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
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Received on Wed Mar 06 2013 - 14:30:03 PST
