Thanks. But I finished running similar 8 simulations with larger system without any memory outage.
_MMPBSA_complex_nm.out.0 file is empty contrast to all other 7 files as below. Please let me know what you think.
[alir02.node2-6 spl_TSHR_prep_calc]$ cat
_MMPBSA_complex_nm.out.0
[alir02.node2-6 spl_TSHR_prep_calc]$ cat _MMPBSA_complex_nm.out.1Reading parm file (spl_TSHR_sim_nw.top)title:default_name mm_options: ntpr=10000 mm_options: diel=C mm_options: kappa=0.103952
mm_options: cut=1000 mm_options: gb=1 mm_options: dielc=4.000000 mm_options: temp0=298.150000scaling charges by 0.500
Processing ASCII traj
iter Total bad vdW elect nonpolar genBorn frms[alir02.node2-6 spl_TSHR_prep_calc]$
--- On Wed, 2/6/13, Jason Swails <jason.swails.gmail.com> wrote:
From: Jason Swails <jason.swails.gmail.com>
Subject: Re: [AMBER] topology file issue with entropy calculation
To: "AMBER Mailing List" <amber.ambermd.org>
Date: Wednesday, February 6, 2013, 9:24 PM
Try running with 1 processor. Normal mode calculations require a lot of
memory, and running 8 simulations at the same time on the same node
requires 8 times a lot of memory.
It's quite possible the computer you are running on does not have enough
memory for that load.
If that is
not the problem, we'll need the error message from the
_MMPBSA_complex_nm.out.0 file -- that might provide more clues about what
went wrong.
Good luck,
Jason
On Wed, Feb 6, 2013 at 8:14 PM, Rejwan <rejwan_88.yahoo.com> wrote:
> Hi,
> Thanks. Following is the job output file. Should you need more info please
> let me know. Again thanks for all your help.
> RA
>
> [alir02.node2-6 spl_TSHR_prep_calc]$ cat spl_nmo.o5290303Running
> MMPBSA.MPI on 8 processorsReading command-line arguments and input
> files...Loading and checking parameter files for compatibility...cpptraj
> found! Using /packages/amber/12n/src/amber12/bin/cpptrajmmpbsa_py_nabnmode
> found! Using
> /packages/amber/12n/src/amber12/bin/mmpbsa_py_nabnmodePreparing
> trajectories for
simulation...
> 200 frames were processed by cpptraj for use in calculation.8 frames were
> processed by cpptraj for nmode calculations.
> Beginning nmode calculations with
> /packages/amber/12n/src/amber12/bin/mmpbsa_py_nabnmode calculating complex
> contribution...[node5-16:20860] 1 more process has sent help message
> help-mpi-runtime.txt / mpi_init:warn-fork[node5-16:20860] Set MCA parameter
> "orte_base_help_aggregate" to 0 to see all help / error messagesCalcError:
> /packages/amber/12n/src/amber12/bin/mmpbsa_py_nabnmode failed with prmtop
> spl_TSHR_sim_nw.top!Error occured on rank 0.Exiting. All files have been
> retained.--------------------------------------------------------------------------MPI_ABORT
> was invoked on rank 0 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 onexactly when Open
> MPI kills
> them.----------------------------------------------------------------------------------------------------------------------------------------------------mpirun
> has exited due to process rank 0 with PID 20861 onnode node5-16 exiting
> without calling "finalize". This mayhave caused other processes in the
> application to beterminated by signals sent by mpirun (as reported
> here).--------------------------------------------------------------------------[node5-16:20860]
> 6 more processes have sent help message help-mpi-runtime.txt /
> mpi_init:warn-fork==> Resources used :
> cput=00:00:24,mem=267660kb,vmem=556632kb,walltime=00:00:20==> Exit status
> : 1 (general error, check job output file)[alir02.node2-6spl_TSHR_prep_calc]$
>
>
>
> --- On Tue, 2/5/13, David A Case <case.biomaps.rutgers.edu> wrote:
>
> From: David A Case <case.biomaps.rutgers.edu>
> Subject: Re: [AMBER] topology file issue with entropy calculation
> To: "AMBER Mailing List" <amber.ambermd.org>
> Date: Tuesday, February 5, 2013, 7:46 AM
>
> On Mon, Feb 04, 2013, Rejwan wrote:
> >
> > I have a ?water stripped topology file that ran fine to calculate
> > decomposition of GB and PB energy components, but giving error while
> > calculating entropy by normal mode. Any suggestions for potential
> > ?failure check are welcome.
>
> Look at the output files to see what the
error is? No one on the list can
> help without more information than this.
>
> ...dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
> 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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Feb 07 2013 - 12:00:02 PST
