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Software Tools
Using PBS
Software toolsPortland compilers pgf77 pgf90 pghpf pgcc pgCC Portland debugger
GNU compilers g77 gcc
Intel ifort icc
…software toolsMPICH (MPI-1, MPI-2MPI compilers mpicc mpiCC mpif77 Mpif90
mpirunYour favorite text editorPBS
Using PBS
PBS an open source job scheduler* and queue manager
PBS – Portable Batch System
Others Torque Sun Grid Engine Platform LSF IBM Load Leveler
PBS/Torque widely used
PBS
openPBS – open source versionPBSpro – commercial versionTorque
qsub [options] script
Submits jobs to a queue (execution)Job specifications in the file scriptMore on pbs scripts laterPbs will queue, schedule and launch job specified in the command/scriptqsub returns jobid -jobnumber.servername (9999.master)
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
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
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.
qsub – common options
-M useraddress - defines mail addresses for email (see –m) -M [email protected]
-S path define the location of the shell to interpret the script-S /bin/csh
qsub – common options
-l job resource list (important)nodes=nppn=m-l nodes=2:ppn=2
qstat - get status of jobs/queues
qstat –a – get status report in alternative format
qstat –a – statesE - 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.
qstat – other options
qstat –an -- lists jobs in queue/running. For running jobs shows nodes/processors assigned to the job.
qstat – options
qstat –q -- list all queues and that status
qdel – deleting a job from the queue
qdel jobidjobid is sequence_number[.server_name]for example –
qdel 9999.master or
qdel 9999
other PBS commands
qhold jobid -- places job jobid on holdqrls jobid -- moves job jobid from hold to queued or executing statusqalter jobid – modifies attributes of the job jobid specified in qsub after it is submitted
** not all attributes may be modified
other PBS commands
qmove dest jobid -- moves job jobid from current queue to the queue dest for example –
qmove short 9999
PBS qsub scripts
Standard (almost) script in whatever shell is supported on the system.Must include the line –
mpirun myprogmay include other statements/directives – like…
PBS qsub scripts – cont.
a simple script – demtest.sh
#!/bin/sh#PBS -N dem#PBS -q parallel#PBS -l nodes=2:ppn=2mpirun -np 4 -machinefile $PBS_NODEFILE
hellocat $PBS_NODEFILE
PBS scripts cont…
then –
qsub demtest.sh
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 0node7node7node6node6
Xpbs
For more information on PBS commands-
System man pages “man qstat”http://www-wisconsin.cern.ch/pbs/commands.htmlhttp://rsusu1.rnd.runnet.ru/opbs/commands.htmlhttp://www.sao.nrc.ca/imsb/rcsg/hpc/sgi_pbs2000/pbs/sld001.htmhttp://www.ccr.buffalo.edu/documents/pbs.PDF
Logging in to the cluster
using a secure shell clientlogin in to-
energy.cluster.wvu.edu
Compiling a MPI program
mpicc myprog.c –o myprog
or
gcc myprog.c –o myprog –lmpi –L/usr/local/packages/mpich/lib –I/usr/local/packages/mpich/include