Found error after running gmx_mpi mdrun -v -deffnm npt -plumed metad.dat , any solution for that?

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1

GROMACS version:
GROMACS modification: Yes/No
Here post your question: Found error after running gmx_mpi mdrun -v -deffnm npt -plumed metad.dat , any solution for that ?
tarting mdrun ‘Protein in water’
75000000 steps, 150000.0 ps.
[ad2-PC:33647] *** Process received signal ***
[ad2-PC:33647] Signal: Segmentation fault (11)
[ad2-PC:33647] Signal code: Address not mapped (1)
[ad2-PC:33647] Failing at address: 0x30
[ad2-PC:33647] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x12980)[0x7f07dbd38980]
[ad2-PC:33647] [ 1] /usr/lib/x86_64-linux-gnu/libmpi.so.20(PMPI_Allreduce+0x189)[0x7f07dc1a3499]
[ad2-PC:33647] [ 2] /usr/local/lib/libplumedKernel.so(_ZN4PLMD6colvar16CoordinationBase9calculateEv+0x470)[0x7f07c91343c0]
[ad2-PC:33647] [ 3] /usr/local/lib/libplumedKernel.so(_ZN4PLMD10PlumedMain13justCalculateEv+0x32d)[0x7f07c91f09fd]
[ad2-PC:33647] [ 4] /usr/local/lib/libplumedKernel.so(_ZN4PLMD10PlumedMain11performCalcEv+0x11)[0x7f07c91f0f41]
[ad2-PC:33647] [ 5] /usr/local/lib/libplumedKernel.so(_ZN4PLMD10PlumedMain3cmdERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPv+0x1133)[0x7f07c91f3303]
[ad2-PC:33647] [ 6] /usr/local/lib/libplumedKernel.so(plumed_plumedmain_cmd+0x8f)[0x7f07c9205d8f]
[ad2-PC:33647] [ 7] /usr/local/gromacs/bin/gmx_mpi(+0x54b031)[0x560e9557f031]
[ad2-PC:33647] [ 8] /usr/local/gromacs/bin/gmx_mpi(+0x5e864e)[0x560e9561c64e]
[ad2-PC:33647] [ 9] /usr/local/gromacs/bin/gmx_mpi(+0x5eaae7)[0x560e9561eae7]
[ad2-PC:33647] [10] /usr/local/gromacs/bin/gmx_mpi(+0x84cee)[0x560e950b8cee]
[ad2-PC:33647] [11] /usr/local/gromacs/bin/gmx_mpi(+0xa5b2e)[0x560e950d9b2e]
[ad2-PC:33647] [12] /usr/local/gromacs/bin/gmx_mpi(+0x8ca90)[0x560e950c0a90]
[ad2-PC:33647] [13] /usr/local/gromacs/bin/gmx_mpi(+0x8d66e)[0x560e950c166e]
[ad2-PC:33647] [14] /usr/local/gromacs/bin/gmx_mpi(+0xb2939)[0x560e950e6939]
[ad2-PC:33647] [15] /usr/local/gromacs/bin/gmx_mpi(+0x7f8dc)[0x560e950b38dc]
[ad2-PC:33647] [16] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7)[0x7f07dabe4c87]
[ad2-PC:33647] [17] /usr/local/gromacs/bin/gmx_mpi(+0x808ca)[0x560e950b48ca]
[ad2-PC:33647] *** End of error message ***
Segmentation fault (core dumped)

2

This is a crash that occurred inside the PLUMED library, I suggest to seek help from the PLUMED community.

3

Anyone found a fix for this? I’m having the same problem. If I run it without plumed, it runs fine, so I dont think it’s the system blowing up.

4

This confirms what @pszilard said above - it’s a PLUMED problem, not a GROMACS problem. Inquire with their help forum.

5

I’ve realized it was because I had the geometry file in the plumed .dat file as .gro, when it has to be in .pdb format. Worth checking if anyone is having a similar problem.