Running motr on a cluster

Note: this is how we use motr on the Univa SGE cluster at Janelia, your mileage may vary.

A. If you are going to access the cluster from Windows, download and install an NX client
http://www.nomachine.com/download.php

B. Login to the cluster

C. qlogin to avoid running MATLAB on the head node
At the command line enter: qlogin -l interactive=true
This will prompt you for your password.

D. make sure your .bashrc file has the correct path to MATLAB
If you get a complaint about finding MATLAB, then you don’t have MATLAB in your path (i.e. you need to go to your .bashrc file and add the following to export PATH=
:/usr/local/matlab-2011b/bin:
e.g. export PATH="$PATH:/usr/local/matlab-2011b/bin"
once you modify the .bashrc file you need to update it by typing [source ~/.bashrc] at the command line and hitting return.

E. if ./build doesn't work
open matlab
>> fnSetUpFolders
>> fnCompile

F. To check on the jobs:
At the cluster command line, type: qstat

e.g. [egnorr@e02u19 egnorlab]$ qstat

r=running, hqw=waiting in the queue
there will be N MouseSingl jobs, and one MouseID job

to monitor the status of the MouseSingl jobs, can cd to the Jobs directory in the experiment directory and type more at the command line (e.g.):
[egnorr@e02u19 Jobs]$ more MouseSingleJob.o1940700

or

[egnorr@e02u19 Jobs]$ tail –f MouseSingleJob.o1940700
(tail looks at the end of a file, and –f = “follow”, so it doesn’t return, but updates)
(note, this never terminates, need to ^C out of it)
other ways to know when done: cursor stops spinning

or

ls –ll at the command line, and look at the size of the error files (e.g. MouseSingleJob.e1940700. You want the error files to have size 0, i.e. no errors).

G. When you run tracking, you should see the following at the MATLAB command line:

Setting initial ellipses for all jobs
Setting ellipses at frame 1
Setting ellipses at frame 5001
Setting ellipses at frame 10001
.
.
.
Setting ellipses at frame 520001
0 key frames will be inserted due to frame drops!
Done!
Generating submit script named /groups/egnor/mousetrack/mousevideo/Jobs/Test_B_1/submitscript
Submitting jobs
qsub -t 1-157 -N MouseJob -e /groups/egnor/mousetrack/mousevideo/Jobs/Test_B_1/ -o /groups/egnor/mousetrack/mousevideo/Jobs/Test_B_1/ -b y -cwd -V '/groups/egnor/mousetrack/mousevideo/Jobs/Test_B_1/submitscript'
Your job-array 586095.1-157:1 ("MouseJob") has been submitted
Generating submit file at /groups/egnor/mousetrack/mousevideo/Jobs/Test_B_1/submitPostProcessScript
Submitting jobs
qsub -N MousePostProcessJob -hold_jid MouseJob -e /groups/egnor/mousetrack/mousevideo/Jobs/Test_B_1 -o /groups/egnor/mousetrack/mousevideo/Jobs/Test_B_1 -b y -cwd -V '/groups/egnor/mousetrack/mousevideo/Jobs/Test_B_1/submitPostProcessScript'
Your job 586096 ("MousePostProcessJob") has been submitted