Re: [AMBER] MMPBSA jobs on a cluster Calcerror:

From: Vivek Shankar Bharadwaj <vbharadw.mymail.mines.edu>
Date: Wed, 6 Mar 2013 13:36:30 -0700

Hi Jason,

I looked up the _MMPBSA_complex_pb.mdout.0 file (also attached) and there
is no error there.

It just ends with
....................................
| PB exmol part c 0.17
| PB exmol part d 0.06
| PB exmol part e 1.26
| PB exmol part f 0.57
| PB epsbnd 0.05
| PB epsmap 0.20
| PB calsa 0.00


  Maximum number of minimization cycles reached.

Vivek



On Wed, Mar 6, 2013 at 1:25 PM, Jason Swails <jason.swails.gmail.com> wrote:

> Look at the _MMPBSA_complex_gb.mdout.0 file -- the error should be in
> there.
>
> On Wed, Mar 6, 2013 at 3:05 PM, Vivek Shankar Bharadwaj <
> vbharadw.mymail.mines.edu> wrote:
>
> > Hi Amber Users,
> >
> > I am trying to run MMPBSA jobs (with decomposition) on our cluster
> > supercomputer with Amber12.
> >
> > The job seems to run for about 3 hours with out error. and suddenly
> > terminates with a calc error (below in red).
> >
> > I have attached the MMPBSA input file used for this job. I also find
> that I
> > am able to run this job on my workstation without any issues.
> >
> > I have attached mmpbsa.in and the script file used for the job.
> >
> > I also recompiled ambertools12 and amber12 with all bug fixes applied and
> > updated.
> >
> > Has anyone come across this error?
> >
> > Thanks
> >
> > ERROR
> > --
> >
> --------------------------------------------------------------------------
> > 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: n102 (PID 3664)
> > MPI_COMM_WORLD rank: 0
> >
> > If you are *absolutely sure* that your application will successfully
> > and correctly survive a call to fork(), you may disable this warning
> > by setting the mpi_warn_on_fork MCA parameter to 0.
> >
> --------------------------------------------------------------------------
> > [n102:03654] 1 more process has sent help message help-mpi-runtime.txt /
> > mpi_init:warn-fork
> > [n102:03654] Set MCA parameter "orte_base_help_aggregate" to 0 to see all
> > help / error messages
> > [n102:03654] 30 more processes have sent help message
> help-mpi-runtime.txt
> > / mpi_init:warn-fork
> > CalcError: /panfs/storage/sets/maupin/common/amber12/bin/sander failed
> with
> > prmtop complex.prmtop!
> >
> >
> > Error occured on rank 21.
> > Exiting. All files have been retained.
> >
> --------------------------------------------------------------------------
> > MPI_ABORT was invoked on rank 21 in communicator MPI_COMM_WORLD
> > with errorcode 1.
> >
> > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> > You may or may not see output from other processes, depending on
> > exactly when Open MPI kills them.
> >
> --------------------------------------------------------------------------
> >
> --------------------------------------------------------------------------
> > mpiexec has exited due to process rank 21 with PID 3684 on
> > node n88 exiting without calling "finalize". This may
> > have caused other processes in the application to be
> > terminated by signals sent by mpiexec (as reported here).
> >
> --------------------------------------------------------------------------
> >
> > Vivek S. Bharadwaj
> > Graduate Student
> > Department of Chemical and Biological Engg.
> > Colorado School of Mines
> > Golden Colorado
> >
> > _______________________________________________
> > 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
>



-- 
Vivek S. Bharadwaj
Graduate Student
Department of Chemical and Biological Engg.
Colorado School of Mines
Golden Colorado



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Received on Wed Mar 06 2013 - 13:00:03 PST
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