[phenixbb] MR_ROSETTA

Wei Shi Wei.Shi.GR at dartmouth.edu
Thu Nov 17 12:07:15 PST 2011

Hi Dr Terwilliger,
I see. Thank you so much!

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 \

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<mailto:terwilliger at LANL.gov>
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