It seems that in my case this is a bug (see Bugzilla, bug # 74) related to using the Intel Math Kernel Library (MKL) v. 8.0.1 for Fourier transforms. The team managing the Altix are trying different FFT libraries. Eric Lindahl says that using a FFT library that is not optimized for Itanium 2 shouldn't hamper the perfomance very much since FT doesn't represent a very big part of the computation. I think the error I get with the version compiled without Fortran is boggus, because this tutorial (John Kerrigan's) was tried sucessfully by many people, so there shouldn't be any mistakes in the .mdp file. Also, the runs I do with that version have strange output and anyway, I don't get that error with the Fortran-enabled version. Segmentation fault has been documented in the position restrained dynamics stage of this tutorial with gromacs 3.3.0 though, and was solved when upgrading to 3.3.1. An exploding system is often caused by extreme forces due to bad contacts, which can be relieved by a minimization step. Have you used a steepest descents minimization step on your system before doing the pr ?
________________________________
De: [EMAIL PROTECTED] de la part de Arneh Babakhani
Date: mar. 2006-05-02 23:21
À: Discussion list for GROMACS users
Objet : Re: RE : [gmx-users] segmentation fault in mdrun when using PME
Hello, I'm experiencing the exact same problem, when trying to do some
restrained molecular dynamics of a small peptide in a water box. Have you had
any luck in trouble-shooting this? (I've pasted my mdp file below, for your
reference). Also running Gromacs 3.3.1
Arneh
title = ResMD
warnings = 10
cpp = /usr/bin/cpp ; location of cpp on SGI
define = -DPOSRES
constraints = all-bonds
integrator = md
dt = 0.002 ; ps !
nsteps = 25000 ; total 50.0 ps.
nstcomm = 1
nstxout = 500 ; output coordinates every 1.0 ps
nstvout = 1000 ; output velocities every 2.0 ps
nstfout = 0
nstlog = 10
nstenergy = 10
nstlist = 10
ns_type = grid
rlist = 0.9
coulombtype = PME
rcoulomb = 0.9
rvdw = 1.0
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 6
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on in four groups
Tcoupl = berendsen
tau_t = 0.1 0.1
tc_grps = protein sol
ref_t = 300 300
; Pressure coupling is on
Pcoupl = berendsen
pcoupltype = isotropic
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529
Diane Fournier wrote:
________________________________
De: [EMAIL PROTECTED] de la part de David van der Spoel
Date: lun. 2006-05-01 13:33
À: Discussion list for GROMACS users
Objet : Re: [gmx-users] segmentation fault in mdrun when using PME
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).
Still doesn't work. logfile ends in the usual way. Except this
time, I get this output:
Reading file trp_em.tpr, VERSION 3.3.1 (single precision)
Steepest Descents:
Tolerance (Fmax) = 1.00000e+03
Number of steps = 500
Warning: 1-4 interaction between 1 and 7 at distance 39513.957 which is
larger than the 1-4 table size 1.000 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
Wrote pdb files with previous and current coordinates
Back Off! I just backed up step0.pdb to ./#step0.pdb.1#
Wrote pdb files with previous and current coordinates
and then these files get written:
step0.pdb
#step0.pdb.1#
step-1.pdb
step1.pdb
Will file a bugzilla.
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________________________________________________________________________
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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