On 4/15/13 3:16 PM, Stephanie Teich-McGoldrick wrote:
Hello Justin,
Thank you for the reply, and I am glad to hear that this is normal output.
Unfortunately, my simulations crash almost immediately when I used v4.6,
and I was assuming it has something to do with the load balancing because
that is the last line in my md.log file.
I have run with the flag "mdrun -debug 1" and find the error:
"mdrun_mpi:13106 terminated with signal 11 at PC=2abd88a03934
SP=7fff6343f170. Backtrace:
/apps/x86_64/mpi/openmpi/intel-12.1-2011.7.256/openmpi-1.4.3_oobpr/lib/libmpi.so.0[0x2abd88a03934]"
I know this is rather vague, but do you have any suggestions on where I
should start tracking down this error? When I use particle decomposition my
simulations run fine.
Standard advice applies:
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
If you want to troubleshoot further, please provide (at minimum) a complete .mdp
file. The simple truth is that systems are not infinitely parallelizable, and
small changes in number of processors can cause subtle instabilities in the DD
algorithm over large numbers of processors. If it worked before, that may have
been a random success that now fails. If there is something more nefarious
going on, we should be able to weed it out with some careful debugging, but
there's no evidence of a bug yet.
-Justin
Message: 3
Date: Mon, 15 Apr 2013 06:08:13 -0400
From: Justin Lemkul <jalem...@vt.edu>
Subject: Re: [gmx-users] Issue with domain decomposition between
v4.5.5 and 4.6.1
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <516bd18d.8000...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 4/14/13 11:23 PM, Stephanie Teich-McGoldrick wrote:
Dear all,
I am running a NPT simulation of 33,534 tip4P waters, and I am using
domain
decomposition as the parallelization scheme. Previously, I had been using
Gromacs version 4.5.5 but have recently installed and switched to Gromacs
version 4.6.1. Using Gromacs 4.5.5 I can successfully run my water box
using domain decomposition over many different processor numbers. However
the same simulation returns the following error when I try Gromacs 4.6.1
"The initial number of communication pulses is: X 1 Y 1 Z 1
The initial domain decomposition cell size is: X 2.48 nm Y 2.48 nm Z 1.46
nm
When dynamic load balancing gets turned on, these settings will change to:
The maximum number of communication pulses is: X 1 Y 1 Z 1
The minimum size for domain decomposition cells is 1.000 nm
The requested allowed shrink of DD cells (option -dds) is: 0.80
The allowed shrink of domain decomposition cells is: X 0.40 Y 0.40 Z 0.68
"
The above error occurred running over 16 nodes / 128 processors. The
system
runs for version 4.6.1 for 1,8, and 16 processors but not for 32,64, or
128
processors.
I have tried other systems (including NVT, Berendsen/PR barostats,
anisotropic/isotropic ) at the higher number of processors using both
version 4.5.5 and 4.6.1 and get the same result - v4.5.5 runs fine while
v4.6.1 returns the error type listed above.
Is anyone else having a similar issue? Is there something I am not
considering? Any help would be greatly appreciated! The details I have
used
to compile each code are below. My log files indicate that I am indeed
calling the correct executable at run time.
Based on what you've posted, I don't see any error. All of the above is
normal
output.
-Justin
--
==============================
==========
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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