[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


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
Building  5  models ...
Running up to  32  jobs in parallel...
Splitting work into 5 jobs and running 32 at a time with csh in

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
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

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
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