From: David Hardy (dhardy_at_ks.uiuc.edu)
Date: Fri Aug 25 2017 - 14:39:24 CDT
I've found and fixed a long-standing bug in the NAMD 2.12 CUDA kernels that may have affected your simulation. You might want to try the NAMD nightly build from http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=NAMD <http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=NAMD> to see if you are able to run on your GPU.
-- David J. Hardy, Ph.D. Theoretical and Computational Biophysics Beckman Institute, University of Illinois dhardy_at_ks.uiuc.edu http://www.ks.uiuc.edu/~dhardy/ > On Jul 20, 2017, at 6:03 AM, James Starlight <jmsstarlight_at_gmail.com> wrote: > > Dear NAMD Users! > > I have faced with a following problem running the lattest NAMD with > GPU quadro 5000k. I am dealing with the GPCR-membrane system > assembling with the CHARM-GUI with all input conf files provided on > the default. > > I took the system just after the equilibration and running it with the > CHARM-GUI parameters obtained the following error: > > FATAL ERROR: Periodic cell has become too small for original patch grid! > Possible solutions are to restart from a recent checkpoint, > increase margin, or disable useFlexibleCell for liquid simulation. > > because this is a membrane-consisting system and disable > useFlexibleCell is not possible I try to increase margin up to 5.0, > obtaining another error: > > FATAL ERROR: High global CUDA exclusion count! (96033 vs 92328) > System unstable or pairlistdist or cutoff too close to periodic cell > size. > > There was no such error with this system running on CPU cluster. How I > should modify conf file to solve the issue? > > Thanks! > > Gleb
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