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[farmshare-discuss] Fwd: difficulty using Stata in barley

Tara Anne Chiatovich tchiatov at stanford.edu
Wed Jan 8 06:56:20 PST 2014


Hi again,

I think the problem was human error. I'm pretty sure I mixed up how Stata and how R handle output when a program is run in Barley. R gives output in the submit-syntax.ojobnumber file, and I was looking for my Stata output in that file when really it was in the stata-do-file.log file. Thanks for the suggestion that I run a simpler program. That allowed me to see where my thinking was off.

Best,
Tara


Tara Chiatovich
Doctoral Candidate
Developmental and Psychological Sciences
Stanford Graduate School of Education

----- Original Message -----
From: "Alex Chekholko" <chekh at stanford.edu>
To: "Open discussion for users of FarmShare" <farmshare-discuss at lists.stanford.edu>
Sent: Monday, January 6, 2014 10:38:31 AM
Subject: Re: [farmshare-discuss] Fwd: difficulty using Stata in barley

Hi Tara,

Sorry to hear that you're having trouble.

First, you should remove the ampersand.

Second, you may need to do a 'module load stata' before your qsub 
command.  You can check if you can find stata with the command "which 
stata".

Third, I would double-check that things are working with a simpler stata 
do file.  Are you able to run the example we have here?:
https://www.stanford.edu/group/farmshare/cgi-bin/wiki/index.php/Stata

Please let us know if we can be of any more help.

Regards,
Alex

On 01/05/2014 12:52 PM, Tara Anne Chiatovich wrote:
> Hello,
>
> I have a Stata do-file titled "StataUncondModels" that I would like to run in barley. I have a file named "StataUncondModelsSubmit" with the following line of code:
>
> stata -b do StataUncondModels &
>
> In the past, I would have been able to run this Stata job in barley by going into corn and entering the following:
>
> qsub -cwd -V StataUncondModelsSubmit
>
> Before, if there were errors in my program, they would appear in a new file titled StataUncondModelsSubmit.ejobnumber. The output would appear in a new file titled StataUncondModelsSubmit.ojobnumber. (If the job could not run, then this new file would not appear.) Now, I get both files, but both are completely blank. Does anyone have suggestions for how I can properly get my do-file to run and be able to access the output?
>
> Thank you,
> Tara
>
>
> Tara Chiatovich
> Doctoral Candidate
> Developmental and Psychological Sciences
> Stanford Graduate School of Education
>
> _______________________________________________
> farmshare-discuss mailing list
> farmshare-discuss at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/farmshare-discuss
>

-- 
Alex Chekholko chekh at stanford.edu 347-401-4860
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