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linux_environment_modules [2020/03/09 13:06] pgh5a |
linux_environment_modules [2021/12/02 14:08] |
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| - | ====== Environment Modules ====== | ||
| - | [[http://modules.sourceforge.net|Environment Modules]] are designed to manage custom package installations. Software in our department is all installed to a network filesystem mounted over NFS where each package available is installed to it's own directory. This allows us to manage a wide range of software across different Linux distributions without users having to deal with any configuration. We can include different versions of software, letting users choose which they want to use. | ||
| - | |||
| - | ===== Available Modules ===== | ||
| - | |||
| - | Please see [[linux_modules:start|Available Modules]] for a listing of available software. | ||
| - | |||
| - | ===== Using Modules ===== | ||
| - | |||
| - | On any Linux system in our department, you can run ''%%module avail%%'' from your shell to get a list of available software. | ||
| - | |||
| - | <code> | ||
| - | [pgh5a@portal04 ~]$ module avail | ||
| - | ------------------------------------------------------------ /sw/centos/Modules/systemModfiles ------------------------------------------------------------- | ||
| - | slurm-client slurm-client-testing | ||
| - | |||
| - | -------------------------------------------------------------- /sw/centos/Modules/modulefiles -------------------------------------------------------------- | ||
| - | afl cmake-3.10 cudnn-7.3.1 gdb-8.1 libav netdata php7 ruby | ||
| - | altera_pro cmake-3.15 cudnn-7.5.0 ghex libtorch nios2eds php7.1.10 ruby2.5.1 | ||
| - | anaconda3 cs6620 dmd git libtorch-1.3.1 nvtop python sbt | ||
| - | anaconda3-2019.10 cuda-toolkit dmd-2.088.0 gradle lua openmpi python2 scala | ||
| - | antlr cuda-toolkit-10 doxygen hashcat lua-5.3.4 openmpi2.1.5 python2.7.15 sqlite3 | ||
| - | atom cuda-toolkit-10.1 eclipse java lxd openmpi4.0.0 python3 storm | ||
| - | boost cuda-toolkit-8.0 emacs java11 modelsim_ae openmpi4.0.2 python3.6.2 svn | ||
| - | boost-1.67.0 cuda-toolkit-9.0 fio java8 modelsim_ase parallel python3.8.0 torch | ||
| - | clang-llvm cuda-toolkit-9.2 gcc java8u161 nano perl qsys verilator | ||
| - | clang-llvm-6.0.0 cudnn gcc-5.5.0 java9 nccl perl-5.26 quartus | ||
| - | clang-llvm-7.1.0 cudnn-7.0.5 gcc-6.3.0 java9.0.4 nccl-10.0 perl-6 R | ||
| - | cmake cudnn-7.1.1 gcc-7.1.0 lammps nccl-9.2 php rstudio | ||
| - | |||
| - | ------------------------------------------------------------ /sw/linux-any/Modules/modulefiles ------------------------------------------------------------- | ||
| - | ant cplex cplex-opl dmd-2.088.0 ripgrep scons-3.0.1 vscode | ||
| - | antlr cplex-concert cplex-studio-all go sbt tmux | ||
| - | apktool cplex-cpoptimizer dmd matlab scons tmux-2.7 | ||
| - | |||
| - | </code> | ||
| - | |||
| - | After deciding what software you want to use, load the package using''%%module load%%''. Now the software is ready to use. | ||
| - | |||
| - | <code> | ||
| - | pgh5a@portal04 ~ $ module load python3 # Load the module for use in your current session | ||
| - | pgh5a@portal04 ~ $ which python | ||
| - | /sw/centos/python/3.6.2/bin/python | ||
| - | pgh5a@portal04 ~ $ python # When you run `python` you get the version that has been loaded | ||
| - | Python 3.6.2 (default, Oct 6 2017, 13:03:05) | ||
| - | [GCC 4.8.5 20150623 (Red Hat 4.8.5-16)] on linux | ||
| - | Type "help", "copyright", "credits" or "license" for more information. | ||
| - | >>> | ||
| - | </code> | ||
| - | |||
| - | After loading several modules in your session, ''%%module list%%'' will show what modules have been loaded. | ||
| - | |||
| - | <code> | ||
| - | ktm5j@applecake ~ $ module load matlab | ||
| - | ktm5j@applecake ~ $ module load php | ||
| - | ktm5j@applecake ~ $ module list | ||
| - | Currently Loaded Modulefiles: | ||
| - | 1) matlab 2) python3 3) php | ||
| - | </code> | ||
| - | |||
| - | ''%%module display%%'' will show specific information about the environment variables that will be modified by a module. | ||
| - | |||
| - | <code> | ||
| - | ktm5j@applecake ~ $ module display python | ||
| - | ------------------------------------------------------------------- | ||
| - | /sw/centos/Modules/modulefiles/python: | ||
| - | |||
| - | module-whatis Python current | ||
| - | prepend-path PATH /sw/centos/python/current/bin | ||
| - | prepend-path LD_LIBRARY_PATH /sw/centos/python/current/lib | ||
| - | prepend-path LD_INCLUDE_PATH /sw/centos/python/current/include | ||
| - | prepend-path MANPATH /sw/centos/python/current/share/man | ||
| - | ------------------------------------------------------------------- | ||
| - | ktm5j@applecake ~ $ echo $LD_LIBRARY_PATH | ||
| - | /sw/centos/python/3.6.2/lib | ||
| - | </code> | ||
| - | |||
| - | You can ''%%switch%%'', changing one version of software for another, or ''%%unload%%'' modules when you are done or no longer want this software. | ||
| - | |||
| - | <code> | ||
| - | ktm5j@applecake ~ $ module switch python3 python2 | ||
| - | ktm5j@applecake ~ $ module unload php | ||
| - | </code> | ||
| - | |||
| - | ===== Things to keep in mind ===== | ||
| - | |||
| - | ==== Shell Scripting/Slurm Batch ==== | ||
| - | |||
| - | If you write shell scripts or slurm batch files that make use of these software packages, remember that you must still load modules from inside of your script. For example, your script must contain the line ''%%module load python3%%'' before you can use python from inside of your script. | ||
| - | |||
| - | === Initialize Modules System === | ||
| - | |||
| - | To make modules work from inside SLURM or scripts, you must including the following line in your script **before** loading any modules: | ||
| - | |||
| - | <code bash> | ||
| - | source /etc/profile.d/modules.sh | ||
| - | </code> | ||