Re: [gmx-users] Simulations on GPU
On Fri, Jan 14, 2011 at 3:58 AM, Rossen Apostolov wrote: > Hi, >> >> I get this error when I try to run mdrun-gpu with a forcefield that >> has GROMOS interaction types: >> >> Fatal error: OpenMM does not support (some) of the provided >> interaction type(s) (G96Angle). >> >> Maybe it's possible to run a short simulation on a small system and >> not encounter the missing interactions? I don't know enough about how >> the forcefields work to know whether that would get past the error. >> >> -Keith >> > > I doesn't matter whether the simulation is short or the system small. You > can exclude certain interaction types from the FF but then you'll end up > with a most likely meaningless model. > > Rossen Thank you, but I think you missed the point of my question. I was only trying to understand why Francesco might get output that is "full of NaN" instead of an error. -Keith >>> >>> Rossen >>> -- >>> 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 >>> > > -- > 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 > -- gmx-users mailing listgmx-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
Re: [gmx-users] Simulations on GPU
OpenMM works with AMBER force-field. Then, to use OpenMM you have to change the force-field Il 13/01/2011 21:42, Keith Callenberg ha scritto: On Tue, Jan 4, 2011 at 3:17 PM, Rossen Apostolov wrote: On 1/4/11 3:16 PM, Francesco Oteri wrote: Maybe the used force-field is wrong. mdrun-gpu is able to use the AMBER forcefield, but it is not possible using gromos force-field. When gromos force-field is used, the output is full of NaN Is that the case? mdrun should complain and exit if the FF isn't supported. I get this error when I try to run mdrun-gpu with a forcefield that has GROMOS interaction types: Fatal error: OpenMM does not support (some) of the provided interaction type(s) (G96Angle). Maybe it's possible to run a short simulation on a small system and not encounter the missing interactions? I don't know enough about how the forcefields work to know whether that would get past the error. -Keith Rossen -- gmx-users mailing listgmx-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 -- gmx-users mailing listgmx-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
Re: [gmx-users] Simulations on GPU
Hi, I get this error when I try to run mdrun-gpu with a forcefield that has GROMOS interaction types: Fatal error: OpenMM does not support (some) of the provided interaction type(s) (G96Angle). Maybe it's possible to run a short simulation on a small system and not encounter the missing interactions? I don't know enough about how the forcefields work to know whether that would get past the error. -Keith I doesn't matter whether the simulation is short or the system small. You can exclude certain interaction types from the FF but then you'll end up with a most likely meaningless model. Rossen Rossen -- gmx-users mailing listgmx-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 -- gmx-users mailing listgmx-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
Re: [gmx-users] Simulations on GPU
On Tue, Jan 4, 2011 at 3:17 PM, Rossen Apostolov wrote: > On 1/4/11 3:16 PM, Francesco Oteri wrote: >> >> Maybe the used force-field is wrong. >> mdrun-gpu is able to use the AMBER forcefield, but it is not possible >> using gromos force-field. >> When gromos force-field is used, the output is full of NaN > > Is that the case? > > mdrun should complain and exit if the FF isn't supported. I get this error when I try to run mdrun-gpu with a forcefield that has GROMOS interaction types: Fatal error: OpenMM does not support (some) of the provided interaction type(s) (G96Angle). Maybe it's possible to run a short simulation on a small system and not encounter the missing interactions? I don't know enough about how the forcefields work to know whether that would get past the error. -Keith > > Rossen > -- > 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 > -- gmx-users mailing listgmx-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
Re: [gmx-users] Simulations on GPU
On 1/4/11 3:16 PM, Francesco Oteri wrote: Maybe the used force-field is wrong. mdrun-gpu is able to use the AMBER forcefield, but it is not possible using gromos force-field. When gromos force-field is used, the output is full of NaN Is that the case? mdrun should complain and exit if the FF isn't supported. Rossen -- gmx-users mailing listgmx-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
Re: [gmx-users] Simulations on GPU
Maybe the used force-field is wrong.
mdrun-gpu is able to use the AMBER forcefield, but it is not possible
using gromos force-field.
When gromos force-field is used, the output is full of NaN
Il 12/10/2010 03:00, Igor Leontyev ha scritto:
Now I am able to run simulations on GPU but the output is weird. For
example, temperature drops down to 270K while ref_t=298
(Tcoupl=andersen). Moreover, after several hours of simulations
mdrun-gpu starts to output "NAN" energies and hangs up. Pre-run and
post-run GPU memory test is always passed. The graphics card is that
provided with HP desktops (might be MSI) NVIDIA GTX260 with 1.8Gb
memory. The output of mdrun and mdrun-gpu versions of Gromacs is given
bellow. Any ideas? Thanks.
Igor
Log file opened on Fri Oct 8 14:46:51 2010
Host: powerpc pid: 32083 nodeid: 0 nnodes: 4
The Gromacs distribution was built Thu Sep 30 14:42:48 PDT 2010 by
leont...@powerpc (Linux 2.6.32-22-generic x86_64)
:-) G R O M A C S (-:
Gromacs Runs One Microsecond At Cannonball Speeds
:-) VERSION 4.5.1 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Peiter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schultz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
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.
:-) /usr/local/opt/bin/gromacs/gromacs-4.5.1/bin/mdrun_mpich2 (-:
Input Parameters:
integrator = md
nsteps = 1
init_step= 0
ns_type = Grid
nstlist = 10
ndelta = 2
nstcomm = 1003
comm_mode= Linear
nstlog = 1000
nstxout = 5000
nstvout = 1000
nstfout = 0
nstcalcenergy= 10
nstenergy= 1000
nstxtcout= 0
init_t = 0
delta_t = 0.001
xtcprec = 1000
nkx = 54
nky = 60
nkz = 90
pme_order= 6
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = TRUE
ePBC = xyz
bPeriodicMols= FALSE
bContinuation= FALSE
bShakeSOR= FALSE
etc = Andersen
nsttcouple = 10
epc = Berendsen
epctype = Isotropic
nstpcouple = 10
tau_p= 0.5
ref_p (3x3):
ref_p[0]={ 1.01325e+00, 0.0e+00, 0.0e+00}
ref_p[1]={ 0.0e+00, 1.01325e+00, 0.0e+00}
ref_p[2]={ 0.0e+00, 0.0e+00, 1.01325e+00}
compress (3x3):
compress[0]={ 4.5e-05, 0.0e+00, 0.0e+00}
compress[1]={ 0.0e+00, 4.5e-05, 0.0e+00}
compress[2]={ 0.0e+00, 0.0e+00, 4.5e-05}
refcoord_scaling = No
posres_com (3):
posres_com[0]= 0.0e+00
posres_com[1]= 0.0e+00
posres_com[2]= 0.0e+00
posres_comB (3):
posres_comB[0]= 0.0e+00
posres_comB[1]= 0.0e+00
posres_comB[2]= 0.0e+00
andersen_seed= 815131
rlist= 1.2
rlistlong= 1.2
rtpi = 0.05
coulombtype = PME
rcoulomb_switch = 0
rcoulomb = 1.2
vdwtype = Cut-off
rvdw_switch = 0
rvdw = 1.2
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 = EnerPres
free_energy = no
init_lambda = 0
delta_lambda = 0
n_foreign_lambda = 0
sc_alpha = 0
sc_power = 0
sc_sigma = 0.3
sc_sigma_min = 0
Re: [gmx-users] Simulations on GPU
Hi, On 10/6/10 3:48 AM, Igor Leontyev wrote: Szilárd wrote: 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 result is the same for both the distribution 4.5.1 and git from the release-4-5-patches. See the output bellow. = PATH=/usr/local/opt/bin/mpi/openmpi-1.4.2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games LD_LIBRARY_PATH=/usr/local/opt/bin/mpi/openmpi-1.4.2/lib:/home/leontyev/programs/bin/cuda/lib64: CPPFLAGS=-I//usr/local/opt/bin/gromacs/fftw-3.2.2/single_sse/include -I//usr/local/opt/bin/mpi/openmpi-1.4.2/include LDFLAGS=-L//usr/local/opt/bin/gromacs/fftw-3.2.2/single_sse/lib -L//usr/local/opt/bin/mpi/openmpi-1.4.2/lib OPENMM_ROOT_DIR=/home/leontyev/programs/bin/gromacs/gromacs-4.5.1-git/openmm cmake src -DGMX_OPENMM=ON -DGMX_THREADS=OFF -DCMAKE_INSTALL_PREFIX=/home/leontyev/programs/bin/gromacs/gromacs-4.5.1-git You have give as an argument to CMake the path the the gromacs/ directory, not the gromacs/src subdirectory! Rossen CMake Error at gmxlib/CMakeLists.txt:124 (set_target_properties): set_target_properties called with incorrect number of arguments. -- gmx-users mailing listgmx-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
Re: [gmx-users] Simulations on GPU
Dear Igor, Your output look _very_ weird, it seems as if CMake internal variable(s) were not initialized, which I have no clue how could have happened - the build generator works just fine for me. The only thing I can think of is that maybe your CMakeCache is corrupted. Could you please rerun cmake in a _clean_ build directory? Also, are you able to run cmake for CPU build (no -D options)? -- Szilárd On Wed, Oct 6, 2010 at 2:48 AM, Igor Leontyev wrote: > Szilárd wrote: >> >> 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 result is the same for both the distribution 4.5.1 and git from the > release-4-5-patches. See the output bellow. > = > > PATH=/usr/local/opt/bin/mpi/openmpi-1.4.2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games > LD_LIBRARY_PATH=/usr/local/opt/bin/mpi/openmpi-1.4.2/lib:/home/leontyev/programs/bin/cuda/lib64: > CPPFLAGS=-I//usr/local/opt/bin/gromacs/fftw-3.2.2/single_sse/include > -I//usr/local/opt/bin/mpi/openmpi-1.4.2/include > LDFLAGS=-L//usr/local/opt/bin/gromacs/fftw-3.2.2/single_sse/lib > -L//usr/local/opt/bin/mpi/openmpi-1.4.2/lib > OPENMM_ROOT_DIR=/home/leontyev/programs/bin/gromacs/gromacs-4.5.1-git/openmm > > cmake src -DGMX_OPENMM=ON -DGMX_THREADS=OFF > -DCMAKE_INSTALL_PREFIX=/home/leontyev/programs/bin/gromacs/gromacs-4.5.1-git > CMake Error at gmxlib/CMakeLists.txt:124 (set_target_properties): > set_target_properties called with incorrect number of arguments. > > > CMake Error at gmxlib/CMakeLists.txt:126 (install): > install TARGETS given no ARCHIVE DESTINATION for static library target > "gmx". > > > CMake Error at mdlib/CMakeLists.txt:11 (set_target_properties): > set_target_properties called with incorrect number of arguments. > > > CMake Error at mdlib/CMakeLists.txt:13 (install): > install TARGETS given no ARCHIVE DESTINATION for static library target > "md". > > > CMake Error at kernel/CMakeLists.txt:43 (set_target_properties): > set_target_properties called with incorrect number of arguments. > > > CMake Error at kernel/CMakeLists.txt:44 (set_target_properties): > set_target_properties called with incorrect number of arguments. > > > CMake Error at kernel/gmx_gpu_utils/CMakeLists.txt:18 > (CUDA_INCLUDE_DIRECTORIES): > Unknown CMake command "CUDA_INCLUDE_DIRECTORIES". > > > CMake Warning (dev) in CMakeLists.txt: > No cmake_minimum_required command is present. A line of code such as > > cmake_minimum_required(VERSION 2.8) > > should be added at the top of the file. The version specified may be lower > if you wish to support older CMake versions for this project. For more > information run "cmake --help-policy CMP". > This warning is for project developers. Use -Wno-dev to suppress it. > > -- Configuring incomplete, errors occurred! > > -- > gmx-users mailing list gmx-us...@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 > -- gmx-users mailing listgmx-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
