[phenixbb] Autobuild error -- merging results of nearly-finished OMIT and autobuild runs

Thomas C. Terwilliger terwilliger at lanl.gov
Fri Apr 15 09:12:38 PDT 2011

Dear Nick,

I'm sorry for the error ("[Errno 5] Input/output error") that you are
getting with your i7-based PC's with Fedora 14.  I have not seen this
error before, but we can try to debug it with "debug=true" and also I have
a work-around for combining the files that you already have created so you
don't need to rerun your whole jobs.

Can you possibly run this quick test job to try and get it to fail:

phenix.autobuild $PHENIX/phenix_regression/wizards/perfect.mtz \
input_labels="FP SIGFP" \
map_file=$PHENIX/phenix_regression/wizards/perfect.mtz \
input_map_labels="FP PHIC FOM" \
seq_file=$PHENIX/phenix_regression/wizards/seq.dat \
resolution=3.0 \
solvent_fraction=.6 \
model=$PHENIX/phenix_regression/wizards/coords.pdb \
rebuild_in_place=True \
n_cycle_rebuild_min=1 \
n_cycle_rebuild_max=1 \
multiple_models=True \
multiple_models_number=1 \
multiple_models_group_number=2 \
highest_resno=200 \

This takes about 5 minutes. If it fails, can you send me
(terwilliger at lanl.gov, not the list) the end out the output where it gives
a traceback of where the error occurred?

     Combining files from a nearly-complete autobuild run with

You can combine models with autobuild, providing all models have exactly
the same set of atoms (aside from any solvent) by editing this script
(basically you run a dummy autobuild run to create a directory and
database entries, then you copy your files there, then you run autobuild
and tell it to carry on and do the combine step):

#!/bin/csh -f

if (-d PDS || -d AutoBuild_run_1_) then
 echo "Please run in a directory without PDS or AutoBuild_run_1_"
 exit 1

echo "Setting up combine models with a dummy run. NOTE:
multiple_models_group_number must be correct"

phenix.autobuild fobs.mtz multiple_models=true seq_file=seq.dat
combine_only=true multiple_models_group_number=2
multiple_models_number=1>& dummy_autobuild.log

echo "Copying files to AutoBuild_run_1_/MULTIPLE_MODELS"
mkdir AutoBuild_run_1_/MULTIPLE_MODELS
cp coords1.pdb AutoBuild_run_1_/MULTIPLE_MODELS/initial_model.pdb_1_1 cp
coords2.pdb AutoBuild_run_1_/MULTIPLE_MODELS/initial_model.pdb_1_2 cp
cp map_coeffs_2.mtz

ls AutoBuild_run_1_/MULTIPLE_MODELS/

echo "Running autobuild to combine files in

phenix.autobuild combine_only=true seq_file=seq.dat carry_on=true run=1 >


    Combining OMIT runs that have been run on separate computers or that
come from a nearly-completed omit run:

You can do this by copying all the individual mtz files with map
coefficients for omit regions to a single directory and running a script
like this 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 "nu nv nw:           32          32          32 " and you copy
those numbers).

#!/bin/csh -f
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

  >> Dear Phenix Developers,
>> I have been experiencing problems with autobuild whenever I try to
>> an MR model or calculate a composite OMIT map. These tasks always end
>> same way: with "[Errno 5] Input/output error". The failure always
>> when the run is basically finished and trying to combine the output
>> multiple tasks. My first thought was that my hard drive was full or
>> to crash, but these problems happen across several machines and have
persisted through multiple official and nightly Phenix releases
>> running 1.7-634). The computers that cannot run autobuild successfully
>> both core i7-based PCs running Fedora 14 (though these problems also
occurred running earlier Fedora versions). My older xeon-based PC runs
autobuild without any trouble, which makes me think this a core
>> problem. I have searched the PhenixBB archive and have not turned up
>> similar problems - have any other users experienced trouble with Phenix
and core i7? Is there a work-around I ca
>>  n use to manually combine the various outputs? The core i7 machines
>> so much faster, I would really like to solve this problem so that I can
stop relying on my aging xeon PC for these long calculations. I have
included the end of two log files for reference. Also, autosol runs fine
>> on the core i7 computers and successfully builds wonderful models from
>> SeMet SAD data. Thank you for Phenix and for any advice you can give.
>> Best wishes,
>> Nick Silvaggi
>> P.S. I apologize if this message appears twice - I sent it once from an
address that was not registered with the BB and decided to re-send from a
>> registered address.
>> Autobuild after MR:
>> -----------------------------------------------------------------------------------------------------
Standard build in parallel  starting with  refine.pdb_1
>> This is the first try at building this model
>> Try:  1 building 1 model
>> Try:  2 building 1 model
>> Try:  3 building 1 model
>> Running up to  3  jobs in parallel... with total of  3  jobs
>> Splitting work into 3 jobs and running with 3 processors using sh
background=True in
>> /home/nicks/projects/r51/phenix_mr/AutoBuild_run_2_/TEMP0
>> Starting job 1...Log will be:
>> /home/nicks/projects/r51/phenix_mr/AutoBuild_run_2_/TEMP0/RUN_FILE_1.log
Starting job 2...Log will be:
>> /home/nicks/projects/r51/phenix_mr/AutoBuild_run_2_/TEMP0/RUN_FILE_2.log
Starting job 3...Log will be:
>> /home/nicks/projects/r51/phenix_mr/AutoBuild_run_2_/TEMP0/RUN_FILE_3.log
Collecting all runs now
>> *************ERROR ENDING *******************
>> ********************************************************************************
Failed to carry out AutoBuild_build_cycle:
>> [Errno 5] Input/output error
>> ********************************************************************************
>> *************ERROR ENDING *******************
>> Calculating SA composite omit map:
>> -----------------------------------------------------------------------------------------------------
Starting job 34...Log will be:
>> /home/nicks/projects/r51/phenix_mr/AutoBuild_run_3_/TEMP0/RUN_FILE_34.log
Starting job 35...Log will be:
>> /home/nicks/projects/r51/phenix_mr/AutoBuild_run_3_/TEMP0/RUN_FILE_35.log
Starting job 36...Log will be:
>> /home/nicks/projects/r51/phenix_mr/AutoBuild_run_3_/TEMP0/RUN_FILE_36.log
Collecting all runs now
>> *************ERROR ENDING *******************
>> ********************************************************************************
Failed to carry out AutoBuild_parallel_omit:
>> [Errno 5] Input/output error
>> ********************************************************************************
>> *************ERROR ENDING *******************
>> Nicholas R Silvaggi, Ph.D.
>> University of Wisconsin, Milwaukee
>> Department of Chemistry and Biochemistry
>> 3210 North Cramer St
>> Milwaukee, WI 53211
>> Office: Chemistry 272B
>> Phone: 414-229-2647
>> silvaggi at uwm.edu
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb

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