As of January 2014, CHPC has a new scheduler - PBSPro.

Main user documentation can be found at http://resources.altair.com/pbs/documentation/support/PBSProUserGuide12.1.pdf

But here is a summary of how to submit jobs at CHPC.

The following must be plain text files, as created by unix programs like nano or vi. If you wish to create them on your desktop and copy them over, ensure they contain no formatting and have unix line endings. Microsoft Word would be a bad choice.

#PBS -N eric.job
#PBS -l select=8:ncpus=1:jobtype=dell,place=free:group=nodetype
#PBS -l select=1:
#PBS -l walltime=1:00:00
#PBS -q workq
#PBS -m be
#PBS -o /export/home/embele/scratch5/eric.out
#PBS -e /export/home/embele/scratch5/eric.err
#PBS

cd $PBS_O_WORKDIR
source /etc/profile.d/modules.sh
module add gaussian/g09.D01
g09 < eric.com > sibusiso.log

#PBS -N eric.job
#PBS -l select=1:mpiprocs=8
#PBS -l walltime=1:00:00
#PBS -q kepla_k20
#PBS -m be
#PBS -o /export/home/embele/amber/amber12/Amber_GPU_Benchmark_Suite/GB/myoglobin/eric.out
#PBS -e /export/home/embele/amber/amber12/Amber_GPU_Benchmark_Suite/GB/myoglobin/eric.err
#PBS
cd $PBS_O_WORKDIR
exe=/export/home/embele/amber/amber12/bin/pmemd.MPI
###exe=/export/home/embele/amber/amber12/bin/pmemd.cuda.MPI
source /etc/profile.d/modules.sh
module add intel-XE/c8000 cuda/5.0-c8000 mvapich2/c8000 amber/k20
module add intel-XE/c8000 cuda/5.0-c8000 mvapich2/c8000 amber/k20
nproc=`cat $PBS_NODEFILE|wc -l`
time mpirun -np $nproc -machinefile $PBS_NODEFILE $exe -O -i mdin -o mdout -p prmtop -c inpcrd

#PBS -N <jobname>
#PBS -l select=<totalcores>:ncpus=1:select=<hosts>:jobtype=<architecture>:place=free:group=nodetype
#PBS -l walltime=<hours>:<minutes>:<seconds>
#PBS -q <queue>
#PBS -m be
#PBS -o <path to your output file>
#PBS -e <path to your error file>
Where
<jobname> = name of the job
<totalcores>= total number of cores
<hosts> = number of hosts
<architecture> = architecture where the jobs will run (nehalem|westmere|dell)
<queue> = submission queue ( workq , priorityq , specialq , intel_mic , spark , kepla_k20 , accelrys)

Note that the M9000 sparc queue is called 'spark'

Syntax

...
#PBS -l walltime=$HOURS:$MINUTES:$SECONDS
#PBS -l select=${NO_OF_HOSTs}:ncpus=${CPUs_PER_HOST}:mpiprocs=${CPUs_PER_HOST}:jobtype=$FEATURE
#PBS -q $QUEUE
...

For more information on qsub

$ man qsub

Additional information on the job queues available

$ qstat -q

A minimal script Dell example would be

$ more mpirun_basic_example
#PBS -l select=2:ncpus=12:mpiprocs=12:jobtype=dell
cat $PBS_NODEFILE

submiting the script

$ qsub mpirun_basic_example

The submitted jobs output file should produce output similar to

cnode-6-33
... repeated 11 times ...
cnode-6-34
... repeated 11 times ...