From: Roy Fernando (roy.nandos_at_gmail.com)
Date: Sat Mar 08 2014 - 10:03:21 CST
I run my simulation in a cluster. I sometimes notice that the simulation
stops without error message in the log file in attempting to connect to all
the processors. However it picks up when I run it again. I wonder if you
are seeing a similar situation?
On Fri, Mar 7, 2014 at 12:45 PM, Morgan, Brittany <
> 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.
> *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: Please visit http://www.ks.uiuc.edu/Research/namd/
> Info: for updates, documentation, and support information.
> Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)
> Info: in all publications reporting results obtained with NAMD.
> 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
> 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 Gregoretti, PhD
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