As Justin said give the command line options for mdrun and also check that your mpi environment is running. Better to run a parallel job and check its output.
Chadnan -- Chandan kumar Choudhury NCL, Pune INDIA On Mon, Feb 8, 2010 at 8:02 PM, Justin A. Lemkul <[email protected]> wrote: > > > Jennifer Williams wrote: > >> >> Dear All, >> >> I am having problems compiling gromacs 4.0.7 in parallel. I am following >> the >> Quick and Dirty Installation instructions on the gromacs webpage. >> I downloaded the the versions of fftw, OpenMPI and gromacs-4.0.7 following >> these instructions. >> >> Everything seems to compile OK and I get all the serial executables >> including mdrun written to my bin directory and they seem to run fine. >> However when I try to run mdrun_mpi on 6 nodes I get the following: >> >> [vlxbig16:08666] [NO-NAME] ORTE_ERROR_LOG: Not found in file >> runtime/orte_init_stage1.c at line 182 >> [vlxbig16:08667] [NO-NAME] ORTE_ERROR_LOG: Not found in file >> runtime/orte_init_stage1.c at line 182 >> [vlxbig16:08700] [NO-NAME] ORTE_ERROR_LOG: Not found in file >> runtime/orte_init_stage1.c at line 182 >> [vlxbig16:08670] [NO-NAME] ORTE_ERROR_LOG: Not found in file >> runtime/orte_init_stage1.c at line 182 >> [vlxbig16:08681] [NO-NAME] ORTE_ERROR_LOG: Not found in file >> runtime/orte_init_stage1.c at line 182 >> [vlxbig16:08659] [NO-NAME] ORTE_ERROR_LOG: Not found in file >> runtime/orte_init_stage1.c at line 182 >> -------------------------------------------------------------------------- >> It looks like orte_init failed for some reason; your parallel process is >> likely to abort. There are many reasons that a parallel process can >> fail during orte_init; some of which are due to configuration or >> environment problems. This failure appears to be an internal failure; >> here's some additional information (which may only be relevant to an >> Open MPI developer): >> >> orte_rml_base_select failed >> --> Returned value -13 instead of ORTE_SUCCESS >> >> >> Does anyone have any idea what is causing this? Computer support at my >> University is not sure. >> >> > How are you launching mdrun_mpi (command line)? > > -Justin > > >> Thanks >> >> >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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