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.node2-6 spl_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
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Received on Wed Feb 06 2013 - 17:30:02 PST
