Yep, then you should run all the tests again with mpirun -np 2 (if you
haven't already). If that continues to give no errors, then it looks like
everything is okay. The way MMPBSA.py.MPI divides up the work on processors
is to divide up the frames evenly for each processor, so you can't use more
processors than frames. And since the tests only have 2 frames, mpirun -np 4
shouldn't work.
I hope that helps.
Good luck!
-Bill
On Tue, Dec 21, 2010 at 11:20 AM, George Tzotzos <gtzotzos.me.com> wrote:
> Hi Bill
>
> Thanks. I had set mpirun to 4.
>
> The error message is as follows:
>
> 2 frames were read in and processed by ptraj for use in calculation.
> Error: You cannot have more MPI threads than frames!
>
> Running on 2 processors gives no error messages
>
> George
>
>
> On Dec 21, 2010, at 4:43 PM, Bill Miller III wrote:
>
> > Try going into one of the test directories (like 01_Generalized_Born) and
> > running the test by hand (i.e. ./Run.GB). You should comment out the end
> of
> > the execution script where the output files are removed. This way you can
> > tell exactly where the error is occurring before the output files are
> > removed by the script. The output files that are produced should give you
> > some kind of indication of what the error might be.
> >
> > Good luck!
> >
> > -Bill
> >
> > On Tue, Dec 21, 2010 at 10:39 AM, George Tzotzos <gtzotzos.me.com>
> wrote:
> >
> >>
> >> Hi,
> >>
> >> I've installed on a new machine MMPBSA.py.MPI as per tutorial 3A
> >> instructions.
> >>
> >> The serial tests run smoothly without error messages. The parallel
> >> implementation of the program gives the following errors
> >>
> >> Any ideas?
> >>
> >> Many thanks
> >>
> >> George
> >>
> >> g:mmpbsa_py george1$ make test
> >> cd 01_Generalized_Born && ./Run.GB
> >> cat: FINAL_RESULTS_MMPBSA.dat: No such file or directory
> >> diffing FINAL_RESULTS_MMPBSA.dat.save with FINAL_RESULTS_MMPBSA.dat
> >> file ddtmp.FINAL_RESULTS_MMPBSA.dat is short
> >> PASSED
> >> rm: FINAL_RESULTS_MMPBSA.dat: No such file or directory
> >> ==============================================================
> >> cd 02_Poisson_Boltzmann && ./Run.PB
> >> cat: FINAL_RESULTS_MMPBSA.dat: No such file or directory
> >> diffing FINAL_RESULTS_MMPBSA.dat.save with FINAL_RESULTS_MMPBSA.dat
> >> file ddtmp.FINAL_RESULTS_MMPBSA.dat is short
> >> PASSED
> >> rm: FINAL_RESULTS_MMPBSA.dat: No such file or directory
> >> ==============================================================
> >> cd 03_Alanine_Scanning && ./Run.ALA
> >> cat: FINAL_RESULTS_MMPBSA.dat: No such file or directory
> >> diffing FINAL_RESULTS_MMPBSA.dat.save with FINAL_RESULTS_MMPBSA.dat
> >> file ddtmp.FINAL_RESULTS_MMPBSA.dat is short
> >> PASSED
> >> rm: FINAL_RESULTS_MMPBSA.dat: No such file or directory
> >> ==============================================================
> >> Mutant mdcrd can only be checked in serial
> >> cd 04_Per_Residue_Decomp && ./Run.PerRes
> >> cat: FINAL_RESULTS_MMPBSA.dat: No such file or directory
> >> diffing ../01_Generalized_Born/FINAL_RESULTS_MMPBSA.dat.save with
> >> FINAL_RESULTS_MMPBSA.dat
> >> file ddtmp.FINAL_RESULTS_MMPBSA.dat is short
> >> PASSED
> >> rm: FINAL_RESULTS_MMPBSA.dat: No such file or directory
> >> ==============================================================
> >> diffing FINAL_DECOMP_MMPBSA.dat.save with FINAL_DECOMP_MMPBSA.dat
> >> PASSED
> >> ==============================================================
> >> cd 05_Pairwise_Decomp && ./Run.Pairwise
> >> cat: FINAL_RESULTS_MMPBSA.dat: No such file or directory
> >> diffing ../01_Generalized_Born/FINAL_RESULTS_MMPBSA.dat.save with
> >> FINAL_RESULTS_MMPBSA.dat
> >> file ddtmp.FINAL_RESULTS_MMPBSA.dat is short
> >> PASSED
> >> rm: FINAL_RESULTS_MMPBSA.dat: No such file or directory
> >> ==============================================================
> >> diffing FINAL_DECOMP_MMPBSA.dat.save with FINAL_DECOMP_MMPBSA.dat
> >> PASSED
> >> ==============================================================
> >> cd 06_NAB_Nmode && ./Run.nmode
> >> diffing FINAL_RESULTS_MMPBSA.dat.save with FINAL_RESULTS_MMPBSA.dat
> >> possible FAILURE: check FINAL_RESULTS_MMPBSA.dat.dif
> >> ==============================================================
> >> cd 07_Comprehensive && ./Run.comprehensive
> >> diffing FINAL_RESULTS_MMPBSA_1.dat.save with FINAL_RESULTS_MMPBSA_1.dat
> >> possible FAILURE: check FINAL_RESULTS_MMPBSA_1.dat.dif
> >> ==============================================================
> >> diffing FINAL_RESULTS_MMPBSA_2.dat.save with FINAL_RESULTS_MMPBSA_2.dat
> >> possible FAILURE: check FINAL_RESULTS_MMPBSA_2.dat.dif
> >> ==============================================================
> >> diffing FINAL_DECOMP_MMPBSA.dat.save with FINAL_DECOMP_MMPBSA.dat
> >> PASSED
> >> ==============================================================
> >>
> >> _______________________________________________
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> >> 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
>
>
> _______________________________________________
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> 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
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Received on Tue Dec 21 2010 - 09:00:03 PST
