Matlab ====== Matlab is a bit of a problem child on the Tardis. While the `MATLAB Distributed Computing Server`_ product aims to implement a compatibility layer to a number of PBS based clusters it just doesn't work reliably for a number of reasons. Because there are only a limited number of shared licenses available, it's generally not feasible to run an arbitrary number of Matlab sessions in the form of jobs. A workaround is to "compile" a script and create a standalone redistribution environment, which does not require a license to run. .. important:: You can check https://lipsupport.mpib-berlin.mpg.de/licstat for the current license usage at the institute. Keep in mind that *one* license is necessary for each user on each unique host. So 3 users, each submitting jobs to any 4 hosts will result in 12 licenses. Different Matlab versions are available via environment modules. You can list them with :program:`module avail matlab` and activate a specific version with :program:`module load matlab/`. Regular sessions ---------------- **If** there are free licenses available and you just need a quick way to spawn a single Matlab session, there is nothing wrong with just running Matlab as is. This might especially be useful if you simply need a node with lot's of memory or if you want to test your code. In an interactive job you could simply enter "matlab" and it will warn you about there not being a display available and start in command line mode. .. code-block:: bash srun --mem 100gb -p test --pty /bin/bash # run an interactive job module load matlab/R2012b # in that job, run matlab matlab < M A T L A B (R) > Copyright 1984-2012 The MathWorks, Inc. R2012a (7.14.0.739) 64-bit (glnxa64) February 9, 2012 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> _ In a job context you would just run :program:`matlab -r main` with main.m containing your script: .. code-block:: bash sbatch --wrap "module load matlab/R2014b; matlab -r main" Compiling --------- Once you leave the testing stage and would like to spawn an arbitrary number of matlab jobs/processes you have to compile your script with :program:`mcc`. A reliable pattern is to create a main file :file:`project.m` that contains a function with the same name and expects some arguments you would like to loop over. A little like this maybe: .. code-block:: matlab function project(subject_id, sigma) % % my main program implementing foo % % arguments % --------- % % subject_id: a string encoding the subject id % sigma: a string encoding values for sigma sigma = str2num(sigma); repmat(cellstr(subject_id), 1, sigma) Running :program:`mcc -m project.m` would then "compile" (or rather encrypt and package) your function and output a system dependent binary named :file:`project` and a wrapper script :file:`run_project.sh`. To run it you now have to combine the wrapper script, the location of a Matlab Compile Runtime or the local installation path of the Matlab instance, that was used by mcc, and a sufficient number of arguments for the function project(). Example: .. code-block:: matlab mcc -m project.m ./run_project.sh /opt/matlab/interactive 42 5 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/opt/matlab/interactive/runtime/glnxa64:/opt/matlab/interactive/bin/glnxa64:/opt/matlab/interactive/sys/os/glnxa64:/opt/matlab/interactive/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/opt/matlab/interactive/sys/java/jre/glnxa64/jre/lib/amd64/server:/opt/matlab/interactive/sys/java/jre/glnxa64/jre/lib/amd64/client:/opt/matlab/interactive/sys/java/jre/glnxa64/jre/lib/amd64 Warning: No display specified. You will not be able to display graphics on the screen. ans = '42' '42' '42' '42' '42' To include toolboxes in your script you have to add them during the compile step so they get included in your package. Matlab built-in toolboxes such as signal processing or statistics are detected automatically by scanning the functions used in your script and don't need to be added explicitly. Compiled scripts can't use the :program:`addpath()` function at runtime. You can guard those calls however with the function :program:`isdeployed()`, which will return 1 when Matlab detects that it runs as a compiled script and 0 otherwise. Example: Suppose you collect your project library in a toolbox called project, which in turn uses the function :program:`normrnd()` from the statistics package: .. code-block:: bash cat matlab/tools/project/myrnd.m function X = myrnd(arg) X = normrnd(0, 1, arg, arg); You can then either use the "-a" or the "-I" switch of mcc to add your own toolbox. + **-a** will add the functions or directories listed directly to the compiled package/archive + **-I** (uppercase i) will add the location to the mcc search path so it get's included implicitly Both options should work fine. The example below uses mcc from matlab R2014b, but you can use any version. The important part is to use the same Matlab version as MCR upon script invocation with :program:`run_project.sh`. .. code-block:: matlab module load matlab/R2014b cat project.m function project(arg1) myrnd(str2num(arg1)) mcc -m project.m -a matlab/tools/project [...] ./run_project.sh /opt/matlab/R2014b 3 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/opt/matlab/R2014b/runtime/glnxa64:/opt/matlab/R2014b/bin/glnxa64:/opt/matlab/R2014b/sys/os/glnxa64:/opt/matlab/R2014b/sys/opengl/lib/glnxa64 ans = 0.5377 0.8622 -0.4336 1.8339 0.3188 0.3426 -2.2588 -1.3077 3.5784 .. note:: You only have to compile your project once and can then use it any number of times. Matlab extracts your package to a shared hidden folder called `.mcrCache`. Those folders sometimes get corrupted by Matlab, especially when multiple jobs start at exactly the same time. The only workaround so far is to add a sleep 1s between qsub/sbatch calls and hope there is no collision. Also, it makes sense to regularly remove those directories. But make sure all your jobs have finished before removing them with :file:`rm -rf .mcrCache*`. SPM --- SPM already comes as a pre-compiled version and can, identical to the examples above, be started with :program:`run_spm12.sh`. Usually users are exporting a number of batch files with the spm gui on their local machine, change the paths to reflect the names on the tardis and then call :program:`run_spm12.sh` with the **run** parameter for each batch file. Example: segmentation for a number of nifti images. The file batch.template contains the string :`%%IMAGE%%` as a placeholder so we can easily replace it with the current image path and create a number of new batches from a single template: .. code-block:: bash #!/bin/bash i=0 for image in tp2/Old/*.nii ; do fullpath=$PWD/$image sed "s#%%IMAGE%%#$fullpath#" batch.template > batch_${i}.m sbatch --wrap "run_spm12.sh /opt/matlab/interactive run $PWD/batch_${i}.m" i=$((i+1)) done Sometimes it ***might be*** necessary to recompile the spm toolbox yourself, for instance if you need a specific version or if you want to add external toolboxes to SPM (e.g. cat12). .. code-block:: matlab matlab Warning: No display specified. You will not be able to display graphics on the screen. < M A T L A B (R) > Copyright 1984-2012 The MathWorks, Inc. R2012a (7.14.0.739) 64-bit (glnxa64) February 9, 2012 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> addpath(genpath('/home/mpib/krause/matlab/tools/spm12')) >> spm_make_standalone() [... lot's of output and warnings ...] Processing /opt/matlab/R2012a/toolbox/matlab/mcc.enc [... lot's of output and warnings ...] Generating file "/home/mpib/krause/matlab/tools/spm_exec/readme.txt".Gen Generating file "/home/mpib/krause/matlab/tools/spm12/../spm_exec/run_spm12.sh". >> This should create a folder :file:`spm_exec` below the spm toolbox location containing the fresh :program:`spm12` and :program:`run_spm12.sh` which you can then use in your jobs just like above. Fieldtrip --------- To properly add the fieldtrip toolbox we have to jump through some more hoops. For now the only reliable and flexible way is to run :program:`mcc()` from within a Matlab session and make sure to run :program:`ft_defaults()` first. Also, some of the provided mex files won't work out of the box, so we have to recompile them using :program:`ft_compile_mex()`. This however stumbles over some external C file called :file:`CalcMD5.c` using non-standard comments. The following Matlab Script has been successfully used to create a compiled script from a :file:`main.m` file, which relies on internal fieldtrip functions. .. code-block:: matlab % setup path basepath='/home/mpib/krause/matlab/tools/ConMemEEGTools/' addpath([basepath, '/fieldtrip-20150930']) ft_defaults() % re-compile mex functions (this has to be done only once per fieldtrip version) % "fix" the CalcMD5.c file system(['sed -i ''s#//.*##g'' ', basepath, '/fieldtrip-20150930/external/fileexchange/CalcMD5.c']) % and compile ft_compile_mex(true) % build the runtime environment mcc('-m', 'main.m') .. _`MATLAB Distributed Computing Server`: http://de.mathworks.com/help/mdce/index.html