From: Alexandre A. Vakhrouchev (makaveli.lcf_at_gmail.com)
Date: Thu May 15 2008 - 13:41:21 CDT
Hi all!
During 2000K atoms system simulation I got following error message:
namd2: Rank 0:29: MPI_Iprobe: ibv_poll_cq(): bad status 12
namd2: Rank 0:28: MPI_Iprobe: ibv_poll_cq(): bad status 12
namd2: Rank 0:28: MPI_Iprobe: self node9.eth0.mvs50k.jscc.ru peer
node26.eth0.mvs50k.jscc.ru (rank: 115)
namd2: Rank 0:28: MPI_Iprobe: error message: transport retry exceeded error
namd2: Rank 0:29: MPI_Iprobe: self node9.eth0.mvs50k.jscc.ru peer
node26.eth0.mvs50k.jscc.ru (rank: 117)
namd2: Rank 0:29: MPI_Iprobe: error message: transport retry exceeded error
namd2: Rank 0:28: MPI_Iprobe: Internal MPI error
namd2: Rank 0:29: MPI_Iprobe: Internal MPI error
MPI Application rank 29 exited before MPI_Finalize() with status 16
NAMD runs for different number of steps before getting this error and
fail. Sometimes it hangs at startup phase. Other simulations work good
for less number of atoms (I tried up to 200K atoms). Cluster is dual
quadcore Xeon on Infiniband. I built NAMD for Linux-amd64-MPI
according to Wiki
http://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?NamdOnInfiniBand
Francly speaking the only thing I didn't use was "-thread pthreads"
for CHARMOPTS because linker exited with error that there was no
pthreads found. May it be the case?
-- Best regards, Dr. Alexander Vakhrushev Institute of Applied Mechanics Dep. of Mech. and Phys.-Chem. of heterogeneous mediums UB of Russian Academy of Sciences 34 T. Baramzinoy St. Izhevsk, Russia 426067
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:49:28 CST