[gmx-users] query for gromacs-4.5.4

[Mark Abraham]

It could be anything. But until we see some GROMACS diagnostic messages,
nobody can tell.

Mark

On Tue, Mar 12, 2013 at 10:08 AM, Chaitali Chandratre <chaitujoshi at gmail.com
> wrote:

> 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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