Hoffman2:MATLAB - Revision history

Jpdiaz: /* Software Versions */ update matlab versions available after centos7 upgrade

2021-11-11T19:07:21Z

Software Versions: update matlab versions available after centos7 upgrade

← Older revision		Revision as of 19:07, 11 November 2021
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	# You can also load different versions of MATLAB:		# You can also load different versions of MATLAB:
	# module load matlab/7.14		# module load matlab/8.6
	# or		# or
	# module load matlab/~~8.1~~		# module load matlab/R2020b
	# Try using "module help" for more information		# Try using "module help" for more information

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	==Software Versions==		==Software Versions==
	The current default version of MATLAB on Hoffman2 is ~~R2015b~~, but ~~more recent~~ versions are also available for use:		The current default version of MATLAB on Hoffman2 is R2020a, but other versions are also available for use:

	~~R2016b or matlab/9.1~~
	~~R2019b or matlab/9.7~~
	~~R2020a or matlab/9.8~~


			R2015b or matlab/8.6
			R2020b or matlab/R2020b

	==External Links==		==External Links==
	*[https://www.hoffman2.idre.ucla.edu/Using-H2/Software/Software.html#matlab MATLAB on Hoffman2]		*[https://www.hoffman2.idre.ucla.edu/Using-H2/Software/Software.html#matlab MATLAB on Hoffman2]

Hwang: /* Large Computations */

2021-07-26T18:00:41Z

Large Computations

← Older revision		Revision as of 18:00, 26 July 2021
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	<pre>		<pre>
	# Request an interactive node with time and memory required. In this case, 10 hours and 4GB RAM		# Request an interactive node with time and memory required. In this case, 10 hours and 4GB RAM
	~~'''~~$ qrsh -l i,h_rt=10:00:00,h_data=4G		<!--$ qrsh -l i,h_rt=10:00:00,h_data=4G-->
	$ qrsh -l h_rt=10:00:00,h_data=4G		$ qrsh -l h_rt=10:00:00,h_data=4G

Hwang: /* Large Computations */

2021-07-26T17:59:45Z

Large Computations

← Older revision		Revision as of 17:59, 26 July 2021
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	<pre>		<pre>
	# Request an interactive node with time and memory required. In this case, 10 hours and 4GB RAM		# Request an interactive node with time and memory required. In this case, 10 hours and 4GB RAM
	'''$ qrsh -l i,h_rt=10:00:00,h_data=4G~~'''~~		'''$ qrsh -l i,h_rt=10:00:00,h_data=4G
	$ qrsh -l h_rt=10:00:00,h_data=4G		$ qrsh -l h_rt=10:00:00,h_data=4G

Hwang: /* Large Computations */

2021-07-26T17:59:10Z

Large Computations

← Older revision		Revision as of 17:59, 26 July 2021
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	<pre>		<pre>
	# Request an interactive node with time and memory required. In this case, 10 hours and 4GB RAM		# Request an interactive node with time and memory required. In this case, 10 hours and 4GB RAM
	$ qrsh -l i,h_rt=10:00:00,h_data=4G		'''$ qrsh -l i,h_rt=10:00:00,h_data=4G'''
			$ qrsh -l h_rt=10:00:00,h_data=4G

	# Load the module MATLAB		# Load the module MATLAB
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	or requesting it across several processors <code>h_data=4G -pe shared 5</code> (total 5 * 4G = 20GB memory).		or requesting it across several processors <code>h_data=4G -pe shared 5</code> (total 5 * 4G = 20GB memory).
	<br>If the GUI is not necessary for running your scripts, then consider launching matlab via text-based interface by issuing the command <code>matlab -nojvm -nodisplay -nosplash</code>.		<br>If the GUI is not necessary for running your scripts, then consider launching matlab via text-based interface by issuing the command <code>matlab -nojvm -nodisplay -nosplash</code>.


	==Running Parallel Jobs==		==Running Parallel Jobs==

Hwang: /* Running Parallel Jobs */

2021-05-06T22:18:53Z

Running Parallel Jobs

← Older revision		Revision as of 22:18, 6 May 2021
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	5) To familiarize with the submission procedure you could copy the content of the directory:		5) To familiarize with the submission procedure you could copy the content of the directory:
	#* cp /u/local/apps/submit_scripts/MATLAB_PARALLEL_BATCH_SUBMISSION/* ./		#* $cp /u/local/apps/submit_scripts/MATLAB_PARALLEL_BATCH_SUBMISSION/* ./

	7) In a local test directory and issue:		7) In a local test directory and issue:
	#* ./matlab_batch_parallel_job_submit.sh -t 3 -s 20 -m 4 -v 9.7 -f ./myparpooltest_batch.m		#* $./matlab_batch_parallel_job_submit.sh -t 3 -s 20 -m 4 -v 9.7 -f ./myparpooltest_batch.m
	(Path: /u/local/apps/submit_scripts/MATLAB_PARALLEL_BATCH_SUBMISSION/myparpooltest_batch.m)		(Path: /u/local/apps/submit_scripts/MATLAB_PARALLEL_BATCH_SUBMISSION/myparpooltest_batch.m)

Hwang at 22:16, 6 May 2021

2021-05-06T22:16:20Z

← Older revision		Revision as of 22:16, 6 May 2021
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	5) To familiarize with the submission procedure you could copy the content of the directory:		5) To familiarize with the submission procedure you could copy the content of the directory:
	#* /u/local/apps/submit_scripts/MATLAB_PARALLEL_BATCH_SUBMISSION		#* cp /u/local/apps/submit_scripts/MATLAB_PARALLEL_BATCH_SUBMISSION/* ./

	7) In a local test directory and issue:		7) In a local test directory and issue:
	#* ./matlab_batch_parallel_job_submit.sh -t 3 -s 20 -m 4 -v 9.7 -f ~~/PATH/TO~~/myparpooltest_batch.m		#* ./matlab_batch_parallel_job_submit.sh -t 3 -s 20 -m 4 -v 9.7 -f ./myparpooltest_batch.m
	(Path ~~in Hoffman~~: /u/local/apps/submit_scripts/MATLAB_PARALLEL_BATCH_SUBMISSION/myparpooltest_batch.m)		(Path: /u/local/apps/submit_scripts/MATLAB_PARALLEL_BATCH_SUBMISSION/myparpooltest_batch.m)

Hwang: /* Running Parallel Jobs */

2021-05-06T17:35:06Z

Running Parallel Jobs

← Older revision		Revision as of 17:35, 6 May 2021
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	1) Request an interactive session with for example:		1) Request an interactive session with for example:
	#* $qrsh -l h_data=4G -pe shared 1		#* $qrsh -l h_data=4G -pe shared 2

	2) When the interactive session is awarded issue:		2) When the interactive session is awarded issue:

Hwang: /* Running Parallel Jobs */

2021-05-05T22:44:40Z

Running Parallel Jobs

← Older revision		Revision as of 22:44, 5 May 2021
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	7) In a local test directory and issue:		7) In a local test directory and issue:
	#* ./matlab_batch_parallel_job_submit.sh -t 3 -s 20 -m 4 -v 9.7 -f myparpooltest_batch.m		#* ./matlab_batch_parallel_job_submit.sh -t 3 -s 20 -m 4 -v 9.7 -f /PATH/TO/myparpooltest_batch.m
	(Path in Hoffman: /u/local/apps/submit_scripts/MATLAB_PARALLEL_BATCH_SUBMISSION/myparpooltest_batch.m)		(Path in Hoffman: /u/local/apps/submit_scripts/MATLAB_PARALLEL_BATCH_SUBMISSION/myparpooltest_batch.m)

Hwang: /* Running Parallel Jobs */

2021-05-05T22:40:16Z

Running Parallel Jobs

← Older revision		Revision as of 22:40, 5 May 2021
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	7) In a local test directory and issue:		7) In a local test directory and issue:
	#* ./matlab_batch_parallel_job_submit.sh -t 3 -s 20 -m 4 -v 9.7 -f myparpooltest_batch.m		#* ./matlab_batch_parallel_job_submit.sh -t 3 -s 20 -m 4 -v 9.7 -f myparpooltest_batch.m
	(~~myparpooltest.batch.m can be found~~ in Hoffman ~~under~~ /u/local/apps/submit_scripts/MATLAB_PARALLEL_BATCH_SUBMISSION/myparpooltest_batch.m)		(Path in Hoffman: /u/local/apps/submit_scripts/MATLAB_PARALLEL_BATCH_SUBMISSION/myparpooltest_batch.m)

Hwang: /* Running Parallel Jobs */

2021-05-05T22:39:00Z

Running Parallel Jobs

← Older revision		Revision as of 22:39, 5 May 2021
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	==Running Parallel Jobs==		==Running Parallel Jobs==
	IDRE team provided the following solution to use parallel pool in Matlab version 9.7.		IDRE team provided the following solution to use parallel pool in Matlab version 9.7.
	Please ~~create~~ the ~~[[Hoffman2:parpoolexample~~.m ~~\| parpoolexample.m]]~~ first~~, where you initiate a pool with the number of workers needed to run~~ the ~~job~~.		Please copy the sample file "myparpooltest_batch.m" first from the path shown below in Hoffman.
	* Make sure to not run the ~~papoolexample~~.m in MATLAB		* Make sure to not run the myparpooltest_batch.m in MATLAB

	1) Request an interactive session with for example:		1) Request an interactive session with for example:
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	7) In a local test directory and issue:		7) In a local test directory and issue:
	#* ./matlab_batch_parallel_job_submit.sh -t 3 -s 20 -m 4 -v 9.7 -f ~~[[Hoffman2:parpoolexample~~.m ~~\| parpoolexample~~.m]]		#* ./matlab_batch_parallel_job_submit.sh -t 3 -s 20 -m 4 -v 9.7 -f myparpooltest_batch.m
			(myparpooltest.batch.m can be found in Hoffman under /u/local/apps/submit_scripts/MATLAB_PARALLEL_BATCH_SUBMISSION/myparpooltest_batch.m)


	8) Look into the file:		8) Look into the file:
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	For older versions of Matlab, the [https://www.fieldtriptoolbox.org/faq/how_to_get_started_with_distributed_computing_using_qsub/ Fieldtrip qsub toolbox] can be used to facilitate batch submissions. Please see [[Hoffman2:MATLAB:qsubjobarray.m \| qsubjobarray.m]] for an example.		For older versions of Matlab, the [https://www.fieldtriptoolbox.org/faq/how_to_get_started_with_distributed_computing_using_qsub/ Fieldtrip qsub toolbox] can be used to facilitate batch submissions. Please see [[Hoffman2:MATLAB:qsubjobarray.m \| qsubjobarray.m]] for an example.


	==Software Versions==		==Software Versions==