Template PBS script.

#!/bin/csh # # file: pbs.template # # purpose: template for PBS (Portable Batch System) script # # remarks: a line beginning with # is a comment; # a line beginning with #PBS is a pbs command; # assume (upper/lower) case to be sensitive; # # use: submit job with # qsub pbs.template # # job name (default is name of pbs script file) #PBS -N myjob # # resource limits: number of CPUs to be used #PBS -l ncpus=25 # # resource limits: number of nodes to be used #PBS -l nodes=25:p4 # # resource limits: amount of memory to be used #PBS -l mem=256mb # # resource limits: max. wall clock time during which job can be running #PBS -l walltime=2:30:00 # # path/filename for standard output #PBS -o mypath/my.out # # path/filename for standard error #PBS -e mypath/my.err # # queue name, one of {dque} # The default queue, "dque", need not be specified #PBS -q dque # # files to be copied to execution server before script processing starts # usage: -W stagein=local-filename@remotehost:remote-filename #PBS -W [email protected]:/raid3/simon/runs/input/my.input # # files to be copied from execution server after script processing # usage: -W stageout=local-filename@remotehost:remote-filename #PBS -W [email protected]:raid3/simon/runs/output/my.outout # # start job only after MMDDhhmm, where M=Month, D=Day, h=hour, m=minute # e.g., November 30th, 17:30 #PBS -a 11301730 # # send me mail when job begins #PBS -m b # send me mail when job ends #PBS -m e # send me mail when job aborts (with an error) #PBS -m a # if you want more than one message, you must group flags on one line, # otherwise, only the last flag selected executes: #PBS -mba # # do not rerun this job if it fails #PBS -r n # # export all my environment variables to the job #PBS -V # # Using PBS - Environment Variables # When a batch job starts execution, a number of environment variables are # predefined, which include: # # Variables defined on the execution host. # Variables exported from the submission host with # -v (selected variables) and -V (all variables). # Variables defined by PBS. # # The following reflect the environment where the user ran qsub: # PBS_O_HOST The host where you ran the qsub command. # PBS_O_LOGNAME Your user ID where you ran qsub. # PBS_O_HOME Your home directory where you ran qsub. # PBS_O_WORKDIR The working directory where you ran qsub. # # These reflect the environment where the job is executing: # PBS_ENVIRONMENT Set to PBS_BATCH to indicate the job is a batch job, or # to PBS_INTERACTIVE to indicate the job is a PBS interactive job. # PBS_O_QUEUE The original queue you submitted to. # PBS_QUEUE The queue the job is executing from. # PBS_JOBID The job's PBS identifier. # PBS_JOBNAME The job's name. # # ------------------------------------------------------------ # Log some interesting information # ------------------------------------------------------------ # echo " " echo "-------------------" echo "This is a $PBS_ENVIRONMENT job" echo "This job was submitted to the queue: $PBS_QUEUE" echo "The job's id is: $PBS_JOBID" echo "-------------------" echo "The master node of this job is: $PBS_O_HOST" # --- the nodes allocated to this job are listed in the # file $PBS_NODEFILE # --- count the number of processors allocated to this run # --- $NPROCS is required by mpirun. NPROCS=`wc -l NNODES=`uniq $PBS_NODEFILE | wc -l` echo "This job is using $NPROCS CPU(s) on the following $NNODES node(s):" echo "-----------------------" uniq $PBS_NODEFILE | sort echo "-----------------------" # ------------------------------------------------------------ # Setup execution variables # ------------------------------------------------------------ # # --- define standard output and error files for the job # default is .o and .e ##PBS -o petrel_test.out ##PBS -e petrel_test.err # --- or combine both output and error streams into one file #PBS -j oe # --- PBS_O_WORKDIR is the current working directory from # which this job was submitted using 'qsub' echo The working directory is $PBS_O_WORKDIR # # --- the path of your executable EXEPATH="" # --- declare any program arguments ARGS="" # --- set the path for the correct version of mpirun # (it depends on compiler choice) # # --- Portland Group Fortran90 compiler # MPIPATH="/usr/local/pgf90/mpich-1.2.5.2/bin/mpirun" # --- other fortran compilers (LFF95, etc.) MPIPATH="/usr/local/lff95/mpi/bin/mpirun" # --- echo the command syntax echo "The command syntax for this job is:" echo $MPIPATH -np $NPROCS $EXEPATH $ARGS echo " " # ------------------------------------------------------------ # Run the program # ------------------------------------------------------------ # # --- 'cd' to the current working directory (by default, qsub # starts from the home directory of the user). # this is useful if you have input files in the working # directory. cd $PBS_O_WORKDIR # --- print out the current time, then use the 'time' command # to start the program and print useful stats # echo -n 'Started program at : ' ; date time $MPIPATH -np $NPROCS $EXEPATH $ARGS echo -n 'Ended program at : ' ; date echo " " exit