[phenixbb] Autobuild requires more then 24 hrs to run on 32 cpu?

[Tatyana Sysoeva]

Thank you for the explanations!

I set the job with new parameters. In case it would not be enough I will try
to limit part of the sequence meant for rebuilding or just do loops fitting.

Sincerely,
Tanya

On Mon, Jun 29, 2009 at 8:33 PM, Thomas C. Terwilliger <terwilliger at lanl.gov
> wrote:

> Hi Tanya,
>
> Autobuild can take quite a while for a large structure such yours, yes.
>
> The command you set up makes 5 models and merges them to make one good
> composite model.  Each of the  5 models is made by running 5 cycles of
> rebuild-in-place, which rebuilds the entire model in overlapping
> 6-residue segments.
>
> This particular process is parallelized only up to the number of models,
> so your 32 processors unfortunately don't help you; you are using only 5
> of them and getting only 5-fold improvement over one processor.
>
> This run seems like it was going fine and was 95% of the way done:
>
> 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
>
> This run doesn't look good:
>
> >> or with error *
> >> TRIED resolve_extra_huge ...but not OK
> >>
> >>
> ********************************************************************************
> >> Failed to carry out AutoBuild_build_cycle:
> >>
> >>
>
> but my guess is that if you use a recent "nightly build" of phenix
> (available on the web site) the error may go away or at least it *should*
> give you a more informative error message if not.
>
> You can speed up your job by saying "n_cycle_rebuild_max=1" or =2 (instead
> of =5); that will be 5x or 2.5x faster.  I am guessing your job could take
> about a day on 5 processors (just more than you had), depending on
> resolution.
>
> All the best,
> Tom T
>
> >> 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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> >> phenixbb at phenix-online.org
> >> http://www.phenix-online.org/mailman/listinfo/phenixbb
> >>
>
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