{"id":979,"date":"2021-03-29T16:28:10","date_gmt":"2021-03-29T16:28:10","guid":{"rendered":"http:\/\/wordpress.ubi.pt\/clusterdem\/?page_id=979"},"modified":"2025-02-04T09:32:29","modified_gmt":"2025-02-04T09:32:29","slug":"computation-section","status":"publish","type":"page","link":"https:\/\/clusterdem.ubi.pt\/?page_id=979","title":{"rendered":"Computational Resources"},"content":{"rendered":"

At ClusterDEM, we leverage advanced computational power to support our research in numerical modeling and simulation. Our mini HPC system, OCTOPUS500 <\/strong><\/em>, is a 768-core <\/strong><\/em> cluster with 2TB of RAM <\/strong><\/em>, running CentOS<\/strong> and built upon ROCKS<\/strong> Cluster. This system enables parallel computing for large-scale simulations, including computational fluid dynamics (CFD) and multiphysics applications.
\n\"\"<\/p>\n

<\/h4>\n

Running Your Case on OCTOPUS500<\/strong><\/h4>\n

To efficiently use our cluster, follow the guidelines below.<\/p>\n

Available Parallel Environments<\/strong><\/h5>\n

OCTOPUS500 uses a parallel environment defined as mpiX<\/code>, where X<\/code> represents the number of CPUs per node (from 1 to 10). Ensure that the number of requested slots is a multiple of X<\/code>.<\/p>\n

\u2705 Example (Valid Submission):<\/p>\n

\n
\n
\n
<\/div>\n<\/div>\n<\/div>\n
-pe mpi5 25
\n<\/code><\/div>\n<\/div>\n

This launches a run with 5 compute nodes, each using 5 CPUs<\/strong>.<\/p>\n

\u274c Invalid Cases:<\/p>\n

\n
-pe mpi5 22 # Incorrect, not a multiple of 5<\/span>
\n-pe mpi2 5 # Incorrect, not a multiple of 2<\/span>
\n<\/code><\/div>\n
\n

Cluster Node Selection<\/strong><\/h4>\n

This can be done with the command:<\/p>\n

\n
-l h=compute-0-x<\/span>
\n<\/code><\/div>\n<\/div>\n

where x<\/code> is the specific node number<\/strong> you want to use.<\/p>\n<\/div>\n

<\/code><\/div>\n<\/div>\n

\ud83d\udca1 Rule:\u00a0To optimize resource usage, you should always check the cluster status using Ganglia before submitting jobs:
\n\ud83d\udd17 Ganglia Monitoring System<\/a> (Accessible within the UBI network)<\/em><\/strong><\/p>\n

\n

Job Submission and Management<\/strong><\/h3>\n

Submitting a Job<\/strong><\/h4>\n

Use the following command to submit jobs:<\/p>\n

\n
qsub RUN.sh
\n<\/code><\/div>\n<\/div>\n

After submitting a job with qsub, SGE will respond with something like:<\/p>\n

Your job 624556 (“myjob.cmd”) has been submitted<\/p>\n

where 624556 is the job number assigned by SGE to your job.<\/p>\n

Example OpenFOAM Submission Script<\/strong><\/h4>\n

Below is a sample job submission script for OpenFOAM:<\/p>\n

\n
#!\/bin\/bash<\/span>
\n#$ -S \/bin\/bash<\/span>
\n#$ -pe mpi5 10<\/span>
\n#$ -cwd<\/span>
\n#$ -N MySimulation<\/span>
\n#$ -o log<\/span>
\n#$ -e error.err<\/span>
\n#$ -p 0<\/span>
\n#$ -M youremail@ubi.pt<\/span>
\n#$ -m bea<\/span><\/code><\/code><\/p>\n

<\/code><\/code>. $HOME<\/span>\/OpenFOAM\/OpenFOAM-2.0.x\/etc\/bashrc # Ensure correct path<\/span>
\nARGS=“–mca btl ^openib –mca btl_tcp_if_include eth0”<\/span><\/p>\n


\n<\/code># Run the solver<\/span>
\nSOLVER=clusterMHDFoam
\nmpirun -np $NSLOTS<\/span> $ARGS<\/span> $SOLVER<\/span> -parallel
\n<\/code><\/p>\n<\/div>\n<\/div>\n

\ud83d\udccc Note:<\/strong> This script should be run inside the case folder.<\/p>\n

\ud83d\udca1 Best Practices:<\/strong><\/p>\n