{"type":"doc","content":[{"type":"extension","attrs":{"layout":"default","extensionType":"com.atlassian.confluence.macro.core","extensionKey":"toc","parameters":{"macroParams":{"minLevel":{"value":"1"},"maxLevel":{"value":"3"},"outline":{"value":"false"},"style":{"value":"none"},"type":{"value":"list"},"printable":{"value":"true"}},"macroMetadata":{"macroId":{"value":"e83e71a8-6699-4267-abfd-648c429d9808"},"schemaVersion":{"value":"1"},"title":"Table of Contents"}},"localId":"7da47ff8-d1b7-42b3-9d78-63e2bf438414"}},{"type":"paragraph","content":[{"text":"Local module is a beneficial approach to efficiently organize your self-installed libraries. Additionally, ","type":"text"},{"text":"EasyBuild","type":"text","marks":[{"type":"link","attrs":{"href":"https://github.com/easybuilders/easybuild"}}]},{"text":" serves as a framework for building and installing software, particularly those with dependencies. The following sections provide general guidelines on how to use local modules and EasyBuild to install and run software on LANTA.","type":"text"}]},{"type":"paragraph","content":[{"text":"Updated: May 2024","type":"text"}]},{"type":"rule"},{"type":"heading","attrs":{"level":3},"content":[{"text":"0. Define local module command ","type":"text"},{"text":"(only once)","type":"text","marks":[{"type":"textColor","attrs":{"color":"#bf2600"}}]}]},{"type":"paragraph","content":[{"text":"To utilize local modules, we suggest creating a bash command such as ","type":"text"},{"text":"localmod","type":"text","marks":[{"type":"code"}]},{"text":" that contains essential setup within your ","type":"text"},{"text":"$HOME/.bashrc","type":"text","marks":[{"type":"code"}]},{"text":". The provided set of commands below will create a local module directory based on ","type":"text"},{"text":"LOCALMOD_DIR","type":"text","marks":[{"type":"code"}]},{"text":" and then define the ","type":"text"},{"text":"localmod","type":"text","marks":[{"type":"code"}]},{"text":" command in your ","type":"text"},{"text":"$HOME/.bashrc","type":"text","marks":[{"type":"code"}]},{"text":".","type":"text"}]},{"type":"paragraph","content":[{"text":"This ","type":"text","marks":[{"type":"strong"}]},{"text":"localmod","type":"text","marks":[{"type":"code"}]},{"text":" command is needed to be executed to activate local modules","type":"text","marks":[{"type":"strong"}]},{"text":", before installing software in ","type":"text"},{"text":"Step 1","type":"text","marks":[{"type":"link","attrs":{"href":"https://thaisc.atlassian.net/wiki/spaces/~6278ba6723d61e006fc39e39/pages/290783233/Local+module+EasyBuild#1.-Prepare-environment"}}]},{"text":" and before using local modules in your job script (see ","type":"text"},{"text":"below","type":"text","marks":[{"type":"link","attrs":{"href":"https://thaisc.atlassian.net/wiki/spaces/~6278ba6723d61e006fc39e39/pages/290783233/Local+module+EasyBuild#5.-Example%3A-Job-script-template-for-local-modules"}}]},{"text":").","type":"text"}]},{"type":"codeBlock","attrs":{"language":"shell"},"content":[{"text":"LOCALMOD_DIR=$HOME/localmod # *** EDITABLE, set to an empty path ***\n\nmkdir -p ${LOCALMOD_DIR} # Create the directory if not already exist\ncat << Eof >> $HOME/.bashrc # Define the below \"localmod\" function in your .bashrc\nfunction localmod(){\n export EASYBUILD_PREFIX=${LOCALMOD_DIR} \n module use \\${EASYBUILD_PREFIX}/modules/all\n export EASYBUILD_OPTARCH=x86-milan\n echo \"*** Import modules at \\${EASYBUILD_PREFIX} on LANTA ***\"\n}\nEof","type":"text"}]},{"type":"expand","attrs":{"title":"Note & Check"},"content":[{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"If you copy the above ","type":"text"},{"text":"localmod","type":"text","marks":[{"type":"code"}]},{"text":" function directly and paste it in your ","type":"text"},{"text":".bashrc","type":"text","marks":[{"type":"code"}]},{"text":", don’t forget to remove ","type":"text"},{"text":"\\","type":"text","marks":[{"type":"code"}]},{"text":" before ","type":"text"},{"text":"$","type":"text","marks":[{"type":"code"}]},{"text":".","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"After this step, if you execute ","type":"text"},{"text":"cat $HOME/.bashrc","type":"text","marks":[{"type":"code"}]},{"text":", the output should contain.","type":"text"}]},{"type":"codeBlock","attrs":{"language":"shell"},"content":[{"text":"function localmod(){\n export EASYBUILD_PREFIX= \n module use ${EASYBUILD_PREFIX}/modules/all\n export EASYBUILD_OPTARCH=x86-milan\n echo \"*** Import modules at ${EASYBUILD_PREFIX} on LANTA ***\"\n}","type":"text"}]}]}]}]},{"type":"expand","attrs":{"title":"More explanation"},"content":[{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"module use","type":"text","marks":[{"type":"code"}]},{"text":" will import extra modules to your Lmod system, i.e., ","type":"text"},{"text":"MODULEPATH","type":"text","marks":[{"type":"code"}]},{"text":".","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"EASYBUILD_PREFIX","type":"text","marks":[{"type":"code"}]},{"text":" variable is for setting default paths when using EasyBuild. ","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"EASYBUILD_OPTARCH","type":"text","marks":[{"type":"code"}]},{"text":" variable must be set to ","type":"text"},{"text":"x86-milan","type":"text","marks":[{"type":"code"}]},{"text":" to be consistent with LANTA hardware.","type":"text"}]}]}]}]},{"type":"expand","attrs":{"title":"Shared local modules among project members"},"content":[{"type":"paragraph","content":[{"text":"LOCALMOD_DIR","type":"text","marks":[{"type":"code"}]},{"text":" could be set to any preferred directory. To share your local modules with your project members, you could use a directory in your project path, like ","type":"text"},{"text":"LOCALMOD_DIR=/project/ltxxxxxx-yyyyyy/localmod","type":"text","marks":[{"type":"code"}]},{"text":", for example. ","type":"text"}]},{"type":"paragraph","content":[{"text":"By default, only you, the person who create the directory, have permission to install modules in it. However, your project members can access and use your modules by executing ","type":"text"},{"text":"module use /project/ltxxxxxx-yyyyyy/localmod/modules/all","type":"text","marks":[{"type":"code"}]},{"text":" directly or by setting the ","type":"text"},{"text":"localmod","type":"text","marks":[{"type":"code"}]},{"text":" command with the same ","type":"text"},{"text":"LOCALMOD_DIR","type":"text","marks":[{"type":"code"}]},{"text":" as you have done.","type":"text"}]}]},{"type":"panel","attrs":{"panelType":"warning"},"content":[{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"You need to ","type":"text"},{"text":"re-login","type":"text","marks":[{"type":"strong"}]},{"text":" or execute ","type":"text"},{"text":"source $HOME/.bashrc","type":"text","marks":[{"type":"code"}]},{"text":" for the changes to take effects.","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"The above step needs to be done ","type":"text"},{"text":"only once","type":"text","marks":[{"type":"underline"}]},{"text":".","type":"text"}]}]}]}]},{"type":"heading","attrs":{"level":3},"content":[{"text":"1. Prepare environment","type":"text"}]},{"type":"panel","attrs":{"panelType":"note"},"content":[{"type":"paragraph","content":[{"text":"To install a new software, it is strongly recommended to clean your environment by re-login or open a new bash session, then execute ","type":"text"},{"text":"module purge","type":"text","marks":[{"type":"code"}]},{"text":".","type":"text"}]}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Enable local module by executing the command defined in ","type":"text"},{"text":"Step 0","type":"text","marks":[{"type":"link","attrs":{"href":"https://thaisc.atlassian.net/wiki/spaces/~6278ba6723d61e006fc39e39/pages/290783233/Local+module+EasyBuild#0.-Define-local-module-command"}}]},{"text":" → ","type":"text"},{"text":"localmod","type":"text","marks":[{"type":"code"}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Load EasyBuild → ","type":"text"},{"text":"module load EasyBuild","type":"text","marks":[{"type":"code"}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Check your current EasyBuild configuration → ","type":"text"},{"text":"eb --show-config","type":"text","marks":[{"type":"code"}]},{"type":"hardBreak"},{"text":"Note: the ","type":"text"},{"text":"installpath","type":"text","marks":[{"type":"code"}]},{"text":" should be set to a local directory that you have write permission.","type":"text"}]}]}]},{"type":"codeBlock","attrs":{"language":"shell"},"content":[{"text":"localmod\nmodule load EasyBuild/4.7.0\neb --show-config","type":"text"}]},{"type":"panel","attrs":{"panelType":"warning"},"content":[{"type":"paragraph","content":[{"text":"Only ","type":"text"},{"text":"EasyBuild/4.7.0","type":"text","marks":[{"type":"code"}]},{"text":" recognizes the CPE toolchains (cpeXXX) at the moment. ","type":"text"}]}]},{"type":"heading","attrs":{"level":3},"content":[{"text":"2. Get EasyConfig file","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Visit ","type":"text"},{"text":"EasyConfig Standard Repo","type":"text","marks":[{"type":"link","attrs":{"href":"https://github.com/easybuilders/easybuild-easyconfigs/tree/develop/easybuild/easyconfigs"}}]},{"text":" or other repositories.","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Download the latest .eb file of the software that you would like to install, then rename it to","type":"text"},{"type":"hardBreak"},{"text":"---.eb","type":"text","marks":[{"type":"code"}]},{"text":" ","type":"text"},{"type":"hardBreak"},{"text":"where CPE toolchain name is ","type":"text"},{"text":"cpeGNU","type":"text","marks":[{"type":"code"}]},{"text":", ","type":"text"},{"text":"cpeIntel","type":"text","marks":[{"type":"code"}]},{"text":", ","type":"text"},{"text":"cpeCray","type":"text","marks":[{"type":"code"}]},{"text":" or others, corresponding to the compiler that you would like to use. For their available version, use ","type":"text"},{"text":"module spider cpeXXX","type":"text","marks":[{"type":"code"}]},{"text":" or see ","type":"text"},{"text":"Current CPE toolchains","type":"text","marks":[{"type":"link","attrs":{"href":"https://thaisc.atlassian.net/wiki/spaces/~6278ba6723d61e006fc39e39/pages/374407170/Software+installation+guideline#1.2-ThaiSC-pre-built-modules"}}]},{"text":".","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"For example, download ","type":"text"},{"text":"giflib-5.2.1-GCCcore-13.2.0.eb","type":"text","marks":[{"type":"code"}]},{"text":" and rename it to ","type":"text"},{"text":"giflib-5.2.1-cpeCray-23.03.eb","type":"text","marks":[{"type":"code"}]}]}]}]},{"type":"expand","attrs":{"title":"Extra note"},"content":[{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Employing the CPE toolchain with the same compiler as utilized in the original EasyConfig file should minimize potential issues and changes in Step 3. 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Edit EasyConfig file","type":"text"}]},{"type":"paragraph","content":[{"text":"Open the .eb file using a text editor such as ","type":"text"},{"text":"vi","type":"text","marks":[{"type":"code"}]},{"text":", then edit the following","type":"text"}]},{"type":"orderedList","attrs":{"order":1},"content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"toolchain","type":"text","marks":[{"type":"strong"}]},{"type":"hardBreak"},{"text":"Correct the toolchain information, e.g., ","type":"text"},{"text":"toolchain = {'name': 'cpeCray', 'version': '23.03'}","type":"text","marks":[{"type":"code"}]},{"text":". This must be consistent with the CPE toolchain and file name chosen in ","type":"text"},{"text":"Step 2","type":"text","marks":[{"type":"link","attrs":{"href":"https://thaisc.atlassian.net/wiki/spaces/~6278ba6723d61e006fc39e39/pages/290783233/Local+module+EasyBuild#2.-Get-EasyConfig-file"}}]},{"text":".","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"builddependencies","type":"text","marks":[{"type":"strong"}]},{"text":" and/or ","type":"text"},{"text":"dependencies","type":"text","marks":[{"type":"strong"}]},{"type":"hardBreak"},{"text":"Check if the software dependencies are available in ","type":"text"},{"text":"ThaiSC modules","type":"text","marks":[{"type":"link","attrs":{"href":"https://thaisc.atlassian.net/wiki/spaces/LANTA/pages/383582209/Software+installation+guideline#ThaiSC-modules"}}]},{"text":" by using ","type":"text"},{"text":"module spider ","type":"text","marks":[{"type":"code"}]},{"text":".","type":"text"},{"type":"hardBreak"},{"text":"For example, ","type":"text"},{"text":"module spider binutils","type":"text","marks":[{"type":"code"}]},{"text":". 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The default will use the same toolchain as in Step 3.1 without any suffix. This is recommended. 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This is to ensure that they are consistent across your module chain. A summary table is provided below. ","type":"text"},{"type":"hardBreak"},{"text":"Additionally, you have to sort ","type":"text"},{"text":"cray-*","type":"text","marks":[{"type":"code"}]},{"text":" modules according to its hierarchy as well (","type":"text"},{"text":"see","type":"text","marks":[{"type":"link","attrs":{"href":"https://thaisc.atlassian.net/wiki/spaces/~6278ba6723d61e006fc39e39/pages/374407170/Software+installation+guideline#Cray-optimized-libraries"}}]},{"text":").","type":"text"}]}]}]},{"type":"table","attrs":{"layout":"default","width":760.0,"localId":"57562a73-637e-43e0-8d29-afcae37df0ea"},"content":[{"type":"tableRow","content":[{"type":"tableHeader","attrs":{"colspan":1,"rowspan":1},"content":[{"type":"paragraph","marks":[{"type":"alignment","attrs":{"align":"center"}}],"content":[{"text":"cray-* 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Install the software","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Execute ","type":"text"},{"text":"eb -D --robot-paths=$(pwd) .eb","type":"text","marks":[{"type":"code"}]},{"text":" to do a short dry run and check for dependencies. ","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"If the command run successfully, it will display build status of the software’s dependencies. 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","type":"text"},{"text":"That is, you need to repeatedly do Step 2 and 3 for all unavailable dependencies required by the target software, and put them in the same directory.","type":"text","marks":[{"type":"underline"}]}]}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"To install the software, execute ","type":"text"}]},{"type":"codeBlock","attrs":{"language":"shell"},"content":[{"text":"eb -r --robot-paths=$(pwd) --parallel=1 --trace --tmpdir=$(pwd) .eb","type":"text"}]}]}]},{"type":"expand","attrs":{"title":"More explanation"},"content":[{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"-D","type":"text","marks":[{"type":"code"}]},{"text":" : ","type":"text"},{"type":"hardBreak"},{"text":"Do a short dry run to check EasyConfig hierarchy. 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","type":"text"},{"type":"hardBreak"},{"text":"Note: you may use ","type":"text"},{"text":"-r $(pwd)","type":"text","marks":[{"type":"code"}]},{"text":" instead of ","type":"text"},{"text":"-r --robot-paths=$(pwd)","type":"text","marks":[{"type":"code"}]},{"text":".","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"--parallel=N","type":"text","marks":[{"type":"code"}]},{"text":": ","type":"text"},{"type":"hardBreak"},{"text":"Build the software using ","type":"text"},{"text":"N","type":"text","marks":[{"type":"code"}]},{"text":" CPU cores, e.g., ","type":"text"},{"text":"make -j N","type":"text","marks":[{"type":"code"}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"--trace --tmpdir=$(pwd)","type":"text","marks":[{"type":"code"}]},{"text":": (Optional) ","type":"text"},{"type":"hardBreak"},{"text":"Provide more information on progress and save logs to the current path. Recommend using them together.","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"For more information, execute ","type":"text"},{"text":"eb --help","type":"text","marks":[{"type":"code"}]},{"text":", ","type":"text"},{"text":"eb -a","type":"text","marks":[{"type":"code"}]},{"text":" and others in ","type":"text"},{"text":"eb --help | grep 'avail'","type":"text","marks":[{"type":"code"}]}]}]}]}]},{"type":"panel","attrs":{"panelType":"warning"},"content":[{"type":"paragraph","content":[{"text":"--parallel=N","type":"text","marks":[{"type":"code"}]},{"text":" where ","type":"text"},{"text":"N<8","type":"text","marks":[{"type":"code"}]},{"text":" is essential since the default 128 would put a burden on the frontend node, prompting admins to kill your process. ","type":"text"}]},{"type":"paragraph","content":[{"text":"Some software may not support parallel build; therefore, ","type":"text"},{"text":"--parallel=1","type":"text","marks":[{"type":"code"}]},{"text":" is recommended.","type":"text"}]}]},{"type":"heading","attrs":{"level":3},"content":[{"text":"5. Job script template for using local modules","type":"text"}]},{"type":"panel","attrs":{"panelType":"note"},"content":[{"type":"paragraph","content":[{"text":"Use ","type":"text"},{"text":"module --ignore-cache avail","type":"text","marks":[{"type":"code"}]},{"text":" to check if the module is available. ","type":"text"}]}]},{"type":"panel","attrs":{"panelType":"warning"},"content":[{"type":"paragraph","content":[{"text":"Don’t forget to enable local module by executing the ","type":"text"},{"text":"localmod","type":"text","marks":[{"type":"code"}]},{"text":" command defined in ","type":"text"},{"text":"Step 0","type":"text","marks":[{"type":"link","attrs":{"href":"https://thaisc.atlassian.net/wiki/spaces/~6278ba6723d61e006fc39e39/pages/290783233/Local+module+EasyBuild#0.-Define-local-module-command"}}]}]}]},{"type":"codeBlock","attrs":{"language":"shell"},"content":[{"text":"#!/bin/bash\n#SBATCH -p compute # Partition\n#SBATCH -N 1 # Number of nodes\n#SBATCH --ntasks-per-node=128 # Number of MPI processes per node\n#SBATCH --cpus-per-task=1 # Number of OpenMP threads per MPI process\n#SBATCH -t 5-00:00:00 # Job runtime limit\n#SBATCH -J MyJob # Job name\n#SBATCH -A ltxxxxxx # Account *** {USER EDIT} *** \n\nsource $HOME/.bashrc\nlocalmod\n\nmodule purge\nmodule load \n\nexport OMP_NUM_THREADS=${SLURM_CPUS_PER_TASK}\n\nsrun -c${SLURM_CPUS_PER_TASK} ","type":"text"}]},{"type":"rule"},{"type":"paragraph","content":[{"text":"Reference","type":"text","marks":[{"type":"strong"}]}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"type":"inlineCard","attrs":{"url":"https://docs.easybuild.io/writing-easyconfig-files/"}},{"text":" ","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"type":"inlineCard","attrs":{"url":"https://mdc-easybuild.readthedocs.io/en/eb462/version-specific/easyconfig_parameters.html"}},{"text":" ","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"type":"inlineCard","attrs":{"url":"https://ulhpc-tutorials.readthedocs.io/en/latest/tools/easybuild/"}},{"text":" ","type":"text"}]}]}]},{"type":"paragraph","content":[{"text":"EasyConfig repositories","type":"text","marks":[{"type":"strong"}]}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"type":"inlineCard","attrs":{"url":"https://github.com/easybuilders/easybuild-easyconfigs/tree/develop/easybuild/easyconfigs"}},{"text":" ","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"type":"inlineCard","attrs":{"url":"https://github.com/Lumi-supercomputer/LUMI-EasyBuild-contrib/tree/main/easybuild/easyconfigs"}},{"text":" (Software may be in a different name.)","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"type":"inlineCard","attrs":{"url":"https://github.com/eth-cscs/production/tree/master/easybuild/easyconfigs"}},{"text":" (Software may be in a different name.)","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"type":"inlineCard","attrs":{"url":"https://github.com/hpc-unibe-ch/ubelix-easyconfigs"}},{"text":" ","type":"text"}]}]}]}],"version":1}

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