Re: [gmx-users] Floating point exception with mdrun-gpu on CUDA
On 1/9/13 10:54 AM, Roland Schulz wrote: Hi, it seems you are using OpenMM. The recommended approach is to compile with GMX_OPENMM=off and GMX_GPU=on. ...with version 4.6beta3. The version shown is an outdated development version from the 4.5.1 era. OpenMM was the only choice at that point for running on GPU, unless I'm mistaken. Whatever the case, it's probably better for the OP to be using a more current version of the software. -Justin On Wed, Jan 9, 2013 at 10:45 AM, sdlonga wrote: Hi, I succesfully built the mdrun-gpu on a MacOS MountainLion having one CUDA NVIDIA GeForce GTX 660 platform. When I try to run one of the GPU benchmarks (e.g. dhfr-impl-1nm.bench) a floating point exception occurs. The same happens for all the benchmarks. I have already tested the functionality of the CUDA GPU with the CUDA toolkit samples. Hope someone can help me to understand what is going wrong.. thanks in advance! The last part of the output of mdrun-gpu is as follows: .. -[no]ionize bool no Do a simulation including the effect of an X-Ray bombardment on your system -device string Device option string Reading file topol.tpr, VERSION 4.5.1-dev-20100917-b1d66 (single precision) WARNING: OpenMM does not support leap-frog, will use velocity-verlet integrator. WARNING: OpenMM supports only Andersen thermostat with the md/md-vv/md-vv-avek integrators. WARNING: OpenMM provides contraints as a combination of SHAKE, SETTLE and CCMA. Accuracy is based on the SHAKE tolerance set by the "shake_tol" option. Floating point exception: 8 -- View this message in context: http://gromacs.5086.n6.nabble.com/Floating-point-exception-with-mdrun-gpu-on-CUDA-tp5004393.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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 -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Floating point exception with mdrun-gpu on CUDA
Hi, it seems you are using OpenMM. The recommended approach is to compile with GMX_OPENMM=off and GMX_GPU=on. Roland On Wed, Jan 9, 2013 at 10:45 AM, sdlonga wrote: > Hi, > > I succesfully built the mdrun-gpu on a MacOS MountainLion having one CUDA > NVIDIA GeForce GTX 660 platform. When I try to run one of the GPU > benchmarks > (e.g. dhfr-impl-1nm.bench) a floating point exception occurs. The same > happens for all the benchmarks. I have already tested the functionality of > the CUDA GPU with the CUDA toolkit samples. > Hope someone can help me to understand what is going wrong.. thanks in > advance! > The last part of the output of mdrun-gpu is as follows: > > .. > -[no]ionize bool no Do a simulation including the effect of an > X-Ray > bombardment on your system > -device string Device option string > > Reading file topol.tpr, VERSION 4.5.1-dev-20100917-b1d66 (single precision) > > WARNING: OpenMM does not support leap-frog, will use velocity-verlet > integrator. > > > WARNING: OpenMM supports only Andersen thermostat with the > md/md-vv/md-vv-avek integrators. > > > WARNING: OpenMM provides contraints as a combination of SHAKE, SETTLE and > CCMA. Accuracy is based on the SHAKE tolerance set by the "shake_tol" > option. > > Floating point exception: 8 > > > > > > > -- > View this message in context: > http://gromacs.5086.n6.nabble.com/Floating-point-exception-with-mdrun-gpu-on-CUDA-tp5004393.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > 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 > > > > > -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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] Floating point exception with mdrun-gpu on CUDA
Hi, I succesfully built the mdrun-gpu on a MacOS MountainLion having one CUDA NVIDIA GeForce GTX 660 platform. When I try to run one of the GPU benchmarks (e.g. dhfr-impl-1nm.bench) a floating point exception occurs. The same happens for all the benchmarks. I have already tested the functionality of the CUDA GPU with the CUDA toolkit samples. Hope someone can help me to understand what is going wrong.. thanks in advance! The last part of the output of mdrun-gpu is as follows: .. -[no]ionize bool no Do a simulation including the effect of an X-Ray bombardment on your system -device string Device option string Reading file topol.tpr, VERSION 4.5.1-dev-20100917-b1d66 (single precision) WARNING: OpenMM does not support leap-frog, will use velocity-verlet integrator. WARNING: OpenMM supports only Andersen thermostat with the md/md-vv/md-vv-avek integrators. WARNING: OpenMM provides contraints as a combination of SHAKE, SETTLE and CCMA. Accuracy is based on the SHAKE tolerance set by the "shake_tol" option. Floating point exception: 8 > -- View this message in context: http://gromacs.5086.n6.nabble.com/Floating-point-exception-with-mdrun-gpu-on-CUDA-tp5004393.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
