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 <jalem...@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> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
