What about _MMPBSA_complex_gb.mdout.0? Of course the GB calculation should
have been done first...
Try running the test suite in parallel (with 2 cores only) on your system
by submitting it to the queue.
Does it work?
On Wed, Mar 6, 2013 at 3:36 PM, Vivek Shankar Bharadwaj <
vbharadw.mymail.mines.edu> wrote:
> 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
>
> _______________________________________________
> 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
Received on Wed Mar 06 2013 - 14:00:02 PST
