Well your input file had a GB section...
In any case, do the tests pass when submitted through the queue?
On Wed, Mar 6, 2013 at 5:00 PM, Vivek Shankar Bharadwaj <
vbharadw.mymail.mines.edu> wrote:
> Hi Jason,
>
> I decided to to PBSA calculations only.
> Should I be doing GBSA calculations before doing PBSA calculations?
>
> Vivek
>
> On Wed, Mar 6, 2013 at 2:47 PM, Jason Swails <jason.swails.gmail.com>
> wrote:
>
> > 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
> >
>
>
>
> --
> 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 - 14:30:04 PST
