MATLAB [MATrix LABoratory] is an integrated technical computing environment from The Mathworks that combines numeric computation, 2- and 3-d graphics & visualisation, and a high-level programming language.<\/p>\n
Version 2017a is the most up to date version installed on the CSF.<\/p>\n
Only compiled MATLAB applications should be used on the CSF; interactive use of MATLAB is strongly discouraged. The only MATLAB components you should run on the login node are the Please note that a MATLAB job cannot run on more than one CSF node. This is because the University does not have licenses for the distributed computing server product. The maximum job size is therefore 12 cores. Please get in touch if you would like help assessing the requirements of your job.<\/p>\n To set up the MATLAB environment, you need to issue the following command<\/p>\n gcc version 4.9.x is requried for MATLAB 2017a:\u00a0loading the MATLAB module (e.g. by using the command above) will automatically load this for you.<\/p>\n gcc version 4.7.x is required for MATLAB 2016a, 2015a and 2014a; loading the MATLAB module (e.g. by using the command above) will automatically load this for you.<\/p>\n Older versions of MATLAB are available using one of:<\/p>\n You must<\/strong> compile your MATLAB code before running it on the CSF in the batch system.<\/p>\n NOTE: If you are running an application that uses random numbers, it is suggested that you read and understand the article Parallel Random Numbers in MATLAB<\/a><\/p>\n The following toolboxes are available in MATLAB R2016a and R2015a<\/p>\n The following toolboxes are available in MATLAB 2014a<\/p>\n The following toolboxes are available in MATLAB 2013a and below<\/p>\n Please note that some of these toolboxes have extremely limited numbers of licenses. For example, there are only two licenses for the Bioinformatics toolbox site-wide.<\/p>\n If you can’t access one of the above toolboxes, or if you need to use a toolbox that isn’t included here, please read the advice given at the following URL. It gives advice on how to use alternatives to toolboxes along with contact details of IS Staff who can facilitate the purchase of extra toolboxes.<\/p>\n The following are available:<\/p>\n Version 12 latest:<\/p>\n Version 12 revision 6906: Version 12 revision 5953: After loading the SPM module file, the SPM toolbox should be compiled as follows:<\/p>\n If you need to use code from your own toolbox, you will need to modify the compilation command above to include your toolbox folder using the After compilation, change directory to your SPM12 standalone directory so that our jobscript can find the files we compiled above:<\/p>\n Then use this line in your job script (instead of the usual matlab commands):<\/p>\n The compiled spm12 code will run the matlab code you have written in yourscript.m<\/em> but this is still essentially a compiled matlab job so will be kind to the license servers.<\/p>\n You should set your <\/p>\n Overview MATLAB [MATrix LABoratory] is an integrated technical computing environment from The Mathworks that combines numeric computation, 2- and 3-d graphics & visualisation, and a high-level programming language. Version 2017a is the most up to date version installed on the CSF. Restrictions on use Only compiled MATLAB applications should be used on the CSF; interactive use of MATLAB is strongly discouraged. The only MATLAB components you should run on the login node are the mcc\u00a0and.. Read more »<\/a><\/p>\n","protected":false},"author":2,"featured_media":0,"parent":31,"menu_order":0,"comment_status":"open","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-233","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/233","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/comments?post=233"}],"version-history":[{"count":21,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/233\/revisions"}],"predecessor-version":[{"id":3731,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/233\/revisions\/3731"}],"up":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/31"}],"wp:attachment":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/media?parent=233"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}mcc<\/code>\u00a0and mex compilers.<\/p>\nSet up procedure<\/h2>\n
module load apps\/binapps\/matlab\/R2017a<\/pre>\n
Change in behaviour<\/h4>\n
module load apps\/binapps\/matlab\/R2016a\r\nmodule load apps\/binapps\/matlab\/R2015a\r\nmodule load apps\/binapps\/matlab\/R2014a\r\nmodule load apps\/binapps\/matlab\/R2013a\r\nmodule load apps\/binapps\/matlab\/R2012a\r\nmodule load apps\/binapps\/matlab\/R2011a\r\nmodule load apps\/binapps\/matlab\/R2010a\r\n\r\n<\/pre>\n
Running the application<\/h2>\n
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Official Toolboxes<\/h2>\n
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Additional Toolboxes<\/h2>\n
CVX<\/a><\/h3>\n
module load apps\/binapps\/matlab\/thirdparty\/cvx\/2.1<\/code><\/p>\nYALMIP<\/a><\/h3>\n
module load apps\/binapps\/matlab\/thirdparty\/yalmip\/R20160930<\/code><\/p>\nSDETools<\/a><\/h3>\n
module load apps\/binapps\/matlab\/thirdparty\/sdetools\/1.2<\/code><\/p>\nSPM<\/a><\/h3>\n
\r\nmodule load apps\/binapps\/matlab\/thirdparty\/spm\/12-latest\r\n #\r\n # !!! Note this will always point to the most recent version we have added\r\n # If you need a specific version or do not want anything to unexpectedly change\r\n # please ensure you use a specific modulefile from those below\r\n<\/pre>\n
module load apps\/binapps\/matlab\/thirdparty\/spm\/12-r6906<\/code><\/p>\nmodule load apps\/binapps\/matlab\/thirdparty\/spm\/12b<\/code><\/p>\nCompilation (basic usage)<\/h4>\n
\r\n# Create a directory in your scratch area and use that directory name in all commands.\r\n# This is easy to do if we set an environment variable:\r\nexport SPM12_STANDALONE=~\/scratch\/SPM12-standalone\r\nmkdir -p $SPM12_STANDALONE\r\n\r\n# Now compile the spm12 wrapper script in to our directory:\r\nmcc -m -C -v -o spm12 -d $SPM12_STANDALONE -N -p $MATLAB_HOME\/toolbox\/signal\/ -R singleCompThread \\\r\n -a $SPM12_ROOT $SPM12_ROOT\/spm_standalone.m\r\n<\/pre>\n
Compilation (including your own toolbox code)<\/h3>\n
-a<\/code> flag as follows:<\/p>\n\r\n# Create a directory in your scratch area and use that directory name in all commands.\r\n# This is easy to do if we set an environment variable:\r\nexport SPM12_STANDALONE=~\/scratch\/SPM12-standalone\r\nmkdir -p $SPM12_STANDALONE\r\n\r\nmcc -m -C -v -o spm12 -d $SPM12_STANDALONE -N -p $MATLAB_HOME\/toolbox\/signal -R singleCompThread \\\r\n -a $SPM12_ROOT -a path\/to\/yourtoolbox<\/strong> $SPM12_ROOT\/spm_standalone.m\r\n<\/pre>\n
Submitting a job<\/h3>\n
cd $SPM12_STANDALONE<\/pre>\n
.\/run_spm12.sh $MATLAB_HOME script yourscript.m<\/em> # Replace yourscript.m<\/em> with the name of your script\r\n<\/pre>\n
Marsbar<\/a> and fieldtrip<\/a><\/h3>\n
\/opt\/gridware\/apps\/binapps\/matlab\/third_party_toolboxes\/marsbar<\/code>
\n\/opt\/gridware\/apps\/binapps\/matlab\/third_party_toolboxes\/fieldtrip<\/code><\/p>\nMATLABPATH<\/code> appropriately to use them.<\/p>\nNAG<\/a><\/h3>\n
module load apps\/binapps\/matlab\/thirdparty\/nag\/25<\/code><\/p>\nFurther information<\/h2>\n
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