[gmx-developers] Simulations on GPU
Igor Leontyev
ileontyev at ucdavis.edu
Tue Oct 5 08:42:03 CEST 2010
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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