Cbb/Baobab: Difference between revisions
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After you have done this, you can ssh ssh into the baobab headnode. You can do this from any machine connected to the internal CBB network. | |||
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ssh baobab.cbb.lan | ssh baobab.cbb.lan |
Revision as of 14:18, 6 November 2014
The Baobab Cluster
CBB's internal cluster.
The new cluster is made up of 6 nodes with 24 cores and 64 GB RAM on each node.
To use the baobab cluster setup your environment to use mpi. I generally recommend you add this to your .bashrc file before you get started.
module add openmpi-x86_64
After you have done this, you can ssh ssh into the baobab headnode. You can do this from any machine connected to the internal CBB network.
ssh baobab.cbb.lan
Please use the PBS submission system to run your jobs. Here is a quick rundown of what you will need to know.
Make yourself a PBS submission script like the following:
#PBS -l nodes=6:ppn=24,walltime=00:01:00 ## nodes = total number of nodes you need ## ppn = processors per node that you will need ## walltime = amount of time your job will be allowed before being forcefully removed ##################################################################################### cd $PBS_O_WORKDIR ## How many cores total do we have? NO_OF_CORES=`cat $PBS_NODEFILE | egrep -v '^#'\|'^$' | wc -l | awk '{print $1}'` ## ## Main execution echo "Job Started at: `date`" mpiexec -np $NO_OF_CORES -machinefile $PBS_NODEFILE hello echo "Job Ended at: `date`"
To submit the jobs to the cluster from the headnode:
qsub <yoursPBSscript>
To check the status of your jobs:
qstat -a
To delete your jobs from the queue:
qdel <Job_Number/Identifier>
For more examples look here: https://wiki.cs.vt.edu/wiki/Cbb/Baobab/examples