Re: Minimization failing on one machine only

From: Ajasja Ljubetič (
Date: Sat Oct 15 2016 - 01:50:29 CDT


Try to run a non-CUDA NAMD on the linux box, so
NAMD 2.11 for Linux-x86_64-multicore

I remember I used to have similar problems with CUDA not minimizing in
certain circumstances.


On 14 October 2016 at 22:34, Chris Goedde <> wrote:

> Hi all,
> Why might a system that minimizes successfully on one machine fail on a
> different machine?
> The two machines are an iMac and and linux box. The linux box has an
> Nvidia GPU in it. The versions of namd are (from the log file):
> NAMD 2.11 for MacOSX-x86_64-multicore
> NAMD 2.11 for Linux-x86_64-multicore-CUDA
> All input files (conf, pdb, psf, etc) are *identical* for the two
> machines. (Checked with diff.)
> On the mac, namd is called as:
> namd2 +p4 +isomalloc_sync run.conf > run.log &
> On the linux box, it’s
> namd2 +p16 +isomalloc_sync run.conf > run.log &
> On the mac the system minimizes correctly, relaxing from the initial
> configuration to the expected minimum energy state. On the linux box, the
> system never minimizes (configuration doesn’t appreciably change), and in
> the log file I see:
> interspersed throughout the minimization process. Of course I don’t see
> this at all in the log files from the mac.
> The system is fairly simple, just water and carbon nanotubes; I don’t
> think the trouble is that the initial state is badly configured. But, if I
> wanted to troubleshoot the minimization process, I’m not sure what exactly
> to look for.
> I don’t see what I’m doing wrong (or what’s happening differently on the
> two machines, other than the different versions of namd). Any suggestions
> appreciated; I’m really stuck here as to what’s happening--001a1139e68c32a87c053ee1c2ed--

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