[phenixbb] MR_ROSETTA

[Francois Berenger]

qsub is a Sun Grid Engine (SGE) command.
It is used to send a job to a cluster (meaning submit to job queue I guess).

Regards,
F.

On 11/18/2011 05:07 AM, Wei Shi wrote:
> Hi DrTerwilliger,
> I see. Thank you so much!
>
> Best,
> Wei
> ------------------------------------------------------------------------
> *From:* phenixbb-bounces at phenix-online.org
> [phenixbb-bounces at phenix-online.org] on behalf of Tom Terwilliger
> [terwilliger at lanl.gov]
> *Sent:* Thursday, November 17, 2011 2:57 PM
> *To:* PHENIX user mailing list
> *Subject:* Re: [phenixbb] MR_ROSETTA
>
> Hi Wei,
>
> I think that you may not have "qsub" as a command on your machine. In
> that case, then you can use "group_run_command=sh" and then it should work.
>
> Note that if it takes "forever" with 1 processor, it will still take a
> long time with 4... It may be useful to run your job on a cluster with
> more processors.
>
> All the best,
> Tom T
>
> On Nov 17, 2011, at 12:49 PM, Wei Shi wrote:
>
>> Hi all,
>>
>> I am trying to run phenix.mr_rosetta using the following script for
>> rebuilding the model with Rosetta before MR from phenix website except
>> omitting specifying ncs_copies number. Following is the script I am using:
>>
>> phenix.mr_rosetta \
>> seq_file = seq.dat \
>> data=coords1.mtz \
>> search_models=coords1.pdb \
>> run_prerefine=True \
>> number_of_prerefine_models=1000 \
>> fragment_files = test3.gz \
>> fragment_files = test9.gz \
>> rescore_mr.relax=False \
>> rosetta_models=20 \
>> space_group=p222\
>> use_all_plausible_sg=False \
>> nproc=4 \
>> group_run_command=qsub\
>>
>> When I run the above script, it gives the following error message:
>>
>> child process stderr output:
>>
>> command: 'qsub /home/wei/MR_ROSETTA_14/GROUP_OF_PLACE_MODEL_1/RUN_FILE_1'
>>
>> /bin/sh: qsub: not found
>>
>> Then, I omit the last line in the command “group_run_command=qsub\”.
>> MR_ROSETTA seems to be running.But, it takes forever to run.
>>
>> My questions is:
>> 1.Does anyone happen to know why it tells me “qsub: not found” when I
>> include“group_run_command=qsub” in my script?
>> 2.When I omit “group_run_command=qsub” in the script, mr_rosetta seems
>> to be running.Butit just gives me the following message and it takes
>> forever to run. Almost 10h later, no job is finished. I don’t know
>> whether this is normal. If not, any idea about why it’s so slow and
>> any suggestions about how to speed up the run? Thank you so much!
>>
>> Splitting work into 1 jobs and running with 4 processors using sh
>> background=True in /home/wei/MR_ROSETTA_15/GROUP_OF_PLACE_MODEL_1
>>
>> Starting job 1...Log will be:
>> /home/wei/MR_ROSETTA_15/GROUP_OF_PLACE_MODEL_1/RUN_FILE_1.log
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>
>
> Thomas C. Terwilliger
> Mail Stop M888
> Los Alamos National Laboratory
> Los Alamos, NM 87545
>
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