Yes, this is user error that is caught by the CUDA code. The FORTRAN code should catch this as well IMO. One or more of your waters is incorrectly named and not correctly picked up for the specialized SHAKE algorithm for waters. So what I've detected is a hydrogen that is supposedly in a water molecule but which has more than one bond attached to it.
-----Original Message-----
From: Marc van der Kamp [mailto:marcvanderkamp.gmail.com]
Sent: Friday, April 08, 2011 8:07 AM
To: amber.ambermd.org
Subject: [AMBER] pmemd.cuda crashes due to "Inconsistent hydrogen network"
Hi all,
I have previously successfully run pmemd.cuda_SPDP using an AMBER force
field.
I'm now trying to do the same using the CHARMM force field. After converting
psf/crd using CHAMBER to prmtop/inpcrd, sander.MPI and pmemd.MPI have no
problems with my system/files. However, when I try to run the same on a GPU,
pmemd.cuda_SPDP crashes with the following message:
Inconsistent hydrogen network, exiting.
I noticed this error message was introduced (or altered) in the
comprehensive Bugfix.9 (BTW, all current bugfixes, i.e. up to 12, are
applied):
if ((my_nonfastwat_bond_dat[j].atm_i == atm_j) ||
(my_nonfastwat_bond_dat[j].atm_i == atm_j))
{
printf("Inconsistent hydrogen network,
exiting.\n");
+ gpu_shutdown_();
exit(-1);
}
The error occurs right after the number of triangulated waters are reported
in the output ("Number of triangulated 3-point waters found")
FYI, I'm running on an NVIDIA Tesla M2050.
Any suggestions on how to fix this?
Many thanks in advance,
Marc
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Received on Fri Apr 08 2011 - 16:30:03 PDT
