[gmx-developers] gromacs on opensolaris - compiles but does not really run
Karsten Meyer
zifsocket at gmx.de
Sun Aug 30 17:30:53 CEST 2009
Hi guys,
as an admin I don't much knowledge about chemistry, but I have to install gromacs. Runs on Ubuntu, but on opensolaris I am getting fatal errors when I try to use mdrun. Below I have attached some Output of md.log generated by running the demo in tutor/gmxdemo of gromacs-4.0.5
How do I fix this ?
K.
=============================================================
cat \#md.log.3\#
Log file opened on Sun Aug 30 17:04:26 2009
Host: opensolaris pid: 23810 nodeid: 0 nnodes: 1
The Gromacs distribution was built Sun Aug 30 16:17:54 CEST 2009 by
zifsocket at opensolaris (SunOS 5.11 i86pc)
:-) G R O M A C S (-:
Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
:-) VERSION 4.0.5 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2008, The GROMACS development team,
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) mdrun (-:
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
molecular simulation
J. Chem. Theory Comput. 4 (2008) pp. 435-447
-------- -------- --- Thank You --- -------- --------
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
Berendsen
GROMACS: Fast, Flexible and Free
J. Comp. Chem. 26 (2005) pp. 1701-1719
-------- -------- --- Thank You --- -------- --------
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
E. Lindahl and B. Hess and D. van der Spoel
GROMACS 3.0: A package for molecular simulation and trajectory analysis
J. Mol. Mod. 7 (2001) pp. 306-317
-------- -------- --- Thank You --- -------- --------
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
H. J. C. Berendsen, D. van der Spoel and R. van Drunen
GROMACS: A message-passing parallel molecular dynamics implementation
Comp. Phys. Comm. 91 (1995) pp. 43-56
-------- -------- --- Thank You --- -------- --------
Input Parameters:
integrator = steep
nsteps = 100
init_step = 0
ns_type = Grid
nstlist = 10
ndelta = 2
nstcomm = 1
comm_mode = Linear
nstlog = 100
nstxout = 100
nstvout = 100
nstfout = 0
nstenergy = 100
nstxtcout = 0
init_t = 5.87747e-39
delta_t = 0.002
xtcprec = 1000
nkx = 0
nky = 0
nkz = 0
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 5.87747e-39
optimize_fft = FALSE
ePBC = xyz
bPeriodicMols = FALSE
bContinuation = FALSE
bShakeSOR = FALSE
etc = No
epc = No
epctype = Isotropic
tau_p = 1
ref_p (3x3):
ref_p[ 0]={ 5.87747e-39, 5.87747e-39, 5.87747e-39}
ref_p[ 1]={ 5.87747e-39, 5.87747e-39, 5.87747e-39}
ref_p[ 2]={ 5.87747e-39, 5.87747e-39, 5.87747e-39}
compress (3x3):
compress[ 0]={ 5.87747e-39, 5.87747e-39, 5.87747e-39}
compress[ 1]={ 5.87747e-39, 5.87747e-39, 5.87747e-39}
compress[ 2]={ 5.87747e-39, 5.87747e-39, 5.87747e-39}
refcoord_scaling = No
posres_com (3):
posres_com[0]= 5.87747e-39
posres_com[1]= 5.87747e-39
posres_com[2]= 5.87747e-39
posres_comB (3):
posres_comB[0]= 5.87747e-39
posres_comB[1]= 5.87747e-39
posres_comB[2]= 5.87747e-39
andersen_seed = 815131
rlist = 1
rtpi = 0.05
coulombtype = Cut-off
rcoulomb_switch = 5.87747e-39
rcoulomb = 1
vdwtype = Cut-off
rvdw_switch = 5.87747e-39
rvdw = 1
epsilon_r = 1
epsilon_rf = 1
tabext = 1
implicit_solvent = No
gb_algorithm = Still
gb_epsilon_solvent = 80
nstgbradii = 1
rgbradii = 2
gb_saltconc = 5.87747e-39
gb_obc_alpha = 1
gb_obc_beta = 0.8
gb_obc_gamma = 4.85
sa_surface_tension = 2.092
DispCorr = No
free_energy = no
init_lambda = 5.87747e-39
sc_alpha = 5.87747e-39
sc_power = 0
sc_sigma = 0.3
delta_lambda = 5.87747e-39
nwall = 0
wall_type = 9-3
wall_atomtype[0] = -1
wall_atomtype[1] = -1
wall_density[0] = 5.87747e-39
wall_density[1] = 5.87747e-39
wall_ewald_zfac = 3
pull = no
disre = No
disre_weighting = Conservative
disre_mixed = FALSE
dr_fc = 1000
dr_tau = 5.87747e-39
nstdisreout = 100
orires_fc = 5.87747e-39
orires_tau = 5.87747e-39
nstorireout = 100
dihre-fc = 1000
em_stepsize = 0.01
em_tol = 1000
niter = 20
fc_stepsize = 5.87747e-39
nstcgsteep = 1000
nbfgscorr = 10
ConstAlg = Lincs
shake_tol = 0.0001
lincs_order = 4
lincs_warnangle = 30
lincs_iter = 1
bd_fric = 5.87747e-39
ld_seed = 1993
cos_accel = 5.87747e-39
deform (3x3):
deform[ 0]={ 5.87747e-39, 5.87747e-39, 5.87747e-39}
deform[ 1]={ 5.87747e-39, 5.87747e-39, 5.87747e-39}
deform[ 2]={ 5.87747e-39, 5.87747e-39, 5.87747e-39}
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1 = 5.87747e-39
userreal2 = 5.87747e-39
userreal3 = 5.87747e-39
userreal4 = 5.87747e-39
grpopts:
nrdf: 3348
ref_t: 5.87747e-39
tau_t: 5.87747e-39
anneal: No
ann_npoints: 0
acc: 5.87747e-39 5.87747e-39 5.87747e-39
nfreeze: N N N
energygrp_flags[ 0]: 0
efield-x:
n = 0
efield-xt:
n = 0
efield-y:
n = 0
efield-yt:
n = 0
efield-z:
n = 0
efield-zt:
n = 0
bQMMM = FALSE
QMconstraints = 0
QMMMscheme = 0
scalefactor = 1
qm_opts:
ngQM = 0
-------------------------------------------------------
Program mdrun, VERSION 4.0.5
Source code file: force.c, line: 1057
Fatal error:
Only triclinic boxes with the first vector parallel to the x-axis and the second vector in the xy-plane are supported.
-------------------------------------------------------
"It Just Tastes Better" (Burger King)
=============================================================
Hardware is a 32/64bit Intel System with opensolaris 2009.06
$ uname -a
SunOS opensolaris 5.11 snv_111b i86pc i386 i86pc Solaris
$ isainfo -v
64-bit amd64 applications
ssse3 cx16 mon sse3 sse2 sse fxsr mmx cmov amd_sysc cx8 tsc fpu
32-bit i386 applications
ssse3 ahf cx16 mon sse3 sse2 sse fxsr mmx cmov sep cx8 tsc fpu
sunstudio's compiler used (installed via package manager)
fftw compiled with
$ ./configure CFLAGS=-m64 --prefix=/usr/local --enable-sse --enable-single --enable-openmp
gromacs compiled with
$ ./configure CFLAGS='-m64 -I/usr/local/include' LDFLAGS=-L/usr/local/lib --prefix=/usr/local --disable-ia32-3dnow --disable-ia32-sse
--
GRATIS für alle GMX-Mitglieder: Die maxdome Movie-FLAT!
Jetzt freischalten unter http://portal.gmx.net/de/go/maxdome01
More information about the gromacs.org_gmx-developers
mailing list