Hi Jason,
I checked, they only have GB in the remark section. The flags are all for
the PBSA calculations.
Yes, the jobs get accepted by the queue. Are you referring to the tests
performed during amber12 compilation? I preformed those on the head node
itself.
Vivek
On Wed, Mar 6, 2013 at 3:13 PM, Jason Swails <jason.swails.gmail.com> wrote:
> 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
>
--
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
Received on Wed Mar 06 2013 - 14:30:05 PST
