[gmx-users] query for gromacs-4.5.4

[Chaitali Chandratre]

Sir,

Thanks for your reply....
But the same script runs on some other cluster with apprx same
configuration but not on cluster on which I am doing set up.

Also job hangs after some 16000 steps but not come out immediately.
It might be problem with configuration or what?

Thanks...

Chaitali

On Tue, Mar 12, 2013 at 2:18 PM, Mark Abraham <mark.j.abraham at gmail.com>wrote:

> They're just MPI error messages and don't provide any useful GROMACS
> diagnostics. Look in the end of the .log file, stderr and stdout for clues.
>
> One possibility is that your user's system is too small to scale
> effectively. Below about 1000 atoms/core you're wasting your time unless
> you've balanced the load really well. There is a
> simulation-system-dependent point below which fatal GROMACS errors are
> assured.
>
> Mark
>
> On Tue, Mar 12, 2013 at 6:17 AM, Chaitali Chandratre
> <chaitujoshi at gmail.com>wrote:
>
> > Hello Sir,
> >
> > Actually I have been given work to setup gromacs-4.5.4 in our cluster
> which
> > is being used
> > by users.I am not gromacs user and not aware of its internal details.
> > I have got only .tpr file from user and I need to test my installation
> > using that .tpr file.
> >
> > It works fine for 2 nodes 8 processes , 1 node 8 processes.
> >  But when number of processes are equal to 16 it gives segmentation fault
> > and
> >  if number of processes are equal to 32 it gives
> > error message like
> > " HYD_pmcd_pmiserv_send_signal (./pm/pmiserv/pmiserv_cb.c:221): assert
> > (!closed) failed
> >  ui_cmd_cb (./pm/pmiserv/pmiserv_pmci.c:128): unable to send SIGUSR1
> > downstream
> >  HYDT_dmxu_poll_wait_for_event (./tools/demux/demux_poll.c:77): callback
> > returned error status
> >  HYD_pmci_wait_for_completion (./pm/pmiserv/pmiserv_pmci.c:388): error
> > waiting for event
> > [ main (./ui/mpich/mpiexec.c:718): process manager error waiting for
> > completion"
> >
> > I am not clear like whether problem is there in my installation or what?
> >
> > Thanks and Regards,
> >    Chaitalij
> >
> > On Wed, Mar 6, 2013 at 5:41 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> > >
> > >
> > > On 3/6/13 4:20 AM, Chaitali Chandratre wrote:
> > >
> > >> Dear Sir ,
> > >>
> > >> I am new to this installation and setup area. I need some information
> > for
> > >> -stepout option for
> > >>
> > >
> > > What more information do you need?
> > >
> > >
> > >  mdrun_mpi and also probable causes for segmentation fault in
> > >>  gromacs-4.5.4.
> > >> (my node having 64 GB mem running with 16 processes, nsteps =
> 20000000)
> > >>
> > >>
> > > There are too many causes to name.  Please consult
> > http://www.gromacs.org/
> > > **Documentation/Terminology/**Blowing_Up<
> > http://www.gromacs.org/Documentation/Terminology/Blowing_Up>.
> > >  If you need further help, please be more specific, including a
> > description
> > > of the system, steps taken to minimize and/or equilibrate it, and any
> > > complete .mdp file(s) that you are using.
> > >
> > > -Justin
> > >
> > > --
> > > ==============================**==========
> > >
> > > Justin A. Lemkul, Ph.D.
> > > Research Scientist
> > > Department of Biochemistry
> > > Virginia Tech
> > > Blacksburg, VA
> > > jalemkul[at]vt.edu | (540) 231-9080
> > > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> > >
> > > ==============================**==========
> > > --
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