On 4/1/2012, at 5:03 p.m., Ben Roberts wrote:
> Hi,
>
> This is apparently the cause of the recent troubles I had when running pmemd.CUDA on Longhorn. These were covered in an earlier thread, and ultimately appeared as bug #172 on the bugzilla.
>
> The upshot of the bug hunting (thanks Scott!) is that it's not a real bug at all, but a hydrogen connected to more than one oxygen, or else an oxygen connected to more than two hydrogens. This is, apparently, a problem for SHAKE, that is caught in the CUDA executable but not in the regular executable.
>
> However, this surprised me, because I thought I had taken good care of my topology. And, indeed, when I checked my topology using rdparm, I found that the only hydrogens bonded to more than one atom of any kind were those in the rigid TIP3P waters, where there's a known H-H bond.
>
> There were a number of oxygens with three substituents. This is because the system I'm simulating involves a dinickel cluster, and each nickel has bonded to it a water molecule, so that the oxygens in these water molecules each have two hydrogen substituents plus a nickel. Also, there's a bridging hydroxide, in which the oxygen has two nickel substituents plus a hydrogen.
>
> These are the only oxygen atoms with three substituents in the system.
>
> Now, this presents a problem to me, because it seems to me that SHAKE oughtn't to whinge and moan about too many hydrogens in such cases. Scott suggested, though, that the nickels could be wrongly identified as hydrogens. If so, how could that be? And is it because of a problem in my input, for example, my PREPI file that I used to construct topologies?
>
> On the other hand, is there perhaps a section in the PRMTOP that lists, either explicitly or as part of a section that serves multiple purposes, which atoms should be considered hydrogens?
>
> And can I get around this problem (even if just as a temporary workaround) by just putting the nickel ions in my system into a NOSHAKEMASK?
Actually, no, I can't. If I try running with the following NOSHAKEMASK:
noshakemask = ':768,769,1540,1541,2312,2313'
I get this error (from STDOUT):
TACC: Done.
TACC: Starting up job 121069
TACC: Setting up parallel environment for MVAPICH ssh-based mpirun.
TACC: Setup complete. Running job script.
TACC: starting parallel tasks...
cudaGetDeviceCount failed unknown error
TACC: MPI job exited with code: 1
TACC: Shutting down parallel environment.
TACC: Shutdown complete. Exiting.
TACC: Cleaning up after job: 121069
TACC: Done.
Any thoughts? Should I file a new ticket on the bugzilla?
Cheers,
Ben
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Received on Wed Jan 04 2012 - 15:00:03 PST
