{"type":"doc","content":[{"type":"layoutSection","content":[{"type":"layoutColumn","attrs":{"width":50.0},"content":[{"type":"paragraph","content":[{"text":"This section explains how to make use of the system-wide available software stack which is organized in modules.","type":"text"}]},{"type":"paragraph","content":[{"text":"A ","type":"text"},{"text":"module","type":"text","marks":[{"type":"em"}]},{"text":" is a self-contained description of a software package - it contains the settings required to run a software package and, usually, encodes required dependencies on other software packages.","type":"text"}]},{"type":"paragraph","content":[{"text":"There are a number of different environment module implementations commonly used on HPC systems: the two most common are ","type":"text"},{"text":"TCL modules","type":"text","marks":[{"type":"em"}]},{"text":" and ","type":"text"},{"text":"Lmod","type":"text","marks":[{"type":"em"}]},{"text":". Both of these use similar syntax and the concepts are the same so learning to use one will allow you to use whichever is installed on the system you are using. 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Check the help for module to see all commands with a description.","type":"text"}]},{"type":"table","attrs":{"layout":"default","width":1800.0,"localId":"ebc9e6f0-a150-4532-991d-a863f4d11b73"},"content":[{"type":"tableRow","content":[{"type":"tableHeader","attrs":{"colspan":1,"rowspan":1,"colwidth":[340.0]},"content":[{"type":"paragraph","content":[{"text":"Command","type":"text","marks":[{"type":"strong"}]}]}]},{"type":"tableHeader","attrs":{"colspan":1,"rowspan":1,"colwidth":[340.0]},"content":[{"type":"paragraph","content":[{"text":"Description","type":"text","marks":[{"type":"strong"}]}]}]}]},{"type":"tableRow","content":[{"type":"tableCell","attrs":{"colspan":1,"rowspan":1,"colwidth":[340.0]},"content":[{"type":"paragraph","content":[{"text":"module -h","type":"text","marks":[{"type":"code"}]},{"text":" or ","type":"text"},{"text":"module 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SHARK","type":"text"}]},{"type":"paragraph","content":[{"text":"ALICE and SHARK have different module structures. This is partly related to how the system-wide software stack is being managed on both clusters. However, the basic usage of environment modules is the same on both clusters.","type":"text"}]},{"type":"paragraph","content":[{"text":"Once you are familiar with how modules are organized on the cluster that you are using, it will not be difficult for you to find the modules that you are looking for.","type":"text"}]},{"type":"layoutSection","content":[{"type":"layoutColumn","attrs":{"width":50.0},"content":[{"type":"rule"},{"type":"paragraph","content":[{"text":"ALICE","type":"text","marks":[{"type":"strong"}]}]},{"type":"paragraph","content":[{"text":"On ALICE modules are organized as different module trees. The software behind each module is build and maintained using ","type":"text"},{"text":"EasyBuild ","type":"text","marks":[{"type":"em"}]},{"text":"(","type":"text"},{"type":"inlineCard","attrs":{"url":"https://easybuild.io/"}},{"text":").","type":"text"}]},{"type":"paragraph","content":[{"text":"In each tree, the modules are organized as ","type":"text"},{"text":"/","type":"text","marks":[{"type":"code"}]},{"text":" where ","type":"text"},{"text":"","type":"text","marks":[{"type":"code"}]},{"text":" can also include additional information about what was used to build the module ","type":"text"},{"text":"","type":"text","marks":[{"type":"code"}]}]},{"type":"paragraph","content":[{"text":"The ","type":"text"},{"text":"default trees","type":"text","marks":[{"type":"strong"}]},{"text":" are ","type":"text"}]},{"type":"table","attrs":{"layout":"default","localId":"112b356c-b19f-419e-9577-06375dc5b6ea"},"content":[{"type":"tableRow","content":[{"type":"tableHeader","attrs":{"colspan":1,"rowspan":1},"content":[{"type":"paragraph","content":[{"text":"Tree","type":"text","marks":[{"type":"strong"}]}]}]},{"type":"tableHeader","attrs":{"colspan":1,"rowspan":1},"content":[{"type":"paragraph","content":[{"text":"Description","type":"text","marks":[{"type":"strong"}]}]}]}]},{"type":"tableRow","content":[{"type":"tableCell","attrs":{"colspan":1,"rowspan":1},"content":[{"type":"paragraph","content":[{"text":"/easybuild/modules/all","type":"text","marks":[{"type":"code"}]}]},{"type":"paragraph"}]},{"type":"tableCell","attrs":{"colspan":1,"rowspan":1},"content":[{"type":"paragraph","content":[{"text":"Default tree, containing all of the system-wide software build with ","type":"text"},{"text":"EasyBuild ","type":"text","marks":[{"type":"em"}]},{"text":"for all nodes with Intel CPU","type":"text"},{"text":". ","type":"text","marks":[{"type":"em"}]},{"text":"Available by default or after loading ","type":"text"},{"text":"ALICE/default","type":"text","marks":[{"type":"code"}]},{"text":" module.","type":"text"}]}]}]},{"type":"tableRow","content":[{"type":"tableCell","attrs":{"colspan":1,"rowspan":1},"content":[{"type":"paragraph","content":[{"text":"/cm/shared/modulefiles","type":"text","marks":[{"type":"code"}]}]}]},{"type":"tableCell","attrs":{"colspan":1,"rowspan":1},"content":[{"type":"paragraph","content":[{"text":"Containing the modules for Slurm and LUMC/FSL software","type":"text"}]}]}]}]},{"type":"paragraph","content":[{"text":"Additionally available trees","type":"text","marks":[{"type":"strong"}]},{"text":" that need to be loaded manually are:","type":"text"}]},{"type":"table","attrs":{"layout":"default","localId":"8d374ff2-aa71-4bbe-b708-69d73be22c10"},"content":[{"type":"tableRow","content":[{"type":"tableHeader","attrs":{"colspan":1,"rowspan":1},"content":[{"type":"paragraph","content":[{"text":"Tree","type":"text","marks":[{"type":"strong"}]}]}]},{"type":"tableHeader","attrs":{"colspan":1,"rowspan":1},"content":[{"type":"paragraph","content":[{"text":"Description","type":"text","marks":[{"type":"strong"}]}]}]}]},{"type":"tableRow","content":[{"type":"tableCell","attrs":{"colspan":1,"rowspan":1},"content":[{"type":"paragraph","content":[{"text":"/cm/shared/LUMC/modulefiles","type":"text","marks":[{"type":"code"}]}]}]},{"type":"tableCell","attrs":{"colspan":1,"rowspan":1},"content":[{"type":"paragraph","content":[{"text":"Containing all LUMC-provided modules including FSL. Available after loading the module ","type":"text"},{"text":"LUMC","type":"text","marks":[{"type":"code"}]}]}]}]},{"type":"tableRow","content":[{"type":"tableCell","attrs":{"colspan":1,"rowspan":1},"content":[{"type":"paragraph","content":[{"text":"/cm/shared/easybuild/GenuineIntel/modules/all","type":"text","marks":[{"type":"code"}]}]},{"type":"paragraph","content":[{"text":"and","type":"text"},{"type":"hardBreak"},{"text":"/cm/shared/easybuild/AuthenticAMD/modules/all","type":"text","marks":[{"type":"code"}]}]}]},{"type":"tableCell","attrs":{"colspan":1,"rowspan":1},"content":[{"type":"paragraph","content":[{"text":"Old modules for Intel and AMD nodes prior to maintenance of May 2024. Because they were build on the old operating system they may or may not work. You can access them by loading the ALICE/legacy module. The module tree is chosen based on the CPU type.","type":"text"}]}]}]}]}]},{"type":"layoutColumn","attrs":{"width":50.0},"content":[{"type":"rule"},{"type":"paragraph","content":[{"text":"SHARK","type":"text","marks":[{"type":"strong"}]}]},{"type":"paragraph","content":[{"text":"On SHARK, all software is contained in the tree ","type":"text"},{"text":"/share/modulefiles","type":"text","marks":[{"type":"code"}]}]},{"type":"paragraph","content":[{"text":"Modules are being organized in a hierarchical structure, i.e., ","type":"text"},{"text":"//","type":"text","marks":[{"type":"code"}]},{"text":" where ","type":"text"},{"text":"","type":"text","marks":[{"type":"code"}]},{"text":" is the class to which the module belong to, ","type":"text"},{"text":"","type":"text","marks":[{"type":"code"}]},{"text":" the name of the module, and ","type":"text"},{"text":"","type":"text","marks":[{"type":"code"}]},{"text":" the installed version of the module ","type":"text"},{"text":"","type":"text","marks":[{"type":"code"}]}]},{"type":"paragraph","content":[{"text":"The different module classes currently are:","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"benchmark","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"bioimage","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"bioinformatics","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"container","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"cryogenicEM","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"genomics","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"graphics","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"gwas","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"library","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"mathematical","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"medicalImaging","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"neuroImaging","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"pharmaceutical","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"statistical","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"system","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"tools","type":"text"}]}]}]}]}]},{"type":"rule"},{"type":"heading","attrs":{"level":1},"content":[{"text":"List currently loaded modules","type":"text"}]},{"type":"paragraph","content":[{"text":"On login, you might start out with a default set of modules.","type":"text"}]},{"type":"paragraph","content":[{"text":"The ","type":"text"},{"text":"module list","type":"text","marks":[{"type":"code"}]},{"text":" command shows which modules you currently have loaded in your environment. ","type":"text"}]},{"type":"layoutSection","content":[{"type":"layoutColumn","attrs":{"width":50.0},"content":[{"type":"rule"},{"type":"paragraph","content":[{"text":"ALICE","type":"text","marks":[{"type":"strong"}]}]},{"type":"paragraph","content":[{"text":"This is what you will most likely see after logging into ALICE.","type":"text"}]},{"type":"codeBlock","content":[{"text":"[me@nodelogin02~]$ module list\n \n Currently Loaded Modules:\n 1) shared 2) DefaultModules 3) gcc/8.2.0 4) slurm/19.05.1","type":"text"}]},{"type":"paragraph","content":[{"text":"You can see that by default the module for Slurm and the gcc compiler is loaded. The number behind the slash sign represent the version number.","type":"text"}]}]},{"type":"layoutColumn","attrs":{"width":50.0},"content":[{"type":"rule"},{"type":"paragraph","content":[{"text":"SHARK","type":"text","marks":[{"type":"strong"}]}]},{"type":"paragraph","content":[{"text":"On SHARK, no modules are being loaded by default. After login, you would see","type":"text"}]},{"type":"codeBlock","content":[{"text":"[me@res-hpc-lo02 ~]$ module list\nNo modules loaded","type":"text"}]}]}]},{"type":"rule"},{"type":"heading","attrs":{"level":1},"content":[{"text":"List available modules","type":"text"}]},{"type":"paragraph","content":[{"text":"To see the available modules, use ","type":"text"},{"text":"module -d avail","type":"text","marks":[{"type":"code"}]},{"text":". With the ","type":"text"},{"text":"-d","type":"text","marks":[{"type":"code"}]},{"text":" option, you will only get the default versions of the modules. For various software packages, there are also older/other versions available, that might be used if necessary. You can see all version by omitting the ","type":"text"},{"text":"-d","type":"text","marks":[{"type":"code"}]},{"text":" option.","type":"text"}]},{"type":"layoutSection","content":[{"type":"layoutColumn","attrs":{"width":50.0},"content":[{"type":"rule"},{"type":"paragraph","content":[{"text":"ALICE","type":"text","marks":[{"type":"strong"}]}]},{"type":"codeBlock","content":[{"text":" [me@nodelogin02~]$ module -d avail\n ---------------------------------------------------------------------- /cm/shared/easybuild/GenuineIntel/modules/all ----------------------------------------------------------------------\n 4ti2/1.6.9-GCC-8.2.0-2.31.1 Miniconda2/4.7.10 flatbuffers/1.12.0-GCCcore-10.2.0\n ALICE/default (L) Miniconda3/4.9.2 flex/2.6.4\n AMUSE-GPU/12.0.0-foss-2018a-Python-2.7.14 MotionCor2/1.3.0-GCCcore-8.2.0 fontconfig/2.13.93-GCCcore-10.3.0\n AMUSE-Miniconda2/4.7.10 MrBayes/3.2.6-foss-2017a foss/2021a\n AMUSE-VADER/12.0.0-foss-2018a-Python-2.7.14 MultiQC/1.7-foss-2018b-Python-3.6.6 fosscuda/2020b\n AMUSE/2021.7-Miniconda3-4.9.2 NASM/2.15.05-GCCcore-10.3.0 freeglut/3.2.1-GCCcore-8.3.0\n ANTs/2.3.5-foss-2019b-Python-3.7.4 NCCL/2.10.3-GCCcore-10.3.0-CUDA-11.3.1 freetype/2.10.4-GCCcore-10.3.0\n APR-util/1.6.1-GCCcore-8.2.0 NGS/2.10.0-GCCcore-8.2.0-Java-11 gc/7.6.12-GCCcore-9.3.0\n APR/1.7.0-GCCcore-8.2.0 NLTK/3.2.4-foss-2019a-Python-3.7.2 gcccuda/2020b\n ARPwARP/8.0 NLopt/2.6.2-GCCcore-10.2.0 gensim/3.7.3-foss-2019a-Python-3.7.2\n# etc...","type":"text"}]}]},{"type":"layoutColumn","attrs":{"width":50.0},"content":[{"type":"rule"},{"type":"paragraph","content":[{"text":"SHARK","type":"text","marks":[{"type":"strong"}]}]},{"type":"codeBlock","content":[{"text":"[rfschulz@res-hpc-lo02 ~]$ module -d avail\n----------------------------------------------------------------------------------- /share/modulefiles ------------------------------------------------------------------------------------\n benckmarks/disk/ior/3.4.0/gcc-8.3.1 library/cuda/11.0/gcc.8.3.1 neuroImaging/MRtrix3/3.0.3/gcc-8.3.1\n benckmarks/disk/iozone/3.491/gcc-8.3.1 library/cuda/11.1/gcc.8.3.1 neuroImaging/SimpleElastix/0.10.0/python3.6.8\n bioimage/CellProfiler/4.2.1/gcc-8.3.1 library/cuda/11.2/gcc.8.3.1 neuroImaging/dsi-studio/2021.10.05/gcc-8.3.1\n bioimage/QuPath/0.2.3 library/cuda/11.3/gcc.8.3.1 neuroImaging/freesurfer/7.2.0\n bioimage/bftools/6.8.1 library/cuda/11.4.1/gcc.8.3.1 neuroImaging/fsl/5.0.10\n bioimage/slideToolkit/1.1 library/cuda/11.6.1/gcc.8.3.1 neuroImaging/fsl/5.0.11\n bioinformatics/tools/SNP/flashpca/2.1/gcc-8.3.1 library/cuda/7.5/gcc.8.3.1 neuroImaging/fsl/5.0.9\n bioinformatics/tools/assembly-stats/1.0.1/gcc-8.3.1 library/cuda/8.0/gcc.8.3.1 neuroImaging/fsl/6.0.0\n bioinformatics/tools/ncbi/sra/2.10.9 library/cuda/9.0/gcc.8.3.1 neuroImaging/fsl/6.0.1\n container/singularity/3.10.0/gcc.8.5.0 library/cuda/9.1/gcc.8.3.1 neuroImaging/fsl/6.0.2\n# etc...","type":"text"}]}]}]},{"type":"rule"},{"type":"heading","attrs":{"level":1},"content":[{"text":"Finding specific modules","type":"text"}]},{"type":"paragraph","content":[{"text":"If you are searching for a specific software package or tool you can search for the full module name like this:","type":"text"}]},{"type":"layoutSection","content":[{"type":"layoutColumn","attrs":{"width":50.0},"content":[{"type":"rule"},{"type":"paragraph","content":[{"text":"ALICE","type":"text","marks":[{"type":"strong"}]}]},{"type":"codeBlock","content":[{"text":"[me@nodelogin02~]$ module avail python\n ---------------------------------------- /cm/shared/easybuild/modules/all -----------------------------------------\n AMUSE-GPU/12.0.0-foss-2018a-Python-2.7.14\n AMUSE-VADER/12.0.0-foss-2018a-Python-2.7.14\n AMUSE/12.0.0-foss-2018a-Python-2.7.14\n AMUSE/13.1.0-foss-2018a-Python-3.6.4 (D)\n Biopython/1.71-foss-2018a-Python-2.7.14\n Biopython/1.73-foss-2019a\n Biopython/1.75-foss-2019b-Python-3.7.4 (D)\n Boost.Python/1.67.0-foss-2018b-Python-3.6.6\n CGAL/4.11.1-foss-2018b-Python-3.6.6\n CONCOCT/1.1.0-foss-2019a-Python-2.7.15\n CheckM/1.0.18-foss-2019a-Python-2.7.15\n Cython/0.25.2-foss-2018a-Python-2.7.14\n Cython/0.25.2-foss-2018a-Python-3.6.4\n Cython/0.29.3-foss-2019a-Python-3.7.2 (D)\n DAS_Tool/1.1.1-foss-2019a-R-3.6.0-Python-3.7.2\n Docutils/0.9.1-foss-2018a-Python-2.7.14\n Docutils/0.9.1-foss-2018a-Python-3.6.4 (D)\n GObject-Introspection/1.60.1-GCCcore-8.2.0-Python-3.7.2\n IPython/5.7.0-foss-2018a-Python-2.7.14\n IPython/6.4.0-foss-2018a-Python-3.6.4\n IPython/7.7.0-foss-2019a-Python-3.7.2 (D)\n Keras/2.2.4-foss-2019a-Python-3.7.2\n Mako/1.0.7-foss-2017b-Python-2.7.14\n Mako/1.0.7-foss-2018a-Python-2.7.14\n Mako/1.0.7-foss-2018b-Python-2.7.15\n Meson/0.50.0-GCCcore-8.2.0-Python-3.7.2\n Meson/0.51.2-GCCcore-8.3.0-Python-3.7.4 (D)\n MultiQC/1.7-foss-2018b-Python-3.6.6\n NLTK/3.2.4-foss-2018a-Python-3.6.4\n NLTK/3.2.4-foss-2019a-Python-3.7.2 (D)\n PyCairo/1.18.0-foss-2018b-Python-3.6.6\n PyTorch/1.3.1-fosscuda-2019b-Python-3.7.4\n PyYAML/3.13-foss-2018b-Python-3.6.6\n Python/2.7.14-foss-2017b\n Python/2.7.14-foss-2018a\n Python/2.7.14-GCCcore-6.4.0-bare\n Python/2.7.15-foss-2018b\n Python/2.7.15-GCCcore-7.3.0-bare\n Python/2.7.15-GCCcore-8.2.0\n Python/2.7.16-GCCcore-8.3.0\n Python/3.6.4-foss-2018a\n Python/3.6.6-foss-2018b\n Python/3.7.2-GCCcore-8.2.0\n Python/3.7.4-GCCcore-8.3.0 (D)\n etc etc etc .......","type":"text"}]},{"type":"paragraph","content":[{"text":"To only search for the module Python itself, use","type":"text"}]},{"type":"codeBlock","content":[{"text":" module -r avail '^Python/'","type":"text"}]}]},{"type":"layoutColumn","attrs":{"width":50.0},"content":[{"type":"rule"},{"type":"paragraph","content":[{"text":"SHARK","type":"text","marks":[{"type":"strong"}]}]},{"type":"codeBlock","content":[{"text":"me@res-hpc-lo02 ~]$ module avail python\n\n--------------------- /share/modulefiles ----------------------\n genomics/ngs/tools/liftoff/1.5.1/python-3.8\n library/wxpython/4.1.0/gcc-8.3.1\n library/wxpython/4.1.1/gcc-8.3.1\n neuroImaging/SimpleElastix/0.10.0/python3.6.8\n system/python/2.7.17\n system/python/3.7.6\n system/python/3.8.1\n system/python/3.9.12\n system/python/3.9.13\n system/python/3.10.2 (L,D)\n tools/miniconda/python2.7/4.7.12\n tools/miniconda/python3.8/4.8.5\n tools/miniconda/python3.8/4.9.2 (D)\n tools/miniconda/python3.9/4.12.0","type":"text"}]}]}]},{"type":"rule"},{"type":"paragraph","content":[{"text":"In the above output, you can see that there are modules with the flag \"(D)\". This indicates that this is the default module for a software package for which modules for different versions exists.","type":"text"}]},{"type":"paragraph","content":[{"text":"If you want to get more information about a specific module, you can use the ","type":"text"},{"text":"whatis","type":"text","marks":[{"type":"code"}]},{"text":" sub-command, e.g.","type":"text"}]},{"type":"layoutSection","content":[{"type":"layoutColumn","attrs":{"width":50.0},"content":[{"type":"rule"},{"type":"paragraph","content":[{"text":"ALICE","type":"text","marks":[{"type":"strong"}]}]},{"type":"codeBlock","content":[{"text":"[me@nodelogin02 ~]$ module whatis Python/3.7.4-GCCcore-8.3.0","type":"text"}]}]},{"type":"layoutColumn","attrs":{"width":50.0},"content":[{"type":"rule"},{"type":"paragraph","content":[{"text":"SHARK","type":"text","marks":[{"type":"strong"}]}]},{"type":"codeBlock","content":[{"text":"[me@res-hpc-lo02 ~]$ module whatis system/python/3.10.2","type":"text"}]}]}]},{"type":"rule"},{"type":"heading","attrs":{"level":1},"content":[{"text":"Load modules","type":"text"}]},{"type":"paragraph","content":[{"text":"To load a module, use ","type":"text"},{"text":"module load","type":"text","marks":[{"type":"code"}]},{"text":". ","type":"text"}]},{"type":"paragraph","content":[{"text":"In the example below, we will use R to demonstrate how the module system works and what it does to your user environment.","type":"text"}]},{"type":"paragraph","content":[{"text":"Initially, R is not loaded and therefore the command ","type":"text"},{"text":"Rscript","type":"text","marks":[{"type":"code"}]},{"text":" is not available for use. We can test this by using the command ","type":"text"},{"text":"which","type":"text","marks":[{"type":"code"}]},{"text":" that looks for programs the same way that Bash does. We can use it to tell us where a particular piece of software is stored.","type":"text"}]},{"type":"layoutSection","content":[{"type":"layoutColumn","attrs":{"width":50.0},"content":[{"type":"rule"},{"type":"paragraph","content":[{"text":"ALICE","type":"text","marks":[{"type":"strong"}]}]},{"type":"codeBlock","content":[{"text":"[me@nodelogin02 ~]$ which Rscript\n/usr/bin/which: no Rscript in (/cm/shared/apps/slurm/20.11.9/sbin:/cm/shared/apps/slurm/20.11.9/bin:/cm/local/apps/gcc/8.2.0/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/me/.local/bin:/home/me/bin)","type":"text"}]}]},{"type":"layoutColumn","attrs":{"width":50.0},"content":[{"type":"rule"},{"type":"paragraph","content":[{"text":"SHARK","type":"text","marks":[{"type":"strong"}]}]},{"type":"codeBlock","content":[{"text":"[me@res-hpc-lo02 ~]$ which Rscript\n/usr/bin/which: no Rscript in (/share/software/system/python/3.10.2/bin:/home/me/.local/bin:/home/me/bin:/opt/TurboVNC/bin:/opt/VirtualGL/bin:/share/software/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/me/.dotnet/tools)","type":"text"}]}]}]},{"type":"rule"},{"type":"paragraph","content":[{"text":"The list of paths in the brackets after “no Rscript in” comes from the environment variable ","type":"text"},{"text":"$PATH","type":"text","marks":[{"type":"code"}]},{"text":".","type":"text"}]},{"type":"paragraph","content":[{"text":"Let us first find the a module for ","type":"text"},{"text":"R","type":"text","marks":[{"type":"code"}]},{"text":" which contains the ","type":"text"},{"text":"Rscript","type":"text","marks":[{"type":"code"}]},{"text":" command","type":"text"}]},{"type":"layoutSection","content":[{"type":"layoutColumn","attrs":{"width":50.0},"content":[{"type":"rule"},{"type":"paragraph","content":[{"text":"ALICE","type":"text","marks":[{"type":"strong"}]}]},{"type":"codeBlock","content":[{"text":"[me@nodelogin02 ~]$ module -r avail '^R/'\n\n----------------------------------------------------------------------------- /cm/shared/easybuild/modules/all -----------------------------------------------------------------------------\n R/3.6.0-foss-2019a-Python-3.7.2 R/3.6.0-foss-2019a R/3.6.2-foss-2019b R/3.6.2-fosscuda-2019b R/4.0.0-foss-2020a R/4.0.5-foss-2020b (D)","type":"text"}]}]},{"type":"layoutColumn","attrs":{"width":50.0},"content":[{"type":"rule"},{"type":"paragraph","content":[{"text":"SHARK","type":"text","marks":[{"type":"strong"}]}]},{"type":"codeBlock","content":[{"text":"[me@res-hpc-lo02 ~]$ module -r avail '/R/'\n\n------------------------------------------------------------------------------------ /share/modulefiles ------------------------------------------------------------------------------------\n statistical/R/3.4.4/gcc.8.3.1 statistical/R/3.6.0/gcc.8.3.1 statistical/R/3.6.3/gcc.8.3.1 statistical/R/4.1.0/gcc.8.3.1\n statistical/R/3.5.3/gcc.8.3.1 statistical/R/3.6.2/gcc.8.3.1 statistical/R/4.0.2/gcc.8.3.1 statistical/R/4.1.2/gcc.8.3.1","type":"text"}]}]}]},{"type":"rule"},{"type":"paragraph","content":[{"text":"Now that we have found the module, we can load it, list all loaded modules just to make sure and check whether ","type":"text"},{"text":"Rscript","type":"text","marks":[{"type":"code"}]},{"text":" is now available:","type":"text"}]},{"type":"layoutSection","content":[{"type":"layoutColumn","attrs":{"width":50.0},"content":[{"type":"rule"},{"type":"paragraph","content":[{"text":"ALICE","type":"text","marks":[{"type":"strong"}]}]},{"type":"codeBlock","content":[{"text":"[schulzrf@nodelogin02 ~]$ module load R/4.0.5-foss-2020b\n[schulzrf@nodelogin02 ~]$ module list\n\nCurrently Loaded Modules:\n 1) shared 23) foss/2020b 45) gettext/0.21-GCCcore-10.2.0 67) Szip/2.1.1-GCCcore-10.2.0\n 2) DefaultModules 24) bzip2/1.0.8-GCCcore-10.2.0 46) PCRE/8.44-GCCcore-10.2.0 68) HDF5/1.10.7-gompi-2020b\n 3) gcc/8.2.0 25) expat/2.2.9-GCCcore-10.2.0 47) GLib/2.66.1-GCCcore-10.2.0 69) UDUNITS/2.2.26-GCCcore-10.2.0\n 4) slurm/20.11.9 26) libpng/1.6.37-GCCcore-10.2.0 48) cairo/1.16.0-GCCcore-10.2.0 70) GSL/2.6-GCC-10.2.0\n 5) GCCcore/10.2.0 27) Brotli/1.0.9-GCCcore-10.2.0 49) libreadline/8.0-GCCcore-10.2.0 71) Ghostscript/9.53.3-GCCcore-10.2.0\n 6) zlib/1.2.11-GCCcore-10.2.0 28) freetype/2.10.3-GCCcore-10.2.0 50) Tcl/8.6.10-GCCcore-10.2.0 72) JasPer/2.0.24-GCCcore-10.2.0\n 7) binutils/2.35-GCCcore-10.2.0 29) ncurses/6.2-GCCcore-10.2.0 51) SQLite/3.33.0-GCCcore-10.2.0 73) LittleCMS/2.11-GCCcore-10.2.0\n 8) GCC/10.2.0 30) util-linux/2.36-GCCcore-10.2.0 52) PCRE2/10.35-GCCcore-10.2.0 74) ImageMagick/7.0.10-35-GCCcore-10.2.0\n 9) numactl/2.0.13-GCCcore-10.2.0 31) fontconfig/2.13.92-GCCcore-10.2.0 53) NASM/2.15.05-GCCcore-10.2.0 75) GLPK/4.65-GCCcore-10.2.0\n 10) XZ/5.2.5-GCCcore-10.2.0 32) xorg-macros/1.19.2-GCCcore-10.2.0 54) libjpeg-turbo/2.0.5-GCCcore-10.2.0 76) nodejs/12.19.0-GCCcore-10.2.0\n 11) libxml2/2.9.10-GCCcore-10.2.0 33) X11/20201008-GCCcore-10.2.0 55) jbigkit/2.1-GCCcore-10.2.0 77) Python/3.8.6-GCCcore-10.2.0\n 12) libpciaccess/0.16-GCCcore-10.2.0 34) gzip/1.10-GCCcore-10.2.0 56) LibTIFF/4.1.0-GCCcore-10.2.0 78) netCDF/4.7.4-gompi-2020b\n 13) hwloc/2.2.0-GCCcore-10.2.0 35) lz4/1.9.2-GCCcore-10.2.0 57) Java/11.0.2 79) GEOS/3.9.1-GCC-10.2.0\n 14) libevent/2.1.12-GCCcore-10.2.0 36) zstd/1.4.5-GCCcore-10.2.0 58) Tk/8.6.10-GCCcore-10.2.0 80) PROJ/7.2.1-GCCcore-10.2.0\n 15) UCX/1.9.0-GCCcore-10.2.0 37) libdrm/2.4.102-GCCcore-10.2.0 59) cURL/7.72.0-GCCcore-10.2.0 81) libgeotiff/1.6.0-GCCcore-10.2.0\n 16) libfabric/1.11.0-GCCcore-10.2.0 38) libglvnd/1.3.2-GCCcore-10.2.0 60) GMP/6.2.0-GCCcore-10.2.0 82) pybind11/2.6.0-GCCcore-10.2.0\n 17) PMIx/3.1.5-GCCcore-10.2.0 39) libunwind/1.4.0-GCCcore-10.2.0 61) NLopt/2.6.2-GCCcore-10.2.0 83) SciPy-bundle/2020.11-foss-2020b\n 18) OpenMPI/4.0.5-GCC-10.2.0 40) LLVM/11.0.0-GCCcore-10.2.0 62) libogg/1.3.4-GCCcore-10.2.0 84) libtirpc/1.3.1-GCCcore-10.2.0\n 19) OpenBLAS/0.3.12-GCC-10.2.0 41) Mesa/20.2.1-GCCcore-10.2.0 63) FLAC/1.3.3-GCCcore-10.2.0 85) HDF/4.2.15-GCCcore-10.2.0\n 20) gompi/2020b 42) libGLU/9.0.1-GCCcore-10.2.0 64) libvorbis/1.3.7-GCCcore-10.2.0 86) GDAL/3.2.1-foss-2020b\n 21) FFTW/3.3.8-gompi-2020b 43) pixman/0.40.0-GCCcore-10.2.0 65) libsndfile/1.0.28-GCCcore-10.2.0 87) R/4.0.5-foss-2020b\n 22) ScaLAPACK/2.1.0-gompi-2020b 44) libffi/3.3-GCCcore-10.2.0 66) ICU/67.1-GCCcore-10.2.0\n \n[me@nodelogin02 ~]$ which Rscript\n/cm/shared/easybuild/GenuineIntel/software/R/4.0.5-foss-2020b/bin/Rscript","type":"text"}]},{"type":"panel","attrs":{"panelType":"warning"},"content":[{"type":"paragraph","content":[{"text":"While you can also just use ","type":"text"},{"text":"module load R","type":"text","marks":[{"type":"code"}]},{"text":", this is not recommended because this command will always load the default version of a module and the default may change when newer versions are being added.","type":"text"}]}]},{"type":"panel","attrs":{"panelType":"info"},"content":[{"type":"paragraph","content":[{"text":"On ALICE, the long list of modules is completely fine because the module R depends on several other modules which have to be loaded in order for R to properly work.","type":"text"}]}]}]},{"type":"layoutColumn","attrs":{"width":50.0},"content":[{"type":"rule"},{"type":"paragraph","content":[{"text":"SHARK","type":"text","marks":[{"type":"strong"}]}]},{"type":"codeBlock","content":[{"text":"[me@res-hpc-lo02 ~]$ module load statistical/R/4.1.2\n[me@res-hpc-lo02 ~]$ module list\n\nCurrently Loaded Modules:\n\nstatistical/R/4.1.2/gcc.8.3.1\n\n[em@res-hpc-lo02 ~]$ which Rscript\n/share/software/statistical/R/R-4.1.2/bin/Rscript","type":"text"}]}]}]},{"type":"rule"},{"type":"paragraph","content":[{"text":"So what just happened? To understand the output, first we need to understand the nature of the ","type":"text"},{"text":"$PATH","type":"text","marks":[{"type":"code"}]},{"text":" environment variable. ","type":"text"},{"text":"$PATH","type":"text","marks":[{"type":"code"}]},{"text":" is a special environment variable that controls where a Linux ","type":"text"},{"text":"operating system","type":"text","marks":[{"type":"em"}]},{"text":" (OS) looks for software. Specifically ","type":"text"},{"text":"$PATH","type":"text","marks":[{"type":"code"}]},{"text":" is a list of directories (separated by ","type":"text"},{"text":":","type":"text","marks":[{"type":"code"}]},{"text":") that the OS searches through for a command. As with all environment variables, we can print it using ","type":"text"},{"text":"echo","type":"text","marks":[{"type":"code"}]},{"text":".","type":"text"}]},{"type":"layoutSection","content":[{"type":"layoutColumn","attrs":{"width":50.0},"content":[{"type":"rule"},{"type":"paragraph","content":[{"text":"ALICE","type":"text","marks":[{"type":"strong"}]}]},{"type":"paragraph","content":[{"text":"This is how ","type":"text"},{"text":"$PATH","type":"text","marks":[{"type":"code"}]},{"text":" looks like after loading R on ALICE","type":"text"}]},{"type":"codeBlock","content":[{"text":"[me@nodelogin02 ~]$ echo $PATH\n/cm/shared/easybuild/GenuineIntel/software/R/4.0.5-foss-2020b/bin:/cm/shared/easybuild/GenuineIntel/software/GDAL/3.2.1-foss-2020b/bin:/cm/shared/easybuild/GenuineIntel/software/HDF/4.2.15-GCCcore-10.2.0/bin:/cm/shared/easybuild/GenuineIntel/software/SciPy-bundle/2020.11-foss-2020b/bin:/cm/shared/easybuild/GenuineIntel/software/pybind11/2.6.0-GCCcore-10.2.0/bin:/cm/shared/easybuild/GenuineIntel/software/libgeotiff/1.6.0-GCCcore-10.2.0/bin:/cm/shared/easybuild/GenuineIntel/software/PROJ/7.2.1-GCCcore-10.2.0/bin:/cm/shared/easybuild/GenuineIntel/software/GEOS/3.9.1-GCC-10.2.0/bin:/cm/shared/easybuild/GenuineIntel/software/netCDF/4.7.4-gompi-2020b/bin:/cm/shared/easybuild/GenuineIntel/software/Python/3.8.6-GCCcore-10.2.0/bin:/cm/shared/easybuild/GenuineIntel/software/nodejs/12.19.0-GCCcore-10.2.0/bin:/cm/shared/easybuild/GenuineIntel/software/GLPK/4.65-GCCcore-10.2.0/bin:/cm/shared/easybuild/GenuineIntel/software/ImageMagick/7.0.10-35-GCCcore-10.2.0/bin:/cm/shared/easybuild/GenuineIntel/software/LittleCMS/2.11-GCCcore-10.2.0/bin:/cm/shared/easybuild/GenuineIntel/software/JasPer/2.0.24-GCCcore-10.2.0/bin:/cm/shared/easybuild/GenuineIntel/software/Ghostscript/9.53.3-GCCcore-10.2.0/bin:/cm/shared/easybuild/GenuineIntel/software/GSL/2.6-GCC-10.2.0/bin:/cm/shared/easybuild/GenuineIntel/software/UDUNITS/2.2.26-GCCcore-10.2.0/bin:/cm/shared/easybuild/GenuineIntel/software/HDF5/1.10.7-gompi-2020b/bin:/cm/shared/easybuild/GenuineIntel/software/ICU/67.1-GCCcore-10.2.0/sbin:/cm/shared/easybuild/GenuineIntel/software/ICU/67.1-GCCcore-10.2.0/bin:/cm/shared/easybuild/GenuineIntel/software/libsndfile/1.0.28-GCCcore-10.2.0/bin:/cm/shared/easybuild/GenuineIntel/software/FLAC/1.3.3-GCCcore-10.2.0/bin:/cm/shared/easybuild/GenuineIntel/software/cURL/7.72.0-GCCcore-10.2.0/bin:/cm/shared/easybuild/GenuineIntel/software/Tk/8.6.10-GCCcore-10.2.0/bin:/cm/shared/easybuild/software/Java/11.0.2:/cm/shared/easybuild/software/Java/11.0.2/bin:/cm/shared/easybuild/GenuineIntel/software/LibTIFF/4.1.0-GCCcore-10.2.0/bin:/cm/shared/easybuild/GenuineIntel/software/jbigkit/2.1-GCCcore-10.2.0/bin:/cm/shared/easybuild/GenuineIntel/software/libjpeg-turbo/2.0.5-GCCcore-10.2.0/bin:/cm/shared/easybuild/GenuineIntel/software/NASM/2.15.05-GCCcore-10.2.0/bin:/cm/shared/easybuild/GenuineIntel/software/PCRE2/10.35-GCCcore-10.2.0/bin:/cm/shared/easybuild/GenuineIntel/software/SQLite/3.33.0-GCCcore-10.2.0/bin:/cm/shared/easybuild/GenuineIntel/software/Tcl/8.6.10-GCCcore-10.2.0/bin:/cm/shared/easybuild/GenuineIntel/software/cairo/1.16.0-GCCcore-10.2.0/bin:/cm/shared/easybuild/GenuineIntel/software/GLib/2.66.1-GCCcore-10.2.0/bin:/cm/shared/easybuild/GenuineIntel/software/PCRE/8.44-GCCcore-10.2.0/bin:/cm/shared/easybuild/GenuineIntel/software/gettext/0.21-GCCcore-10.2.0/bin:/cm/shared/easybuild/GenuineIntel/software/LLVM/11.0.0-GCCcore-10.2.0/bin:/cm/shared/easybuild/GenuineIntel/software/zstd/1.4.5-GCCcore-10.2.0/bin:/cm/shared/easybuild/GenuineIntel/software/lz4/1.9.2-GCCcore-10.2.0/bin:/cm/shared/easybuild/GenuineIntel/software/gzip/1.10-GCCcore-10.2.0/bin:/cm/shared/easybuild/GenuineIntel/software/X11/20201008-GCCcore-10.2.0/bin:/cm/shared/easybuild/GenuineIntel/software/fontconfig/2.13.92-GCCcore-10.2.0/bin:/cm/shared/easybuild/GenuineIntel/software/util-linux/2.36-GCCcore-10.2.0/sbin:/cm/shared/easybuild/GenuineIntel/software/util-linux/2.36-GCCcore-10.2.0/bin:/cm/shared/easybuild/software/ncurses/6.2-GCCcore-10.2.0/bin:/cm/shared/easybuild/GenuineIntel/software/freetype/2.10.3-GCCcore-10.2.0/bin:/cm/shared/easybuild/GenuineIntel/software/Brotli/1.0.9-GCCcore-10.2.0/bin:/cm/shared/easybuild/GenuineIntel/software/libpng/1.6.37-GCCcore-10.2.0/bin:/cm/shared/easybuild/GenuineIntel/software/expat/2.2.9-GCCcore-10.2.0/bin:/cm/shared/easybuild/GenuineIntel/software/bzip2/1.0.8-GCCcore-10.2.0/bin:/cm/shared/easybuild/GenuineIntel/software/FFTW/3.3.8-gompi-2020b/bin:/cm/shared/easybuild/GenuineIntel/software/OpenMPI/4.0.5-GCC-10.2.0/bin:/cm/shared/easybuild/GenuineIntel/software/PMIx/3.1.5-GCCcore-10.2.0/bin:/cm/shared/easybuild/GenuineIntel/software/libfabric/1.11.0-GCCcore-10.2.0/bin:/cm/shared/easybuild/GenuineIntel/software/UCX/1.9.0-GCCcore-10.2.0/bin:/cm/shared/easybuild/GenuineIntel/software/libevent/2.1.12-GCCcore-10.2.0/bin:/cm/shared/easybuild/GenuineIntel/software/hwloc/2.2.0-GCCcore-10.2.0/sbin:/cm/shared/easybuild/GenuineIntel/software/hwloc/2.2.0-GCCcore-10.2.0/bin:/cm/shared/easybuild/GenuineIntel/software/libxml2/2.9.10-GCCcore-10.2.0/bin:/cm/shared/easybuild/GenuineIntel/software/XZ/5.2.5-GCCcore-10.2.0/bin:/cm/shared/easybuild/GenuineIntel/software/numactl/2.0.13-GCCcore-10.2.0/bin:/cm/shared/easybuild/software/binutils/2.35-GCCcore-10.2.0/bin:/cm/shared/easybuild/software/GCCcore/10.2.0/bin:/cm/shared/apps/slurm/20.11.9/sbin:/cm/shared/apps/slurm/20.11.9/bin:/cm/local/apps/gcc/8.2.0/bin:/usr/lib/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/me/.local/bin:/home/me/bin","type":"text"}]}]},{"type":"layoutColumn","attrs":{"width":50.0},"content":[{"type":"rule"},{"type":"paragraph","content":[{"text":"SHARK","type":"text","marks":[{"type":"strong"}]}]},{"type":"paragraph","content":[{"text":"This is how ","type":"text"},{"text":"$PATH","type":"text","marks":[{"type":"code"}]},{"text":" looks like after loading R on SHARK","type":"text"}]},{"type":"codeBlock","content":[{"text":"[rfschulz@res-hpc-lo02 ~]$ echo $PATH\n/share/software/statistical/R/R-4.1.2/bin:/home/me/.local/bin:/home/me/bin:/opt/TurboVNC/bin:/opt/VirtualGL/bin:/share/software/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/me/.dotnet/tools","type":"text"}]}]}]},{"type":"rule"},{"type":"paragraph","content":[{"text":"After loading the module for R, the ","type":"text"},{"text":"$PATH","type":"text","marks":[{"type":"code"}]},{"text":" variable has been changed to include the directories holding executables of the newly loaded modules.","type":"text"}]},{"type":"paragraph","content":[{"text":"Taking this to its conclusion, ","type":"text"},{"text":"module load","type":"text","marks":[{"type":"code"}]},{"text":" adds software to your ","type":"text"},{"text":"$PATH","type":"text","marks":[{"type":"code"}]},{"text":". It “loads” software.","type":"text"}]},{"type":"panel","attrs":{"panelType":"warning"},"content":[{"type":"paragraph","content":[{"text":"Careful when you load several modules. It is possible that their dependencies can cause conflicts in particular with respect to different compilers which can create problems later on. It is best to always check what other modules have been automatically loaded.","type":"text"}]}]},{"type":"paragraph","content":[{"text":"Also a note of warning: When you load several modules, it is possible that their dependencies can cause conflicts and problems later on. It is best to always check what other modules have been automatically loaded.","type":"text"}]},{"type":"heading","attrs":{"level":1},"content":[{"text":"Unload modules","type":"text"}]},{"type":"paragraph","content":[{"text":"The command ","type":"text"},{"text":"module unload","type":"text","marks":[{"type":"code"}]},{"text":" “un-loads” a module. Using the above example of R","type":"text"}]},{"type":"layoutSection","content":[{"type":"layoutColumn","attrs":{"width":50.0},"content":[{"type":"rule"},{"type":"paragraph","content":[{"text":"ALICE","type":"text","marks":[{"type":"strong"}]}]},{"type":"codeBlock","content":[{"text":"[m@nodelogin02 ~]$ module unload R/4.0.5-foss-2020b\n[me@nodelogin02 ~]$ module list\n\nCurrently Loaded Modules:\n 1) shared 23) foss/2020b 45) gettext/0.21-GCCcore-10.2.0 67) HDF5/1.10.7-gompi-2020b\n 2) DefaultModules 24) bzip2/1.0.8-GCCcore-10.2.0 46) PCRE/8.44-GCCcore-10.2.0 68) UDUNITS/2.2.26-GCCcore-10.2.0\n 3) gcc/8.2.0 25) expat/2.2.9-GCCcore-10.2.0 47) GLib/2.66.1-GCCcore-10.2.0 69) GSL/2.6-GCC-10.2.0\n 4) slurm/20.11.9 26) libpng/1.6.37-GCCcore-10.2.0 48) cairo/1.16.0-GCCcore-10.2.0 70) Ghostscript/9.53.3-GCCcore-10.2.0\n 5) GCCcore/10.2.0 27) Brotli/1.0.9-GCCcore-10.2.0 49) libreadline/8.0-GCCcore-10.2.0 71) JasPer/2.0.24-GCCcore-10.2.0\n 6) zlib/1.2.11-GCCcore-10.2.0 28) freetype/2.10.3-GCCcore-10.2.0 50) Tcl/8.6.10-GCCcore-10.2.0 72) LittleCMS/2.11-GCCcore-10.2.0\n 7) binutils/2.35-GCCcore-10.2.0 29) ncurses/6.2-GCCcore-10.2.0 51) SQLite/3.33.0-GCCcore-10.2.0 73) ImageMagick/7.0.10-35-GCCcore-10.2.0\n 8) GCC/10.2.0 30) util-linux/2.36-GCCcore-10.2.0 52) PCRE2/10.35-GCCcore-10.2.0 74) GLPK/4.65-GCCcore-10.2.0\n 9) numactl/2.0.13-GCCcore-10.2.0 31) fontconfig/2.13.92-GCCcore-10.2.0 53) NASM/2.15.05-GCCcore-10.2.0 75) nodejs/12.19.0-GCCcore-10.2.0\n 10) XZ/5.2.5-GCCcore-10.2.0 32) xorg-macros/1.19.2-GCCcore-10.2.0 54) libjpeg-turbo/2.0.5-GCCcore-10.2.0 76) Python/3.8.6-GCCcore-10.2.0\n 11) libxml2/2.9.10-GCCcore-10.2.0 33) X11/20201008-GCCcore-10.2.0 55) jbigkit/2.1-GCCcore-10.2.0 77) netCDF/4.7.4-gompi-2020b\n 12) libpciaccess/0.16-GCCcore-10.2.0 34) gzip/1.10-GCCcore-10.2.0 56) LibTIFF/4.1.0-GCCcore-10.2.0 78) GEOS/3.9.1-GCC-10.2.0\n 13) hwloc/2.2.0-GCCcore-10.2.0 35) lz4/1.9.2-GCCcore-10.2.0 57) Tk/8.6.10-GCCcore-10.2.0 79) PROJ/7.2.1-GCCcore-10.2.0\n 14) libevent/2.1.12-GCCcore-10.2.0 36) zstd/1.4.5-GCCcore-10.2.0 58) cURL/7.72.0-GCCcore-10.2.0 80) libgeotiff/1.6.0-GCCcore-10.2.0\n 15) UCX/1.9.0-GCCcore-10.2.0 37) libdrm/2.4.102-GCCcore-10.2.0 59) GMP/6.2.0-GCCcore-10.2.0 81) pybind11/2.6.0-GCCcore-10.2.0\n 16) libfabric/1.11.0-GCCcore-10.2.0 38) libglvnd/1.3.2-GCCcore-10.2.0 60) NLopt/2.6.2-GCCcore-10.2.0 82) SciPy-bundle/2020.11-foss-2020b\n 17) PMIx/3.1.5-GCCcore-10.2.0 39) libunwind/1.4.0-GCCcore-10.2.0 61) libogg/1.3.4-GCCcore-10.2.0 83) libtirpc/1.3.1-GCCcore-10.2.0\n 18) OpenMPI/4.0.5-GCC-10.2.0 40) LLVM/11.0.0-GCCcore-10.2.0 62) FLAC/1.3.3-GCCcore-10.2.0 84) HDF/4.2.15-GCCcore-10.2.0\n 19) OpenBLAS/0.3.12-GCC-10.2.0 41) Mesa/20.2.1-GCCcore-10.2.0 63) libvorbis/1.3.7-GCCcore-10.2.0 85) GDAL/3.2.1-foss-2020b\n 20) gompi/2020b 42) libGLU/9.0.1-GCCcore-10.2.0 64) libsndfile/1.0.28-GCCcore-10.2.0\n 21) FFTW/3.3.8-gompi-2020b 43) pixman/0.40.0-GCCcore-10.2.0 65) ICU/67.1-GCCcore-10.2.0\n 22) ScaLAPACK/2.1.0-gompi-2020b 44) libffi/3.3-GCCcore-10.2.0 66) Szip/2.1.1-GCCcore-10.2.0","type":"text"}]},{"type":"paragraph","content":[{"text":"As you can see, the module for R was “unloaded”.","type":"text"}]}]},{"type":"layoutColumn","attrs":{"width":50.0},"content":[{"type":"rule"},{"type":"paragraph","content":[{"text":"SHARK","type":"text","marks":[{"type":"strong"}]}]},{"type":"codeBlock","content":[{"text":"[me@res-hpc-lo02 ~]$ module unload statistical/R/4.1.2/gcc.8.3.1\n[me@res-hpc-lo02 ~]$ module list\nNo modules loaded","type":"text"}]}]}]},{"type":"rule"},{"type":"panel","attrs":{"panelType":"warning"},"content":[{"type":"paragraph","content":[{"text":"IMPORTANT: Unloading a module does not unload its dependencies.","type":"text"}]}]},{"type":"paragraph","content":[{"text":"If you want to unload all currently loaded modules, you can use the command ","type":"text"},{"text":"module purge","type":"text","marks":[{"type":"code"}]},{"text":".","type":"text"}]},{"type":"panel","attrs":{"panelType":"warning"},"content":[{"type":"paragraph","content":[{"text":"For ALICE users","type":"text"}]},{"type":"paragraph","content":[{"text":"Using ","type":"text"},{"text":"module purge","type":"text","marks":[{"type":"code"}]},{"text":" will also remove the module for Slurm, but you can quickly load it again by running ","type":"text"},{"text":"module load slurm","type":"text","marks":[{"type":"code"}]},{"text":" (There is only one version of slurm available on the cluster, so no need to specify the version here)","type":"text"}]}]},{"type":"panel","attrs":{"panelType":"info"},"content":[{"type":"paragraph","content":[{"text":"Pro tip","type":"text"}]},{"type":"paragraph","content":[{"text":"You can also use ","type":"text"},{"text":"module purge","type":"text","marks":[{"type":"code"}]},{"text":" in your batch script before loading the modules that you need in order to make sure that no other modules can interfere with your job environment.","type":"text"}]}]},{"type":"heading","attrs":{"level":1},"content":[{"text":"Saving and restoring (default) modules","type":"text"}]},{"type":"paragraph","content":[{"text":"If you work with a standard set of modules quite a lot, you can save and restore to the list of modules at any time.","type":"text"}]},{"type":"paragraph","content":[{"text":"Let’s start from a clean module environment:","type":"text"}]},{"type":"codeBlock","content":[{"text":"module purge","type":"text"}]},{"type":"layoutSection","content":[{"type":"layoutColumn","attrs":{"width":50.0},"content":[{"type":"rule"},{"type":"paragraph","content":[{"text":"ALICE","type":"text","marks":[{"type":"strong"}]}]},{"type":"panel","attrs":{"panelType":"warning"},"content":[{"type":"paragraph","content":[{"text":"On ALICE, you should always include the module ","type":"text"},{"text":"slurm","type":"text","marks":[{"type":"code"}]},{"text":". Otherwise, you will not be able to access Slurm commands when you restore the module environment","type":"text"}]}]},{"type":"paragraph","content":[{"text":"Load a set of modules and save them as default","type":"text"}]},{"type":"codeBlock","content":[{"text":"[me@nodelogin02 ~]$ module load slurm Python/3.10.4-GCCcore-11.3.0 git/2.36.0-GCCcore-11.3.0-nodocs\n[me@nodelogin02 ~]$ module save\nSaved current collection of modules to: \"default\"","type":"text"}]},{"type":"paragraph","content":[{"text":"If you need to restore them:","type":"text"}]},{"type":"codeBlock","content":[{"text":"[me@nodelogin02 ~]$ module restore\nRestoring modules from user's default","type":"text"}]},{"type":"paragraph","content":[{"text":"To test the effect of restoring them, either load another module or purge the module environment. You can check with ","type":"text"},{"text":"module list","type":"text","marks":[{"type":"code"}]},{"text":" that the default modules have been loaded.","type":"text"}]},{"type":"paragraph","content":[{"text":"You can can also define multiple different module environments by specifying a name when saving the module list:","type":"text"}]},{"type":"codeBlock","content":[{"text":"[me@nodelogin02 ~]$ module load slurm Python/3.10.4-GCCcore-11.3.0 git/2.36.0-GCCcore-11.3.0-nodocs\n[me@nodelogin02 ~]$ module save python\nSaved current collection of modules to: \"python\"","type":"text"}]},{"type":"paragraph","content":[{"text":"And restoring works like this:","type":"text"}]},{"type":"codeBlock","content":[{"text":"[me@nodelogin02 ~]$ module restore python\nRestoring modules from user's python","type":"text"}]}]},{"type":"layoutColumn","attrs":{"width":50.0},"content":[{"type":"rule"},{"type":"paragraph","content":[{"text":"SHARK","type":"text","marks":[{"type":"strong"}]}]},{"type":"paragraph","content":[{"text":"Load a set of modules and save them as default","type":"text"}]},{"type":"codeBlock","content":[{"text":"[me@res-hpc-lo02 ~]$ module load system/python/3.10.2\n[me@res-hpc-lo02 ~]$ module save\nSaved current collection of modules to: \"default\"","type":"text"}]},{"type":"paragraph","content":[{"text":"If you need to restore them:","type":"text"}]},{"type":"codeBlock","content":[{"text":"[me@res-hpc-lo02 ~]$ module restore\nRestoring modules from user's default","type":"text"}]},{"type":"paragraph","content":[{"text":"To test the effect of restoring them, either load another module or purge the module environment. You can check with ","type":"text"},{"text":"module list","type":"text","marks":[{"type":"code"}]},{"text":" that the default modules have been loaded.","type":"text"}]},{"type":"paragraph","content":[{"text":"You can can also define multiple different module environments by specifying a name when saving the module list:","type":"text"}]},{"type":"codeBlock","content":[{"text":"[me@res-hpc-lo02 ~]$ module load system/python/3.10.2\n[me@res-hpc-lo02 ~]$ module save python\nSaved current collection of modules to: \"python\"","type":"text"}]},{"type":"paragraph","content":[{"text":"And restoring works like this:","type":"text"}]},{"type":"codeBlock","content":[{"text":"[me@res-hpc-lo02 ~]$ module restore python\nRestoring modules from user's python","type":"text"}]}]}]},{"type":"rule"},{"type":"panel","attrs":{"panelType":"warning"},"content":[{"type":"paragraph","content":[{"text":"Note that using ","type":"text"},{"text":"module restore","type":"text","marks":[{"type":"code"}]},{"text":" in your batch scripts has an impact on the reproducibility of your batch scripts. When you want to check later on what modules (and versions) were loaded for a job, this information is no longer available in your batch script.","type":"text"}]},{"type":"paragraph","content":[{"text":"If you want to make use of ","type":"text"},{"text":"module restore","type":"text","marks":[{"type":"code"}]},{"text":", we recommend to add the command ","type":"text"},{"text":"module list","type":"text","marks":[{"type":"code"}]},{"text":" after the restore command in your batch script. This way, the Slurm output file for the job will contain the list of modules and versions used.","type":"text"}]}]},{"type":"panel","attrs":{"panelType":"warning"},"content":[{"type":"paragraph","content":[{"text":"The command ","type":"text"},{"text":"module save","type":"text","marks":[{"type":"code"}]},{"text":" will always save the full list of modules with the version used even if you loaded the modules without specifying a version.","type":"text"}]}]},{"type":"paragraph","content":[{"text":"You can get a full list of saved module environments like this:","type":"text"}]},{"type":"codeBlock","content":[{"text":"module savelist","type":"text"}]},{"type":"paragraph","content":[{"text":"Disabling an saved collection of modules can be done with ","type":"text"}]},{"type":"codeBlock","content":[{"text":"module disable ","type":"text"}]},{"type":"paragraph","content":[{"text":"where ","type":"text"},{"text":"","type":"text","marks":[{"type":"code"}]},{"text":" should be replaced by the name of the collection. This will not entirely remove the file though. This has to be done manually.","type":"text"}]},{"type":"paragraph","content":[{"text":"The various collections of modules are stored in your home directory in: ","type":"text"},{"text":"~/.lmod.d","type":"text","marks":[{"type":"code"}]}]},{"type":"paragraph"}],"version":1}

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