Výpočetní cluster a úložiště Botanického ústavu & MetaCentra

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en:prace [2020/06/10 15:35]
Vojtěch Zeisek created
en:prace [2020/08/18 10:00] (current)
Vojtěch Zeisek
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 > :!: **Basic information about work in MetaCentrum are on [[https://wiki.metacentrum.cz/wiki/Categorized_list_of_topics|its wiki]].** Prior you start work on MetaCentrum, reads its documentation and learn how to work in Linux command line. :!: > :!: **Basic information about work in MetaCentrum are on [[https://wiki.metacentrum.cz/wiki/Categorized_list_of_topics|its wiki]].** Prior you start work on MetaCentrum, reads its documentation and learn how to work in Linux command line. :!:
  
-MetaCentrum, and therefore the Průhonice cluster, run in a [[https://wiki.metacentrum.cz/wiki/Categorized_list_of_topics|Linux environment]] (use logs in via **SSH**), which implies that users must [[https://wiki.metacentrum.cz/wiki/Beginners_guide|master the basic UNIX commands]] in order to interact with the operating system. The user must prepare in advance a script containing all commands and operations that will be performed during the analysis. The job is executed by submitting the script with the ''qsub'' command. To submit a job to a queue on our cluster the user must add to the ''qsub'' command the ''-q ibot'' parameter. The node on which the computations will be carried out can be specified such as ''-l cluster=carex'', ''-l cluster=draba'' or ''-l cluster=vinca''. Other parameters are available and can be obtained from the [[https://metavo.metacentrum.cz/pbsmon2/qsub_pbspro|qsub assembler tool]]. E.g.:+MetaCentrum, and therefore the Průhonice cluster, run in a [[https://wiki.metacentrum.cz/wiki/Categorized_list_of_topics|Linux environment]] (use logs in via **SSH**), which implies that users must [[https://wiki.metacentrum.cz/wiki/Beginners_guide|master]] the [[en:zaklady-prikazove-radky|basic UNIX commands]] in order to interact with the operating system. The user must prepare in advance a script containing all commands and operations that will be performed during the analysis. The job is executed by submitting the script with the ''qsub'' command.
  
-<code bash spusteni_ulohy.sh>+To submit a job to a queue on our cluster the user must add to the ''qsub'' command the ''-q ibot'' parameter. The node on which the computations will be carried out can be specified such as ''-l cluster=carex'', ''-l cluster=draba'' or ''-l cluster=vinca''. Other parameters are available and can be obtained from the [[https://metavo.metacentrum.cz/pbsmon2/qsub_pbspro|qsub assembler tool]]. E.g.: 
 + 
 +<code bash submitting_tasks.sh>
 # Login to fronend # Login to fronend
 ssh USER@tilia.ibot.cas.cz ssh USER@tilia.ibot.cas.cz
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 # ...and run it: # ...and run it:
 qsub ... -q ibot ... qsub ... -q ibot ...
-qsub ... -q ibot -l cluster=carex ... +qsub ... -l select=...:cluster=carex -l -q ibot ... 
-qsub ... -q ibot -l cluster=draba ... +qsub ... -l select=...:cluster=draba -l -q ibot ... 
-qsub ... -q ibot -l cluster=vinca ...+qsub ... -l select=...:cluster=vinca -l -q ibot ...
 qsub -l walltime=1:0:0 -q ibot -l select=1:ncpus=4:mem=4gb:scratch_local=1gb -m abe script.sh qsub -l walltime=1:0:0 -q ibot -l select=1:ncpus=4:mem=4gb:scratch_local=1gb -m abe script.sh
 </code> </code>
en/prace.1591803309.txt.gz · Last modified: 2020/06/10 15:35 by Vojtěch Zeisek