From: Morgan, Brittany (Brittany.Morgan_at_umassmed.edu)
Date: Fri Mar 07 2014 - 11:45:15 CST
Ivan,
I've had similar output if I hit a hard quota on physical memory. In my experience, if there is no error message it means that the problem is external to NAMD.
Brittany
________________________________
From: owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] On Behalf Of Ivan Gregoretti [ivangreg_at_gmail.com]
Sent: Friday, March 07, 2014 12:36 PM
To: namd-l_at_ks.uiuc.edu list
Subject: namd-l: NAMD 2.9 quits early without error message.
Hello everybody,
I bring you a riddle here to help me solve.
I am trying to run a 100000 simulation but NAMD 2.9 quits early.
My configuration file requests
# dynamics
numsteps 100000
but the last line of the output to the log file states
WRITING COORDINATES TO DCD FILE AT STEP 67000
The velocities and coordinate files did not get written. It is clearly an unwanted early termination. No error message.
The head of the log file says
Charm++: standalone mode (not using charmrun)
Converse/Charm++ Commit ID: v6.4.0-beta1-0-g5776d21
CharmLB> Load balancer assumes all CPUs are same.
Charm++> Running on 1 unique compute nodes (32-way SMP).
Charm++> cpu topology info is gathered in 0.094 seconds.
Info: NAMD 2.9 for Linux-x86_64-multicore
Info:
Info: Please visit http://www.ks.uiuc.edu/Research/namd/
Info: for updates, documentation, and support information.
Info:
Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)
Info: in all publications reporting results obtained with NAMD.
Info:
Info: Based on Charm++/Converse 60400 for multicore-linux64-iccstatic
Info: Built Mon Apr 30 14:00:48 CDT 2012 by jim on naiad.ks.uiuc.edu<http://naiad.ks.uiuc.edu>
Info: 1 NAMD 2.9 Linux-x86_64-multicore 32 inca igregore
Info: Running on 32 processors, 1 nodes, 1 physical nodes.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 0.169809 s
Info: 2265.71 MB of memory in use based on /proc/self/stat
I am running this on a 32 core Linux 64 machine with 256GB RAM. Notice that this is NAMD 2.9 release.
Has anybody seen anything like this?
Thank you,
Ivan
Ivan Gregoretti, PhD
Bioinformatics
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