Autobuild requires more then 24 hrs to run on 32 cpu?
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
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 _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
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 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
_______________________________________________
phenixbb mailing list
[email protected]
http://www.phenix-online.org/mailman/listinfo/phenixbb _______________________________________________
phenixbb mailing list
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http://www.phenix-online.org/mailman/listinfo/phenixbb
participants (2)
-
Tatyana Sysoeva -
Thomas C. Terwilliger