From: Bryan Roessler (roessler_at_uab.edu)
Date: Fri Feb 03 2017 - 14:17:51 CST
FWIW, it appears that this issue has been resolved in the nightlies
(2017-02-03).
*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
On Tue, Jan 31, 2017 at 10:12 AM, Bryan Roessler <roessler_at_uab.edu> wrote:
> 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
> issue.
>
> Thanks,
> Bryan
>
> *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
>
> On Tue, Jan 31, 2017 at 12:52 AM, Bryan Roessler <roessler_at_uab.edu> wrote:
>
>> Hello,
>>
>> 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.
>>
>> Thanks,
>> Bryan
>>
>>
>> *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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