[gmx-users] query for gromacs-4.5.4

[Chaitali Chandratre]

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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