From: Bryan Roessler (roessler_at_uab.edu)
Date: Tue Jan 31 2017 - 10:12:07 CST
OK, it appears the issue is with the new nonbonded CUDA kernel in 2.12.
Passing the "useCUDA2 no" option in the configuration file has fixed the
*Bryan Roessler | Graduate Research Assistant*
UAB | The University of Alabama at Birmingham
Knowledge that will change your world
On Tue, Jan 31, 2017 at 12:52 AM, Bryan Roessler <roessler_at_uab.edu> wrote:
> I've been having problems with my free MD simulations in 2.12 and 2.12b1
> that do not happen in 2.11. According to my logs the last known good build
> that I was using was the 2015-10-29 nightly that did not have this problem.
> I am using the CUDA enabled linux builds.
> The problem is that immediately when I begin (or restart) a simulation
> using one of the affected builds I see a large depression form in the
> solvation box (it's not a PBC artifact, there is plenty of padding) and my
> system temperature rises from ~310K to ~335K (and higher) and eventually my
> simulation fails due to RATTLE constraints on some of the exterior
> hydrogens of my protein.
> I have tried restarting stable ~20ns simulations from the 2015-10-29 build
> and they will usually fail within 100-1000 timesteps on 2.12 or 2.12b1. If
> I restart the simulations in 2.11 they proceed perfectly. I thought that
> there might be some compatibility issue between the binary files so I've
> also exported the restart files as a PDB in VMD and reinitialized my
> temperatures but this hasn't helped.
> I thought that perhaps CUDA versioning was giving me problems so I made
> sure to specify the correct LD_LIBRARY_PATH with the linked cuda.so
> included with NAMD.
> I have also tried building NAMD but I will need to fire up a VM since
> there are compatibility issues between GCC 5.3 and CUDA 8.0 and I don't
> want to muck with my environment too much. I was hoping that maybe someone
> could shed some light on this problem before I go that route.
> The KISS in me says to just keep using 2.11 for the time being but I'd
> very much like to utilize the GPU performance optimizations and I'm curious
> why this happening. 2015-10-29 has decent performance too without the
> associated problem so I will likely continue to use that version going
> forward. I'd also be curious to find a ftp or some other site where I can
> download older nightly builds so maybe I could narrow down when this
> problem was introduced.
> *Bryan Roessler | Graduate Research Assistant*
> UAB | The University of Alabama at Birmingham
> *uab.edu/cmdb <http://uab.edu/cmdb>*
> Knowledge that will change your world
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