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:
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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
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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/ -
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Received on Wed Mar 07 2007 - 06:07:45 PST
