[gmx-developers] gromacs on opensolaris - compiles but does not really run
Mark Abraham
Mark.Abraham at anu.edu.au
Mon Aug 31 04:05:50 CEST 2009
Karsten Meyer wrote:
> 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.
> -------------------------------------------------------
The most likely cause for this problem is an incorrectly formatted
coordinate file supplied to grompp. Perhaps you need to find a more
reliable source of inputs, since a successful test will require
well-conditioned input. Possibilities include the GROMACS test set,
GROMACS benchmark set or some tutorial material. Google is your friend.
Mark
> "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
>
>
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