[phenixbb] mr_rosetta

[Thomas C. Terwilliger]

Hi Jermaine,
Thank you!  That helps eliminate a lot of possible reasons for the problem.

Now your mr_rosetta log file should look something like the one below near
the end, as you mention that it got as far as rescoring. My next quesetion
is...is the part "Collecting all runs now" there?

Also what is in the file

.../MR_ROSETTA_1/GROUP_OF_RESCORE_MR_ROSETTA_1/JOBS_RUNNING
(Does it indicate all jobs finished)?

It's fine to continue this off-list until we figure out the answer if you
like.

All the best,
Tom

Starting sub-processes Group of rescore MR rosetta:Rescoring set of
rosetta
models...==============================================================================
Splitting work into 4 jobs and running with 20 processors using
qsubbackground=False in
/net/omega/raid1/scratch1/terwill/blind_tests/all_cases/mr_r
osetta_from_templates/3_cab55348/MR_ROSETTA_7/GROUP_OF_RESCORE_MR_ROSETTA_1

Starting job 1...Log will be:
/net/omega/raid1/scratch1/terwill/blind_tests/all_
cases/mr_rosetta_from_templates/3_cab55348/MR_ROSETTA_7/GROUP_OF_RESCORE_MR_ROSETTA_1/RUN_FILE_1.logStarting
job 2...Log will be: /net/omega/raid1/scratch1/terwill/blind_tests/all_
cases/mr_rosetta_from_templates/3_cab55348/MR_ROSETTA_7/GROUP_OF_RESCORE_MR_ROSETTA_1/RUN_FILE_2.log
Collecting all runs now
Collecting run_file:
/net/omega/raid1/scratch1/terwill/blind_tests/all_cases/mr_
rosetta_from_templates/3_cab55348/MR_ROSETTA_7/GROUP_OF_RESCORE_MR_ROSETTA_1/RUN_FILE_1info_file:
/net/omega/raid1/scratch1/terwill/blind_tests/all_cases/mr_rosetta_fr
om_templates/3_cab55348/MR_ROSETTA_7/GROUP_OF_RESCORE_MR_ROSETTA_1/INFO_FILE_1
method: mr_rosettalogfile:
/net/omega/raid1/scratch1/terwill/blind_tests/all_cases/mr_rosetta_from_templates/3_cab55348/MR_ROSETTA_7/GROUP_OF_RESCORE_MR_ROSETTA_1/RUN_FILE_1.log
Reading pickle file from
/net/omega/raid1/scratch1/terwill/blind_tests/all_cases/mr_rosetta_from_templates/3_cab55348/MR_ROSETTA_7/GROUP_OF_RESCORE_MR_ROSETTA_1
/RUN_1/results.pkl


>> I ran the tests as requested and got an  "ALL COMMAND_LINE TESTS OK" so
>> things appear to be working fine. I am submitting my job to a cluster
>> using
>> a script that qsubs nodes=1:ppn=4,walltime=160:00:00. Then executes
>> another
>> script that sources phenix,  sets an export phenix_rosetta path an runs
>> "phenix.mr_rosetta mr_rosetta_params.eff ".
>>
>>
>> JJ
>>
>> On Tue, May 10, 2011 at 9:56 PM, Thomas C. Terwilliger
>> <terwilliger at lanl.gov
>>> wrote:
>>
>>> Hi Jermaine,
>>> I am sorry for the trouble!  I am wondering if rosetta is working quite
>>> right? Can you possibly run the regression tests on mr_rosetta:
>>>
>>> phenix_regression.wizards.test_command_line_rosetta_quick_tests
>>>
>>> and see if that helps diagnose the problem?
>>> All the best,
>>> Tom T
>>>
>>> >> I have been trying a standard run of mr_rosetta and I have stopped at
>>> the
>>> >> same point (output below). 32 folders were created in the
>>> >> GROUP_OF_RESCORE_MR_ROSETTA_1 folder and the mr_rosetta.log files all
>>> say
>>> >> that saved overall results to a  .../results.pkl and the Run log file
>>> >> states
>>> >> that each job finished. But no further files were written in the Work
>>> >> folder
>>> >> under each RUN folder and I am assuming there should be a folder with
>>> my
>>> >> final 20 Rosetta models somewhere. Does this mean there was a failure
>>> in
>>> a
>>> >> subscript?
>>> >>
>>> ==============================================================================
>>> >>
>>> >> Starting sub-processes Group of rescore MR rosetta:Rescoring set of
>>> >> rosetta
>>> >> models...
>>> >>
>>> ==============================================================================
>>> >>
>>> >> Splitting work into 32 jobs and running with 4 processors using sh
>>> >> background=True in ....MR_ROSETTA_1/GROUP_OF_RESCORE_MR_ROSETTA_1
>>> >>
>>> >> Starting job 1...Log will be:
>>> >> ..../MR_ROSETTA_1/GROUP_OF_RESCORE_MR_ROSETTA_1/RUN_FILE_1.log
>>> >> Starting job 2...Log will be:
>>> >> ..../MR_ROSETTA_1/GROUP_OF_RESCORE_MR_ROSETTA_1/RUN_FILE_2.log
>>> >>
>>> >> thanks,
>>> >> JJ
>>> >> _______________________________________________
>>> >> phenixbb mailing list
>>> >> phenixbb at phenix-online.org
>>> >> http://phenix-online.org/mailman/listinfo/phenixbb
>>> >>
>>>
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