AMBER Archive (2006)

Subject: AMBER: job crashes

From: Xiaowei (David) Li (xl3a_at_virginia.edu)
Date: Tue Sep 26 2006 - 22:09:04 CDT

Dear all:
  I have met intensive (almost every job I submitted) MD job crashes
during recent simulation work. The job crashes always happend upon the
completion points of simulations (for example, the crash happens around
950 ps for a 1 ns simulation). All of the errors messages have the
"semop lock failed" information as following.
Job is running on node(s):
------------------------
compute-2-5 compute-2-6 compute-2-7 compute-2-9
------------------------
    p4_error: latest msg from perror: Invalid argument
p0_9469: p4_error: OOPS: semop lock failed: -1
forrtl: error (69): process interrupted (SIGINT)
forrtl: error (69): process interrupted (SIGINT)
forrtl: error (69): process interrupted (SIGINT)
forrtl: error (69): process interrupted (SIGINT)
p3_28418: (207846.623829) net_send: could not write to fd=5, errno = 32
forrtl: error (69): process interrupted (SIGINT)
p0_9469: (207848.918605) net_send: could not write to fd=4, errno = 32:

I was running the parallel simulation with MPI on a linux cluster with
Athlon Opteron 244 processors. The input file is:
&cntrl
  imin = 0,
  irest = 1,
  ntx = 5,
  ntb = 2,
  pres0 = 1.0,
  ntp = 1,
  tautp=5
  taup =5,
  cut = 10,
  ntr = 0,
  ntc = 2,
  ntf = 2,
  tempi = 300.0,
  temp0 = 300.0,
  ntt = 1,
  nstlim =500000,
  dt = 0.002,
  ntpr = 100,
  ntwx = 100,
  ntwr = 1000,
  nscm=1,
 &end
Any help or suggestion will be deeply appreciated. Thanks.

Best,
Xiaowei Li
University of Virginia

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu