Hi, There's nothing GROMACS-specific here - something about your MPI installation, configuration or use is pretty wrong, but we can't help work out what.
Mark On Sun, Nov 10, 2013 at 12:31 PM, S.Chandra Shekar < chandrashe...@iisertvm.ac.in> wrote: > Dear all > > I encounter a problem while running command mdrun_mpi -v -deffnm em in > gromacs. > > I am new to the gromacs. i just ran test calculation, *simulation of > lyzozyme in water*. i am able to generate gro, tpr files. But in the final > step i got following error. > > Thanks in advance. > > > [localhost.localdomain:23122] mca: base: component_find: paffinity > "mca_paffinity_linux" uses an MCA interface that is not recognized > (component MCA v1.0.0 != supported MCA v2.0.0) -- ignored > [localhost.localdomain:23123] mca: base: component_find: paffinity > "mca_paffinity_linux" uses an MCA interface that is not recognized > (component MCA v1.0.0 != supported MCA v2.0.0) -- ignored > [localhost.localdomain:23123] mca: base: component_find: ras > "mca_ras_dash_host" uses an MCA interface that is not recognized (component > MCA v1.0.0 != supported MCA v2.0.0) -- ignored > [localhost.localdomain:23123] mca: base: component_find: ras > "mca_ras_gridengine" uses an MCA interface that is not recognized > (component MCA v1.0.0 != supported MCA v2.0.0) -- ignored > [localhost.localdomain:23123] mca: base: component_find: ras > "mca_ras_localhost" uses an MCA interface that is not recognized (component > MCA v1.0.0 != supported MCA v2.0.0) -- ignored > [localhost.localdomain:23123] mca: base: component_find: errmgr > "mca_errmgr_hnp" uses an MCA interface that is not recognized (component > MCA v1.0.0 != supported MCA v2.0.0) -- ignored > [localhost.localdomain:23123] mca: base: component_find: errmgr > "mca_errmgr_orted" uses an MCA interface that is not recognized (component > MCA v1.0.0 != supported MCA v2.0.0) -- ignored > [localhost.localdomain:23123] mca: base: component_find: errmgr > "mca_errmgr_proxy" uses an MCA interface that is not recognized (component > MCA v1.0.0 != supported MCA v2.0.0) -- ignored > [localhost.localdomain:23123] mca: base: component_find: iof > "mca_iof_proxy" uses an MCA interface that is not recognized (component MCA > v1.0.0 != supported MCA v2.0.0) -- ignored > [localhost.localdomain:23123] mca: base: component_find: iof "mca_iof_svc" > uses an MCA interface that is not recognized (component MCA v1.0.0 != > supported MCA v2.0.0) -- ignored > [localhost.localdomain:23122] mca: base: component_find: rcache > "mca_rcache_rb" uses an MCA interface that is not recognized (component MCA > v1.0.0 != supported MCA v2.0.0) -- ignored > [localhost:23122] *** Process received signal *** > [localhost:23122] Signal: Segmentation fault (11) > [localhost:23122] Signal code: Address not mapped (1) > [localhost:23122] Failing at address: 0x44000098 > [localhost:23122] [ 0] /lib64/libpthread.so.0() [0x3fcee0f500] > [localhost:23122] [ 1] /usr/local/lib/libmpi.so.1(PMPI_Comm_size+0x4e) > [0x2acc6d93727e] > [localhost:23122] [ 2] > /usr/local/gromacs/bin/../lib/libgmx_mpi.so.8(gmx_setup+0x32) > [0x2acc6d195e02] > [localhost:23122] [ 3] > /usr/local/gromacs/bin/../lib/libgmx_mpi.so.8(init_par+0x51) > [0x2acc6d234251] > [localhost:23122] [ 4] mdrun_mpi(cmain+0x11f9) [0x435799] > [localhost:23122] [ 5] /lib64/libc.so.6(__libc_start_main+0xfd) > [0x3fcea1ecdd] > [localhost:23122] [ 6] mdrun_mpi() [0x406ee9] > [localhost:23122] *** End of error message *** > Segmentation fault (core dumped) > -- > 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 > -- 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
