[gmx-users] About system requirement to gromacs

[Mark Abraham]

On 2/08/2012 1:02 AM, rama david wrote:
> Thank you for reply and your suggestion..
>
> As I mentioned earlier I installed Gromacs-openmpi 4.5.5  from Ubuntu
> software package manager
>
> So I want to just check is it performing REMD or  not???
>
> So as per previous suggestion of Mark ...
> I made two tpr file that has two different temp 300 k and 310
> k..topol0.tpr and topol1.tpr  respectively

mdrun disagrees with you. Use gmxcheck to compare your .tpr files.

Mark

>
>
> I used command line....
>
>   mpirun -c 4   mdrun_mpi  -v -multi 2 -replex 10
>
> output as follow.....
>
>
> node 0 par_fn 'topol0.tpr'
> node 0 par_fn 'topol1.tpr'
> node 0 par_fn 'traj1.trr'
> node 0 par_fn 'traj1.xtc'
> node 0 par_fn 'state1.cpt'
> node 0 par_fn 'state1.cpt'
> node 0 par_fn 'confout1.gro'
> node 0 par_fn 'ener1.edr'
> node 0 par_fn 'traj0.trr'
> node 0 par_fn 'md1.log'
> log
> node 0 par_fn 'traj0.xtc'
> node 0 par_fn 'dhdl1.xvg'
> node 0 par_fn 'field1.xvg'
> node 0 par_fn 'state0.cpt'
> node 0 par_fn 'rerun1.xtc'
> node 0 par_fn 'tpi1.xvg'
> node 0 par_fn 'tpidist1.xvg'
> node 0 par_fn 'state0.cpt'
> node 0 par_fn 'sam1.edo'
> node 0 par_fn 'confout0.gro'
> node 0 par_fn 'bam1.gct'
> node 0 par_fn 'gct1.xvg'
> node 0 par_fn 'ener0.edr'
> node 0 par_fn 'deviatie1.xvg'
> node 0 par_fn 'runaver1.xvg'
> node 0 par_fn 'md0.log'
> node 0 par_fn 'pullx1.xvg'
> node 0 par_fn 'pullf1.xvg'
> node 0 par_fn 'nm1.mtx'
> log
> node 0 par_fn 'dipole1.ndx'
> node 0 par_fn 'dhdl0.xvg'
>
> Back Off! I just backed up md1.log to ./#md1.log.4#
> Getting Loaded...
> Reading file topol1.tpr, VERSION 4.5.5 (single precision)
> node 0 par_fn 'field0.xvg'
> node 0 par_fn 'rerun0.xtc'
> node 0 par_fn 'tpi0.xvg'
> node 0 par_fn 'tpidist0.xvg'
> node 0 par_fn 'sam0.edo'
> node 0 par_fn 'bam0.gct'
> node 0 par_fn 'gct0.xvg'
> node 0 par_fn 'deviatie0.xvg'
> node 0 par_fn 'runaver0.xvg'
> node 0 par_fn 'pullx0.xvg'
> node 0 par_fn 'pullf0.xvg'
> node 0 par_fn 'nm0.mtx'
> node 0 par_fn 'dipole0.ndx'
>
> Back Off! I just backed up md0.log to ./#md0.log.4#
> Getting Loaded...
> Reading file topol0.tpr, VERSION 4.5.5 (single precision)
> Loaded with Money
>
> Loaded with Money
>
> Making 1D domain decomposition 2 x 1 x 1
>
> Back Off! I just backed up traj0.trr to ./#traj0.trr.4#
>
> Back Off! I just backed up ener0.edr to ./#ener0.edr.4#
> Making 1D domain decomposition 2 x 1 x 1
>
> Back Off! I just backed up traj1.trr to ./#traj1.trr.4#
>
> Back Off! I just backed up ener1.edr to ./#ener1.edr.4#
>
> -------------------------------------------------------
> Program mdrun_mpi, VERSION 4.5.5
> Source code file: /build/buildd/gromacs-4.5.5/src/kernel/repl_ex.c, line: 177
>
> Fatal error:
> The properties of the 2 systems are all the same, there is nothing to exchange
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> "I Do It All the Time" (Magnapop)
>
>
> -------------------------------------------------------
> Program mdrun_mpi, VERSION 4.5.5
> Source code file: /build/buildd/gromacs-4.5.5/src/kernel/repl_ex.c, line: 177
>
> Fatal error:
> The properties of the 2 systems are all the same, there is nothing to exchange
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> "I Do It All the Time" (Magnapop)
>
> Error on node 2, will try to stop all the nodes
> Halting parallel program mdrun_mpi on CPU 2 out of 4
> Error on node 0, will try to stop all the nodes
> Halting parallel program mdrun_mpi on CPU 0 out of 4
>
> gcq#197: "I Do It All the Time" (Magnapop)
>
>
> gcq#197: "I Do It All the Time" (Magnapop)
>
> --------------------------------------------------------------------------
> 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 on
> exactly when Open MPI kills them.
> --------------------------------------------------------------------------
> --------------------------------------------------------------------------
> mpirun has exited due to process rank 0 with PID 9919 on
> node VPCEB34EN exiting without calling "finalize". This may
> have caused other processes in the application to be
> terminated by signals sent by mpirun (as reported here).
> --------------------------------------------------------------------------
> [VPCEB34EN:09918] 1 more process has sent help message
> help-mpi-api.txt / mpi-abort
> [VPCEB34EN:09918] Set MCA parameter "orte_base_help_aggregate" to 0 to
> see all help / error messag
>
>
>
> Thanks a lot for hearing my problem
>
> So from above output is it able to perform REMD or not ?????
> Is the gromacs installation  on my system is right for open-mpi????
>
>
> With Best Wishes and regards
>
> Rama david