Hi! В письме от 16 февраля 2013 23:27:45 пользователь Tomek Wlodarski написал: > Hi! > > I have problem in running gromacs 4.6 in PBS queue... > I end up with error: > > > [n370:03036] [[19430,0],0]-[[19430,1],8] mca_oob_tcp_msg_recv: readv > failed: Connection reset by peer (104) > -------------------------------------------------------------------------- > mpirun noticed that process rank 18 with PID 616 on node n344 exited on > signal 4 (Illegal instruction).
Aha. Your mdrun process got SIGILL. This means that your nodes have different instruction set then head node. So try to use different acceleration level. Can you share details about your hw? > -------------------------------------------------------------------------- > [n370:03036] 3 more processes have sent help message > help-opal-shmem-mmap.txt / mmap on nfs > [n370:03036] Set MCA parameter "orte_base_help_aggregate" to 0 to see all > help / error messages > 3 total processes killed (some possibly by mpirun during cleanup) > > I run the same pbs files with older gromacs 4.5.5 (installed with the same > openmpi, gcc and fftw) and everything is working.. > > also when I am running gromacs directly on the access node: > > mpirun -np 32 /home/users/didymos/gromacs/bin/mdrun_mpi -v -deffnm > protein-EM-solvated -c protein-EM-solvated.gro > > it is running OK. > Any ideas? > Thank you! > Best! > > tomek -- Best Regards, Alexey 'Alexxy' Shvetsov Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, Gatchina, Russia Department of Molecular and Radiation Biophysics Gentoo Team Ru Gentoo Linux Dev mailto:[email protected] mailto:[email protected] mailto:[email protected]
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