{"type":"doc","content":[{"type":"layoutSection","content":[{"type":"layoutColumn","attrs":{"width":66.66},"content":[{"type":"heading","attrs":{"level":1},"content":[{"text":"About this tutorial","type":"text"}]},{"type":"paragraph","content":[{"text":"This tutorial will guide you through running a job with MATLAB on ALICE. ","type":"text"}]},{"type":"heading","attrs":{"level":2},"content":[{"text":"What you will learn?","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Setting up the batch script for running a MATLAB script","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Loading the necessary modules","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Submitting your job","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Monitoring your job","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Collect information about your job","type":"text"}]}]}]},{"type":"heading","attrs":{"level":2},"content":[{"text":"What this example will not cover?","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Writing MATLAB scripts","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Optimize MATLAB jobs for HPC","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Running an interactive job for MATLAB","type":"text"}]}]}]},{"type":"heading","attrs":{"level":2},"content":[{"text":"What you should know before starting?","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Basic MATLAB knowledge.","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Basic knowledge of how to use a Linux OS from the command line.","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"How to connect to ALICE or SHARK: ","type":"text"},{"type":"inlineCard","attrs":{"url":"https://pubappslu.atlassian.net/wiki/spaces/HPCWIKI/pages/37748771"}},{"text":" ","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"How to move files to and from ALICE or SHARK: ","type":"text"},{"type":"inlineCard","attrs":{"url":"https://pubappslu.atlassian.net/wiki/spaces/HPCWIKI/pages/37749117"}},{"text":" ","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"How to setup a simple batch job as shown in ","type":"text"},{"type":"inlineCard","attrs":{"url":"https://pubappslu.atlassian.net/wiki/spaces/HPCWIKI/pages/37027928"}},{"text":" ","type":"text"}]}]}]}]},{"type":"layoutColumn","attrs":{"width":33.33},"content":[{"type":"extension","attrs":{"layout":"default","extensionType":"com.atlassian.confluence.macro.core","extensionKey":"toc","parameters":{"macroParams":{"minLevel":{"value":"1"},"maxLevel":{"value":"7"}},"macroMetadata":{"macroId":{"value":"639e9bde-94bd-4c94-8b59-33be0e007c1d"},"schemaVersion":{"value":"1"},"title":"Table of Contents"}},"localId":"e492b20d-d769-4beb-aaaf-dc376a4a7789"}}]}]},{"type":"heading","attrs":{"level":1},"content":[{"text":"MATLAB on ALICE and SHARK","type":"text"}]},{"type":"paragraph","content":[{"text":"The availability of MATLAB on ALICE and SHARK differs because MATLAB is a paid-for licensed software ","type":"text"}]},{"type":"layoutSection","content":[{"type":"layoutColumn","attrs":{"width":50.0},"content":[{"type":"rule"},{"type":"paragraph","content":[{"text":"ALICE","type":"text","marks":[{"type":"strong"}]}]},{"type":"paragraph","content":[{"text":"Leiden University has a campus license for MATLAB and the software is available on ALICE as a module. ","type":"text"}]},{"type":"paragraph","content":[{"text":"You can find a list of available versions with","type":"text"}]},{"type":"codeBlock","content":[{"text":"module avail MATLAB","type":"text"}]},{"type":"paragraph","content":[{"text":"but we recommend that you use the most recent one. Older versions might not work anymore.","type":"text"}]},{"type":"codeBlock","content":[{"text":"module load MATLAB/2023b","type":"text"}]}]},{"type":"layoutColumn","attrs":{"width":50.0},"content":[{"type":"rule"},{"type":"paragraph","content":[{"text":"SHARK","type":"text","marks":[{"type":"strong"}]}]},{"type":"paragraph","content":[{"text":"MATLAB on SHARK is not available for all SHARK users. Please check that your group is covered by the license. Check with the SHARK team.","type":"text"}]},{"type":"codeBlock","content":[{"text":"module avail MATLAB","type":"text"}]},{"type":"paragraph","content":[{"text":"Choose a module and add it to your environment by loading it, e.g.,:","type":"text"}]},{"type":"codeBlock","content":[{"text":"moduel load statistical/MATLAB/R2021a","type":"text"}]}]}]},{"type":"rule"},{"type":"heading","attrs":{"level":1},"content":[{"text":"Preparations","type":"text"}]},{"type":"paragraph","content":[{"text":"It is always a good idea to start by looking at the load of the cluster when you want to submit a job. Also, it helps to run some short, resource-friendly tests to see if your set up is working and you have a correct batch file. ","type":"text"}]},{"type":"paragraph","content":[{"text":"The “testing”-partition on ALICE or the “short” partition on SHARK can be used for such purpose. The examples in this tutorial are save to use on those partitions. ","type":"text"}]},{"type":"paragraph","content":[{"text":"Here, we will assume that you have already created a directory called ","type":"text"},{"text":"user_guide_tutorials","type":"text","marks":[{"type":"code"}]},{"text":" in your ","type":"text"},{"text":"$HOME","type":"text","marks":[{"type":"code"}]},{"text":" from the previous tutorials. For this job, let's create a sub-directory and change into it:","type":"text"}]},{"type":"codeBlock","content":[{"text":"mkdir -p $HOME/user_guide_tutorials/first_matlab_job\ncd $HOME/user_guide_tutorials/first_matlab_job","type":"text"}]},{"type":"heading","attrs":{"level":1},"content":[{"text":"A simple MATLAB job","type":"text"}]},{"type":"paragraph","content":[{"text":"In this example, we will create a very basic MATLAB script that will just print out some information and then run it through a slurm batch job. ","type":"text"}]},{"type":"heading","attrs":{"level":2},"content":[{"text":"Preparations","type":"text"}]},{"type":"heading","attrs":{"level":3},"content":[{"text":"Directory for example","type":"text"}]},{"type":"paragraph","content":[{"text":"Because this section contains further tutorials, we will create a sub-directory and change into it.","type":"text"}]},{"type":"codeBlock","content":[{"text":"mkdir -p $HOME/user_guide_tutorials/first_matlab_job/test_matlab_simple\ncd $HOME/user_guide_tutorials/first_matlab_job/test_matlab_simple","type":"text"}]},{"type":"heading","attrs":{"level":3},"content":[{"text":"The MATLAB script","type":"text"}]},{"type":"paragraph","content":[{"text":"We will use the following MATLAB script for this example and save it as ","type":"text"},{"text":"test_matlab_simple.m","type":"text","marks":[{"type":"code"}]},{"text":".","type":"text"}]},{"type":"codeBlock","attrs":{"language":"python"},"content":[{"text":"% Example for a simple MATLAB script\n\nfprintf('MATLAB script started\\n');\n\n% getting the number of cores set for the job\ncpus = str2num(getenv(\"SLURM_CPUS_PER_TASK\"));\nfprintf('Number of CPUS from Slurm job: %g\\n', cpus);\n\n% Just saying hello here\nfprintf('Hello World from MATLAB\\n');\n\nfprintf('MATLAB script finished\\n');\nexit;","type":"text"}]},{"type":"paragraph","content":[{"text":"For demonstration purposes, the script shows how to read the number of cores set for the Slurm job. The fprintf statements will write everything out to the Slurm output file.","type":"text"}]},{"type":"heading","attrs":{"level":3},"content":[{"text":"The Slurm batch file","type":"text"}]},{"type":"paragraph","content":[{"text":"The next step is to create the corresponding Slurm batch file which we will name ","type":"text"},{"text":"test_matlab_simple.slurm","type":"text","marks":[{"type":"code"}]},{"text":". We will make use of the ","type":"text"},{"text":"testing","type":"text","marks":[{"type":"em"}]},{"text":" partition on ALICE or the ","type":"text"},{"text":"short ","type":"text","marks":[{"type":"em"}]},{"text":"partition on SHARK. Make sure to change the partition and resources requirements for your production jobs. The running time and amount of memory have already been set in a way that fits to the resources that this job needs. If you do not know this, it is best to use a conservative estimate at first and then reduce the resource requirements.","type":"text"}]},{"type":"layoutSection","content":[{"type":"layoutColumn","attrs":{"width":50.0},"content":[{"type":"rule"},{"type":"paragraph","content":[{"text":"ALICE","type":"text","marks":[{"type":"strong"}]}]},{"type":"codeBlock","content":[{"text":"#!/bin/bash\n#SBATCH --job-name=test_matlab_simple\n#SBATCH --output=%x_%j.out\n#SBATCH --mail-user=\"\"\n#SBATCH --mail-type=\"ALL\"\n#SBATCH --mem=1G\n#SBATCH --time=00:05:00\n#SBATCH --partition=testing\n#SBATCH --ntasks=1\n#SBATCH --cpus-per-task=1\n\n# load modules (assuming you start from the default environment)\n# we explicitly call the modules to improve reproducibility\n# in case the default settings change\nmodule load MMATLAB/2023b\n\necho \"[$SHELL] #### Starting MATLAB test\"\necho \"[$SHELL] ## This is $SLURM_JOB_USER on $HOSTNAME and this job has the ID $SLURM_JOB_ID\"\n# get the current working directory\nexport CWD=$(pwd)\necho \"[$SHELL] ## current working directory: \"$CWD\n\n# Run the file\necho \"[$SHELL] ## Run MATLAB script\"\n# there different ways to start a matlab script\n# here we use -batch\n# Just the name of the script without \".m\"\nmatlab -batch test_matlab_simple\necho \"[$SHELL] ## Script finished\"\n\necho \"[$SHELL] #### Finished MATLAB test. Have a nice day\"","type":"text"}]}]},{"type":"layoutColumn","attrs":{"width":50.0},"content":[{"type":"rule"},{"type":"paragraph","content":[{"text":"SHARK","type":"text","marks":[{"type":"strong"}]}]},{"type":"codeBlock","content":[{"text":"#!/bin/bash\n#SBATCH --job-name=test_matlab_simple\n#SBATCH --output=%x_%j.out\n#SBATCH --mail-user=\"\"\n#SBATCH --mail-type=\"ALL\"\n#SBATCH --mem=1G\n#SBATCH --time=00:05:00\n#SBATCH --partition=short\n#SBATCH --ntasks=1\n#SBATCH --cpus-per-task=1\n\n# load modules (assuming you start from the default environment)\n# we explicitly call the modules to improve reproducibility\n# in case the default settings change\nmodule load statistical/MATLAB/R2021a\n\necho \"[$SHELL] #### Starting MATLAB test\"\necho \"[$SHELL] ## This is $SLURM_JOB_USER on $HOSTNAME and this job has the ID $SLURM_JOB_ID\"\n# get the current working directory\nexport CWD=$(pwd)\necho \"[$SHELL] ## current working directory: \"$CWD\n\n# Run the file\necho \"[$SHELL] ## Run MATLAB script\"\n# there different ways to start a matlab script\n# here we use -batch\n# Just the name of the script without \".m\"\nmatlab -batch test_matlab_simple\necho \"[$SHELL] ## Script finished\"\n\necho \"[$SHELL] #### Finished MATLAB test. Have a nice day\"","type":"text"}]}]}]},{"type":"rule"},{"type":"paragraph","content":[{"text":"where you should replace ","type":"text"},{"text":"","type":"text","marks":[{"type":"code"}]},{"text":" by an actual e-mail address of yours. ","type":"text"}]},{"type":"paragraph","content":[{"text":"The batch file will also print out some information to the Slurm output file. To separate the output from what the MATLAB script will produce, we use ","type":"text"},{"text":"[$SHELL]","type":"text","marks":[{"type":"code"}]},{"text":" here.","type":"text"}]},{"type":"paragraph","content":[{"text":"While there are different ways to run MATLAB script non-interactively, here we have used the option ","type":"text"},{"text":"-batch","type":"text","marks":[{"type":"code"}]},{"text":". It automatically prevents MATLAB from trying to start the GUI. It also does not add the splash screen output and returns a proper exit code for the MATLAB script.","type":"text"}]},{"type":"heading","attrs":{"level":2},"content":[{"text":"Job submission","type":"text"}]},{"type":"paragraph","content":[{"text":"Let us submit this MATLAB job to slurm:","type":"text"}]},{"type":"codeBlock","content":[{"text":"sbatch test_matlab_simple.slurm","type":"text"}]},{"type":"paragraph","content":[{"text":"Immediately after you have submitted this job, you should see something like this:","type":"text"}]},{"type":"codeBlock","content":[{"text":"[me@ test_matlab_sim[le]]$ sbatch test_matlab_simple.slurm\nSubmitted batch job ","type":"text"}]},{"type":"heading","attrs":{"level":2},"content":[{"text":"Job output","type":"text"}]},{"type":"paragraph","content":[{"text":"In the directory where you launched your job, there should be new file created by Slurm: ","type":"text"},{"text":"test_matlab_simple_.out","type":"text","marks":[{"type":"code"}]},{"text":". It contains all the output from your job which would have normally written to the command line. Check the file for any possible error messages. The content of the file should look something like this:","type":"text"}]},{"type":"codeBlock","content":[{"text":"[/bin/bash] #### Starting MATLAB test\n[/bin/bash] ## This is on nodelogin01 and this job has the ID \n[/bin/bash] ## current working directory: /home//user-guide-tutorials/first_matlab_job/test_matlab_simple\n[/bin/bash] ## Run MATLAB script\nMATLAB script started\nNumber of CPUS from Slurm job: 1\nHello World from MATLAB\nMATLAB script finished\n[/bin/bash] ## Script finished\n[/bin/bash] #### Finished MATLAB test. Have a nice day","type":"text"}]},{"type":"paragraph","content":[{"text":"The running time might differ when you run it. ","type":"text"}]},{"type":"paragraph","content":[{"text":"You can get a quick overview of the resources actually used by your job by running:","type":"text"}]},{"type":"codeBlock","content":[{"text":" seff ","type":"text"}]},{"type":"paragraph","content":[{"text":"The output from ","type":"text"},{"text":"seff","type":"text","marks":[{"type":"code"}]},{"text":" will probably look something like this:","type":"text"}]},{"type":"codeBlock","content":[{"text":"Job ID: \nCluster: \nUser/Group: /\nState: COMPLETED (exit code 0)\nCores: 1\nCPU Utilized: 00:00:11\nCPU Efficiency: 84.62% of 00:00:13 core-walltime\nJob Wall-clock time: 00:00:13\nMemory Utilized: 1.30 MB\nMemory Efficiency: 0.13% of 1.00 GB","type":"text"}]},{"type":"heading","attrs":{"level":1},"content":[{"text":"A MATLAB job to create a plot","type":"text"}]},{"type":"paragraph","content":[{"text":"In this example, we will create a MATLAB script that will produce a plot and run it through a slurm batch job. ","type":"text"}]},{"type":"heading","attrs":{"level":2},"content":[{"text":"Preparations","type":"text"}]},{"type":"heading","attrs":{"level":3},"content":[{"text":"Directory for example","type":"text"}]},{"type":"paragraph","content":[{"text":"As we have done for the previous example, we will create a sub-directory and change into it.","type":"text"}]},{"type":"codeBlock","content":[{"text":"mkdir -p $HOME/user_guide_tutorials/first_matlab_job/test_matlab_plot\ncd $HOME/user_guide_tutorials/first_matlab_job/test_matlab_plot","type":"text"}]},{"type":"heading","attrs":{"level":3},"content":[{"text":"The MATLAB script","type":"text"}]},{"type":"paragraph","content":[{"text":"We will use the following MATLAB script for this example and save it as ","type":"text"},{"text":"test_matlab_simple.m","type":"text","marks":[{"type":"code"}]},{"text":".","type":"text"}]},{"type":"codeBlock","attrs":{"language":"python"},"content":[{"text":"% Simple MATLAB script to create a plot\n\nfprintf(\"Generating data\\n\");\nFS=20;\nCgray = gray(10);\n\nalpha=4.0;\nbeta=1.0;\ndelta=linspace(1,50,1000);\nr=linspace(0.01,10,1000);\nTD=sqrt(alpha.*delta)+alpha./delta-beta;\nTF=2*sqrt(alpha)-beta;\nTT=alpha/beta/beta;\nYY2=sqrt(alpha./delta)-beta+alpha./beta;\nYY3=alpha./beta;\n\nfprintf(\"Creating figure\\n\");\nfigure('position',[100 100 600 500]);\nhold on;\nplot(TD,delta,'k-','linewidth',2)\nxline(TF,'-r','linewidth',2);\n% xline(TT,'--g','linewidth',2);\nplot(YY2,delta,'k-','linewidth',2)\nxline(YY3,'--','linewidth',2)\n\nfill([TD YY2(end:-1:1)], [delta delta(end:-1:1)],Cgray(9,:))\n\nxlabel('global density, $\\langle\\tau\\rangle$','Interpreter','latex','fontsize',FS)\nylabel('diffusion ratio, $\\delta$','Interpreter','latex','fontsize',FS)\nxlim([0 15])\ntext(4.5,30,'spinodal region','fontsize',FS,'Interpreter','latex');\nbox on\nset(gca,'fontsize',FS,'linewidth',2,'xminortick','off','yminortick','off',...\n 'ticklength',[0.020 0.01])\n% set(gca,'fontsize',FS,'YScale','log')\nset(gca, 'Layer', 'top');\n\nfprintf(\"Saving figure\\n\");\nsaveas(gca, 'Fig.pdf');\n\nfprintf(\"Done\\n\");\nexit;","type":"text"}]},{"type":"heading","attrs":{"level":3},"content":[{"text":"The Slurm batch file","type":"text"}]},{"type":"paragraph","content":[{"text":"For this example, we will name the slurm batch file ","type":"text"},{"text":"test_matlab_plot.slurm","type":"text","marks":[{"type":"code"}]},{"text":". We can more-or-less re-use the job script from the previous example, but for completeness the entire batch job is shown. ","type":"text"}]},{"type":"paragraph","content":[{"text":"Again, we will make use of the ","type":"text"},{"text":"testing","type":"text","marks":[{"type":"em"}]},{"text":" partition on ALICE or the ","type":"text"},{"text":"short ","type":"text","marks":[{"type":"em"}]},{"text":"partition on SHARK. Make sure to change the partition and resources requirements for your production jobs. The running time and amount of memory have already been set in a way that fits to the resources that this job needs. If you do not know this, it is best to use a conservative estimate at first and then reduce the resource requirements.","type":"text"}]},{"type":"layoutSection","content":[{"type":"layoutColumn","attrs":{"width":50.0},"content":[{"type":"rule"},{"type":"paragraph","content":[{"text":"ALICE","type":"text","marks":[{"type":"strong"}]}]},{"type":"codeBlock","content":[{"text":"#!/bin/bash\n#SBATCH --job-name=test_matlab_plot\n#SBATCH --output=%x_%j.out\n#SBATCH --mail-user=\"\"\n#SBATCH --mail-type=\"ALL\"\n#SBATCH --mem=1G\n#SBATCH --time=00:05:00\n#SBATCH --partition=testing\n#SBATCH --ntasks=1\n#SBATCH --cpus-per-task=1\n\n# load modules (assuming you start from the default environment)\n# we explicitly call the modules to improve reproducibility\n# in case the default settings change\nmodule load MATLAB/2023b\n\necho \"[$SHELL] #### Starting MATLAB test\"\necho \"[$SHELL] ## This is $SLURM_JOB_USER on $HOSTNAME and this job has the ID $SLURM_JOB_ID\"\n# get the current working directory\nexport CWD=$(pwd)\necho \"[$SHELL] ## current working directory: \"$CWD\n\n# Run the file\necho \"[$SHELL] ## Run MATLAB script\"\n# there different ways to start a matlab script\n# here we use -batch\n# Just the name of the script without \".m\"\nmatlab -batch test_matlab_plot\necho \"[$SHELL] ## Script finished\"\n\necho \"[$SHELL] #### Finished MATLAB test. Have a nice day\"","type":"text"}]}]},{"type":"layoutColumn","attrs":{"width":50.0},"content":[{"type":"rule"},{"type":"paragraph","content":[{"text":"SHARK","type":"text","marks":[{"type":"strong"}]}]},{"type":"codeBlock","content":[{"text":"#!/bin/bash\n#SBATCH --job-name=test_matlab_plot\n#SBATCH --output=%x_%j.out\n#SBATCH --mail-user=\"\"\n#SBATCH --mail-type=\"ALL\"\n#SBATCH --mem=1G\n#SBATCH --time=00:05:00\n#SBATCH --partition=short\n#SBATCH --ntasks=1\n#SBATCH --cpus-per-task=1\n\n# load modules (assuming you start from the default environment)\n# we explicitly call the modules to improve reproducibility\n# in case the default settings change\nmodule load statistical/MATLAB/R2021a\n\necho \"[$SHELL] #### Starting MATLAB test\"\necho \"[$SHELL] ## This is $SLURM_JOB_USER on $HOSTNAME and this job has the ID $SLURM_JOB_ID\"\n# get the current working directory\nexport CWD=$(pwd)\necho \"[$SHELL] ## current working directory: \"$CWD\n\n# Run the file\necho \"[$SHELL] ## Run MATLAB script\"\n# there different ways to start a matlab script\n# here we use -batch\n# Just the name of the script without \".m\"\nmatlab -batch test_matlab_plot\necho \"[$SHELL] ## Script finished\"\n\necho \"[$SHELL] #### Finished MATLAB test. Have a nice day\"","type":"text"}]}]}]},{"type":"rule"},{"type":"paragraph","content":[{"text":"where you should replace ","type":"text"},{"text":"","type":"text","marks":[{"type":"code"}]},{"text":" by an actual e-mail address of yours. ","type":"text"}]},{"type":"heading","attrs":{"level":2},"content":[{"text":"Job submission","type":"text"}]},{"type":"paragraph","content":[{"text":"Let us submit this MATLAB job to slurm:","type":"text"}]},{"type":"codeBlock","content":[{"text":"sbatch test_matlab_plot.slurm","type":"text"}]},{"type":"paragraph","content":[{"text":"Immediately after you have submitted this job, you should see something like this:","type":"text"}]},{"type":"codeBlock","content":[{"text":"[me@ test_matlab_plot]$ sbatch test_matlab_plot.slurm\nSubmitted batch job ","type":"text"}]},{"type":"heading","attrs":{"level":2},"content":[{"text":"Job output","type":"text"}]},{"type":"paragraph","content":[{"text":"In the directory where you launched your job, there should be new file created by Slurm: ","type":"text"},{"text":"test_matlab_simple_.out","type":"text","marks":[{"type":"code"}]},{"text":". It contains all the output from your job which would have normally written to the command line. Check the file for any possible error messages. The content of the file should look something like this:","type":"text"}]},{"type":"codeBlock","content":[{"text":"[/bin/bash] #### Starting MATLAB test\n[/bin/bash] ## This is on nodelogin01 and this job has the ID \n[/bin/bash] ## current working directory: /home//user-guide-tutorials/first_matlab_job/test_matlab_plot\n[/bin/bash] ## Run MATLAB script\nGenerating data\nCreating figure\nWarning: MATLAB has disabled some advanced graphics rendering features by\nswitching to software OpenGL. For more information, click here.\nSaving figure\nDone\n[/bin/bash] ## Script finished\n[/bin/bash] #### Finished MATLAB test. Have a nice day","type":"text"}]},{"type":"paragraph","content":[{"text":"The running time might differ when you run it. ","type":"text"}]},{"type":"paragraph","content":[{"text":"You can get a quick overview of the resources actually used by your job by running:","type":"text"}]},{"type":"codeBlock","content":[{"text":" seff ","type":"text"}]},{"type":"paragraph","content":[{"text":"The output from ","type":"text"},{"text":"seff","type":"text","marks":[{"type":"code"}]},{"text":" will probably look something like this:","type":"text"}]},{"type":"codeBlock","content":[{"text":"Job ID: \nCluster: \nUser/Group: /\nState: COMPLETED (exit code 0)\nCores: 1\nCPU Utilized: 00:00:20\nCPU Efficiency: 95.24% of 00:00:21 core-walltime\nJob Wall-clock time: 00:00:21\nMemory Utilized: 1.30 MB\nMemory Efficiency: 0.13% of 1.00 GB","type":"text"}]},{"type":"heading","attrs":{"level":1},"content":[{"text":"A simple parallel MATLAB job","type":"text"}]},{"type":"paragraph","content":[{"text":"In this example, we will create a simple MATLAB script which does parallel calculations and run it through a slurm batch job. ","type":"text"}]},{"type":"heading","attrs":{"level":2},"content":[{"text":"Preparations","type":"text"}]},{"type":"heading","attrs":{"level":3},"content":[{"text":"Directory for example","type":"text"}]},{"type":"paragraph","content":[{"text":"As we have done for the previous example, we will create a sub-directory and change into it.","type":"text"}]},{"type":"codeBlock","content":[{"text":"mkdir -p $HOME/user_guide_tutorials/first_matlab_job/test_matlab_parallel\ncd $HOME/user_guide_tutorials/first_matlab_job/test_matlab_parallel","type":"text"}]},{"type":"heading","attrs":{"level":3},"content":[{"text":"The MATLAB script","type":"text"}]},{"type":"paragraph","content":[{"text":"We will use the following MATLAB script for this example and save it as ","type":"text"},{"text":"test_matlab_simple.m","type":"text","marks":[{"type":"code"}]},{"text":".","type":"text"}]},{"type":"codeBlock","attrs":{"language":"python"},"content":[{"text":"% Example of a parallel MATLAB script with parpool\n% Based on https://researchcomputing.princeton.edu/support/knowledge-base/matlab#slurm\n\ncpus = str2num(getenv(\"SLURM_CPUS_PER_TASK\"));\nfprintf('Number of CPUS from Slurm job: %g\\n', cpus);\n\ncluster = parcluster;\npoolobj = parpool(cluster,cpus-1);\nfprintf('Number of workers: %g\\n', poolobj.NumWorkers);\n\nn = 20;\nA = 50;\na = zeros(n);\n\nfprintf('Starting parallel processing\\n');\nparfor (i=1:n,cluster)\n start_time = datetime;\n a(i) = max(abs(eig(rand(A))));\n % just for demonstration purposes\n fprintf('Iteration %g started %s: %g (took %gs)\\n', i, start_time, a(i), seconds(datetime - start_time));\n\nend\nfprintf('Finished parallel processing\\n');\nexit;","type":"text"}]},{"type":"paragraph","content":[{"text":" Here, we use ","type":"text"},{"text":"parpool","type":"text","marks":[{"type":"code"}]},{"text":" to create pool of Process workers (not Thread workers). This script is just an example for parallel processing in MATLAB and not optimized in any way. For example, it is generally not a good idea to print out information at every iteration because the print statements are executed in parallel, but they write to the same file. This is done here only for demonstrating the parallelization.","type":"text"}]},{"type":"heading","attrs":{"level":3},"content":[{"text":"The Slurm batch file","type":"text"}]},{"type":"paragraph","content":[{"text":"For this example, we will name the slurm batch file ","type":"text"},{"text":"test_matlab_parallel.slurm","type":"text","marks":[{"type":"code"}]},{"text":". Once again, we can re-use the job script from the previous example and adjust it slightly.","type":"text"}]},{"type":"paragraph","content":[{"text":"The most important change is that we set ","type":"text"},{"text":"#SBATCH --cpus-per-task=4","type":"text","marks":[{"type":"code"}]},{"text":" so that Slurm assigns multiple cores (here 4) to our job. We also switched from ","type":"text"},{"text":"#SBATCH --mem","type":"text","marks":[{"type":"code"}]},{"text":" to ","type":"text"},{"text":"#SBATCH --mem-per-cpu","type":"text","marks":[{"type":"code"}]},{"text":" to specify the amount of memory. Of course, we also changed the name of the job and MATLAB script.","type":"text"}]},{"type":"paragraph","content":[{"text":"Again, we will make use of the ","type":"text"},{"text":"testing","type":"text","marks":[{"type":"em"}]},{"text":" partition on ALICE or the ","type":"text"},{"text":"short ","type":"text","marks":[{"type":"em"}]},{"text":"partition on SHARK. Make sure to change the partition and resources requirements for your production jobs. The running time and amount of memory have already been set in a way that fits to the resources that this job needs. If you do not know this, it is best to use a conservative estimate at first and then reduce the resource requirements.","type":"text"}]},{"type":"layoutSection","content":[{"type":"layoutColumn","attrs":{"width":50.0},"content":[{"type":"rule"},{"type":"paragraph","content":[{"text":"ALICE","type":"text","marks":[{"type":"strong"}]}]},{"type":"codeBlock","content":[{"text":"#!/bin/bash\n#SBATCH --job-name=test_matlab_parallel\n#SBATCH --output=%x_%j.out\n##SBATCH --mail-user=\"\"\n##SBATCH --mail-type=\"ALL\"\n#SBATCH --mem-per-cpu=4G\n#SBATCH --time=00:05:00\n#SBATCH --partition=testing\n#SBATCH --ntasks=1\n#SBATCH --cpus-per-task=4\n\n# load modules (assuming you start from the default environment)\n# we explicitly call the modules to improve reproducibility\n# in case the default settings change\nmodule load MATLAB/2023b\n\necho \"[$SHELL] #### Starting MATLAB test\"\necho \"[$SHELL] ## This is $SLURM_JOB_USER on $HOSTNAME and this job has the ID $SLURM_JOB_ID\"\n# get the current working directory\nexport CWD=$(pwd)\necho \"[$SHELL] ## current working directory: \"$CWD\n\n# Run the file\necho \"[$SHELL] ## Run MATLAB script\"\nmatlab -batch test_matlab_parallel\necho \"[$SHELL] ## Script finished\"\n\necho \"[$SHELL] #### Finished MATLAB test. Have a nice day\"","type":"text"}]}]},{"type":"layoutColumn","attrs":{"width":50.0},"content":[{"type":"rule"},{"type":"paragraph","content":[{"text":"SHARK","type":"text","marks":[{"type":"strong"}]}]},{"type":"codeBlock","content":[{"text":"#!/bin/bash\n#SBATCH --job-name=test_matlab_parallel\n#SBATCH --output=%x_%j.out\n##SBATCH --mail-user=\"\"\n##SBATCH --mail-type=\"ALL\"\n#SBATCH --mem-per-cpu=1G\n#SBATCH --time=00:05:00\n#SBATCH --partition=short\n#SBATCH --ntasks=1\n#SBATCH --cpus-per-task=4\n\n# load modules (assuming you start from the default environment)\n# we explicitly call the modules to improve reproducibility\n# in case the default settings change\nmodule load MATLAB/2022b\n\necho \"[$SHELL] #### Starting MATLAB test\"\necho \"[$SHELL] ## This is $SLURM_JOB_USER on $HOSTNAME and this job has the ID $SLURM_JOB_ID\"\n# get the current working directory\nexport CWD=$(pwd)\necho \"[$SHELL] ## current working directory: \"$CWD\n\n# Run the file\necho \"[$SHELL] ## Run MATLAB script\"\nmatlab -batch test_matlab_parallel\necho \"[$SHELL] ## Script finished\"\n\necho \"[$SHELL] #### Finished MATLAB test. Have a nice day\"","type":"text"}]}]}]},{"type":"rule"},{"type":"paragraph","content":[{"text":"where you should replace ","type":"text"},{"text":"","type":"text","marks":[{"type":"code"}]},{"text":" by an actual e-mail address of yours. ","type":"text"}]},{"type":"heading","attrs":{"level":2},"content":[{"text":"Job submission","type":"text"}]},{"type":"paragraph","content":[{"text":"Let us submit this MATLAB job to slurm:","type":"text"}]},{"type":"codeBlock","content":[{"text":"sbatch test_matlab_parallel.slurm","type":"text"}]},{"type":"paragraph","content":[{"text":"Immediately after you have submitted this job, you should see something like this:","type":"text"}]},{"type":"codeBlock","content":[{"text":"[me@ test_matlab_plot]$ sbatch test_matlab_parallel.slurm\nSubmitted batch job ","type":"text"}]},{"type":"heading","attrs":{"level":2},"content":[{"text":"Job output","type":"text"}]},{"type":"paragraph","content":[{"text":"In the directory where you launched your job, there should be new file created by Slurm: ","type":"text"},{"text":"test_matlab_simple_.out","type":"text","marks":[{"type":"code"}]},{"text":". It contains all the output from your job which would have normally written to the command line. Check the file for any possible error messages. The content of the file should look something like this:","type":"text"}]},{"type":"codeBlock","content":[{"text":"[/bin/bash] #### Starting MATLAB test\n[/bin/bash] ## This is on nodelogin01 and this job has the ID \n[/bin/bash] ## current working directory: /home//user-guide-tutorials/first_matlab_job/test_matlab_parallel\n[/bin/bash] ## Run MATLAB script\nNumber of CPUS from Slurm job: 4\nStarting parallel pool (parpool) using the 'Processes' profile ...\nConnected to the parallel pool (number of workers: 4).\nNumber of workers: 4\nStarting parallel processing\nIteration 2 started 10-Nov-2023 14:12:35: 25.1099 (took 0.257216s)\nIteration 4 started 10-Nov-2023 14:12:39: 24.9113 (took 0.216974s)\nIteration 1 started 10-Nov-2023 14:12:40: 25.0373 (took 0.22236s)\nIteration 3 started 10-Nov-2023 14:12:41: 24.9415 (took 0.244377s)\nIteration 5 started 10-Nov-2023 14:12:54: 24.789 (took 0.173497s)\nIteration 6 started 10-Nov-2023 14:13:02: 25.1175 (took 0.195869s)\nIteration 7 started 10-Nov-2023 14:13:04: 24.9419 (took 0.268012s)\nIteration 8 started 10-Nov-2023 14:13:06: 25.5467 (took 0.241785s)\nIteration 9 started 10-Nov-2023 14:13:16: 25.0073 (took 0.194753s)\nIteration 10 started 10-Nov-2023 14:13:25: 24.7405 (took 0.289914s)\nIteration 11 started 10-Nov-2023 14:13:25: 24.7002 (took 0.182165s)\nIteration 12 started 10-Nov-2023 14:13:25: 25.2093 (took 0.184685s)\nIteration 13 started 10-Nov-2023 14:13:35: 24.9931 (took 0.17234s)\nIteration 14 started 10-Nov-2023 14:13:43: 25.3847 (took 0.207539s)\nIteration 15 started 10-Nov-2023 14:13:43: 24.6339 (took 0.184508s)\nIteration 16 started 10-Nov-2023 14:13:43: 25.1662 (took 0.203561s)\nIteration 17 started 10-Nov-2023 14:13:52: 25.0236 (took 0.210807s)\nIteration 18 started 10-Nov-2023 14:14:00: 24.7586 (took 0.153341s)\nIteration 19 started 10-Nov-2023 14:14:00: 25.3056 (took 0.199779s)\nIteration 20 started 10-Nov-2023 14:14:00: 25.2567 (took 0.159019s)\nFinished parallel processing\n[/bin/bash] ## Script finished\n[/bin/bash] #### Finished Python test. Have a nice day","type":"text"}]},{"type":"paragraph","content":[{"text":"The running time might differ when you run it. ","type":"text"}]},{"type":"paragraph","content":[{"text":"You can get a quick overview of the resources actually used by your job by running:","type":"text"}]},{"type":"codeBlock","content":[{"text":" seff ","type":"text"}]},{"type":"paragraph","content":[{"text":"The output from ","type":"text"},{"text":"seff","type":"text","marks":[{"type":"code"}]},{"text":" will probably look something like this:","type":"text"}]},{"type":"codeBlock","content":[{"text":"Job ID: \nCluster: \nUser/Group: /\nState: COMPLETED (exit code 0)\nNodes: 1\nCores per node: 4\nCPU Utilized: 00:05:53\nCPU Efficiency: 92.89% of 00:06:20 core-walltime\nJob Wall-clock time: 00:01:35\nMemory Utilized: 11.02 GB\nMemory Efficiency: 68.85% of 16.00 GB","type":"text"}]},{"type":"paragraph"},{"type":"paragraph","content":[{"text":"Further reading: ","type":"text"},{"type":"hardBreak"},{"text":"* Howto run Matlab in an interactive shell: ","type":"text"},{"text":"Calling MATLAB Functions From the Command Line in Linux","type":"text","marks":[{"type":"link","attrs":{"href":"https://www.baeldung.com/linux/matlab-functions-terminal"}}]}]}],"version":1}

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