tech:slurm
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tech:slurm [2021/03/19 12:14] – kohofer | tech:slurm [2022/11/24 16:17] (current) – [Compute Nodes] kohofer | ||
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===== Installation ===== | ===== Installation ===== | ||
+ | |||
===== Controller name: slurm-ctrl ===== | ===== Controller name: slurm-ctrl ===== | ||
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debug* | debug* | ||
- | If computer node is **<color # | + | If computer node is <color # |
< | < | ||
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PARTITION AVAIL TIMELIMIT | PARTITION AVAIL TIMELIMIT | ||
debug* | debug* | ||
+ | </ | ||
+ | |||
+ | < | ||
+ | sinfo -o " | ||
+ | NODELIST | ||
+ | gpu[02-03] | ||
+ | gpu04 | ||
+ | hpcmoi01, | ||
</ | </ | ||
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chown root: / | chown root: / | ||
- | | + | |
+ | === Directories === | ||
+ | |||
+ | Be sure that the nfs mounted partitions are, all there: | ||
+ | |||
+ | < | ||
+ | /data | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | /scratch | ||
+ | </ | ||
===== Modify user accounts ===== | ===== Modify user accounts ===== | ||
+ | |||
+ | Display the accounts created: | ||
+ | |||
+ | # Show also associations in the accounts | ||
+ | sacctmgr show account -s | ||
+ | # Show all columns separated by pipe | symbol | ||
+ | sacctmgr show account -s -P | ||
+ | # | ||
+ | sacctmgr show user -s | ||
Add user | Add user | ||
- | sacctmgr add user <usernme> Account=gpu-users Partition=gpu | + | sacctmgr add user <username> Account=gpu-users Partition=gpu |
Modify user, give 12000 minutes/200 hours for usage | Modify user, give 12000 minutes/200 hours for usage | ||
- | sacctmgr modify user misegata | + | sacctmgr modify user < |
+ | |||
+ | Modify user by removing it from certain account | ||
+ | |||
+ | sacctmgr remove user where user=< | ||
+ | |||
+ | Delete user | ||
+ | |||
+ | sacctmgr delete user ivmilan | ||
+ | Deleting users... | ||
+ | ivmilan | ||
+ | Would you like to commit changes? (You have 30 seconds to decide) | ||
+ | (N/y): y | ||
Restart the services: | Restart the services: | ||
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systemctl status slurmdbd.service | systemctl status slurmdbd.service | ||
+ | ==== Submit a job to a specific node using Slurm' | ||
+ | |||
+ | To run a job on a specific Node use this option in the job script | ||
+ | |||
+ | #SBATCH --nodelist=gpu03 | ||
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====== Modules ====== | ====== Modules ====== | ||
+ | |||
+ | The Environment Modules package provides for the dynamic modification of a user's environment via modulefiles. | ||
+ | |||
+ | Installing Modules on Unix | ||
+ | |||
+ | Login into slurm-ctrl and become root | ||
+ | |||
+ | ssh slurm-ctrl | ||
+ | sudo -i | ||
+ | |||
+ | Download modules | ||
+ | |||
+ | curl -LJO https:// | ||
+ | tar xfz modules-4.6.0.tar.gz | ||
+ | cd modules-4.6.0 | ||
+ | |||
+ | |||
+ | $ ./configure --prefix=/ | ||
+ | $ make | ||
+ | $ make install | ||
+ | |||
+ | |||
+ | |||
+ | https:// | ||
+ | |||
+ | |||
+ | ---- | ||
+ | |||
+ | ===== SPACK ===== | ||
+ | |||
Add different python versions using spack! | Add different python versions using spack! | ||
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1. First see which python versions are available: | 1. First see which python versions are available: | ||
- | spack versions python | + | |
==> Safe versions (already checksummed): | ==> Safe versions (already checksummed): | ||
3.8.2 3.7.7 3.7.4 3.7.1 3.6.7 3.6.4 3.6.1 3.5.2 3.4.10 | 3.8.2 3.7.7 3.7.4 3.7.1 3.6.7 3.6.4 3.6.1 3.5.2 3.4.10 | ||
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3.10.0a6 | 3.10.0a6 | ||
3.10.0a5 | 3.10.0a5 | ||
- | ..... | + | ... |
+ | | ||
2. now select the python version you would like to install: | 2. now select the python version you would like to install: | ||
- | spack install python@3.8.2 | + | |
+ | ==> 23834: Installing libiconv | ||
+ | ==> Using cached archive: / | ||
+ | ==> Staging archive: / | ||
+ | ==> Created stage in / | ||
+ | ==> No patches needed for libiconv | ||
+ | ==> 23834: libiconv: Building libiconv [AutotoolsPackage] | ||
+ | ==> 23834: libiconv: Executing phase: ' | ||
+ | ==> 23834: libiconv: Executing phase: ' | ||
+ | ==> 23834: libiconv: Executing phase: ' | ||
+ | ==> 23834: libiconv: Executing phase: ' | ||
+ | ==> 23834: libiconv: Successfully installed libiconv | ||
+ | Fetch: 0.04s. | ||
+ | [+] / | ||
+ | ==> 23834: Installing libbsd | ||
+ | ... | ||
+ | ... | ||
+ | ... | ||
+ | ==> 23834: Installing python | ||
+ | ==> Fetching https:// | ||
+ | ############################################################################################################ | ||
+ | ==> Staging archive: / | ||
+ | ==> Created stage in / | ||
+ | ==> Ran patch() for python | ||
+ | ==> 23834: python: Building python [AutotoolsPackage] | ||
+ | ==> 23834: python: Executing phase: ' | ||
+ | ==> 23834: python: Executing phase: ' | ||
+ | ==> 23834: python: Executing phase: ' | ||
+ | ==> 23834: python: Executing phase: ' | ||
+ | ==> 23834: python: Successfully installed python | ||
+ | Fetch: 1.81s. | ||
+ | [+] / | ||
+ | |||
+ | |||
+ | This will take some minutes time, depending on the type of version | ||
3. Now you need to add a modules file | 3. Now you need to add a modules file | ||
+ | root@slurm-ctrl: | ||
+ | |||
+ | < | ||
+ | #%Module1.0 | ||
+ | proc ModulesHelp { } { | ||
+ | global dotversion | ||
+ | | ||
+ | puts stderr " | ||
+ | } | ||
+ | |||
+ | module-whatis " | ||
+ | |||
+ | set | ||
+ | set-alias | ||
+ | |||
+ | prepend-path | ||
+ | prepend-path | ||
+ | |||
+ | </ | ||
+ | |||
+ | 4. New module should now be available: | ||
+ | |||
+ | root@slurm-ctrl: | ||
+ | -------------------------------------------- / | ||
+ | anaconda3 | ||
+ | bzip | ||
+ | cuda-10.2 | ||
+ | cuda-11.0 | ||
+ | |||
+ | 5. Load the new module | ||
+ | |||
+ | root@slurm-ctrl: | ||
+ | |||
+ | 6. Verify it works | ||
+ | |||
+ | root@slurm-ctrl: | ||
+ | Python 3.8.2 (default, Mar 19 2021, 11:05:37) | ||
+ | [GCC 9.3.0] on linux | ||
+ | Type " | ||
+ | >>> | ||
+ | |||
+ | 7. Unload the new module | ||
+ | module unload python-3.8.2 | ||
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===== Links ===== | ===== Links ===== | ||
+ | |||
+ | [[https:// | ||
+ | |||
+ | [[https:// | ||
+ | |||
https:// | https:// |
/data/www/wiki.inf.unibz.it/data/attic/tech/slurm.1616152469.txt.gz · Last modified: 2021/03/19 12:14 by kohofer