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Software Tools Using PBS

Software Tools Using PBS. Software tools. Portland compilers pgf77 pgf90 pghpf pgcc pgCC Portland debugger GNU compilers g77 gcc Intel ifort icc. …software tools. MPICH MPI compilers mpicc mpiCC mpif77 Mpif90 mpirun Your favorite text editor PBS. Using PBS.

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Software Tools Using PBS

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  1. Software ToolsUsing PBS

  2. Software tools • Portland compilers • pgf77 • pgf90 • pghpf • pgcc pgCC • Portland debugger • GNU compilers • g77 • gcc • Intel • ifort • icc

  3. …software tools • MPICH • MPI compilers • mpicc • mpiCC • mpif77 • Mpif90 • mpirun • Your favorite text editor • PBS

  4. Using PBS PBS an open source job scheduler* and queue manager

  5. PBS – Portable Batch System • Others • Torque • Sun Grid Engine • Platform LSF • IBM Load Leveler • PBS/Torque widely used

  6. PBS • openPBS – open source version • PBSpro – commercial version

  7. qsub [options] script • Submits jobs to a queue (execution) • Job specifications in the file script • More on pbs scripts later • Pbs will queue, schedule and launch job specified in the command/script • qsub returns jobid -jobnumber.servername (9999.master)

  8. qsub – common options • -q queuename -- submit to the queue queuename • -q parallel@master • -N name -- give the job the name name • -N mybigjob1 • -I – run the job in interactive mode rather than batch

  9. qsub – common options • -o path -- location of pbs output, defaults to ~owner • -e path -- location of pbs error file, defaults to ~owner • -a datetime --places job in a wait state until datetime • datetime is [[[[CC]YY]MM]DD]hhmm[.SS] -- run a job on/after 5:00 pm on Feb. 14 -a 0214 1700

  10. qsub – common options • -m [a,b,e] a --mail is sent when the job is aborted by the batch system*. b --mail is sent when the job begins execution. e --mail is sent when the job terminates.

  11. qsub – common options • -M useraddress - defines mail addresses for email (see –m) • -M Don.McLaughlin@mail.wvu.edu • -S path define the location of the shell to interpret the script -S /bin/csh

  12. qsub – common options • -l job resource list (important) nodes=n ppn=m -l nodes=2:ppn=2

  13. qstat - get status of jobs/queues • qstat –a – get status report in alternative format

  14. qstat –a – states E - Job is exiting after having run. H - Job is held. Q - job is queued, eligible to run or routed. R - job is running. T - job is being moved to new location. (not here) W - job is waiting for its execution time (qsub -a option) to be reached.

  15. qstat – other options • qstat –an -- lists jobs in queue/running. For running jobs shows nodes/processors assigned to the job.

  16. qstat – options • qstat –q -- list all queues and that status

  17. qdel – deleting a job from the queue • qdel jobid jobid is sequence_number[.server_name] for example – qdel 9999.master or qdel 9999

  18. other PBS commands • qhold jobid -- places job jobid on hold • qrls jobid -- moves job jobid from hold to queued or executing status • qalter jobid – modifies attributes of the job jobid specified in qsub after it is submitted ** not all attributes may be modified

  19. other PBS commands • qmove dest jobid -- moves job jobid from current queue to the queue dest • for example – qmove short 9999

  20. PBS qsub scripts • Standard (almost) shell in whatever shell is supported on the system. • Must include the line – mpirun myprog may include other statements/directives – like…

  21. PBS qsub scripts – cont. • a simple script – demtest.sh #!/bin/sh #PBS -N dem #PBS -q parallel #PBS -l nodes=2:ppn=2 mpirun -np 4 -machinefile $PBS_NODEFILE hello cat $PBS_NODEFILE

  22. PBS scripts cont… • then – qsub demtest.sh

  23. PBS scripts cont… • and your get dem.o3975 --- Hello world! I'm node 1 Hello world! I'm node 2 Hello world! I'm node 3 Hello world! I'm node 0 node7 node7 node6 node6

  24. Xpbs

  25. For more information on PBS commands- • System man pages “man qstat” • http://www-wisconsin.cern.ch/pbs/commands.html • http://rsusu1.rnd.runnet.ru/opbs/commands.html • http://www.sao.nrc.ca/imsb/rcsg/hpc/sgi_pbs2000/pbs/sld001.htm • http://www.ccr.buffalo.edu/documents/pbs.PDF

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