Dear Phenix Developers,
I have been experiencing problems with autobuild whenever I try to rebuild an MR model or calculate a composite OMIT map. These tasks always end
same way: with "[Errno 5] Input/output error". The failure always happens when the run is basically finished and trying to combine the output from multiple tasks. My first thought was that my hard drive was full or fixing to crash, but these problems happen across several machines and have
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 \
debug=true
This takes about 5 minutes. If it fails, can you send me
([email protected], 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
rebuild-in-place=true
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
#COMBINE_MODELS SCRIPT
if (-d PDS || -d AutoBuild_run_1_) then
echo "Please run in a directory without PDS or AutoBuild_run_1_"
exit 1
endif
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
map_coeffs_1.mtz
AutoBuild_run_1_/MULTIPLE_MODELS/initial_model.mtz_1_1
cp map_coeffs_2.mtz
AutoBuild_run_1_/MULTIPLE_MODELS/initial_model.mtz_1_2
ls AutoBuild_run_1_/MULTIPLE_MODELS/
echo "Running autobuild to combine files in
AutoBuild_run_1_/MULTIPLE_MODELS"
phenix.autobuild combine_only=true seq_file=seq.dat carry_on=true run=1 >
autobuild_combine.log
# END OF COMBINE_MODELS SCRIPT
-------------------------------------------------------
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
# COMBINE OMIT SCRIPT
phenix.resolve< running 1.7-634). The computers that cannot run autobuild successfully
are
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
i7-related
problem. I have searched the PhenixBB archive and have not turned up
any
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
are
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
my
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
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