This should take only seconds, since all it has to do is rewrite the output.
I'm guessing that it's stuck at a barrier after a couple threads quit
out... Try concatenating all of the thread-specific output files into
output files of the same name (but with no numerical suffix) and running the
same command but in serial (you can run it straight from the command-line
without submitting it since it should only take a second or two).
What I mean by this is:
cat _MMPBSA_receptor_nm.out.[0-3] > _MMPBSA_receptor_nm.out
cat _MMPBSA_complex_nm.out.[0-3] > _MMPBSA_complex_nm.out
cat _MMPBSA_ligand_nm.out.[0-3] > _MMPBSA_ligand_nm.out
and then run it in serial.
Hope this helps,
Jason
On Tue, Feb 22, 2011 at 4:51 AM, mish <smncbr.gmail.com> wrote:
> I ran with the statistics calculation with flag "-rewrite-output" like :
>
> mpiexec -np 4 -machinefile MMPBSA.py.MPI -rewrite-output -O -i
> mmpbsa_nm.in-o FINAL_RESULTS_MMPBSA.dat -sp rsl_lig2_wat.prmtop -cp
> rsl_lig2.prmtop -rp
> rsl.prmtop -lp lig2.prmtop -y prod_lig2.mdcrd > progress.log
>
> but its running from last 20 hours and the only output i can see in the log
> file is "MMPBSA.py.MPI being run on 4 processors
> ". Do u think it should take so much time ?
>
> Sincerely
> ..mish
>
> On Mon, Feb 21, 2011 at 8:05 PM, Jason Swails <jason.swails.gmail.com
> >wrote:
>
> > On Mon, Feb 21, 2011 at 1:18 PM, mish <smncbr.gmail.com> wrote:
> >
> > > If we look at output file (_MMPBSA_complex_nm.out.[0-3]), it have the
> > > fallowing statistics for each snapshot (probably) -
> > >
> > >
> > > freq. E Cv S
> > > cm**-1 kcal/mol cal/mol-K cal/mol-K
> > > Total: 20127.098 7989.218 9654.238
> > > translational: 0.888 2.979 56.561
> > > rotational: 0.888 2.979 57.775
> > > vibrational: 21829.391 7983.261 9539.901
> > > ff energy: -1704.069
> > >
> > > Do you think that average of all the terms (or Total) and computing the
> > > delta (complex-receptor-ligand) over all the snapshots for all 4
> thread
> > > will give the entropy term ? or there is some other statistics /
> formulae
> > > used to get the entropy from these values ?
> > >
> >
> > That will work, but I don't know if MMPBSA.py.MPI actually uses the
> length
> > of the arrays or if it uses the number taken from the ptraj output files
> to
> > determine how many frames were analyzed. I can't remember how it's done
> in
> > the currently released version anymore.
> >
> > Good luck!
> > Jason
> >
> >
> > >
> > > ..mish
> > >
> > >
> > > On Mon, Feb 21, 2011 at 6:08 PM, Jason Swails <jason.swails.gmail.com
> > > >wrote:
> > >
> > > > Hello,
> > > >
> > > > All threads should be running concurrently (which is why you have the
> > > files
> > > > for all 4 threads; .0, .1, .2, and .3). You would have to look at
> each
> > > of
> > > > those input files separately to see where the calculation died (on
> > which
> > > > frame).
> > > >
> > > > There is no way of *easily* computing the statistics from *finished*
> > > > frames,
> > > > I don't think. You can try using the same command you used to run
> > > > MMPBSA.py.MPI the first time and just add the flag "-rewrite-output"
> to
> > > the
> > > > command line. I can't remember whether it counts the frames as it
> adds
> > > > them, or parses it from the ptraj output files.
> > > >
> > > > Just be careful and make sure that the output makes sense.
> > > >
> > > > Good luck!
> > > > Jason
> > > >
> > > > On Mon, Feb 21, 2011 at 10:38 AM, mish <smncbr.gmail.com> wrote:
> > > >
> > > > > Hi,
> > > > >
> > > > > I was doing Entropy calculation in nabmode. I used parallel version
> > of
> > > > the
> > > > > python script to do so using 4CPU. Unfortunately my calculation got
> > > > killed
> > > > > due to lime limit and now it copied only -
> > > > >
> > > > > _MMPBSA_complex_nm.out.[0-3]
> > > > > _MMPBSA_receptor_nm.out.[0-3]
> > > > > _MMPBSA_ligand_nm.out.[0-3]
> > > > >
> > > > > If I look in the progress.log then i can see that calculation were
> > > killed
> > > > > during last thread so I think It will have the data up to second
> last
> > > > > thread. Is it possible by someway to generate the final results
> from
> > > this
> > > > > data stored in these 12 files ?
> > > > >
> > > > >
> > > > > Sincerely
> > > > > ..mish
> > > > > _______________________________________________
> > > > > AMBER mailing list
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> > > > >
> > > >
> > > >
> > > >
> > > > --
> > > > 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
> > > >
> > > _______________________________________________
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> > >
> >
> >
> >
> > --
> > 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
> >
> _______________________________________________
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> 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 Tue Feb 22 2011 - 07:30:04 PST
