MATLAB is a high-performance language for technical computing. It integrates computation, visualization, and programming in an easy-to-use environment where problems and solutions are expressed in familiar mathematical notation. MATLAB features a family of add-on application-specific solutions called toolboxes. Toolboxes are comprehensive collections of MATLAB functions (M-files) that extend the MATLAB environment to solve particular classes of problems. These are the toolboxes installed in NERSC MATLAB, along with the number of licenses.
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The name MATLAB stands for matrix laboratory. MATLAB was originally written to provide easy access to matrix software developed by the LINPACK and EISPACK projects. Today, MATLAB engines incorporate the LAPACK and BLAS libraries, embedding the state of the art in software for matrix computation.
How to Use MATLAB on Cori¶
MATLAB is available at NERSC on Cori (and Edison until it retires). The number of MATLAB licenses at NERSC is not very large (currently 16), so users should not be running a MATLAB session when it is not being actively used. If you use NX, it's particularly easy to think you've released your license when you haven't, since license checkouts persist between NX sessions.
MATLAB can be run interactively or in batch mode. MATLAB can run on a compute node with exclusive access to the full usable memory (about 62 GB on Edison nodes and 120 GB on Cori Phase 1 nodes) by submitting a batch job to the regular queue.
To run MATLAB interactively on Cori, connect with ssh -X or via NX, and do the following:
salloc -q interactive -N 1 -c 32 -C haswell -t 30:00 module load matlab matlab
It is also possible to run MATLAB on a Cori login node directly. Production computing should not be undertaken on login nodes, however. For long-running or compute intensive jobs, use a batch script.
module load matlab matlab
To run one instance of MATLAB non-intearctively through a batch job, you can use the following job script on Cori:
#!/bin/bash -l #SBATCH -q regular #SBATCH -N 1 #SBATCH -c 32 #SBATCH -C haswell #SBATCH -t 00:30:00 cd $SLURM_SUBMIT_DIR # optional, since this is the default behavior module load matlab srun -n 1 -c 32 matlab -nodisplay -r < myjob.m -logfile myjob.log
myjob.m is your MATLAB script.
Parallelism in MATLAB¶
To prepare a MATLAB cluster with 32 cores (within MATLAB) do:
cluster = parcluster('local') cluster.NumWorkers = 32 saveAsProfile(cluster,'cori_cluster') pp = parpool('cori_cluster', 32)
Running MATLAB Parallel Commands¶
The following program illustrates how MATLAB parallel commands can be used on Cori. NERSC's license currently limits parallel use to a single node and the number of threads that one node supports.
% hello-world.m pc = parcluster('local'); parpool(pc, 32); spmd rank = labindex; fprintf(1,'Hello %d\n',rank); end
For loop-level parallelism, MATLAB provides the parfor construct.
In order to make MATLAB work in parallel on Edison, you need to make sure it will access the MATLAB libraries before the standard cray libraries. You can do this by running this command for bash:
export LD_PRELOAD="/global/common/sw/cray/cnl6/ivybridge/matlab/R2016b/bin/glnxa64/libmpichnem.so /global/common/sw/cray/cnl6/ivybridge/matlab/R2016b/bin/glnxa64/libmpichsock.so"
or for csh / tcsh:
setenv LD_PRELOAD "/global/common/sw/cray/cnl6/ivybridge/matlab/R2016b/bin/glnxa64/libmpichnem.so /global/common/sw/cray/cnl6/ivybridge/matlab/R2016b/bin/glnxa64/libmpichsock.so"
However, if you have
LD_PRELOAD set on a login node, this will interfere with the regular Edison and Cori environment. It's important that you only set the
LD_PRELOAD variable in your parallel MATLAB job script (or interactive job).
Parallelism with the MATLAB Compiler¶
Another way to run MATLAB in parallel is to run multiple instances of a compiled MATLAB program. By compiling, you create a stand-alone application that doesn't need to obtain a separate license from the NERSC license server to run. See MATLAB Compiler for details.