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[farmshare-discuss] Submitting simple MATLAB script

Jason Bishop bishopj at stanford.edu
Thu Jan 16 09:21:03 PST 2014


Hi Jeff, i'll bet you a dollar it is because of windows line ending characters.  You can tell because they end in ^M's.

to see if this is the case, use cat -ve as in:


$ cat -ve jjacobs3.submit
#!/bin/bash^M$
^M$
#$ -N gameinvite_grid^M$
#$ -m bes^M$
#$ -M jjacobs3 at stanford.edu^M$
#$ -cwd^M$
^M$
module load matlab^M$
matlab -nodesktop -singleCompThread < ./blah.m^M$
^M$


If yours looks like above run dos2unix on it and it should qsub fine.

Jason


----- Original Message -----
From: "Jeff Jacobs" <jjacobs3 at stanford.edu>
To: farmshare-discuss at lists.stanford.edu
Sent: Thursday, January 16, 2014 2:31:58 AM
Subject: [farmshare-discuss] Submitting simple MATLAB script

Hello, I'm not sure what I'm doing wrong, but I've written a self-contained matlab script and then attempted to submit it via qsub and received the following email (I tried several times, and got it each time): 

Job 1308602 (gameinvite_grid) Set in error state 
Exit Status = -1 
Signal = unknown signal 
User = jjacobs3 
Queue = raring.q at barley18.Stanford.EDU 
Host = barley18.Stanford.EDU 
Start Time = <unknown> 
End Time = <unknown> 
CPU = NA 
Max vmem = NA 
failed searching requested shell because: 
01/16/2014 02:26:35 [30981:25623]: execvp(/farmshare/software/ free/oge/2011.11p1/FSraring/ spool/barl 
Use "qmod -c <jobid>" to clear job error state 
once the problem is fixed. 

The script I submitted (runBootstrapGridC.script) was: 

#!/bin/bash 

#$ -N gameinvite_grid 
#$ -m bes 
#$ -M jjacobs3 at stanford.edu 
#$ -cwd 

module load matlab 
matlab -nodesktop -singleCompThread < ./generateBootstrapGridNoWealthC.m 

and the command I issued was: 

qsub ./runBootstrapGridC.script 

I'm guessing it's something really stupid, so please let me know if you see anything glaring. Thanks! 

-- 
Jeff Jacobs 
jjacobs3 at stanford.edu 

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