[gmx-developers] Simulations on GPU
Szilárd Páll
szilard.pall at cbr.su.se
Tue Oct 5 10:15:18 CEST 2010
I think this mail belongs to the user's list, CC-d will continue the
discussion there.
--
Szilárd
2010/10/5 Igor Leontyev <ileontyev at 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
> 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
> -------------------------------------------------------
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