does it work when you are not using multisander?
On 3/6/07, Ilyas Yildirim <yildirim.pas.rochester.edu> wrote:
> Dear All,
>
> Using sander.MPI in a minimization with 2 cpu's work fine, but if I try to
> use 4/8/... cpu's, it is giving me the following error:
>
> ---------------------------------------------------------------------
> arde00:/home/yildirim/test/l_0.2>runmin &
> [1] 2428
> arde00:/home/yildirim/test/l_0.2>/bin/rm: No match.
> mpirun -stdin /dev/null -np 4 -nolocal -machinefile /tmp/tmp.mpi.2434
> /home/yildirim/amber9/exe/sander.MPI -ng 2 -groupfile
> /home/yildirim/test/l_0.2/groups_min1; rm -f /tmp/tmp.mpi.2434
> running on arde11:1 arde12:1 arde13:2
>
> Running multisander version of sander amber9
> Total processors = 4
> Number of groups = 2
>
> Looping over processors:
> WorldRank is the global PE rank
> NodeID is the local PE rank in current group
>
> Group = 0
> WorldRank = 0
> NodeID = 0
>
> WorldRank = 1
> NodeID = 1
>
> Group = 1
> WorldRank = 2
> NodeID = 0
>
> WorldRank = 3
> NodeID = 1
>
> p3_19669: p4_error: : 14
> 3 - MPI_BCAST : Message truncated
> [3] Aborting program !
> [3] Aborting program!
> p1_7187: p4_error: : 14
> 1 - MPI_BCAST : Message truncated
> [1] Aborting program !
> [1] Aborting program!
> rm_l_3_19670: (2.024163) net_send: could not write to fd=5, errno = 32
> rm_l_1_7188: (2.869610) net_send: could not write to fd=5, errno = 32
> p2_12533: p4_error: net_recv read: probable EOF on socket: 1
> rm_l_2_12534: (2.259215) net_send: could not write to fd=5, errno = 32
> p1_7187: (2.871182) net_send: could not write to fd=5, errno = 32
> p2_12533: (6.264409) net_send: could not write to fd=5, errno = 32
> mpirun -stdin /dev/null -np 4 -nolocal -machinefile /tmp/tmp.mpi.2595
> /home/yildirim/amber9/exe/sander.MPI -ng 2 -groupfile
> /home/yildirim/test/l_0.2/groups_min2; rm -f /tmp/tmp.mpi.2595
> ---------------------------------------------------------------------
>
> For the md runs, I dont see any problems (can run with 4/8/... cpu's). The
> system is an 8-mer solvated with water. I was wondering if this is normal
> for AMBER9, or if I am missing something. Thanks.
>
> --
> Ilyas Yildirim
> ---------------------------------------------------------------
> - Department of Chemisty - -
> - University of Rochester - -
> - Hutchison Hall, # B10 - -
> - Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) -
> - http://www.pas.rochester.edu/~yildirim/ -
> ---------------------------------------------------------------
>
>
--
Received on Wed Mar 07 2007 - 06:07:46 PST
