[phenixbb] MR_ROSETTA

Tom Terwilliger terwilliger at lanl.gov
Thu Nov 17 11:57:12 PST 2011

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.  But it 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

Tel:  505-667-0072                 email: terwilliger at LANL.gov
Fax: 505-665-3024                 SOLVE web site: http://solve.lanl.gov
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ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu
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