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>> configCluster Must set WallTimeQueueName and QueueNameWallTime before submitting jobs to O2. E.g. >> c = parcluster; >> c.AdditionalProperties.QueueName = 'queue-name'; >> % 5 hourhours walltime >> c.AdditionalProperties.WallTime = '05:00:00'; >> c.AdditionalProperties.QueueName = 'queue-name'; >> c.saveProfile >>saveProfile Complete. Default cluster profile set to "o2 R2023a". |
now your default cluster profile is set to o2 local R2019a R2023a and you should be able to verify it by running the command parclustercommand parcluster
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>> parcluster
ans =
Generic Cluster
Properties:
Profile: o2 R2019aR2023a
Modified: false
Host: compute-a-16-22161
NumWorkers: 100000
NumThreads: 1
JobStorageLocation: /home/abc123/MdcsDataLocationabc/.matlab/3p_cluster_jobs/o2/R2023a/R2019ashared
ClusterMatlabRoot: /n/app/matlab/2019a2023a-v2
OperatingSystem: unix
RequiresOnlineLicensing: false
IntegrationScriptsLocation PreferredPoolNumWorkers: 32
PluginScriptsLocation: /n/app/matlab/2019a/toolbox/localsupport-packages/matlab-parallel-server/scripts/IntegrationScripts/o2
AdditionalProperties: List properties
Associated Jobs:
Number Pending: 0
Number Queued: 0
Number Running: 0
Number Finished: 0
>> |
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Note 2: After running the configCluster command, the default cluster profile is set to the O2 cluster, ; if you want to go back and use the "local" cluster profile, you can change the default profile using the command parallelcommand parallel.defaultClusterProfile('local')
Note 3: Running the configCluster command sets the cluster profile only for the currently used MATLAB version. If later on you use a different version of MATLAB you will need to run configCluster again Note 4: O2 MATLAB cluster profile is not compatible with Orchestra profile. If you plan to run on both clusters it is recommended to use a different version of MATLAB in each cluster (for example 2016b in Orchestra and 2017a in O2)again.
Setting the submission parameter for the O2 MATLAB cluster profile
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>> c=parcluster; % Specify the walltime (e.g. 48 hours) >> c.AdditionalProperties.WallTime = '48:00:00'; % Specify a partition to use for MATLAB jobs >> c.AdditionalProperties.QueueName = 'partition-name'; % Optional flags % Specify memory to use for MATLAB jobs, per node (MB) >> c.AdditionalProperties.Mem = '4000'; % Specify memory to use for MATLAB jobs, per CPU core (MB) >> c.AdditionalProperties.MemUsageMemPerCPU = '40002000'; % Specify the GPU card to run on >> c.AdditionalProperties.GpuCard = 'gpu-card-to-use'; % Request 2 GPUs per node >> c.AdditionalProperties.GpusPerNode = 2; % addAdd directly any sbatch supported flag manually (for example, mem per node and Num tasks per node):. % The "AdditionalSubmitArgs" field can be used for any Slurm flag except the walltime and partition. % This is the method we recommend. >> c.AdditionalProperties.AdditionalSubmitArgs = '--mem=4000 --tasks-per-node=2' % Save changes after modifying AdditionalProperties for the above changes to persist between MATLAB sessions >> c.saveProfile |
Note that set parameters by default will not be retained by default and will need to must be re-entered if the c object is deleted. To save permanently the submission parameter you must execute the command c.saveProfile
Important: Use --mem-per-cpu (or the flag c.AdditionalProperties.MemUsageMemPerCPU) instead of --mem to request a custom amount of memory when using the mpi partitionthe mpi partition. The slurm flag --mem is used to request a given amount of memory per node, so , unless you are enforcing a balanced distribution of tasks (i.e. MATLAB workers) per node, you might end up with too much or not enough memory on a given node, depending on how the tasks are allocated.
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