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

[Shahaan Ayyub <shahaan@xxxxxxxxx>]

Hi Dmitry,

  If the job gets submitted, then check what does the "condor_q -better-analyze" say, generally you can troubleshoot things using that. However, if it's not very clear, then it is possible that the script actually executed but failed, it's better to print the whole "argv" to see what exactly got executed on the execute node and then test that to see if everything worked as expected.

You mentioned that you are using OSX, if you have already tested it on OSX, well, then the problem might be somewhere else.

Kind regards,

Shahaan 

On Sat, Sep 8, 2012 at 1:11 AM, Dmitry Rodionov <dmitry.rodionov@xxxxxxxxxxxxxx> wrote:

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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