This example runs PAUP on the input file input.nex that resides in the current working directory. A file (here we'll name it pbsjob) is created with the contents:
#!/bin/bash
#PBS -c s
#PBS -j oe
#PBS -m ae
#PBS -N jobname
#PBS -l pmem=5gb
#PBS -l walltime=500:00:00
#PBS -M your.name@jcu.edu.au
ncpu=`wc -l $PBS_NODEFILE | awk '{print $1}'`
echo "------------------------------------------------------"
echo " This job is allocated "$ncpu" CPU cores on "
cat $PBS_NODEFILE | uniq
echo "------------------------------------------------------"
echo "PBS: Submitted to $PBS_QUEUE@$PBS_O_HOST"
echo "PBS: Working directory is $PBS_O_WORKDIR"
echo "PBS: Job identifier is $PBS_JOBID"
echo "PBS: Job name is $PBS_JOBNAME"
echo "------------------------------------------------------"
cd $PBS_O_WORKDIR
source /etc/profile.d/modules.sh
module load paup
paup -n input.nex
To submit the job for execution on a HPRC compute node simply enter the command:
qsub pbsjob
If you know this job will require more than 4GB but less than 8GB of RAM, you could use the command:
qsub -l nodes=1:ppn=2 pbsjob
If you know this job will require more than 8GB but less than 16GB of RAM, you could use the command:
qsub -l nodes=1:ppn=8 pbsjob
The reason for the special cases (latter two) is to guarantee memory resources for your job. If memory on a node is overallocated, swap will be used. Job(s) that are actively using swap (disk) to simulate memory could take more than 1000 times longer to finish than a job running on dedicated memory. In most cases, this will mean your job will never finish.
Using Job Arrays
Users with a knowledge of shell scripting (e.g., bash) may choose to take advantage of job arrays. This feature significantly reduces load on our Torque/Maui server (compared to lots of individual job submissions). The example below (assume the file name is pbsjob), will only be useful as a guide
#!/bin/bash #PBS -c s #PBS -j oe #PBS -m ae #PBS -N jobarray #PBS -M your.name@jcu.edu.au #PBS -l pmem=2gb #PBS -l walltime=9:00:00 cd $PBS_O_WORKDIR source /etc/profile.d/modules.sh module load matlab matlab -r myjob$PBS_ARRAYID
Issuing the command
qsub -S /bin/bash -t 1-8 pbsjob
will see 8 jobs run under one major identifier. To view status of individual jobs in the array. The above example is identical (in terms of what jobs would be executed) to the one in the "Do It Yourself" section below.
Chances are you may need more advanced features of the scripting language than what is shown above. HPRC staff will endeavour to provide assistance with job arrays, if requested.
Do It Yourself
There are several legitimate reasons for wanting to run multiple single processor jobs in parallel within a single PBS script. For example, you may want to run 8 MATLAB jobs which require a toolbox that only has 4 licensed users. Only 1 MATLAB license is checked out if all 8 jobs are run on the same system. An example PBS script to do this task would look like
#!/bin/bash #PBS -c s #PBS -j oe #PBS -m ae #PBS -N jobname #PBS -M your.name@jcu.edu.au #PBS -l walltime=1000:00:00 #PBS -l nodes=1:ppn=8 #PBS -l pmem=32gb ncpu=`wc -l $PBS_NODEFILE` echo "------------------------------------------------------" echo " This job is allocated "$ncpu" CPU cores on " cat $PBS_NODEFILE | uniq echo "------------------------------------------------------" echo "PBS: Submitted to $PBS_QUEUE@$PBS_O_HOST" echo "PBS: Working directory is $PBS_O_WORKDIR" echo "PBS: Job identifier is $PBS_JOBID" echo "PBS: Job name is $PBS_JOBNAME" echo "------------------------------------------------------" cd $PBS_O_WORKDIR source /etc/profile.d/modules.sh module load matlab matlab -r myjob1 & matlab -r myjob2 & matlab -r myjob3 & matlab -r myjob4 & matlab -r myjob5 & matlab -r myjob6 & matlab -r myjob7 & matlab -r myjob8 & wait # Wait for background jobs to finish.
To submit the job for execution on a HPRC compute node simply enter the command:
qsub pbsjob
Note: The echo commands in the PBS script example above are informational only.
#!/bin/bash #PBS -V #PBS -m abe #PBS -N migrate #PBS -l pmem=62GB #PBS -l nodes=1:ppn=24 #PBS -l walltime=240:00:00 #PBS -M your.email@my.jcu.edu.au cd #PBS_O_WORKDIR module load openmpi module load migrate mpirun -np 24 -machinefile $PBS_NODEFILE migrate-n-mpi ...