During In 2012, several new nodes with Intel i7 quad-core processors (with hyperthreading) have been added to the Deltares H4 cluster. These new nodes are significantly faster than the old ones, and are accessible via a separate queue: 'normal-i7'. Since these nodes have 4 cores, they are most efficient when dealing with parallel jobs, for instance XBeach in MPI mode.
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Submitting a job to the cluster is done as usual, by submitting a shell script. The easiest way to create these shell scripts is using the XBeach MATLAB toolbox (for more information, see Matlab Toolbox, make sure to use an up-to-date version). The command used is xb_write_sh_scripts.
To create scripts for the i7 nodes use the syntax: xb
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xb_write_sh_scripts('localpath', 'runpath', 'binary','XBeach_binarypath', 'mpitype', 'openmpi', 'nodes', |
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nr_of_nodes, 'name', 'runname', 'queuetype', 'normal-i7'); |
When . When choosing the normal-i7 queue, the job is split into 4 separate processes per node (so if you select 2 nodes, the job will be split up into 8 processes, in order to use all the cores on every node). Currently, this only works for 'openmpi' and not for 'mpich2'.
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To submit the job to the cluster, use putty, go to the folder containing the shell scripts and use . Submit the job by using the command: qsub -q normal-i7 xbeach.sh
By adding
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-q normal-i7 |
, the job is sent to the normal-i7 queue instead of the default queue (which is named 'normal'). xbeach.sh in turn automatically submits mpi.sh to the 'normal-i7' queue. Usage of all nodes can be viewed at the H4 cluster staus page. If all went well, the nodes that your xbeach simulation runs on have a load greater than 1 (actual load > maximum load of 1 core, so multiple cores are in use).