On Wed, Aug 20, 2014 at 5:11 PM, Hallel Freedman <hfreedma.ualberta.ca>
wrote:
> Hi Jason,
> Here is the list of files that were created:
>
> -rw-rw-r-- 1 freedman freedman 262 Aug 20 11:34
> _MMPBSA_gb_decomp_rec.mdin
> -rw-rw-r-- 1 freedman freedman 251 Aug 20 11:34
> _MMPBSA_gb_decomp_lig.mdin
> -rw-rw-r-- 1 freedman freedman 307 Aug 20 11:34
> _MMPBSA_gb_decomp_com.mdin
> -rw-rw-r-- 1 freedman freedman 657295 Aug 20 11:35 _MMPBSA_receptor.pdb
> -rw-rw-r-- 1 freedman freedman 1971541 Aug 20 11:35
> _MMPBSA_receptor.mdcrd.0
> -rw-rw-r-- 1 freedman freedman 7722 Aug 20 11:35
> _MMPBSA_normal_traj_cpptraj.out
> -rw-rw-r-- 1 freedman freedman 3571 Aug 20 11:35 _MMPBSA_ligand.pdb
> -rw-rw-r-- 1 freedman freedman 10781 Aug 20 11:35 _MMPBSA_ligand.mdcrd.0
> -rw-rw-r-- 1 freedman freedman 296227 Aug 20 11:35
> _MMPBSA_dummyreceptor.inpcrd
> -rw-rw-r-- 1 freedman freedman 1708 Aug 20 11:35
> _MMPBSA_dummyligand.inpcrd
> -rw-rw-r-- 1 freedman freedman 297833 Aug 20 11:35
> _MMPBSA_dummycomplex.inpcrd
> -rw-rw-r-- 1 freedman freedman 660886 Aug 20 11:35 _MMPBSA_complex.pdb
> -rw-rw-r-- 1 freedman freedman 1982241 Aug 20 11:35 _MMPBSA_complex.mdcrd.0
> -rw-rw-r-- 1 freedman freedman 439 Aug 20 11:35 progress.log
>
You can try running the command that MMPBSA.py attempts by hand and see if
you get a more helpful error message that way:
/global/software/amber/amber14/bin/sander -O -i _MMPBSA_gb_decomp_com.mdin
-p nw.complex.top -c _MMPBSA_dummycomplex.inpcrd -o
_MMPBSA_complex_gb.mdout.0
Do you get any error messages there?
> Thanks,
> Holly
>
>
> On Wed, Aug 20, 2014 at 3:08 PM, Jason Swails <jason.swails.gmail.com>
> wrote:
>
> > On Wed, Aug 20, 2014 at 3:17 PM, Hallel Freedman <hfreedma.ualberta.ca>
> > wrote:
> >
> > > Hi Jason,
> > > We were in fact using a serial version of MMPBSA.py, and it passes all
> of
> > > the serial tests. Do you have any other suggestions for me please?
> > >
> >
> > What intermediate files _were_ made?
> >
> >
> > > Thanks,
> > > Holly
> > >
> > >
> > > On Wed, Aug 20, 2014 at 11:41 AM, Jason Swails <jason.swails.gmail.com
> >
> > > wrote:
> > >
> > > > On Wed, Aug 20, 2014 at 1:37 PM, Hallel Freedman <
> hfreedma.ualberta.ca
> > >
> > > > wrote:
> > > >
> > > > > It doesn't seem to be getting that far - there is no file with that
> > > name.
> > > > > Maybe I should mention that I am getting a warning:
> > > > > An MPI process has executed an operation involving a call to the
> > > > > "fork()" system call to create a child process. Open MPI is
> > currently
> > > > > operating in a condition that could result in memory corruption or
> > > > > other system errors; your MPI job may hang, crash, or produce
> silent
> > > > > data corruption. The use of fork() (or system() or other calls
> that
> > > > > create child processes) is strongly discouraged.
> > > > >
> > > > > The process that invoked fork was:
> > > > >
> > > > > Local host: jasper.westgrid.ca (PID 19790)
> > > > > MPI_COMM_WORLD rank: 0
> > > > >
> > > > > Could this be related to the problem?
> > > > >
> > > >
> > > > If you're having trouble in parallel, the first thing to do (if
> > > possible)
> > > > is to run in serial. It's a very simple way to help reduce the
> number
> > of
> > > > places one has to look for the source of the problem.
> > > >
> > > > I can't recall the exact name of the output file off the top of my
> > head,
> > > > but the name should indicate it is the mdout file of rank 0
> (.mdout.0)
> > > for
> > > > the complex. The output files often hide the true error messages.
> > > >
> > > > --
> > > > Jason M. Swails
> > > > BioMaPS,
> > > > Rutgers University
> > > > Postdoctoral Researcher
> > > > _______________________________________________
> > > > 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
> > BioMaPS,
> > Rutgers University
> > Postdoctoral Researcher
> > _______________________________________________
> > 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
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Aug 20 2014 - 14:30:03 PDT
