This page will guide you through the serial computing with Matlab at Triton cluster. (Note (2017): We used to have the Matlab Distributed Computing Server (MDCS), but because of low use we no longer have a license. You can still run in parallel on one node, up to 20-28 cores depending on how new.)
Matlab writes session data, compiled code and additional toolboxes to
~/.matlab. This can quicky fill up your
$HOME quota. To fix this
we recommend that you replace the folder with a symlink that points to
a directory in your working directory.
rsync -lrt ~/.matlab/ $WRKDIR/matlab-config/ && rm -r ~/.matlab ln -sT $WRKDIR/matlab-config ~/.matlab quotafix -gs --fix $WRKDIR/matlab-config
Interactive usage is currently available via the sinteractive tool. Do not use the cluster front-end for doing heavy task. Only meant for submitting jobs/compiling. Using MDCS for sending jobs is ok.
ssh -X email@example.com sinteractive module load matlab matlab &
Simple serial script¶
Running a single core Matlab job is easy through the slurm queue. A sample slurm script is provided underneath:
#!/bin/bash -l #SBATCH -p short #SBATCH -t 00:05:00 #SBATCH -n 1 #SBATCH --mem-per-cpu=100 #SBATCH -o serial_Matlab.out module load matlab n=3 m=2 srun matlab -nojvm -nosplash -r "serial_Matlab($n,$m) ; exit(0)"
The above script can then be saved as a file (e.g. matlab_test.slrm) and the job can be submitted with
sbatch matlab_test.slrm. The actual calculation is done in
function C = serial_Matlab(n,m) try A=0:(n*m-1); A=reshape(A,[2,3]).' B=2:(n*m+1); B=reshape(B,[2,3]).' C=0.5*ones(n,n) C=A*(B.') + 2.0*C catch error disp(getReport(error)) exit(1) end end
Remember to always set exit into your slurm script so that the program quits
once the function
serial_Matlab has finished. Using a
try-catch-statement will allow your job to finish in case of any error
within the program. If you don’t do this, Matlab will drop into
interactive mode and do nothing while your cluster time wastes.
NOTE: Starting from version r2019a the launch options
-r ...; exit(0) can be easily
replaced with the
-batch option which automatically exits matlab at the end of the command that is passed
(see here for details).
So the last command from the slurm script above for Matlab r2019a will look like:
srun matlab -nojvm -nosplash -batch "serial_Matlab($n,$m);"
Multiple serial batchjobs¶
The most common way to utilize Matlab is to write a single .M-file that can be used to run tasks as a non-interactive batch job. These jobs are then submitted as independent tasks and when the heavy part is done, the results are collected for analysis. For these kinds of jobs the Slurm array jobs is the best choice; For more information on array jobs see Array jobs in the Triton user guide.
Below you will find an example how-to prepare and run such type of jobs.
run.m file doing the actual calculation task
The file below calculates Sin-function in the interval 0-2*PI and stores the results into a file. The interval is divided into blocks that are distributed over the nodes.
function run(blockIndex,pointsPerBlock,totalBlocks) % blockindex runs from 0..totalblocks-1 % range 0..2pi length=2*pi; % values to setup even spacing between given range % and splitting the spacings to even number of points per block totalPoints=pointsPerBlock*totalBlocks; step=length/(totalPoints-1); start=blockIndex*pointsPerBlock*step; % do some calculations, store the resulst so arrays A and B for index=0:pointsPerBlock-1 i=index+1; x=start+index*step; y=sin(x); A(i)=x; B(i)=y; end % save the results based on the blockIndex to a file filename=strcat('output-',int2str(blockIndex)); save( filename, 'A', 'B', 'blockIndex'); % display message to output (log) that we have reached this far. disp(sprintf('SUCCESS blockIndex %d',blockIndex)); % exit as this is a batch-job exit;
Submission of 10 independent tasks
Below the run.m is executed as an array job with 10 array tasks, which will execute independently, potentially in parallel if there are enough idle resources. Note that it is using play partition with 5min time limit.
#!/bin/bash -l #SBATCH --time=0-00:05:00 --mem-per-cpu=500 #SBATCH -p debug #SBATCH -o job-%a.out #SBATCH --array=0-9 module load matlab matlab -nojvm -r "run($SLURM_ARRAY_TASK_ID,100,10); quit"
Submit the job with “sbatch matslurm.sh” (or whatever you called the batch job script above).
Collecting the results
Finally a wrapper script to read in the .mat files and plots you tha Sin-function calculated in parallel with 10 tasks.:
function collectResults(numberOfBlocks) X=; Y=; for index=0:numberOfBlocks-1 % read the output from the jobs filename = strcat( 'output-', int2str( index ) ); load( filename ); % catenate results to a single arrays X=cat(2,X,A); Y=cat(2,Y,B); end plot(X,Y,'b+:')
Seeding the random number generator¶
Note that by default MATLAB always initializes the random number
generator with a constant value. Thus if you launch several matlab
instances e.g. to calculate distinct ensembles, then you need to seed
the random number generator such that it’s distinct for each
instance. In order to do this, you can call the
passing the value of
$SLURM_ARRAY_TASK_ID to it.
Parallel Matlab with Matlab’s internal parallelization¶
Matlab has internal parallelization that can be activated by requesting
more than one cpu per task in the
and using the
matlab_multithread to start the interpreter.
#!/bin/bash -l #SBATCH -p short #SBATCH -t 00:15:00 #SBATCH --nodes=1 #SBATCH --ntasks=1 #SBATCH --cpus-per-task=4 #SBATCH --mem-per-cpu=2G #SBATCH -o int_parallel.out module load matlab srun time -p matlab_multithread -nojvm -nosplash -r "int_parallel() ; exit(0)"
An example function is provided in
function int_parallel() try tic; A = rand(2000,2000); A = A + A.'; B = pinv(A); max(max(B * A)) toc catch error disp('Error occured'); exit(0) end end
Parallel Natlab with parpool¶
Often one uses Matlab’s parallel pool for parallelization. When
parpool one needs to specify the number of workers. This
number should match the number of CPUs requested.
JVM so when launching the interpreter one needs to use
#!/bin/bash -l #SBATCH -p short #SBATCH -t 00:15:00 #SBATCH --nodes=1 #SBATCH --ntasks=1 #SBATCH --cpus-per-task=4 #SBATCH --mem-per-cpu=2G #SBATCH -o parpool_parallel.out module load matlab srun matlab_multithread -nodisplay -r "parpool_parallel($SLURM_CPUS_PER_TASK) ; exit(0)"
An example function is provided in
function parpool_parallel(n) % Try-catch expression that quits the Matlab session if your code crashes try % Initialize the parallel pool c=parcluster(); t=tempname() mkdir(t) c.JobStorageLocation=t; parpool(c,n); % The actual program calls from matlab's example. % The path for r2017b addpath(strcat(matlabroot, '/examples/distcomp/main')); % The path for r2016b % addpath(strcat(matlabroot, '/examples/distcomp')); % simulate 10000 blackjack hands with 100 players tic; pctdemo_aux_parforbench(10000,100,n); toc catch error getReport(error) disp('Error occured'); exit(0) end end
Parallel matlab in exclusive mode¶
#!/bin/bash -l #SBATCH -p short #SBATCH -t 00:15:00 #SBATCH --exclusive #SBATCH -o parallel_Matlab3.out export OMP_NUM_THREADS=$(nproc) module load matlab/r2017b srun -n 1 -c $OMP_NUM_THREADS matlab_multithread -nosplash -r "parallel_Matlab3($OMP_NUM_THREADS) ; exit(0)"
function parallel_Matlab3(n) % Try-catch expression that quits the Matlab session if your code crashes try % Initialize the parallel pool c=parcluster(); t=tempname() mkdir(t) c.JobStorageLocation=t; parpool(c,n); % The actual program calls from matlab's example. % The path for r2017b addpath(strcat(matlabroot, '/examples/distcomp/main')); % The path for r2016b % addpath(strcat(matlabroot, '/examples/distcomp')); pctdemo_aux_parforbench(10000,100,n); catch error getReport(error) disp('Error occured'); exit(0) end end
Hints for Condor users¶
The above example also works (even nicer way) for condor.
A wrapper script to execute matlab on the department workstation.
#!/bin/bash -l # a wrapper to run Matlab with condor block=$1 pointsPerBlock=10 totalBlocks=10 matlab -nojvm -r "run($block,$pointsPerBlock,$totalBlocks)"
Condor submission script
Condor actually contains ArrayJob functionality that makes the task easier.
## Condor submit description (script) file for my_program.exe. ## 1. Specify the [path and] name for the executable file... Executable = run.sh ## 2. Specify Condor execution environment. Universe = vanilla notify = Error ## 3. Specify remote execution machines running Linux (required)... Requirements = ((OpSys == "Linux") || (OpSysName == "Ubuntu")) ## 4. Define input files and arguments #Input = stdin.txt.$(Process) Arguments = $(Process) ## 5. Define output/error/log files Output = log/stdout.$(Process).txt Error = log/stderr.$(Process).txt Log = log/log.$(Process).txt ## 6. Tell Condor which files need to be transferred and when. Transfer_input_files = run.m Transfer_output_files = output-$(Process).mat Transfer_executable = true Should_transfer_files = YES When_to_transfer_output = ON_EXIT ## 7. Add 10 copies of the job to the queue Queue 10
FAQ / troubleshooting¶
If things randomly don’t work, you can try removing or moving either the
~/.matlab directory or
~/.matlab/Rxxxxy directory to see if it’s
caused by configuration.
Random error messages about things not loading and/or something
(Matlab Live Editor maybe) doesn’t work:
ls *.m, do you have any
unexpected files like
pathdef.m in there? Remove them.
Also, check your home quota. Often
.matlab gets large and fills up
your home directory. Check the answer at the very top of the page,
under “Matlab Configuration”.