[gmx-users] problem in running mdrun command

[S.Chandra Shekar]

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)