[gmx-users] Re: [gmx-developers] Simulations on GPU
Szilárd Páll
szilard.pall at cbr.su.se
Tue Oct 5 10:18:22 CEST 2010
Hi,
The beta versions are all outdated, could you please use the latest
source distribution (4.5.1) instead (or git from the
release-4-5-patches branch)?
The instructions are here:
http://www.gromacs.org/gpu#Compiling_and_custom_installation_of_GROMACS-GPU
>> The requested platform "CUDA" could not be found
AFAIR that is generally the sign of a problem with the mismatch
between the CUDA version of the libraries mdrun and openmm are linked
against with.
Let us know if you succeed!
--
Szilárd
>>
>>
>>
>> The output of gmx4.5-beta2 is
>> --------------------------------------------------------------------------
>> Log file opened on Mon Oct 4 21:56:10 2010
>> Host: powerpc pid: 30370 nodeid: 0 nnodes: 1
>> The Gromacs distribution was built @TMP_TIME@ by
>> rossen at mohawk.cbr.su.se [CMAKE] (@TMP_MACHINE@)
>>
>> :-) G R O M A C S (-:
>> GROwing Monsters And Cloning Shrimps
>> :-) VERSION 4.5-GPU-beta2 (-:
>>
>> 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.
>> :-) /home/leontyev/programs/bin/gromacs/gromacs-4.5-beta2/bin/mdrun-gpu (-:
>>
>> ++++ 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 = md
>> nsteps = 100
>> init_step = 0
>> nstcalcenergy = 10
>> ns_type = Simple
>> nstlist = 0
>> ndelta = 2
>> nstcomm = 1003
>> comm_mode = Linear
>> nstlog = 10
>> nstxout = 5000
>> nstvout = 10000000
>> nstfout = 0
>> nstenergy = 1000
>> nstxtcout = 1
>> init_t = 0
>> delta_t = 0.001
>> xtcprec = 1000
>> nkx = 0
>> nky = 0
>> nkz = 0
>> pme_order = 4
>> ewald_rtol = 1e-05
>> ewald_geometry = 0
>> epsilon_surface = 0
>> optimize_fft = FALSE
>> ePBC = xyz
>> bPeriodicMols = FALSE
>> bContinuation = FALSE
>> bShakeSOR = FALSE
>> etc = No
>> nsttcouple = -1
>> epc = No
>> epctype = Isotropic
>> nstpcouple = -1
>> tau_p = 1
>> ref_p (3x3):
>> ref_p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
>> ref_p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
>> ref_p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
>> compress (3x3):
>> compress[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
>> compress[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
>> compress[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
>> refcoord_scaling = No
>> posres_com (3):
>> posres_com[0]= 0.00000e+00
>> posres_com[1]= 0.00000e+00
>> posres_com[2]= 0.00000e+00
>> posres_comB (3):
>> posres_comB[0]= 0.00000e+00
>> posres_comB[1]= 0.00000e+00
>> posres_comB[2]= 0.00000e+00
>> andersen_seed = 815131
>> rlist = 1
>> rlistlong = 1
>> rtpi = 0.05
>> coulombtype = Cut-off
>> rcoulomb_switch = 0
>> rcoulomb = 1
>> vdwtype = Cut-off
>> rvdw_switch = 0
>> rvdw = 1
>> epsilon_r = 1
>> epsilon_rf = 1
>> tabext = 1
>> implicit_solvent = No
>> gb_algorithm = Still
>> gb_epsilon_solvent = 80
>> nstgbradii = 1
>> rgbradii = 1
>> gb_saltconc = 0
>> gb_obc_alpha = 1
>> gb_obc_beta = 0.8
>> gb_obc_gamma = 4.85
>> gb_dielectric_offset = 0.009
>> sa_algorithm = No
>> sa_surface_tension = 2.092
>> DispCorr = No
>> free_energy = no
>> init_lambda = 0
>> delta_lambda = 0
>> n_foreign_lambda = 0
>> sc_alpha = 0
>> sc_power = 0
>> sc_sigma = 0.3
>> nstdhdl = 10
>> dh_table_size = 0
>> dh_table_spacing = 0.1
>> nwall = 0
>> wall_type = 9-3
>> wall_atomtype[0] = -1
>> wall_atomtype[1] = -1
>> wall_density[0] = 0
>> wall_density[1] = 0
>> wall_ewald_zfac = 3
>> pull = no
>> disre = No
>> disre_weighting = Conservative
>> disre_mixed = FALSE
>> dr_fc = 1000
>> dr_tau = 0
>> nstdisreout = 100
>> orires_fc = 0
>> orires_tau = 0
>> nstorireout = 100
>> dihre-fc = 1000
>> em_stepsize = 0.01
>> em_tol = 10
>> niter = 20
>> fc_stepsize = 0
>> nstcgsteep = 1000
>> nbfgscorr = 10
>> ConstAlg = Lincs
>> shake_tol = 0.0001
>> lincs_order = 8
>> lincs_warnangle = 30
>> lincs_iter = 4
>> bd_fric = 0
>> ld_seed = 1993
>> cos_accel = 0
>> deform (3x3):
>> deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
>> deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
>> deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
>> userint1 = 0
>> userint2 = 0
>> userint3 = 0
>> userint4 = 0
>> userreal1 = 0
>> userreal2 = 0
>> userreal3 = 0
>> userreal4 = 0
>> grpopts:
>> nrdf: 99024
>> ref_t: 0
>> tau_t: 0
>> anneal: No
>> ann_npoints: 0
>> acc: 0 0 0
>> nfreeze: N N N
>> energygrp_flags[ 0]: 0 0
>> energygrp_flags[ 1]: 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
>> Table routines are used for coulomb: FALSE
>> Table routines are used for vdw: FALSE
>> Cut-off's: NS: 1 Coulomb: 1 LJ: 1
>> System total charge: -0.000
>> Generated table with 1000 data points for 1-4 COUL.
>> Tabscale = 500 points/nm
>> Generated table with 1000 data points for 1-4 LJ6.
>> Tabscale = 500 points/nm
>> Generated table with 1000 data points for 1-4 LJ12.
>> Tabscale = 500 points/nm
>> Enabling SPC-like water optimization for 11505 molecules.
>> Configuring nonbonded kernels...
>> Configuring standard C nonbonded kernels...
>>
>> Removing pbc first time
>> Initializing LINear Constraint Solver
>> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
>> B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije
>> LINCS: A Linear Constraint Solver for molecular simulations
>> J. Comp. Chem. 18 (1997) pp. 1463-1472
>> -------- -------- --- Thank You --- -------- --------
>> The number of constraints is 5967
>> ++++ 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 --- -------- --------
>> Center of mass motion removal mode is Linear
>> We have the following groups for center of mass motion removal:
>> 0: rest
>> Max number of connections per atom is 91
>> Total number of connections is 387700
>> Max number of graph edges per atom is 6
>> Total number of graph edges is 70330
>> OpenMM plugins loaded from directory
>> /home/leontyev/programs/bin/gromacs/gromacs-4.5-beta2/bin/../openmm/lib/plugins:
>> libOpenMMCuda.so,
>> -------------------------------------------------------
>> Program mdrun-gpu, VERSION 4.5-GPU-beta2
>> Source code file:
>> /home/rossen/Research/Projects/Gromacs-dev/gromacs/src/kernel/openmm_wrapper.cpp,
>> line: 550
>> Fatal error:
>> OpenMM supports only the following methods for electrostatics: NoCutoff
>> (i.e. rcoulomb = rvdw = 0 ),Reaction-Field, Ewald or PME.
>> For more information and tips for troubleshooting, please check the GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>> -------------------------------------------------------
>> --
>> gmx-developers mailing list
>> gmx-developers at gromacs.org
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