Re: long running sim dies

From: Tristan Croll (
Date: Mon Oct 13 2014 - 14:36:37 CDT

Simple question first: you're not just hitting the maximum number of steps specified in your input file? When I do that, my build exits with a similar, counterintuitive "cannot find... " error message.

Tristan Croll
Faculty of Health
School of Biomedical Sciences
Institute of Health and Biomedical Engineering
Queensland University of Technology
60 Musk Ave
Kelvin Grove QLD 4059 Australia
+61 7 3138 6443

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On 13 Oct 2014, at 11:41 pm, "Thomas C. Bishop" <<>> wrote:

Dear NAMD,
we have been doing some benchmarks on my local computers lately and seems they are dieing
after running successfully from some time.
( NAMD 2.9 for Linux-x86_64-multicore, 32-way SMP opteron, 1 node, 1 physical node
Uname 3.11.10-21-desktop #1 SMP PREEMPT ... the machine has LOTS of ram and typically one user )

Nothing seems pathological w/ the system (all energies config etc.. are ok)
There is plenty of disk space for output..etc..

The only error I have was a note from one student
. I checked the output file and found a fatal error occured, it said that cannot find balancer (not sure, need to check it again).

Other runs died w/ no error message.
Could it possibly be that /usr/local/namd2, which is automounted, is disconnecting?
system logs do not indicate a hardware problem.

I presume if the namd2 executable is in same directory as the output that I/O will keep the automount active.
It this true or does namd open/close files between writes?

Just trying to figure this one out... guess I need to dust off the sys-admin manual.

Any ideas/comments appreciated.

   Thomas C. Bishop
    Tel: 318-257-5209
    Fax: 318-257-3823<>

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