From: Ivan Gregoretti (ivangreg_at_gmail.com)
Date: Fri Mar 07 2014 - 11:46:54 CST
I should add, perhaps, that I have plenty of disk space to write to.
Ivan Gregoretti, PhD
Bioinformatics
On Fri, Mar 7, 2014 at 12:36 PM, Ivan Gregoretti <ivangreg_at_gmail.com> wrote:
> 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
> 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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