[phenixbb] Fwd: mr_rosetta and Condor

Dmitry Rodionov dmitry.rodionov at mail.mcgill.ca
Fri Sep 7 11:00:22 PDT 2012

> 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"

1)It appears that the submission problem comes from the Condor job description file:

Universe = vanilla
Error = err.log
Output = out.log
Requirements = Memory > 256
copy_to_spool = False
Initialdir = "/Volumes/condor/Och1/MR_ROSETTA_32/GROUP_OF_PLACE_MODEL_1"
Executable = "/Volumes/condor/Och1/MR_ROSETTA_32/GROUP_OF_PLACE_MODEL_1/RUN_FILE_10.sh"

I am able to submit the job manually if i remove the double quotes from initialdir and executable lines.

Sounds like a very simple problem. Does anyone know how can this be fixed?

2) shortly after submission, the modified (no quotes) job stops with the following:


Rebuilding the model /Volumes/condor/Och1/MR_ROSETTA_32/WORK_1/global_1/2vk9_1_chain.pdb 
with rosetta

Splitting generation of rebuilt models into 1000 jobs 
with 1 structures generated per job


******************* ERROR ENDING ***************
'NoneType' object has no attribute 'endswith'

******************* ERROR ENDING ***************

Oddly enough, if I run the script locally it runs without this problem.

I understand that the error is Python. Does anybody know where it might be coming from?

2)Another thing is that Condor's err.log and out.log are created in the same location and under the same name for all jobs which "may lead to bizarre behaviour" according to the Condor's manual. Might not be a bad idea to name the files something like run_xx_err.log or stick them into the RUN_xx folder for the sake of safety.



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