From: hl332_at_drexel.edu
Date: Fri Apr 20 2007 - 11:22:09 CDT
Hi all,
I am doing an NVE run of my protein with PBC. The version of namd used is 2.5. It was running on 8 processors with a parallel version. My run crashed after 3 million steps giving segmentation fault error listed below. I read a few previous mails from archive but could not make out how to resolve this? NO such problems arise with spherical boundary runs, why so?
I see no bad energy (in the sense too high) vales or any thing else in log file. I am not sure whats going on? Can someone from development team help me out:
ERROR:
==============================
bash: line 1: 26222 Segmentation fault /usr/bin/env MPIRUN_MPD=0 MPIRUN_HOST=node10 MPIRUN_PORT=32927 MPIRUN_PROCESSES='node10:node10:node10:node10:node9:node9:node9:node9:' MPIRUN_RANK=0 MPIRUN_NPROCS=8 MPIRUN_ID=26180 /home/sfw/namd-2.5/bin/namd2 nve.conf
[7] Abort: [node9:7] Got completion with error, code=VAPI_RETRY_EXC_ERR, vendor code=81, dest rank=0
at line 378 in file viacheck.c
[6] Abort: [node9:6] Got completion with error, code=VAPI_RETRY_EXC_ERR, vendor code=81, dest rank=0
at line 378 in file viacheck.c
[4] Abort: [5] Abort: [node9:4] Got completion with error, code=VAPI_RETRY_EXC_ERR, vendor code=81, dest rank=0
at line 378 in file viacheck.c
[node9:5] Got completion with error, code=VAPI_RETRY_EXC_ERR, vendor code=81, dest rank=0
at line 378 in file viacheck.c
done.
-------------------------------------------------
Harish Vashisth (Ph.D Candidate)
CAT-361,Chemical & Biological Engg.
Drexel University, Philadelphia, PA
office: 215-895-5823
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