[gmx-users] Gromacs 4.6 crushes in PBS queue system

Tomek Wlodarski tomek.wlodarski at gmail.com
Sat Feb 16 23:27:45 CET 2013


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).
[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!


More information about the gromacs.org_gmx-users mailing list