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Re: [Condor-users] Troubleshoot Phenix MR_Rosetta+Condor
- Date: Thu, 6 Sep 2012 12:47:51 +1000
- From: Shahaan Ayyub <shahaan@xxxxxxxxx>
- Subject: Re: [Condor-users] Troubleshoot Phenix MR_Rosetta+Condor
Just specify the executable, no need for the absolute path.
On Thu, Sep 6, 2012 at 11:43 AM, Dmitry Rodionov <dmitry.rodionov@xxxxxxxxxxxxxx>
I am new to Condor, and I am trying to submit a Phenix MR_Rosetta job to a Condor pool.
Sadly, the scripts generated by Phenix won't run producing something like this:
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"
I am guessing that my problem is trivial, however I can't figure out what is wrong.
sample description file:
Universe = vanilla
Error = err.log
Output = out.log
Requirements = Memory > 256
copy_to_spool = False
Initialdir = "/Volumes/condor/Sht1/MR_ROSETTA_5/GROUP_OF_PLACE_MODEL_1"
Executable = "/Volumes/condor/Sht1/MR_ROSETTA_5/GROUP_OF_PLACE_MODEL_1/RUN_FILE_2.sh"
sample script looks like this and runs locally just fine:
phenix.mr_rosetta "/Volumes/condor/Sht1/MR_ROSETTA_5/GROUP_OF_PLACE_MODEL_1/PARAMS_2.eff" write_run_directory_to_file="/Volumes/condor/Sht1/MR_ROSETTA_5/GROUP_OF_PLACE_MODEL_1/INFO_FILE_2" > "/Volumes/condor/Sht1/MR_ROSETTA_5/GROUP_OF_PLACE_MODEL_1/RUN_FILE_2".log 2>&1
The NFS share "condor" is mounted on all the nodes and the environment is identical.
Could somebody point me in the right direction?
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