On Tue, May 20, 2014 at 7:26 AM, Sanjib Paul <sanjib88paul.gmail.com> wrote:
> *Warning: Conflicting CPU frequencies detected, using: 2600.000000.Warning:
> Conflicting CPU frequencies detected, using: 2600.000000.*
> In NPT it stopped after giving some message -
This warning isn't from Amber - a quick google search appears to
indicate that it's related to OpenMPI. From what I gather it probably
won't affect your results, except maybe for timing data, though you
should probably run some basic tests of your MPI setup. My
recommendation would be to switch to a different MPI like mpich - I've
never had great luck with OpenMPI.
> ERROR: PMEMD does not support intermolecular
> PRFs!--------------------------------------------------------------------------mpirun
If your system has bonding between different molecules and has extra
points, this is not supported for NPT runs.
> *gpu_download_partial_forces: download failed unspecified launch
> failure--------------------------------------------------------------------------mpirun
The GPU code is more sensitive to bad initial configurations than the
CPU code. I recommend trying a short run with the CPU code to better
diagnose what is happening with the system that fails.
Note that unless you have multiple GPUs in a single box both connected
to PCI-E 2.0 x 16 or better, you probably aren't going to gain much
running pmemd.cuda.MPI for a single MD job. Make sure you've read up
on all the information here:
http://ambermd.org/gpus/
particularly the section 'Running GPU Accelerated Simulations'.
Hope this helps,
-Dan
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue May 20 2014 - 07:30:02 PDT
