[phenixbb] mr_rosetta and Condor

Dmitry Rodionov dmitry.rodionov at mail.mcgill.ca
Wed Sep 5 17:32:08 PDT 2012

With shares out of the way, I started mr_rosetta on home-grown condor pool.
Unfortunately it stopped immediately after submitting the jobs with this error:

Splitting work into 10 jobs and running with 1 processors using /condor/condor-installed/bin/condor_submit
background=None in /Volumes/condor/Sht1/MR_ROSETTA_5/GROUP_OF_PLACE_MODEL_1
Running using condor job submission

Starting job 1...Log will be: /Volumes/condor/Sht1/MR_ROSETTA_5/GROUP_OF_PLACE_MODEL_1/RUN_FILE_1.log

Submitting job(s)
ERROR: No such directory: /Volumes/condor/Sht1/MR_ROSETTA_5/GROUP_OF_PLACE_MODEL_1/"/Volumes/condor/Sht1/MR_ROSETTA_5/GROUP_OF_PLACE_MODEL_1"

The error can be reproduced by submitting the phenix-generated jobs manually. I can run the scripts locally without any problem. Sounds like condor_submit is unhappy with the job description files.

What did I do wrong?
Does anybody know how can this be fixed?

Please find the input files attached.

Thanks a bunch!


On 2012-09-02, at 12:58 AM, Francis E Reyes wrote:

> This is most easily done by allowing your user home directory to be mapped identically on all nodes.
> That is to say that if the user submitting the job could login to all the nodes, the shell / directory/ filesystem environment looks exactly the same as the machine the user is submitting the job from.
> F
> On Sep 1, 2012, at 9:52 PM, Dmitry Rodionov wrote:
>> What exactly has to go on the network share and how would I make the execution nodes aware of it?
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb

-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: mr_rosetta_params-master.txt
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20120906/e6dedcbf/attachment.txt>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: RUN_FILE_2
Type: application/octet-stream
Size: 275 bytes
Desc: RUN_FILE_2
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20120906/e6dedcbf/attachment.obj>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: RUN_FILE_2.sh
Type: application/octet-stream
Size: 569 bytes
Desc: RUN_FILE_2.sh
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20120906/e6dedcbf/attachment-0001.obj>

More information about the phenixbb mailing list