I think this mail belongs to the user's list, CC-d will continue the discussion there.
-- Szilárd 2010/10/5 Igor Leontyev <ileont...@ucdavis.edu>: > Dear gmx-developers, > My first attempt to start GPU-version of gromacs has no success. The reason > is that grompp turns off setting of electrostatics overriding them by > coulombtype=Cut-off and rcoulomb=1, which are not currently supported in gpu > version, despite that in mdp-file coulombtype is set to "PME" and > rcoulomb=1.2. See the log-file bellow. Any suggestions? > > 1) Here a precompiled mdrun-gpu binary from the distributed archive > "gromacs-4.5-GPU-beta2_linux-X86_64.tar.gz" was used along with standard > installation of gromacs version 4.5-beta2. I tried to follow the > instructions given at > http://www.gromacs.org/Downloads/Installation_Instructions/Gromacs_on_GPUs > The output always points to unsupported method of electrostatics > disregarding the fact that both tried methods (PME and NoCutoff) should be > supported. > > 2) I also tried upper versions of grompp: 4.5-beta3, 4.5-beta4, 4.5 and > 4.5.1. > In 4.5-beta3 version grompp does not switch the electrostatics method but > mdrun-gpu yet generate an error: >> >> The requested platform "CUDA" could not be found > > While all upper gmx-versions are not compatible with this mdrun-gpu > executable >> >> Fatal error: >> reading tpx file (CcO_0hcav_3Dch_E242side_OH-_O2-_PM.tpr) version 73 with >> version 71 > > Thanks, > Igor > > > > 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 > ros...@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-develop...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-developers > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-developers-requ...@gromacs.org. > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists