Výpočetní cluster a úložiště Botanického ústavu & MetaCentra

User Tools

Site Tools


en:prace

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision
Previous revision
Last revision Both sides next revision
en:prace [2020/06/11 15:20]
Vojtěch Zeisek
en:prace [2020/08/14 13:22]
Vojtěch Zeisek [Work on the cluster]
Line 7: Line 7:
 > :!: **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 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.:
  
 <code bash submitting_tasks.sh> <code bash submitting_tasks.sh>
Line 15: Line 17:
 # ...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.txt · Last modified: 2020/08/18 10:00 by Vojtěch Zeisek