD_sys=Linux OSVERSION=8.8 MAIL=/var/mail/test PATH=/sNow/snow-tools/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games SLURM_CONF=/etc/slurm/slurm.conf LMOD_SETTARG_CMD=: PWD=/homedtic/test LANG=en_GB.UTF-8 MODULEPATH=/sNow/easybuild/modules/all:/sNow/easybuild/debian/8.8/Broadwell/modules/all:/sNow/easybuild/modulefiles/Linux:/sNow/easybuild/modulefiles/Core:/sNow/easybuild/lmod/lmod/modulefiles/Core LMOD_CMD=/sNow/easybuild/lmod/lmod/libexec/lmod SHLVL=1 HOME=/homedtic/test EASYBUILD_SOURCEPATH=/sNow/easybuild/sources EASYBUILD_TMP_LOGDIR=/sNow/easybuild/tmp BASH_ENV=/sNow/easybuild/lmod/lmod/init/bash PYTHONPATH=/sNow/easybuild/installation/lib/python2.7/site-packages: LOGNAME=test SSH_CONNECTION=10.80.60.5 58918 10.80.61.9 22 MODULESHOME=/sNow/easybuild/lmod/lmod LMOD_FULL_SETTARG_SUPPORT=no ARCHITECTURE=Broadwell LMOD_DIR=/sNow/easybuild/lmod/lmod/libexec
From that extensive list, you'll basically work with the following ones:
HOME=/homedtic/test
PATH=/sNow/snow-tools/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games
LIBRARY_PATH=/sNow/easybuild/debian/8.8/Broadwell/software/CUDA/8.0.61/lib64 LD_LIBRARY_PATH=/sNow/easybuild/debian/8.8/Broadwell/software/CUDA/8.0.61/lib64
The environment variables are managed by the system and inherited from several places at login time. To add or modify the environment variables, we suggest this way:
Edit the file ~/.bashrc. It is placed on your home directory:
test@node009:~$ test@node009:~$ vi .bashrc
and go to the last lines of the file. In the following example, we'll add the environment variables for the Matlab Java JVM and we'll add Matlab to our application path:
# Add the path of matlab's binary to the system PATH export PATH=$PATH:/soft/MATLAB/R2013b/bin:/sge/matlab
To process the new version of our .bashrc, we have to logout and login again, as .bashrc is processed on login time.
Modules
The Modules package provides for the dynamic modification of the user's environment via modulefiles. Remember that to load the modules you must be logged in a calculation node.
To see the available modules you can execute the module av command.
test@node009:~$ module av ------------------------------------------------ /sNow/easybuild/modules/all ------------------------------------------------ EasyBuild/3.2.1 ------------------------------------- /sNow/easybuild/debian/8.8/Broadwell/modules/all -------------------------------------- Autoconf/2.69-foss-2017a Tcl/8.6.5-foss-2017a Automake/1.15-foss-2017a Tk/8.6.5-foss-2017a Autotools/20150215-foss-2017a binutils/2.27-GCCcore-6.3.0 Bison/3.0.4-GCCcore-6.3.0 binutils/2.27 (D) Bison/3.0.4 (D) bzip2/1.0.6-foss-2017a CUDA/8.0.61 flex/2.6.0 EasyBuild/3.3.1 (D) flex/2.6.3-GCCcore-6.3.0 (D) FFTW/3.3.6-gompi-2017a foss/2017a GCC/6.3.0-2.27 gompi/2017a GCCcore/6.3.0 help2man/1.47.4-GCCcore-6.3.0 GMP/6.1.1-foss-2017a hwloc/1.11.5-GCC-6.3.0-2.27 Java/1.8.0_45 libffi/3.2.1-foss-2017a M4/1.4.17-foss-2017a libreadline/6.3-foss-2017a M4/1.4.17 libtool/2.4.6-foss-2017a M4/1.4.18-GCCcore-6.3.0 (D) mdtest/git-foss-2017a OpenBLAS/0.2.19-GCC-6.3.0-2.27-LAPACK-3.7.0 ncurses/6.0-foss-2017a OpenMPI/2.0.2-GCC-6.3.0-2.27 numactl/2.0.11-GCC-6.3.0-2.27 Python/2.7.12-foss-2017a zlib/1.2.8-foss-2017a SQLite/3.13.0-foss-2017a zlib/1.2.8 ScaLAPACK/2.0.2-gompi-2017a-OpenBLAS-0.2.19-LAPACK-3.7.0 zlib/1.2.11-GCCcore-6.3.0 (D) Szip/2.1.1-foss-2017a ---------------------------------------- /sNow/easybuild/lmod/lmod/modulefiles/Core ----------------------------------------- lmod/7.4.20 settarg/7.4.20 Where: 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".
To load cuda module and to check if is really loaded:
test@node019:~$ module load CUDA/8.0.61 test@node019:~$ module list Currently Loaded Modules: 1) CUDA/8.0.61
The modules tool is useful to load and unload environment variables without worrying about .bashrc, but shows its best behavior if you want to dinamically change from two different installed versions of a package in the system. If you look carefully, you'll see that we have two different versions of gcc, and default is 4.92:
test@node009:~$ gcc -v Using built-in specs. COLLECT_GCC=gcc COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/4.9/lto-wrapper Target: x86_64-linux-gnu Thread model: posix gcc version 4.9.2 (Debian 4.9.2-10)
Let’s change the gcc version:
test@node009:~$ test@node009:~$ module load GCC/6.3.0-2.27 test@node009:~$ gcc -v Using built-in specs. COLLECT_GCC=gcc COLLECT_LTO_WRAPPER=/sNow/easybuild/debian/8.8/Broadwell/software/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper Target: x86_64-pc-linux-gnu Thread model: posix gcc version 6.3.0 (GCC) test@node009:~$
