Diane Fournier wrote:
-----Original Message-----
From: [EMAIL PROTECTED] on behalf of David van der Spoel
Sent: Sat 4/29/2006 2:25 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] segmentation fault in mdrun when using PME
Diane Fournier wrote:
Hi, I'm new to Gromacs and I'm trying to run a enzyme-ligand complex
molecular dynamics simulation. I have tried doing John
Kerrigan's Drug-Enzyme tutorial and mdrun crashes with segmentation
fault and core dump at the steepest descents minimization step. However,
mdrun works fine when using cutoff instead of PME.
I'm working with Gromacs v. 3.3.1 on a SGI altix 3700 with 32 Intel
Itanium 2 processors (but I'm currently using a single node, so it's not
a MPI problem) under Red Hat Enterprise Linux AS release 3 with Intel
Math Kernel Librarary (MKL) v. 8.0.1 as FFT library (which is optimized
for Itanium 2).
the em.mdp file looks like:
title = drg_trp
cpp = /usr/bin/cpp
define = -DFLEX_SPC
constraints = none
integrator = steep
dt = 0.002 ; ps !
nsteps = 500
nstlist = 10
ns_type = grid
rlist = 0.9
coulombtype = PME
rcoulomb = 0.9
rvdw = 0.9
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
;
; Energy minimizing stuff
;
emtol = 1000.0
emstep = 0.01
Is it possible this could be related to insufficient memory allocation ?
How demanding is this PME calculation ?
Not likely a memory problem. It could be a compiler issue but we need
more info! Where does it crash? Is it reproducible? DOes the same tpr
file cause a crash on another architecture (e.g. your desktop)?
I installed gromacs 3.3.1 on my desktop (Pentium 4 under linux fedora core 4 and using the fftw3 fourier transform library). I used the .tpr file generated on the altix in mdrun and it worked fine.
When I run that same file on the altix, it crashes every time without any
iteration in the .log file:
Removing pbc first time
Done rmpbc
Initiating Steepest Descents
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
0: rest, initial mass: 14580
Started Steepest Descents on node 0 Mon May 1 11:47:39 2006
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
S. Miyamoto and P. A. Kollman
SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
Water Models
J. Comp. Chem. 13 (1992) pp. 952-962
-------- -------- --- Thank You --- -------- --------
After that the file ends. There is no other error message than segmentation
fault with core dump.
The compilers that are used on the altix are:
C++ Version 9 9.0-023 -> 9.0-031
C++ Version 8 8.1-033 -> 8.1-036
Fortran 9 9.0-021 -> 9.0-032
Fortran 8 8.1-029 -> 8.1-033
IPP 4.1 -> 5.0
Have you enabled fortran at the compilation stage? In that case try it
without, otherwise please file a bugzilla, such that we can document
this problem (and try to fix it of course).
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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