[phenixbb] Autobuild requires more then 24 hrs to run on 32 cpu?
Tatyana Sysoeva
tatyanasysoeva at gmail.com
Mon Jun 29 17:08:12 PDT 2009
Hello!
I am trying to use Autobuild wizard and it seems that it takes longer time
that I expected.
That's why I have next questions:
1. What is "usual" time range estimate for Autobuild run with default
parameters if my model has 7 chains with 284 aa in each?
(if I'm running Autobuild on a single machine it does not finish in 3 days
or on cluster with usage of 32 processors - in 24 hours)
2. Do I use phenix comman correctly for using several machines at once?
I used /phenix-1.4-89, command line
*phenix.autobuild data=e239a.hkl seq_file=seq.dat model=model.pdb nproc=32*
In 24 hrs, which is my limit on cluster time, I get next things -
AutoBuild_run_1_1_/AutoBuild_run_1_1.log ends with
*Setting up to build 5 models to be combined into final model #1
NOTE: input model will be rebuilt in place: nothing will be added or
deleted.
Building 5 models ...
Running up to 32 jobs in parallel...
Splitting work into 5 jobs and running 32 at a time with csh in
/home2/tas354/phenix_runs/20090610/1/AutoBuild_run_1_/TEMP0
Starting job 1...
Starting job 2...
Starting job 3...
Starting job 4...
Starting job 5...*
AutoBuild_run_1_1_/TEMP0/AutoBuild_run_1_N.log ends with
*Copying refined_pdb_in.pdb to composite_model.pdb in
AutoBuild_run_1_/TEMP0
Beginning merge with current best model: refined_pdb_in.pdb
Merging models: composite_model.pdb refine_1.pdb
Refining model: Build_composite_3.pdb
Model: AutoBuild_run_1_/TEMP0/Build_composite_refined_3.pdb
R/Rfree=0.23/0.25
Rebuilding side chains from Build_composite_refined_3.pdb*
or with error *
TRIED resolve_extra_huge ...but not OK
********************************************************************************
Failed to carry out AutoBuild_build_cycle:
********************************************************************************
*
Should I change parameters of the Autobuild which will dramatically reduce
time for computations or should I ask for extension of my time for letting
the programs to run as it is?
I would give more details if it is needed I just could not think of some
other right now. And I would appreciate any advices and suggestions!
Thank you
Tanya
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