Center for Cognitive Neuroscience - User contributions [en]

Instructions

2022-02-15T06:45:53Z

Ravi:

'''Instructions for Creating New User and Adding User Rights'''

* '''1) Login as a Administrator'''

* '''2) Navigate to the "Special Pages" link on the left side toolbar'''
** https://www.ccn.ucla.edu/wiki/index.php/Special:SpecialPages

* '''3) Click on "Create Account" under Login/ create account '''
** https://www.ccn.ucla.edu/wiki/index.php/Special:CreateAccount
*** chose a temporary password for the user for use during first login

* '''4) Navigate back to "Special Pages" and click on "User Rights Management"
** Input the username of the user you created and assign the user to the right user groups

Instructions

2022-02-15T06:31:01Z

Ravi: Created page with "'''Instructions for Creating New User and Adding User Rights''' 1) First Login as a Administrator"

'''Instructions for Creating New User and Adding User Rights'''
1) First Login as a Administrator

Main Page

2022-02-15T06:27:35Z

Ravi:

__NOTOC__
== Center for Cognitive Neuroscience at UCLA ==

Welcome to the Wiki of the Center for Cognitive Neuroscience at UCLA (CCN at UCLA). Please find and contribute helpful information for lab usage here.

=== Classes ===
* [[CCN Workshops]]
* [[Neuroimaging+ Journal Club]]
* [[Principles of Neuroimaging - 2016-2017]]
* [[Principles of Neuroimaging - 2015-2016]]

=== Computing ===
* [[Hoffman2 maintenance and Issues]]
* [[Hoffman2]]
* [[Dicom]]
* [[Psychophysics]]


=== EEG/fMRI ===
* [[EEG]] (includes EEG-fMRI)
* [[MR]]


=== Staglin Center ===
* [[Staglin EEG Suite]]
* [[Staglin MR Suite]]

=== Resources ===
* [[Software Licenses]]


===Instructions For Admins ===
* [[Instructions]]

Hoffman2:MATLAB

2020-04-02T18:47:39Z

Ravi: /* Running Parallel Jobs */

[[Hoffman2|Back to all things Hoffman2]]

MATLAB is not a small program and it can handle some fairly complex graphics. As such, this is not something suitable to be used on a login node of Hoffman2. But that's already been thought of by the great people at ATS.

==GUI==
To run a full GUI session of MATLAB, execute
$ matlab
That's it, no flags, no frills, nothing else. Hoffman2 will automatically check out an appropriate interactive node for you to run MATLAB on. All you have to do is provide a time limit (in hours) when they ask you
Enter a time limit for your session, in hours (default 2)
<or quit>:

==Command Line==
If you don't need the fancy GUI and just want the command line, execute
$ matlab -nodesktop
and then supply a time limit when asked.

'''Since this uses interactive nodes, the maximum time limit you can request is 24 hours.'''

==License Check==
With so many people using Hoffman2 and MATLAB, sometimes licenses run out. Using this helpful script will give you some insight as to the license situation.

[[Hoffman2:Scripts:matlab_license_check.sh|matlab_license_check.sh]]

==Large Computations==
If you are doing a larger computation, '''running MATLAB normally will probably not work well.'''

Using the default method of launching MATLAB on Hoffman2 checks out an [[Hoffman2:Interactive_Sessions | interactive node]] with only 1GB of RAM. This is woefully small if you are working with ten minutes of dense array EEG. Use the following steps to launch a more capable MATLAB session.

<pre>
$ # 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
$ # Load the module MATLAB
$ # You can also load different versions of MATLAB:
$ # module load matlab/7.14
$ # or
$ # module load matlab/8.1
$ # Try using "module help" for more information
$ module load matlab
$ # Launch MATLAB
$ matlab
</pre>

==Running Parallel Jobs==
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 amount of workers needed to run the job.
* Make sure to not run the papoolexample.m in MATLAB

1) Request an interactive session with for example:
#* $qrsh -l h_data=4G -pe shared 1

2) When the interactive session is awarded issue:
#* $module load matlab/9.7
#* $matlab &

3) When the matlab desktop opens, issue at the matlab command prompt:
>> rehash toolboxcache
>> configCluster

4) Close matlab

5) To familiarize with the submission procedure you could copy the content of the directory:
#* /u/local/apps/submit_scripts/MATLAB_PARALLEL_BATCH_SUBMISSION

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]]

8) Look into the file:
#* /u/local/apps/submit_scripts/MATLAB_PARALLEL_BATCH_SUBMISSION/README.HOWTO

9) and/or issues:
#* ./matlab_batch_parallel_job_submit.sh --help

==Software Versions==

The current default version of MATLAB on Hoffman2 is R2015b, but more recent versions are also available for use:

R2016b or matlab/9.1
R2019b or matlab/9.7

==External Links==
*[https://www.hoffman2.idre.ucla.edu/matlab_toolboxes/ MATLAB on Hoffman2]

Hoffman2:MATLAB

2020-04-02T18:46:45Z

Ravi: /* Running Parallel Jobs */

[[Hoffman2|Back to all things Hoffman2]]

MATLAB is not a small program and it can handle some fairly complex graphics. As such, this is not something suitable to be used on a login node of Hoffman2. But that's already been thought of by the great people at ATS.

==GUI==
To run a full GUI session of MATLAB, execute
$ matlab
That's it, no flags, no frills, nothing else. Hoffman2 will automatically check out an appropriate interactive node for you to run MATLAB on. All you have to do is provide a time limit (in hours) when they ask you
Enter a time limit for your session, in hours (default 2)
<or quit>:

==Command Line==
If you don't need the fancy GUI and just want the command line, execute
$ matlab -nodesktop
and then supply a time limit when asked.

'''Since this uses interactive nodes, the maximum time limit you can request is 24 hours.'''

==License Check==
With so many people using Hoffman2 and MATLAB, sometimes licenses run out. Using this helpful script will give you some insight as to the license situation.

[[Hoffman2:Scripts:matlab_license_check.sh|matlab_license_check.sh]]

==Large Computations==
If you are doing a larger computation, '''running MATLAB normally will probably not work well.'''

Using the default method of launching MATLAB on Hoffman2 checks out an [[Hoffman2:Interactive_Sessions | interactive node]] with only 1GB of RAM. This is woefully small if you are working with ten minutes of dense array EEG. Use the following steps to launch a more capable MATLAB session.

<pre>
$ # 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
$ # Load the module MATLAB
$ # You can also load different versions of MATLAB:
$ # module load matlab/7.14
$ # or
$ # module load matlab/8.1
$ # Try using "module help" for more information
$ module load matlab
$ # Launch MATLAB
$ matlab
</pre>

==Running Parallel Jobs==
IDRE team provided the following solution to use parallel pool in Matlab version 9.7.
Please create the [[Hoffman2:parpoolexample.m | parpooltest.m]] first, where you initiate a pool with the amount of workers needed to run the job.
* Make sure to not run the papooltest.m in MATLAB

1) Request an interactive session with for example:
#* $qrsh -l h_data=4G -pe shared 1

2) When the interactive session is awarded issue:
#* $module load matlab/9.7
#* $matlab &

3) When the matlab desktop opens, issue at the matlab command prompt:
>> rehash toolboxcache
>> configCluster

4) Close matlab

5) To familiarize with the submission procedure you could copy the content of the directory:
#* /u/local/apps/submit_scripts/MATLAB_PARALLEL_BATCH_SUBMISSION

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 | myparpooltest.m]]

8) Look into the file:
#* /u/local/apps/submit_scripts/MATLAB_PARALLEL_BATCH_SUBMISSION/README.HOWTO

9) and/or issues:
#* ./matlab_batch_parallel_job_submit.sh --help

==Software Versions==

The current default version of MATLAB on Hoffman2 is R2015b, but more recent versions are also available for use:

R2016b or matlab/9.1
R2019b or matlab/9.7

==External Links==
*[https://www.hoffman2.idre.ucla.edu/matlab_toolboxes/ MATLAB on Hoffman2]

Hoffman2:MATLAB

2020-04-02T18:45:44Z

Ravi: /* Running Parallel Jobs */

[[Hoffman2|Back to all things Hoffman2]]

MATLAB is not a small program and it can handle some fairly complex graphics. As such, this is not something suitable to be used on a login node of Hoffman2. But that's already been thought of by the great people at ATS.

==GUI==
To run a full GUI session of MATLAB, execute
$ matlab
That's it, no flags, no frills, nothing else. Hoffman2 will automatically check out an appropriate interactive node for you to run MATLAB on. All you have to do is provide a time limit (in hours) when they ask you
Enter a time limit for your session, in hours (default 2)
<or quit>:

==Command Line==
If you don't need the fancy GUI and just want the command line, execute
$ matlab -nodesktop
and then supply a time limit when asked.

'''Since this uses interactive nodes, the maximum time limit you can request is 24 hours.'''

==License Check==
With so many people using Hoffman2 and MATLAB, sometimes licenses run out. Using this helpful script will give you some insight as to the license situation.

[[Hoffman2:Scripts:matlab_license_check.sh|matlab_license_check.sh]]

==Large Computations==
If you are doing a larger computation, '''running MATLAB normally will probably not work well.'''

Using the default method of launching MATLAB on Hoffman2 checks out an [[Hoffman2:Interactive_Sessions | interactive node]] with only 1GB of RAM. This is woefully small if you are working with ten minutes of dense array EEG. Use the following steps to launch a more capable MATLAB session.

<pre>
$ # 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
$ # Load the module MATLAB
$ # You can also load different versions of MATLAB:
$ # module load matlab/7.14
$ # or
$ # module load matlab/8.1
$ # Try using "module help" for more information
$ module load matlab
$ # Launch MATLAB
$ matlab
</pre>

==Running Parallel Jobs==
IDRE team provided the following solution to use parallel pool in Matlab version 9.7
Please create the [[Hoffman2:parpoolexample.m | parpooltest.m]] where you initiate a pool with the amount of workers needed to run the job.
* Make sure to not run the papooltest.m in MATLAB

1) Request an interactive session with for example:
#* $qrsh -l h_data=4G -pe shared 1

2) When the interactive session is awarded issue:
#* $module load matlab/9.7
#* $matlab &

3) When the matlab desktop opens, issue at the matlab command prompt:
>> rehash toolboxcache
>> configCluster

4) Close matlab

5) To familiarize with the submission procedure you could copy the content of the directory:
#* /u/local/apps/submit_scripts/MATLAB_PARALLEL_BATCH_SUBMISSION

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 | myparpooltest.m]]

8) Look into the file:
#* /u/local/apps/submit_scripts/MATLAB_PARALLEL_BATCH_SUBMISSION/README.HOWTO

9) and/or issues:
#* ./matlab_batch_parallel_job_submit.sh --help

==Software Versions==

The current default version of MATLAB on Hoffman2 is R2015b, but more recent versions are also available for use:

R2016b or matlab/9.1
R2019b or matlab/9.7

==External Links==
*[https://www.hoffman2.idre.ucla.edu/matlab_toolboxes/ MATLAB on Hoffman2]

Hoffman2:parpoolexample.m

2020-04-02T18:43:03Z

Ravi:

Example Script of using 20 workers:
%%%% parpoolexample.m START %%%%%

n=20
p = parpool('local',n);
poolobj = gcp('nocreate'); % If no pool, do not create new one.
if isempty(poolobj)
poolsize = 0;
else
poolsize = poolobj.NumWorkers
end
tic
ticBytes(gcp);
n = 1024;
A = zeros(n);
parfor (i = 1:n)
A(i,:) = (1:n) .* sin(i*2*pi/1024);
end
tocBytes(gcp)
toc
delete(p)
%%%% parpoolexample.m STOP %%%%%

If the script is run without the steps mentioned in [[Hoffman2:MATLAB#Running_Parallel_Jobs | Running_Parallel_Jobs]], you will run in to an issue where the local pool will start but wouldn't initialize the workers themselves.

**Create this parpoolexample.m before going through the steps mentioned **

Hoffman2:parpoolexample.m

2020-04-02T18:38:59Z

Ravi:

Example Script:
%%%% parpoolexample.m START %%%%%

n=20
p = parpool('local',n);
poolobj = gcp('nocreate'); % If no pool, do not create new one.
if isempty(poolobj)
poolsize = 0;
else
poolsize = poolobj.NumWorkers
end
tic
ticBytes(gcp);
n = 1024;
A = zeros(n);
parfor (i = 1:n)
A(i,:) = (1:n) .* sin(i*2*pi/1024);
end
tocBytes(gcp)
toc
delete(p)
%%%% parpoolexample.m STOP %%%%%

If the script is run without the steps mentioned [[Hoffman2:MATLAB#RunningParallel_Jobs | here]]

Hoffman2:parpoolexample.m

2020-04-02T18:37:23Z

Ravi:

Hoffman2:parpoolexample.m

2020-04-02T18:37:14Z

Ravi:

Hoffman2:MATLAB

2020-04-02T18:31:45Z

Ravi: /* Running Parallel Jobs */

[[Hoffman2|Back to all things Hoffman2]]

MATLAB is not a small program and it can handle some fairly complex graphics. As such, this is not something suitable to be used on a login node of Hoffman2. But that's already been thought of by the great people at ATS.

==GUI==
To run a full GUI session of MATLAB, execute
$ matlab
That's it, no flags, no frills, nothing else. Hoffman2 will automatically check out an appropriate interactive node for you to run MATLAB on. All you have to do is provide a time limit (in hours) when they ask you
Enter a time limit for your session, in hours (default 2)
<or quit>:

==Command Line==
If you don't need the fancy GUI and just want the command line, execute
$ matlab -nodesktop
and then supply a time limit when asked.

'''Since this uses interactive nodes, the maximum time limit you can request is 24 hours.'''

==License Check==
With so many people using Hoffman2 and MATLAB, sometimes licenses run out. Using this helpful script will give you some insight as to the license situation.

[[Hoffman2:Scripts:matlab_license_check.sh|matlab_license_check.sh]]

==Large Computations==
If you are doing a larger computation, '''running MATLAB normally will probably not work well.'''

Using the default method of launching MATLAB on Hoffman2 checks out an [[Hoffman2:Interactive_Sessions | interactive node]] with only 1GB of RAM. This is woefully small if you are working with ten minutes of dense array EEG. Use the following steps to launch a more capable MATLAB session.

<pre>
$ # 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
$ # Load the module MATLAB
$ # You can also load different versions of MATLAB:
$ # module load matlab/7.14
$ # or
$ # module load matlab/8.1
$ # Try using "module help" for more information
$ module load matlab
$ # Launch MATLAB
$ matlab
</pre>

==Running Parallel Jobs==
IDRE team provided the following solution to use parallel pool in Matlab version 9.7

1) Request an interactive session with for example:
#* $qrsh -l h_data=4G -pe shared 1

2) When the interactive session is awarded issue:
#* $module load matlab/9.7
#* $matlab &

3) When the matlab desktop opens, issue at the matlab command prompt:
>> rehash toolboxcache
>> configCluster

4) Close matlab

5) To familiarize with the submission procedure you could copy the content of the directory:
#* /u/local/apps/submit_scripts/MATLAB_PARALLEL_BATCH_SUBMISSION

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 | myparpooltest_batch.m]]

8) Look into the file:
#* /u/local/apps/submit_scripts/MATLAB_PARALLEL_BATCH_SUBMISSION/README.HOWTO

9) and/or issues:
#* ./matlab_batch_parallel_job_submit.sh --help

==Software Versions==

The current default version of MATLAB on Hoffman2 is R2015b, but more recent versions are also available for use:

R2016b or matlab/9.1
R2019b or matlab/9.7

==External Links==
*[https://www.hoffman2.idre.ucla.edu/matlab_toolboxes/ MATLAB on Hoffman2]

Hoffman2:MATLAB

2020-04-02T18:29:28Z

Ravi: /* Running Parallel Jobs */

[[Hoffman2|Back to all things Hoffman2]]

MATLAB is not a small program and it can handle some fairly complex graphics. As such, this is not something suitable to be used on a login node of Hoffman2. But that's already been thought of by the great people at ATS.

==GUI==
To run a full GUI session of MATLAB, execute
$ matlab
That's it, no flags, no frills, nothing else. Hoffman2 will automatically check out an appropriate interactive node for you to run MATLAB on. All you have to do is provide a time limit (in hours) when they ask you
Enter a time limit for your session, in hours (default 2)
<or quit>:

==Command Line==
If you don't need the fancy GUI and just want the command line, execute
$ matlab -nodesktop
and then supply a time limit when asked.

'''Since this uses interactive nodes, the maximum time limit you can request is 24 hours.'''

==License Check==
With so many people using Hoffman2 and MATLAB, sometimes licenses run out. Using this helpful script will give you some insight as to the license situation.

[[Hoffman2:Scripts:matlab_license_check.sh|matlab_license_check.sh]]

==Large Computations==
If you are doing a larger computation, '''running MATLAB normally will probably not work well.'''

Using the default method of launching MATLAB on Hoffman2 checks out an [[Hoffman2:Interactive_Sessions | interactive node]] with only 1GB of RAM. This is woefully small if you are working with ten minutes of dense array EEG. Use the following steps to launch a more capable MATLAB session.

<pre>
$ # 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
$ # Load the module MATLAB
$ # You can also load different versions of MATLAB:
$ # module load matlab/7.14
$ # or
$ # module load matlab/8.1
$ # Try using "module help" for more information
$ module load matlab
$ # Launch MATLAB
$ matlab
</pre>

==Running Parallel Jobs==
IDRE team provided the following solution to use parallel pool in Matlab version 9.7

# request an interactive session with for example:
#* $qrsh -l h_data=4G -pe shared 1

# when the interactive session is awarded issue:
#* $module load matlab/9.7
#* $matlab &

#when the matlab desktop opens, issue at the matlab command prompt:
>>rehash toolboxcache
>>configCluster

#close matlab

#To familiarize with the submission procedure you could copy the content of the directory:
/u/local/apps/submit_scripts/MATLAB_PARALLEL_BATCH_SUBMISSION

#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 | myparpooltest_batch.m]]

#Look into the file:
/u/local/apps/submit_scripts/MATLAB_PARALLEL_BATCH_SUBMISSION/README.HOWTO

and/or issues:

./matlab_batch_parallel_job_submit.sh --help

==Software Versions==

The current default version of MATLAB on Hoffman2 is R2015b, but more recent versions are also available for use:

R2016b or matlab/9.1
R2019b or matlab/9.7

==External Links==
*[https://www.hoffman2.idre.ucla.edu/matlab_toolboxes/ MATLAB on Hoffman2]

Hoffman2:MATLAB

2020-04-02T18:27:07Z

Ravi: /* Running Parallel Jobs */

[[Hoffman2|Back to all things Hoffman2]]

MATLAB is not a small program and it can handle some fairly complex graphics. As such, this is not something suitable to be used on a login node of Hoffman2. But that's already been thought of by the great people at ATS.

==GUI==
To run a full GUI session of MATLAB, execute
$ matlab
That's it, no flags, no frills, nothing else. Hoffman2 will automatically check out an appropriate interactive node for you to run MATLAB on. All you have to do is provide a time limit (in hours) when they ask you
Enter a time limit for your session, in hours (default 2)
<or quit>:

==Command Line==
If you don't need the fancy GUI and just want the command line, execute
$ matlab -nodesktop
and then supply a time limit when asked.

'''Since this uses interactive nodes, the maximum time limit you can request is 24 hours.'''

==License Check==
With so many people using Hoffman2 and MATLAB, sometimes licenses run out. Using this helpful script will give you some insight as to the license situation.

[[Hoffman2:Scripts:matlab_license_check.sh|matlab_license_check.sh]]

==Large Computations==
If you are doing a larger computation, '''running MATLAB normally will probably not work well.'''

Using the default method of launching MATLAB on Hoffman2 checks out an [[Hoffman2:Interactive_Sessions | interactive node]] with only 1GB of RAM. This is woefully small if you are working with ten minutes of dense array EEG. Use the following steps to launch a more capable MATLAB session.

<pre>
$ # 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
$ # Load the module MATLAB
$ # You can also load different versions of MATLAB:
$ # module load matlab/7.14
$ # or
$ # module load matlab/8.1
$ # Try using "module help" for more information
$ module load matlab
$ # Launch MATLAB
$ matlab
</pre>

==Running Parallel Jobs==
IDRE team provided the following solution to use parallel pool in Matlab version 9.7

# request an interactive session with for example:
#* $qrsh -l h_data=4G -pe shared 1

#when the interactive session is awarded issue:
$module load matlab/9.7
$matlab &

#when the matlab desktop opens, issue at the matlab command prompt:
>>rehash toolboxcache
>>configCluster

#close matlab

#To familiarize with the submission procedure you could copy the content of the directory:
/u/local/apps/submit_scripts/MATLAB_PARALLEL_BATCH_SUBMISSION

#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 | myparpooltest_batch.m]]

#Look into the file:
/u/local/apps/submit_scripts/MATLAB_PARALLEL_BATCH_SUBMISSION/README.HOWTO

and/or issues:

./matlab_batch_parallel_job_submit.sh --help

==Software Versions==

The current default version of MATLAB on Hoffman2 is R2015b, but more recent versions are also available for use:

R2016b or matlab/9.1
R2019b or matlab/9.7

==External Links==
*[https://www.hoffman2.idre.ucla.edu/matlab_toolboxes/ MATLAB on Hoffman2]

Hoffman2:MATLAB

2020-04-02T18:26:03Z

Ravi: /* Running Parallel Jobs */

[[Hoffman2|Back to all things Hoffman2]]

MATLAB is not a small program and it can handle some fairly complex graphics. As such, this is not something suitable to be used on a login node of Hoffman2. But that's already been thought of by the great people at ATS.

==GUI==
To run a full GUI session of MATLAB, execute
$ matlab
That's it, no flags, no frills, nothing else. Hoffman2 will automatically check out an appropriate interactive node for you to run MATLAB on. All you have to do is provide a time limit (in hours) when they ask you
Enter a time limit for your session, in hours (default 2)
<or quit>:

==Command Line==
If you don't need the fancy GUI and just want the command line, execute
$ matlab -nodesktop
and then supply a time limit when asked.

'''Since this uses interactive nodes, the maximum time limit you can request is 24 hours.'''

==License Check==
With so many people using Hoffman2 and MATLAB, sometimes licenses run out. Using this helpful script will give you some insight as to the license situation.

[[Hoffman2:Scripts:matlab_license_check.sh|matlab_license_check.sh]]

==Large Computations==
If you are doing a larger computation, '''running MATLAB normally will probably not work well.'''

Using the default method of launching MATLAB on Hoffman2 checks out an [[Hoffman2:Interactive_Sessions | interactive node]] with only 1GB of RAM. This is woefully small if you are working with ten minutes of dense array EEG. Use the following steps to launch a more capable MATLAB session.

<pre>
$ # 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
$ # Load the module MATLAB
$ # You can also load different versions of MATLAB:
$ # module load matlab/7.14
$ # or
$ # module load matlab/8.1
$ # Try using "module help" for more information
$ module load matlab
$ # Launch MATLAB
$ matlab
</pre>

==Running Parallel Jobs==
IDRE team provided the following solution to use parallel pool in Matlab version 9.7

#request an interactive session with for example:
$qrsh -l h_data=4G -pe shared 1

#when the interactive session is awarded issue:
$module load matlab/9.7
$matlab &

#when the matlab desktop opens, issue at the matlab command prompt:
>>rehash toolboxcache
>>configCluster

#close matlab

#To familiarize with the submission procedure you could copy the content of the directory:
/u/local/apps/submit_scripts/MATLAB_PARALLEL_BATCH_SUBMISSION

#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 | myparpooltest_batch.m]]

#Look into the file:
/u/local/apps/submit_scripts/MATLAB_PARALLEL_BATCH_SUBMISSION/README.HOWTO

and/or issues:

./matlab_batch_parallel_job_submit.sh --help

==Software Versions==

The current default version of MATLAB on Hoffman2 is R2015b, but more recent versions are also available for use:

R2016b or matlab/9.1
R2019b or matlab/9.7

==External Links==
*[https://www.hoffman2.idre.ucla.edu/matlab_toolboxes/ MATLAB on Hoffman2]

Hoffman2:MATLAB

2020-04-02T18:23:19Z

Ravi: /* Running Parallel Jobs */

[[Hoffman2|Back to all things Hoffman2]]

MATLAB is not a small program and it can handle some fairly complex graphics. As such, this is not something suitable to be used on a login node of Hoffman2. But that's already been thought of by the great people at ATS.

==GUI==
To run a full GUI session of MATLAB, execute
$ matlab
That's it, no flags, no frills, nothing else. Hoffman2 will automatically check out an appropriate interactive node for you to run MATLAB on. All you have to do is provide a time limit (in hours) when they ask you
Enter a time limit for your session, in hours (default 2)
<or quit>:

==Command Line==
If you don't need the fancy GUI and just want the command line, execute
$ matlab -nodesktop
and then supply a time limit when asked.

'''Since this uses interactive nodes, the maximum time limit you can request is 24 hours.'''

==License Check==
With so many people using Hoffman2 and MATLAB, sometimes licenses run out. Using this helpful script will give you some insight as to the license situation.

[[Hoffman2:Scripts:matlab_license_check.sh|matlab_license_check.sh]]

==Large Computations==
If you are doing a larger computation, '''running MATLAB normally will probably not work well.'''

Using the default method of launching MATLAB on Hoffman2 checks out an [[Hoffman2:Interactive_Sessions | interactive node]] with only 1GB of RAM. This is woefully small if you are working with ten minutes of dense array EEG. Use the following steps to launch a more capable MATLAB session.

<pre>
$ # 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
$ # Load the module MATLAB
$ # You can also load different versions of MATLAB:
$ # module load matlab/7.14
$ # or
$ # module load matlab/8.1
$ # Try using "module help" for more information
$ module load matlab
$ # Launch MATLAB
$ matlab
</pre>

==Running Parallel Jobs==
IDRE team provided the following solution to use parallel pool in Matlab version 9.7

1) request an interactive session with for example:
$qrsh -l h_data=4G -pe shared 1

2) when the interactive session is awarded issue:
$module load matlab/9.7
$matlab &

3) when the matlab desktop opens, issue at the matlab command prompt:
>>rehash toolboxcache
>>configCluster

4) close matlab

5) to familiarize with the submission procedure you could copy the content of the directory:

/u/local/apps/submit_scripts/MATLAB_PARALLEL_BATCH_SUBMISSION

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 | myparpooltest_batch.m]]

look into the file:

/u/local/apps/submit_scripts/MATLAB_PARALLEL_BATCH_SUBMISSION/README.HOWTO

and/or issues:

./matlab_batch_parallel_job_submit.sh --help

==Software Versions==

The current default version of MATLAB on Hoffman2 is R2015b, but more recent versions are also available for use:

R2016b or matlab/9.1
R2019b or matlab/9.7

==External Links==
*[https://www.hoffman2.idre.ucla.edu/matlab_toolboxes/ MATLAB on Hoffman2]

Hoffman2:MATLAB

2020-04-02T18:22:19Z

Ravi: /* Running Parallel Jobs */

[[Hoffman2|Back to all things Hoffman2]]

MATLAB is not a small program and it can handle some fairly complex graphics. As such, this is not something suitable to be used on a login node of Hoffman2. But that's already been thought of by the great people at ATS.

==GUI==
To run a full GUI session of MATLAB, execute
$ matlab
That's it, no flags, no frills, nothing else. Hoffman2 will automatically check out an appropriate interactive node for you to run MATLAB on. All you have to do is provide a time limit (in hours) when they ask you
Enter a time limit for your session, in hours (default 2)
<or quit>:

==Command Line==
If you don't need the fancy GUI and just want the command line, execute
$ matlab -nodesktop
and then supply a time limit when asked.

'''Since this uses interactive nodes, the maximum time limit you can request is 24 hours.'''

==License Check==
With so many people using Hoffman2 and MATLAB, sometimes licenses run out. Using this helpful script will give you some insight as to the license situation.

[[Hoffman2:Scripts:matlab_license_check.sh|matlab_license_check.sh]]

==Large Computations==
If you are doing a larger computation, '''running MATLAB normally will probably not work well.'''

Using the default method of launching MATLAB on Hoffman2 checks out an [[Hoffman2:Interactive_Sessions | interactive node]] with only 1GB of RAM. This is woefully small if you are working with ten minutes of dense array EEG. Use the following steps to launch a more capable MATLAB session.

<pre>
$ # 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
$ # Load the module MATLAB
$ # You can also load different versions of MATLAB:
$ # module load matlab/7.14
$ # or
$ # module load matlab/8.1
$ # Try using "module help" for more information
$ module load matlab
$ # Launch MATLAB
$ matlab
</pre>

==Running Parallel Jobs==
IDRE team provided the following solution to use parallel pool in Matlab version 9.7

1) request an interactive session with for example:
$qrsh -l h_data=4G -pe shared 1

2) when the interactive session is awarded issue:
$module load matlab/9.7
$matlab &

3) when the matlab desktop opens, issue at the matlab command prompt:
>>rehash toolboxcache
>>configCluster

4) close matlab

5) to familiarize with the submission procedure you could copy the content of the directory:

/u/local/apps/submit_scripts/MATLAB_PARALLEL_BATCH_SUBMISSION

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 | myparpooltest_batch.m]]

look into the file:

/u/local/apps/submit_scripts/MATLAB_PARALLEL_BATCH_SUBMISSION/README.HOWTO

and/or issues:

./matlab_batch_parallel_job_submit.sh --help

==Software Versions==

The current default version of MATLAB on Hoffman2 is R2015b, but more recent versions are also available for use:

R2016b or matlab/9.1
R2019b or matlab/9.7

==External Links==
*[https://www.hoffman2.idre.ucla.edu/matlab_toolboxes/ MATLAB on Hoffman2]

Hoffman2:parpoolexample.m

2020-04-02T18:19:26Z

Ravi: Created page with "Example Script: %%%% parpoolexample.m START %%%%% n=20 p = parpool('local',n); poolobj = gcp('nocreate'); % If no pool, do not create new one. if isempty(poolobj)..."

Hoffman2

2020-04-02T18:19:10Z

Ravi: /* Software */

A compilation of lab know-how regarding the Hoffman2 Computing Cluster.



== Getting Started ==
=== Introduction ===
Hoffman2 is a Computing Cluster at UCLA, find out how it generally works so you know how to use it.
: [[Hoffman2:Introduction]]

=== Getting an Account ===
You know what it is, now you want to use it. First you need an account.
: [[Hoffman2:Getting an Account]]

=== Accessing the Cluster ===
Now how do you use that account to access the cluster?
: [[Hoffman2:Accessing the Cluster]]

=== Working in a Linux Environment ===
Never heard of a command line before? Vaguely know what "permissions" are and have no idea how to navigate a filesystem? This page is meant to take the scare out of the words "command line" so you can actually use Hoffman2.
: [[Hoffman2:Linux Tutorial]]

=== Quotas ===
Resources are not infinite, and disk space is a resource. Find out how to manage your disk space usage to stay under quota.
: [[Hoffman2:Quotas]]

=== Environmental Modules ===
How to get access to CCN-supported software.
: [[Hoffman2:Modules]]

=== Changing Passwords ===
How to change your Hoffman2 password.
: [[Hoffman2:Changing Passwords]]

=== Password-less Logins ===
Log in to Hoffman2 without typing your password every time.
: [https://www.hoffman2.idre.ucla.edu/access/passwordless_ssh/ Password-less ssh]

== Computing ==
You can find your way through Hoffman2, now it is time to start making things happen.

=== Software Tools ===
You've got your account, you are logged on, now how do you get to using a real software tool?
: [[Hoffman2:Software Tools]]

=== Run Your Jobs ===
You can run your job by starting an interactive session or submitting it with batch mode.


:[[Hoffman2:Interactive_Sessions]]
:[[Hoffman2:Batch Mode]]
:[[Hoffman2:Job Array]]

=== Monitoring Jobs ===
Right after they zap their robot monster to life, every mad scientist wishes they had the tools to check on or stop their creation. Now that you can submit jobs, you need to be able to check on them and stop them if they start terrorizing downtown Tokyo.
: [[Hoffman2:Monitoring Jobs]]



== Software ==
=== MATLAB ===
How to use MATLAB on the cluster. It is easier than you think. (Well, maybe...)
: [[Hoffman2:MATLAB]]
: [[Hoffman2:parpoolexample.m]]

==== Compiling MATLAB ====
So you have a MATLAB script, but you don't need to GUI open all night to have it process your data. How to submit MATLAB jobs to Hoffman2.
: [[Hoffman2:Compiling MATLAB]]

==== EEGLAB ====
We try to maintain the three most recent versions of EEGLAB for your convenience. Make sure to add it to your MATLAB path.
: [[Hoffman2:MATLAB:EEGLAB]]

===== EEGLAB Jobs =====
Processing multiple subjects through EEGLAB can be tiring and inconvenient if you do it by hand. Learn how to make scripts that run as jobs leveraging the power of Hoffman2.
: [[Hoffman2:MATLAB:EEGLAB:Jobs]]

==== SPM Compiled (Batch) ====
Maybe FSL isn't your cup of tea for neuroimaging work. SPM is a capable alternative and, even though it is MATLAB based, it has a compiled version that will let you leverage the power of the cluster.
: [[Hoffman2:MATLAB:SPM]]

=== R ===
You are probably a statistician, or you just prefer open source software. Here's how to run R on Hoffman2.
: [[Hoffman2:R]]

=== WEKA ===
If machine learning is your thing, maybe you've heard of WEKA. If not, maybe it will be your new best friend.
: [[Hoffman2:WEKA]]

=== FSL ===
FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.
: [[Hoffman2:FSL]]

=== Jupyter Notebook ===
: [[Hoffman2:JupyterNotebook]]

== Productivity ==
How about streamlining some of those tasks, or getting more things done.

=== Scripts ===
All of the difficulties you are experiencing now have probably been experienced before by someone else. And for that reason we already have scripts to simplify your life.
: [[Hoffman2:Scripts]]

=== Data Transfer ===
All dressed up with no where to go? That's how Hoffman2 feels if you don't give it any data to work with. Find out how to avoid hurting the Cluster's feelings.
: [[Hoffman2:Data Transfer]]

=== Sharing Filesystems ===
All you want to do is be able to look at your precious data. But it is locked up on Hoffman2 and you want to use tools on your computer to look at it. There's an app for that.
: [[Hoffman2:Sharing Filesystems]]

=== Tools ===
Simple tools that will help your productivity.
: [[Hoffman2:Tools]]

=== Mailing List ===
Information about the the CCN-Hoffman mailing list, including how to join the list.
: [[Hoffman2:Mailing List]]

Hoffman2:MATLAB

2020-04-02T17:57:11Z

Ravi: /* Running Parallel Jobs */

[[Hoffman2|Back to all things Hoffman2]]

MATLAB is not a small program and it can handle some fairly complex graphics. As such, this is not something suitable to be used on a login node of Hoffman2. But that's already been thought of by the great people at ATS.

==GUI==
To run a full GUI session of MATLAB, execute
$ matlab
That's it, no flags, no frills, nothing else. Hoffman2 will automatically check out an appropriate interactive node for you to run MATLAB on. All you have to do is provide a time limit (in hours) when they ask you
Enter a time limit for your session, in hours (default 2)
<or quit>:

==Command Line==
If you don't need the fancy GUI and just want the command line, execute
$ matlab -nodesktop
and then supply a time limit when asked.

'''Since this uses interactive nodes, the maximum time limit you can request is 24 hours.'''

==License Check==
With so many people using Hoffman2 and MATLAB, sometimes licenses run out. Using this helpful script will give you some insight as to the license situation.

[[Hoffman2:Scripts:matlab_license_check.sh|matlab_license_check.sh]]

==Large Computations==
If you are doing a larger computation, '''running MATLAB normally will probably not work well.'''

Using the default method of launching MATLAB on Hoffman2 checks out an [[Hoffman2:Interactive_Sessions | interactive node]] with only 1GB of RAM. This is woefully small if you are working with ten minutes of dense array EEG. Use the following steps to launch a more capable MATLAB session.

<pre>
$ # 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
$ # Load the module MATLAB
$ # You can also load different versions of MATLAB:
$ # module load matlab/7.14
$ # or
$ # module load matlab/8.1
$ # Try using "module help" for more information
$ module load matlab
$ # Launch MATLAB
$ matlab
</pre>

==Running Parallel Jobs==
IDRE team provided the following solution to use parallel pool in Matlab version 9.7

1) request an interactive session with for example:
$qrsh -l h_data=4G -pe shared 1

2) when the interactive session is awarded issue:
$module load matlab/9.7
$matlab &

3) when the matlab desktop opens, issue at the matlab command prompt:
>>rehash toolboxcache
>>configCluster

4) close matlab

5) to familiarize with the submission procedure you could copy the content of the directory:

/u/local/apps/submit_scripts/MATLAB_PARALLEL_BATCH_SUBMISSION

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

look into the file:

/u/local/apps/submit_scripts/MATLAB_PARALLEL_BATCH_SUBMISSION/README.HOWTO

and/or issues:

./matlab_batch_parallel_job_submit.sh --help

==Software Versions==

The current default version of MATLAB on Hoffman2 is R2015b, but more recent versions are also available for use:

R2016b or matlab/9.1
R2019b or matlab/9.7

==External Links==
*[https://www.hoffman2.idre.ucla.edu/matlab_toolboxes/ MATLAB on Hoffman2]

Hoffman2:MATLAB

2020-04-02T17:56:14Z

Ravi: /* Running Parallel Jobs */

[[Hoffman2|Back to all things Hoffman2]]

MATLAB is not a small program and it can handle some fairly complex graphics. As such, this is not something suitable to be used on a login node of Hoffman2. But that's already been thought of by the great people at ATS.

==GUI==
To run a full GUI session of MATLAB, execute
$ matlab
That's it, no flags, no frills, nothing else. Hoffman2 will automatically check out an appropriate interactive node for you to run MATLAB on. All you have to do is provide a time limit (in hours) when they ask you
Enter a time limit for your session, in hours (default 2)
<or quit>:

==Command Line==
If you don't need the fancy GUI and just want the command line, execute
$ matlab -nodesktop
and then supply a time limit when asked.

'''Since this uses interactive nodes, the maximum time limit you can request is 24 hours.'''

==License Check==
With so many people using Hoffman2 and MATLAB, sometimes licenses run out. Using this helpful script will give you some insight as to the license situation.

[[Hoffman2:Scripts:matlab_license_check.sh|matlab_license_check.sh]]

==Large Computations==
If you are doing a larger computation, '''running MATLAB normally will probably not work well.'''

Using the default method of launching MATLAB on Hoffman2 checks out an [[Hoffman2:Interactive_Sessions | interactive node]] with only 1GB of RAM. This is woefully small if you are working with ten minutes of dense array EEG. Use the following steps to launch a more capable MATLAB session.

<pre>
$ # 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
$ # Load the module MATLAB
$ # You can also load different versions of MATLAB:
$ # module load matlab/7.14
$ # or
$ # module load matlab/8.1
$ # Try using "module help" for more information
$ module load matlab
$ # Launch MATLAB
$ matlab
</pre>

==Running Parallel Jobs==
IDRE team provided the following solution to use parallel pool in Matlab version 9.7

1) request an interactive session with for example:
$qrsh -l h_data=4G -pe shared 1

2) when the interactive session is awarded issue:
$module load matlab/9.7
$matlab &

3) when the matlab desktop opens, issue at the matlab command prompt:
rehash toolboxcache
configCluster

4) close matlab

5) to familiarize with the submission procedure you could copy the content of the directory:

/u/local/apps/submit_scripts/MATLAB_PARALLEL_BATCH_SUBMISSION

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

look into the file:

/u/local/apps/submit_scripts/MATLAB_PARALLEL_BATCH_SUBMISSION/README.HOWTO

and/or issues:

./matlab_batch_parallel_job_submit.sh --help

==Software Versions==

The current default version of MATLAB on Hoffman2 is R2015b, but more recent versions are also available for use:

R2016b or matlab/9.1
R2019b or matlab/9.7

==External Links==
*[https://www.hoffman2.idre.ucla.edu/matlab_toolboxes/ MATLAB on Hoffman2]

Hoffman2:MATLAB

2020-04-02T17:55:19Z

Ravi: /* Running Parallel Jobs */

[[Hoffman2|Back to all things Hoffman2]]

MATLAB is not a small program and it can handle some fairly complex graphics. As such, this is not something suitable to be used on a login node of Hoffman2. But that's already been thought of by the great people at ATS.

==GUI==
To run a full GUI session of MATLAB, execute
$ matlab
That's it, no flags, no frills, nothing else. Hoffman2 will automatically check out an appropriate interactive node for you to run MATLAB on. All you have to do is provide a time limit (in hours) when they ask you
Enter a time limit for your session, in hours (default 2)
<or quit>:

==Command Line==
If you don't need the fancy GUI and just want the command line, execute
$ matlab -nodesktop
and then supply a time limit when asked.

'''Since this uses interactive nodes, the maximum time limit you can request is 24 hours.'''

==License Check==
With so many people using Hoffman2 and MATLAB, sometimes licenses run out. Using this helpful script will give you some insight as to the license situation.

[[Hoffman2:Scripts:matlab_license_check.sh|matlab_license_check.sh]]

==Large Computations==
If you are doing a larger computation, '''running MATLAB normally will probably not work well.'''

Using the default method of launching MATLAB on Hoffman2 checks out an [[Hoffman2:Interactive_Sessions | interactive node]] with only 1GB of RAM. This is woefully small if you are working with ten minutes of dense array EEG. Use the following steps to launch a more capable MATLAB session.

<pre>
$ # 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
$ # Load the module MATLAB
$ # You can also load different versions of MATLAB:
$ # module load matlab/7.14
$ # or
$ # module load matlab/8.1
$ # Try using "module help" for more information
$ module load matlab
$ # Launch MATLAB
$ matlab
</pre>

==Running Parallel Jobs==
IDRE team provided the following solution to use parallel pool in Matlab version 9.7

1) request an interactive session with for example: qrsh -l h_data=4G -pe shared 1

2) when the interactive session is awarded issue:
module load matlab/9.7
matlab &

3) when the matlab desktop opens, issue at the matlab command prompt:
rehash toolboxcache
configCluster

4) close matlab

5) to familiarize with the submission procedure you could copy the content of the directory:

/u/local/apps/submit_scripts/MATLAB_PARALLEL_BATCH_SUBMISSION

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

look into the file:

/u/local/apps/submit_scripts/MATLAB_PARALLEL_BATCH_SUBMISSION/README.HOWTO

and/or issues:

./matlab_batch_parallel_job_submit.sh --help

==Software Versions==

The current default version of MATLAB on Hoffman2 is R2015b, but more recent versions are also available for use:

R2016b or matlab/9.1
R2019b or matlab/9.7

==External Links==
*[https://www.hoffman2.idre.ucla.edu/matlab_toolboxes/ MATLAB on Hoffman2]

Hoffman2:MATLAB

2020-04-02T17:54:11Z

Ravi: /* Running Parallel Jobs */

[[Hoffman2|Back to all things Hoffman2]]

MATLAB is not a small program and it can handle some fairly complex graphics. As such, this is not something suitable to be used on a login node of Hoffman2. But that's already been thought of by the great people at ATS.

==GUI==
To run a full GUI session of MATLAB, execute
$ matlab
That's it, no flags, no frills, nothing else. Hoffman2 will automatically check out an appropriate interactive node for you to run MATLAB on. All you have to do is provide a time limit (in hours) when they ask you
Enter a time limit for your session, in hours (default 2)
<or quit>:

==Command Line==
If you don't need the fancy GUI and just want the command line, execute
$ matlab -nodesktop
and then supply a time limit when asked.

'''Since this uses interactive nodes, the maximum time limit you can request is 24 hours.'''

==License Check==
With so many people using Hoffman2 and MATLAB, sometimes licenses run out. Using this helpful script will give you some insight as to the license situation.

[[Hoffman2:Scripts:matlab_license_check.sh|matlab_license_check.sh]]

==Large Computations==
If you are doing a larger computation, '''running MATLAB normally will probably not work well.'''

Using the default method of launching MATLAB on Hoffman2 checks out an [[Hoffman2:Interactive_Sessions | interactive node]] with only 1GB of RAM. This is woefully small if you are working with ten minutes of dense array EEG. Use the following steps to launch a more capable MATLAB session.

<pre>
$ # 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
$ # Load the module MATLAB
$ # You can also load different versions of MATLAB:
$ # module load matlab/7.14
$ # or
$ # module load matlab/8.1
$ # Try using "module help" for more information
$ module load matlab
$ # Launch MATLAB
$ matlab
</pre>

==Running Parallel Jobs==
IDRE team provided the following solution to use parallel pool in Matlab version 9.7

1) request an interactive session with for example: qrsh -l h_data=4G -pe shared 1

2) when the interactive session is awarded issue:
module load matlab/9.7
matlab &

3) when the matlab desktop opens, issue at the matlab command prompt:
rehash toolboxcache
configCluster

4) close matlab

5) to familiarize with the submission procedure you could copy the content of the directory:

/u/local/apps/submit_scripts/MATLAB_PARALLEL_BATCH_SUBMISSION

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

look into the file:

/u/local/apps/submit_scripts/MATLAB_PARALLEL_BATCH_SUBMISSION/README.HOWTO

and/or issues:

./matlab_batch_parallel_job_submit.sh --help

==Software Versions==

The current default version of MATLAB on Hoffman2 is R2015b, but more recent versions are also available for use:

R2016b or matlab/9.1
R2019b or matlab/9.7

==External Links==
*[https://www.hoffman2.idre.ucla.edu/matlab_toolboxes/ MATLAB on Hoffman2]

Hoffman2:MATLAB

2020-04-02T17:53:18Z

Ravi:

[[Hoffman2|Back to all things Hoffman2]]

MATLAB is not a small program and it can handle some fairly complex graphics. As such, this is not something suitable to be used on a login node of Hoffman2. But that's already been thought of by the great people at ATS.

==GUI==
To run a full GUI session of MATLAB, execute
$ matlab
That's it, no flags, no frills, nothing else. Hoffman2 will automatically check out an appropriate interactive node for you to run MATLAB on. All you have to do is provide a time limit (in hours) when they ask you
Enter a time limit for your session, in hours (default 2)
<or quit>:

==Command Line==
If you don't need the fancy GUI and just want the command line, execute
$ matlab -nodesktop
and then supply a time limit when asked.

'''Since this uses interactive nodes, the maximum time limit you can request is 24 hours.'''

==License Check==
With so many people using Hoffman2 and MATLAB, sometimes licenses run out. Using this helpful script will give you some insight as to the license situation.

[[Hoffman2:Scripts:matlab_license_check.sh|matlab_license_check.sh]]

==Large Computations==
If you are doing a larger computation, '''running MATLAB normally will probably not work well.'''

Using the default method of launching MATLAB on Hoffman2 checks out an [[Hoffman2:Interactive_Sessions | interactive node]] with only 1GB of RAM. This is woefully small if you are working with ten minutes of dense array EEG. Use the following steps to launch a more capable MATLAB session.

<pre>
$ # 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
$ # Load the module MATLAB
$ # You can also load different versions of MATLAB:
$ # module load matlab/7.14
$ # or
$ # module load matlab/8.1
$ # Try using "module help" for more information
$ module load matlab
$ # Launch MATLAB
$ matlab
</pre>

==Running Parallel Jobs==
IDRE team provided the following solution to use parallel pool in Matlab version 9.7

1) request an interactive session with for example:

qrsh -l h_data=4G -pe shared 1

2) when the interactive session is awarded issue:
module load matlab/9.7
matlab &

3) when the matlab desktop opens, issue at the matlab command prompt:
rehash toolboxcache
configCluster

4) close matlab

5) to familiarize with the submission procedure you could copy the content of the directory:

/u/local/apps/submit_scripts/MATLAB_PARALLEL_BATCH_SUBMISSION

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

look into the file:

/u/local/apps/submit_scripts/MATLAB_PARALLEL_BATCH_SUBMISSION/README.HOWTO

and/or issues:

./matlab_batch_parallel_job_submit.sh --help

==Software Versions==

The current default version of MATLAB on Hoffman2 is R2015b, but more recent versions are also available for use:

R2016b or matlab/9.1
R2019b or matlab/9.7

==External Links==
*[https://www.hoffman2.idre.ucla.edu/matlab_toolboxes/ MATLAB on Hoffman2]

Hoffman2:JupyterNotebook

2020-04-02T17:28:35Z

Ravi:

==Use Jupyter Notebook==

===Method 1:===
Run on Hoffman2

Download h2jupynb from [https://gitlab.idre.ucla.edu/dauria/jupyter-notebook git ] to your local drive

chmod u+x h2jupynb

From your laptop, run (Using Python 3.7)

./h2jupynb -u userid -v 3.7.0

(You'll find more details [https://www.hoffman2.idre.ucla.edu/access/jupyter-notebook/ here])

===Method 2:===
Install to your laptop using Anaconda:

[https://jupyter.readthedocs.io/en/latest/install.html Jupyter Official Website]

1. Download [https://www.anaconda.com/distribution/ Anaconda] version 3.7

2. Install it to your MacBook as a regular application

3. then run "jupyter notebook" from the terminal

Main Page

2019-09-25T22:08:19Z

Ravi: Reverted edits by PhillippWeymouth (talk) to last revision by Hwang

__NOTOC__
== Center for Cognitive Neuroscience at UCLA ==

Welcome to the Wiki of the Center for Cognitive Neuroscience at UCLA (CCN at UCLA). Please find and contribute helpful information for lab usage here.

=== Classes ===
* [[Principles of Neuroimaging - 2015-2016]]
* [[Principles of Neuroimaging - 2016-2017]]
* [[Neuroimaging+ Journal Club]]

=== Computing ===
* [[Hoffman2]]
* [[Dicom]]


=== EEG/fMRI ===
* [[EEG]] (includes EEG-fMRI)
* [[MR]]
* [[fNIRS]]

=== Staglin Center ===
* [[Staglin EEG Suite]]
* [[Staglin MR Suite]]