Mark Yes, it was your suggestions that finally set me on the right $PATH. The examples and analyses work as intended. Thanks Paul
> On May 6, 2018, at 2:24 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > > Hi, > > I already referred you to the install guide for ideas on how to access the > version of GROMACS that you want. Did you look there? > > Mark > > On Sun, May 6, 2018, 02:52 paul buscemi <pbusc...@q.com> wrote: > >> Mark, Justin >> >> I was able to access the GPU using simply : >> >> cmake .. -DGMX_BUILD_OWN_FFTW=ON \ >> -DREGRESSIONTEST_DOWNLOAD=ON \ >> -DGMX_MPI=on \ >> -DGMX_GPU=on >> >> the result for the lysozyme MD run ( with the appropriate quote ) was: >> >> >> Core t (s) Wall t (s) (%) >> Time: 281.756 35.220 800.0 >> (ns/day) (hour/ns) >> Performance: 245.323 0.098 >> >> GROMACS reminds you: "You still have to climb to the shoulders of the >> giants" (Vedran Miletic) >> >> >> You were correct, the problem was that the tutorial was accessing an >> earlier install of gromacs 5.1 >> and I had to access gmx-2018 MD by adding the path to the mdrun command >> >> /home/rgb/Desktop/gromacs-gpu-2018/build/bin/gmx mdrun -deffnm md_0_1 >> >> which is not ideal. This is more of a linux question, but can you suggest >> a way to clean up older installations, or is it sufficient to >> ensure the PATH points to the correct version ? >> >> thanks for your help >> Paul >> >> >>> On May 5, 2018, at 12:00 PM, Mark Abraham <mark.j.abra...@gmail.com> >> wrote: >>> >>> Hi, >>> >>> It's also GROMACS 5.1.2 not the 2018 you reported trying to install. You >>> need to make sure your terminal has been given access to the GROMACS that >>> you want to use (see that part of the install guode.). >>> >>> Also, your CMake line tried to use OpenCL which is not what you want for >>> running on an Nvidia GPU (even though you can get it to work). >>> >>> Mark >>> >>> On Sat, May 5, 2018, 00:55 Justin Lemkul <jalem...@vt.edu> wrote: >>> >>>> >>>> >>>> On 5/4/18 6:53 PM, paul buscemi wrote: >>>>> Justin, >>>>> >>>>> Here is the install script and a snippit from the log file . >>>>> >>>>> Gromacs runs normally with this ( fresh ) install but without GPU use >>>>> >>>>> Paul >>>>> >>>>> cmake .. -DGMX_BUILD_OWN_FFTW=ON \ >>>>> -DGMX_GPU=on \ >>>>> -DCUDA_TOOLKIT_ROOT_DIR=/usr/lib/nvidia-cuda-toolkit \ >>>>> -DGMX_USE_OPENCL=on >>>>> >>>>> Command line: >>>>> gmx mdrun -deffnm md_0_1 >>>>> >>>>> GROMACS version: VERSION 5.1.2 >>>>> Precision: single >>>>> Memory model: 64 bit >>>>> MPI library: thread_mpi >>>>> OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 32) >>>>> GPU support: disabled >>>> >>>> Well, here's what you need to know. Something failed in trying to enable >>>> GPU acceleration. Take a look at the cmake output. >>>> >>>> -Justin >>>> >>>> -- >>>> ================================================== >>>> >>>> Justin A. Lemkul, Ph.D. >>>> Assistant Professor >>>> Virginia Tech Department of Biochemistry >>>> >>>> 303 Engel Hall >>>> 340 West Campus Dr. >>>> Blacksburg, VA 24061 >>>> >>>> jalem...@vt.edu | (540) 231-3129 >>>> http://www.thelemkullab.com >>>> >>>> ================================================== >>>> >>>> -- >>>> Gromacs Users mailing list >>>> >>>> * Please search the archive at >>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>>> posting! >>>> >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>> >>>> * For (un)subscribe requests visit >>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>>> send a mail to gmx-users-requ...@gromacs.org. >>>> >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.