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 <chaitujo...@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.abra...@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 > > <chaitujo...@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 <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? 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