Matteo Guglielmi wrote:
Mark Abraham wrote:
Matteo Guglielmi wrote:
I did what you suggest and even more, I decreased the timestep to 0.001
Well the problem doesn't go away.
I've been reading mails from this discussion list... I'm not the only
who's experiencing this kind of problem (ci variable range error)...
actually few gmx users suggest it comes only from parallel runs which
is my case BTW.
I've seen it most often when equilibration hasn't happened properly,
but you'd think 1.5ns would be enough to avoid a crash.
I'm running parallel runs on different clusters... it's happening
everywhere.
Do serial runs do it?
Have you looked at your trajectory visually to see where things start
going wrong?
Mark
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I did no try any serial run yet... trajectory looks fine... but log
files might explain
why parallel runs keep crashing.
Usually I run gromacs on a dual Xeon 5140 cpus machine (2x2-cores) in
double precision.
I did compile gromacs using the intel compilers - 9.1 series:
[EMAIL PROTECTED] ~]$ icc -V
Intel(R) C Compiler for Intel(R) EM64T-based applications, Version
9.1 Build 20070320 Package ID: l_cc_c_9.1.049
Copyright (C) 1985-2007 Intel Corporation. All rights reserved.
[EMAIL PROTECTED] ~]$ icpc -V
Intel(R) C++ Compiler for Intel(R) EM64T-based applications, Version
9.1 Build 20070320 Package ID: l_cc_c_9.1.049
Copyright (C) 1985-2007 Intel Corporation. All rights reserved.
[EMAIL PROTECTED] ~]$ ifort -V
Intel(R) Fortran Compiler for Intel(R) EM64T-based applications, Version
9.1 Build 20070320 Package ID: l_fc_c_9.1.045
Copyright (C) 1985-2007 Intel Corporation. All rights reserved.
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try again with gcc in that case. if that gives the same behavior then
please submit a bugzilla.
--
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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