Thank you for the explanations! <br><br>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.<br><br>Sincerely,<br>Tanya<br>
<br><div class="gmail_quote">On Mon, Jun 29, 2009 at 8:33 PM, Thomas C. Terwilliger <span dir="ltr"><<a href="mailto:terwilliger@lanl.gov">terwilliger@lanl.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi Tanya,<br>
<br>
Autobuild can take quite a while for a large structure such yours, yes.<br>
<br>
The command you set up makes 5 models and merges them to make one good<br>
composite model. �Each of the �5 models is made by running 5 cycles of<br>
rebuild-in-place, which rebuilds the entire model in overlapping<br>
6-residue segments.<br>
<br>
This particular process is parallelized only up to the number of models,<br>
so your 32 processors unfortunately don't help you; you are using only 5<br>
of them and getting only 5-fold improvement over one processor.<br>
<br>
This run seems like it was going fine and was 95% of the way done:<br>
<div class="im"><br>
AutoBuild_run_1_1_/TEMP0/AutoBuild_run_1_N.log ends with<br>
>><br>
>> *Copying �refined_pdb_in.pdb �to �composite_model.pdb �in<br>
>> AutoBuild_run_1_/TEMP0<br>
>> Beginning merge with current best model: �refined_pdb_in.pdb<br>
>> Merging models: composite_model.pdb refine_1.pdb<br>
>> Refining model: �Build_composite_3.pdb<br>
>> Model: AutoBuild_run_1_/TEMP0/Build_composite_refined_3.pdb<br>
>> R/Rfree=0.23/0.25<br>
<br>
</div>This run doesn't look good:<br>
<div class="im"><br>
>> or with error *<br>
>> TRIED resolve_extra_huge ...but not OK<br>
>><br>
>> ********************************************************************************<br>
>> Failed to carry out AutoBuild_build_cycle:<br>
>><br>
>><br>
<br>
</div>but my guess is that if you use a recent "nightly build" of phenix<br>
(available on the web site) the error may go away or at least it *should*<br>
give you a more informative error message if not.<br>
<br>
You can speed up your job by saying "n_cycle_rebuild_max=1" or =2 (instead<br>
of =5); that will be 5x or 2.5x faster. �I am guessing your job could take<br>
about a day on 5 processors (just more than you had), depending on<br>
resolution.<br>
<br>
All the best,<br>
Tom T<br>
<div><div></div><div class="h5"><br>
>> Hello!<br>
>><br>
>> I am trying to use Autobuild wizard and it seems that it takes longer time<br>
>> that I expected.<br>
>> That's why I have next questions:<br>
>><br>
>> 1. What is "usual" time range estimate for Autobuild run with default<br>
>> parameters if my model has 7 chains with 284 aa in each?<br>
>> (if I'm running Autobuild on a single machine it does not finish in 3 days<br>
>> or on cluster with usage of 32 processors - in 24 hours)<br>
>><br>
>> 2. Do I use phenix comman correctly for using several machines at once?<br>
>><br>
>> I used /phenix-1.4-89, command line<br>
>> *phenix.autobuild �data=e239a.hkl seq_file=seq.dat model=model.pdb<br>
>> nproc=32*<br>
>><br>
>><br>
>> In 24 hrs, which is my limit on cluster time, I get next things -<br>
>> AutoBuild_run_1_1_/AutoBuild_run_1_1.log ends with<br>
>><br>
>> *Setting up to build 5 models to be combined into final model #1<br>
>> NOTE: input model will be rebuilt in place: nothing will be added or<br>
>> deleted.<br>
>> Building �5 �models ...<br>
>> Running up to �32 �jobs in parallel...<br>
>> Splitting work into 5 jobs and running 32 at a time with csh in<br>
>> /home2/tas354/phenix_runs/20090610/1/AutoBuild_run_1_/TEMP0<br>
>><br>
>> Starting job 1...<br>
>> Starting job 2...<br>
>> Starting job 3...<br>
>> Starting job 4...<br>
>> Starting job 5...*<br>
>><br>
>> AutoBuild_run_1_1_/TEMP0/AutoBuild_run_1_N.log ends with<br>
>><br>
>> *Copying �refined_pdb_in.pdb �to �composite_model.pdb �in<br>
>> AutoBuild_run_1_/TEMP0<br>
>> Beginning merge with current best model: �refined_pdb_in.pdb<br>
>> Merging models: composite_model.pdb refine_1.pdb<br>
>> Refining model: �Build_composite_3.pdb<br>
>> Model: AutoBuild_run_1_/TEMP0/Build_composite_refined_3.pdb<br>
>> R/Rfree=0.23/0.25<br>
>><br>
>> Rebuilding side chains from �Build_composite_refined_3.pdb*<br>
>><br>
>> or with error *<br>
>> TRIED resolve_extra_huge ...but not OK<br>
>><br>
>> ********************************************************************************<br>
>> Failed to carry out AutoBuild_build_cycle:<br>
>><br>
>><br>
>> ********************************************************************************<br>
>> *<br>
>><br>
>> Should I change parameters of the Autobuild which will dramatically reduce<br>
>> time for computations or should I ask for extension of my time for letting<br>
>> the programs to run as it is?<br>
>><br>
>> I would give more details if it is needed I just could not think of some<br>
>> other right now. And I would appreciate any advices and suggestions!<br>
>><br>
>><br>
>> Thank you<br>
>> Tanya<br>
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</blockquote></div><br>