[gmx-users] problem in running mdrun command

[Mark Abraham]

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 <
chandrashekar at 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)
> --
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