Cbb/Baobab: Difference between revisions

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The new cluster is made up of 6 nodes with 24 cores and 64 GB RAM on each node.
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.
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.
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module add openmpi-x86_64
module add openmpi-x86_64
</PRE>
</PRE>


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.
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
</PRE>
</PRE>


Please use the PBS submission system to run your jobs.  Here is a quick rundown of what you will need to know.
Please use the PBS submission system to run your jobs.  Here is a quick rundown of what you will need to know.
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echo "Job Ended at: `date`"
echo "Job Ended at: `date`"
</PRE>
</PRE>


To submit the jobs to the cluster from the headnode:
To submit the jobs to the cluster from the headnode:
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qsub <yoursPBSscript>
qsub <yoursPBSscript>
</PRE>
</PRE>


To check the status of your jobs:
To check the status of your jobs:
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qstat -a
qstat -a
</PRE>
</PRE>


To delete your jobs from the queue:
To delete your jobs from the queue:
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qdel <Job_Number/Identifier>
qdel <Job_Number/Identifier>
</PRE>
</PRE>


For more examples look here: https://wiki.cs.vt.edu/wiki/Cbb/Baobab/examples
For more examples look here: https://wiki.cs.vt.edu/wiki/Cbb/Baobab/examples

Revision as of 15:19, 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