On Sun, Apr 10, 2011 at 11:01 AM, vani panguluri <vanipanguluri.gmail.com>wrote:
> below is the error msg i got
>
>
> MMPBSA.py.MPI being run on 192 processors
>
Wow. That's a lot of processors for MMPBSA.py.MPI. Especially to be using
on only 300 frames. This will force the first 108 processors to work on 2
frames and the remaining 84 processors to work on 1 frame and wait for the
others to finish. You will almost certainly see better performance using
150 processors (since then MMPBSA has to create fewer intermediate files),
and maybe even fewer.
While this *should* work, if you get problems trying to run on this many
processors, your best bet is to *seriously* scale back the number of
processors you're trying to run on (maybe even run in serial!) and try on a
smaller subset of your frames (maybe try in serial on only 5 frames or so).
Then you can try increasing the processor count and frame count.
As with any parallel amber program, you want to make sure that the serial
version is working (or at the very least, the parallel version with a small
number of processors) to make sure that the problem is actually with the
program.
The error message you got leads me to believe that it's probably an issue
with the master's setup work before the calculations actually start, but the
system/MPI error message kind of swamps that out.
Good luck,
Jason
ptraj found! Using
> /usr/local/packages/amber/11/intel-11.1-mvapich-1.1/exe/ptraj
> sander found! Using
> /usr/local/packages/amber/11/intel-11.1-mvapich-1.1/exe/sander
>
> Preparing trajectories with ptraj...
> 300 frames were read in and processed by ptraj for use in calculation.
> Abort signaled by rank 0: [qb519:0] Got completion with error
> IBV_WC_LOC_LEN_ERR, code=1, dest rank=8
>
> Exit code -3 signaled from qb386
> Killing remote processes...MPI process terminated unexpectedly
> DONE
>
> Regards,
> Vani
>
> On Sun, Apr 10, 2011 at 12:53 PM, Jason Swails <jason.swails.gmail.com>wrote:
>
>> Are you talking about the tutorial? The final results file can be
>> downloaded in several locations on the tutorial site, it's not necessarily
>> included in the zip files (I don't remember exactly where they are).
>>
>> If you're talking about no FINAL_RESULTS_MMPBSA.dat file appearing after
>> you've run the sample calculation, we can't help without more information.
>> The only reason it wouldn't print a final results file is if something
>> went
>> wrong, in which case we'd need the error message that was generated.
>>
>> All the best,
>> Jason
>>
>> On Sun, Apr 10, 2011 at 9:55 AM, vani panguluri <vanipanguluri.gmail.com
>> >wrote:
>>
>> > I got the MMPBSA files but i am not able to found the finalresults.dat
>> file
>> > in my output. can i know why it so happening.........
>> >
>> > Regards,
>> > Vani
>> >
>> > On Fri, Apr 8, 2011 at 1:01 PM, Bill Miller III <brmilleriii.gmail.com
>> > >wrote:
>> >
>> > > In this calculation, mmpbsa.in, 1err.solvated.prmtop, complex.prmtop,
>> > > receptor.prmtop, ligand.prmtop and all files that end in .mdcrd are
>> input
>> > > files for this calculation. Everything except mmpbsa.in can be found
>> in
>> > > that
>> > > zip file that I mentioned previously.
>> > >
>> > > -Bill
>> > >
>> > > On Fri, Apr 8, 2011 at 1:48 PM, vani panguluri <
>> vanipanguluri.gmail.com
>> > > >wrote:
>> > >
>> > > > in this the complex ,receptor and ligand are our input files or else
>> we
>> > > > need
>> > > > to consider those files also from these Zip files.
>> > > >
>> > > > Regards,
>> > > > Vani
>> > > >
>> > > > On Fri, Apr 8, 2011 at 12:15 PM, Bill Miller III <
>> > brmilleriii.gmail.com
>> > > > >wrote:
>> > > >
>> > > > > All of these files can be downloaded from Section 3.2 of the
>> online
>> > > > > tutorial
>> > > > > (
>> > >
>> http://ambermd.org/tutorials/advanced/tutorial3/py_script/section2.htm
>> > > > ).
>> > > > > All of the files necessary to run this MMPBSA.py calculation can
>> be
>> > > > > downloaded on that site as part of the tarball near the top of the
>> > page
>> > > > > called Est_Rec_top_mdcrd.tgz.
>> > > > >
>> > > > > I hope that helps.
>> > > > >
>> > > > > -Bill
>> > > > >
>> > > > > On Fri, Apr 8, 2011 at 1:01 PM, vani panguluri <
>> > > vanipanguluri.gmail.com
>> > > > > >wrote:
>> > > > >
>> > > > > > Hello,
>> > > > > >
>> > > > > > In the MMPBSA.PY in protein- ligand complex how can I get the
>> > > > > > *1err.solvated.prmtop
>> > > > > > that *file i had done the prod steps as shown in the manual but
>> i
>> > got
>> > > > > > stucked over this step
>> > > > > > $AMBERHOME/bin/MMPBSA.py -O -i mmpbsa.in -o
>> > > FINAL_RESULTS_MMPBSA.dat
>> > > > > -sp
>> > > > > > 1err.solvated.prmtop -cp complex.prmtop -rp receptor.prmtop -lp
>> > > > > > ligand.prmtop -y *.mdcrd
>> > > > > >
>> > > > > > Can anyone explain me in detail about this step and how to get
>> > those
>> > > > > files
>> > > > > >
>> > > > > > Regards,
>> > > > > > Vani
>> > > > > > _______________________________________________
>> > > > > > AMBER mailing list
>> > > > > > AMBER.ambermd.org
>> > > > > > http://lists.ambermd.org/mailman/listinfo/amber
>> > > > > >
>> > > > >
>> > > > >
>> > > > >
>> > > > > --
>> > > > > Bill Miller III
>> > > > > Quantum Theory Project,
>> > > > > University of Florida
>> > > > > Ph.D. Graduate Student
>> > > > > 352-392-6715
>> > > > > _______________________________________________
>> > > > > AMBER mailing list
>> > > > > AMBER.ambermd.org
>> > > > > http://lists.ambermd.org/mailman/listinfo/amber
>> > > > >
>> > > > _______________________________________________
>> > > > AMBER mailing list
>> > > > AMBER.ambermd.org
>> > > > http://lists.ambermd.org/mailman/listinfo/amber
>> > > >
>> > >
>> > >
>> > >
>> > > --
>> > > Bill Miller III
>> > > Quantum Theory Project,
>> > > University of Florida
>> > > Ph.D. Graduate Student
>> > > 352-392-6715
>> > > _______________________________________________
>> > > AMBER mailing list
>> > > AMBER.ambermd.org
>> > > http://lists.ambermd.org/mailman/listinfo/amber
>> > >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>>
>> --
>> Jason M. Swails
>> Quantum Theory Project,
>> University of Florida
>> Ph.D. Candidate
>> 352-392-4032
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sun Apr 10 2011 - 11:30:03 PDT
