Dear all:
I'm running an MD of pure tip4p water. The calculation is not very big, so I thought if I could run it without SHAKE. But it turned out I couldn't. Every time I got similar error messages like this:
[cli_0]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
SANDER BOMB in subroutine nonbond_list
SANDER BOMB in subroutine nonbond_list
volume of ucell too big, too many subcells
list grid memory needs to be reallocated, restart sander
SANDER BOMB in subroutine nonbond_list
volume of ucell too big, too many subcells
[cli_3]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 3
volume of ucell too big, too many subcells
list grid memory needs to be reallocated, restart sander
[cli_4]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 4
[cli_1]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 1
[cli_2]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 2
list grid memory needs to be reallocated, restart sander
SANDER BOMB in subroutine nonbond_list
volume of ucell too big, too many subcells
SANDER BOMB in subroutine nonbond_list
volume of ucell too big, too many subcells
list grid memory needs to be reallocated, restart sander
[cli_6]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 6
list grid memory needs to be reallocated, restart sander
SANDER BOMB in subroutine nonbond_list
volume of ucell too big, too many subcells
list grid memory needs to be reallocated, restart sander
[cli_7]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 7
SANDER BOMB in subroutine nonbond_list
volume of ucell too big, too many subcells
list grid memory needs to be reallocated, restart sander
[cli_5]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 5
rank 3 in job 1 dell13_38141 caused collective abort of all ranks
exit status of rank 3: return code 1
rank 2 in job 1 dell13_38141 caused collective abort of all ranks
exit status of rank 2: return code 1
rank 1 in job 1 dell13_38141 caused collective abort of all ranks
exit status of rank 1: return code 1
rank 0 in job 1 dell13_38141 caused collective abort of all ranks
exit status of rank 0: return code 1
Unit 30 Error on OPEN: density.rst
[cli_0]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
rank 0 in job 1 dell13_32985 caused collective abort of all ranks
exit status of rank 0: killed by signal 9
I checked the mailing list but no luck. I've ran similar MD before, the only difference is this time I removed SHAKE. So I added SHAKE back. It worked.
So I'm thinking is SHAKE necessary in running an MD?
Thank you.
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Received on Mon Apr 01 2013 - 02:00:03 PDT
