[phenixbb] unstable phenix?

Tom Terwilliger terwilliger at lanl.gov
Thu Aug 25 08:29:56 PDT 2011

Hi Kas,

I'm sorry for the trouble!  I don't know the answer to the instability problem...but I can help on the job itself.

For a big job like this, scripts can be helpful. You can also run from the GUI and choose to run "detached" (You may have to specify "edit parameters and run/ run detached to get this option).

Also if you are getting partly done with your composite omit map, you can do it in pieces (specifying which omit region to run in each job) and put them all together at the end like this:

Combine composite OMIT files from a set of parallel runs on different computers

If you run a composite OMIT job but it fails at the last step of combining files, or if you run all the individual omit boxes on different machines, you can still combine them all into one single composite omit map.

You can do this by copying all the individual mtz files with map coefficients for omit regions to a single directory.

Here is a script you can edit and use to combine omit maps representing different omit regions into one.

NOTE: you need to ensure that the OMIT regions are defined the same in the runs where you got your overall_best_denmod_map_coeffs.mtz_OMIT_REGION_1 etc files and this run. You ensure that with the n_xyz command that sets the grid. You can copy this from one of your resolve log files created when you ran your omit (i.e., AutoBuild_run_1_/TEMP0/AutoBuild_run_1_/TEMP0/resolve.log will have a line like "nu nv nw: 32 32 32 " and you copy those numbers).  

#!/bin/csh -f
phenix.resolve << EOD
hklin exptl_fobs_phases_freeR_flags.mtz
n_xyz 32 32 32  # YOU MUST SET THIS BASED ON THE nu nv nw in a resolve log
solvent_content 0.85
ha_file NONE
combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_1
combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_2
combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_3
combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_4
combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_5
combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_6
combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_7
combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_8
combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_9
combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_10
combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_11
combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_12
combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_13
combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_14
combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_15
combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_16
combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_17
combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_18
combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_19
combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_20
combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_21
combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_22
combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_23
combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_24

All the best,
Tom T

On Aug 25, 2011, at 9:18 AM, Kenneth A. Satyshur wrote:

> We are running phenix (743) on a RHEL5 dual quad, multithread, making a composite
> omit map pf a very large structure (750 AA) and the system keeps getting locked up.
> Have anyone else seen this type of problem? Does multiprocessing work well on RHEL
> or just FC versions? We needed to install the FC8 version (/phenix-1.7.1-743/build/intel-linux-2.6-x86_64)
> to get it to work. So maybe we are using the wrong version? Shoiuld I recompile it for
> our system?  Why is the gui always open when we are running long jobs (many days)? We need to
> put this stuff in the background and log out so someone else can run. 
> Should scripts be used instead of the gui?
> Great program but too unstable.
> kas
> --
> Kenneth A. Satyshur, M.S.,Ph.D.
> Associate Scientist
> University of Wisconsin
> Madison, Wisconsin 53706
> 608-215-5207
> <satyshur.vcf>_______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb

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
PHENIX web site: http:www.phenix-online.org
ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu
TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB
CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss

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