On Sat, Jun 1, 2013 at 2:22 PM, Marek Maly <marek.maly.ujep.cz> wrote:
> Dear all,
> I just found that in Updates section ( http://ambermd.org/bugfixes12.html
> ) is already record of the
> expected bugfix-18 announced recently by Ross.
>
> i.e.
> --------
> bugfix.18: Fixes a number of issues with pmemd and pmemd.cuda:
> Updates GPU code to v12.3
> Adds check to prevent running ntb=2 with gamma_ln=0 and ntt=3 or 4.
> Fixes Hamiltonian Replica Exchange on GPUs and CPUs in explicit solvent.
> Fixes issue with nmropt DUMPAVE printing in pmemd for H-REMD.
> Fixes extra-points support for the GLYCAM force field which was leading to
> a segfault in pmemd and pmemd.cuda.
> Improves stability for NPT simulations on GPUs.
> Adds check to make sure code quits if skinnb would go negative in GPU
> calculations due to large reductions in box size.
> Fixes issues with restart of NPT simulations on GPUs in cases where the
> box size had shrunk considerably.
> Fixes minimizations on GPUs with the SPFP precision model by truncating
> large forces that occur during the beginning of a minimization.
> Changes pmemd.cuda and pmemd.cuda.MPI links to be relative instead of
> absolute in AMBERHOME/bin directory.
> Updates configure script to optimize for sm35 GPU hardware (Kepler II) in
> cases where cuda v5.0 is detected.
> Makes GTX680 output the gold standard for test cases.
> Fixes incorrect timings that were reported at the end of a run with REMD
> runs in pmemd.
> --------
>
> but it seems that this bugfix was not uploaded to the given server as
> after the attempt
> to click on the given link I have obtained this err.
>
The bugfix is actually uploaded. It's a compressed patch, and I
accidentally referenced the wrong file (without the .bz2_ suffix).
You can get the update via update_amber:
$AMBERHOME/update_amber --update
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Jun 01 2013 - 14:30:03 PDT
