Re: [Condor-users] Troubleshoot Phenix MR_Rosetta+Condor

[Dmitry Rodionov <dmitry.rodionov@xxxxxxxxxxxxxx>]

Hi Shahaan,

That is exactly what I did.
The error is the same.

Submission works fine with as little as removing all the quotes.
Is it a condor-OS X thing?
What do I risk by omitting the quotes other than possibly messed up spaces and such?

Thanks!
Dmitry

On 2012-09-06, at 9:14 PM, Shahaan Ayyub wrote:

Hi Dmitry,
  I was saying this:

Initialdir = "/Volumes/condor/Sht1/MR_ROSETTA_5/GROUP_OF_PLACE_MODEL_1"
Executable = "RUN_FILE_2.sh"


regards,

Shahaan

On Fri, Sep 7, 2012 at 3:43 AM, Dmitry Rodionov <dmitry.rodionov@xxxxxxxxxxxxxx<mailto:dmitry.rodionov@xxxxxxxxxxxxxx>> wrote:
Hi Shahaan,

Thanks for answering.

I get the same error if I remove the path to the executable from the description file.
The job gets submitted but stays in Idle if i remove the double quotes from the Initialdir and executable paths.

Dmitry

On 2012-09-05, at 10:47 PM, Shahaan Ayyub wrote:

Hi Dmitry,
  Just specify the executable, no need for the absolute path.

regards,

On Thu, Sep 6, 2012 at 11:43 AM, Dmitry Rodionov <dmitry.rodionov@xxxxxxxxxxxxxx<mailto:dmitry.rodionov@xxxxxxxxxxxxxx><mailto:dmitry.rodionov@xxxxxxxxxxxxxx<mailto:dmitry.rodionov@xxxxxxxxxxxxxx>>> wrote:
Good day!
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:

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"

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"
Queue


sample script looks like this and runs locally just fine:

#!/bin/sh
cd "/Volumes/condor/Sht1/MR_ROSETTA_5/GROUP_OF_PLACE_MODEL_1"
pwd
export PATH=/usr/local/phenix-dev-1148/build/mac-intel-osx-x86_64/bin:/usr/local/phenix-dev-1148/build/mac-intel-osx-x86_64/bin:/usr/local/phenix-dev-1148/build/mac-intel-osx-x86_64/bin:/usr/bin:/bin:/usr/sbin:/sbin
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?

Thanks!
Dmitry

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