Mark Abraham wrote:
On 12/07/2011 4:51 AM, Justin A. Lemkul wrote:
Hi All,
I'm having a strange problem with some implicit solvent systems and
I'm wondering if anyone's experienced the same problem or if I've
stumbled upon a bug. I'm testing some methodology with a robust
system (everyone's favorite, 1AKI lysozyme). Running simulations with
finite cutoffs works fine (in serial or parallel using DD), but if I
try to call the all-vs-all kernels (e.g. infinite cutoffs), the
simulations instantly crash (at step 0) with LINCS warnings. Running
in serial, however, produces perfectly stable trajectories using
all-vs-all, but the simulations are very slow.
The effects are independent of integrator (tested sd and md) and
hardware/compilers. The problem is reproducible on two very different
systems:
1. x86_64 via OpenMPI 1.4.2 and compiled with cmake with gcc-4.3.4
2. Mac OSX with threads and compiled via autoconf with gcc-4.4.4
All force fields that I've tested (OPLS-AA, CHARMM27, and AMBER03)
give the same result.
The problem is present in version 4.5.4 and the most current
release-4-5-patches. My .mdp file and a gdb backtrace are provided at
the end of this message.
Is there anything else to try, or should I just file a redmine issue
with a .tpr file?
Judging by the .mdp file, I have similar systems working just fine in
parallel. If you upload the .tpr to Redmine, I'll try it out.
Thanks Mark. I've created issue #777 for this.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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