View source for Submitting Matlab scripts to the SGE cluster

Submitting matlab jobs to the SGE cluster is a breeze, just use the following command:

 matlab.q [-t HOURS] [-d MEMORY] [-m MESSAGING] MY_SCRIPT.m

; HOURS
: (optional) This is the number of hours your script will take to run.  Choose a high number, but overestimating by too much can make you wait unnecessarily in the queue
; MEMORY
: (optional) This is the number of megabytes of memory you would like dedicated to your job (e.g. substituting a value of 1024 will give you 1 GB)
; MESSAGING
: (optional) Place the desired messaging flags here
: b = beginning
: e = end
: a = abort
: n = none
: So "-m bea" would send a message to the email account on file for you with Hoffman.  A separate message will come when the job begins, when the job ends, and if the job was aborted.
; MY_SCRIPT.m
: The m-file you want to execute.
; other options
: Try typing "matlab.q" at the command prompt on Hoffman2 and use the Info page to see the other available options.

; Keep in mind that you can only run one of these at a time since it uses a full MATLAB license.  If you are already running MATLAB on Hoffman2 and try to submit a job with matlab.q, it will fail because you are already using a license.

matlab.q will first try to compile your code and then run it.  If the compilation fails, it will run it as a job on its own.  To directly compile your code, see the instructions below.


=Submitting Multiple Jobs without Using Multiple Licenses (aka Compiling)=
The key to this approach is compiling your code using the MATLAB Compiler (MCC) then running it using the queue. Note that the MATLAB Compiler has some limitations to it.

*Each job must have a single associated .m file.
*You CANNOT use the path() function inside the .m file.

Commands to do it:
 qrsh
 module load matlab
 mcc -m my_m_file.m -R -singleCompThread -a top_path
 matexe.q my_m_file

Alternative commands:
 qrsh
 module load matlab
 mcc -m my_m_file.m -R -singleCompThread -a top_path
 matexe.q -ns my_m_file
 qsub my_m_file.cmd

;mcc -m my_m_file.m -a top_path
:This will create an executable called my_m_file
:top_path adds all files inside top_path and inside it's subfolders
:Note that the -a option can make compilation take a long time
::Consider using "-I folder1 -I folder2"
::Note that folder1 and folder2 must contain ALL of the dependencies of the compiled function, excluding the default base that MATLAB gives you.
:This step takes time, but don't try to parallelize it if you're compiling in the same directory. This will lead to errors.
:-R -singleCompThread
::This specifies that the job only needs one cpu to run instead of the default 8.
::If you include this, each job will take more time but it won't need to wait for 8 cpus to be free on a single node.
;matexe.q my_m_file
:This submits to the queue and also does the "module load matlab" command before your script is executed.
:This is the ONLY way to submit a mcc-compiled job. Other attempts to load the module manually will fail.
:-t <hours>
::This argument is 8 hours by default. [1,336] is allowed for highp.
::If you think your job may take longer than 8 hours, you MUST include this or else the job will fail precisely at 8 hours.
:-ns
::This stands for not submit. This allows you to edit your .cmd file as you desire. This is particularly useful for job arrays.

;Without using -a:
 qrsh
 module load matlab
 mcc -m my_m_file.m -I folder1 -I folder2
 matexe.q my_m_file

;L33T tip: 
:As jobs are in the queue, request up to 8 cpus of qrsh sessions at a time. This ensures that you will get, at minimum, 8 cpus of processing power at any one time.
:You are limited to 8x1cpu sessions or 1x8cpu session by ATS.
:To request a single cpu, use "qrsh -l i,time=24:00:00".
:Do this also to ensure that your compiled code works as you expect it to.

If you have more questions and/or want example scripts, ask [mailto:wesleytk@ucla.edu Wesley] and/or Hong-jing.