On Mon, Jul 16, 2018 at 7:43 PM Rajat Desikan <rajatdesi...@gmail.com> wrote:
> Hi Mark, > > Thank you for the quick answer. My group is experimenting with a GPU-heavy > processor-light configuration similar to the Amber machines available from > Exxact (https://www.exxactcorp.com/AMBER-Certified-MD-Systems). In our > understanding, for this configuration to be successful performance-wise, > gromacs would've to do all the calculating on GPUs, and not just > electrostatics. That's why we're looking at openmm enabled versions. > For that you'd need the ~8 year old GROMACS 4.5 with OpenMM 2.x (IIRC) support which is ancient and unsupported so really not a good idea. Instead, use the latest release. Hardware-wise, ddeally you'd want to have 2-3 faster (wokstation) or 3-5 slower (server) cores per GPU for good CPU-GPU balance. -- Szilárd > If you and others have alternate suggestions, we would be really eager to > hear them. Thank you for your time. > > Regards, > Rajat > > On Mon, 16 Jul 2018, 10:25 pm Mark Abraham, <mark.j.abra...@gmail.com> > wrote: > > > Hi, > > > > This code was not ever functional in the 4.6 branch, so if you want it to > > work, try 4.5.7. But really there is no reason to want to build it any > more > > - use the CUDA and OpenCL ports available in more recent GROMACS. > > > > Mark > > > > On Mon, Jul 16, 2018 at 6:47 PM Rajat Desikan <rajatdesi...@gmail.com> > > wrote: > > > > > Dear all, > > > I'm trying to install openmm enabled version of gromacs 4.6.7 on a > 6-core > > > i7 machine with two GTX 1080 Ti GPUs. I am repeatedly facing a rather > > > strange error while running make: > > > > > > /home/sujit/gromacs-4.6.7/src/contrib/mdrun_openmm.c: In function > > ‘cmain’: > > > /home/sujit/gromacs-4.6.7/src/contrib/mdrun_openmm.c:221:23: warning: > > > missing braces around initializer [-Wmissing-braces] > > > gmx_hw_opt_t hw_opt={0,0,0,0,TRUE,FALSE,0,NULL}; > > > ^ > > > */home/sujit/gromacs-4.6.7/src/contrib/mdrun_openmm.c:221:23: note: > (near > > > initialization for ‘hw_opt’)* > > > */home/sujit/gromacs-4.6.7/src/contrib/mdrun_openmm.c:247:41: error: > > > ‘gmx_hw_opt_t {aka struct <anonymous>}’ has no member named ‘gpu_id’; > did > > > you mean ‘gpu_opt’?* > > > * { "-gpu_id", FALSE, etSTR, {&hw_opt.gpu_id},* > > > ^ > > > src/kernel/CMakeFiles/mdrun.dir/build.make:302: recipe for target > > > 'src/kernel/CMakeFiles/mdrun.dir/__/contrib/mdrun_openmm.c.o' failed > > > make[2]: *** > > [src/kernel/CMakeFiles/mdrun.dir/__/contrib/mdrun_openmm.c.o] > > > Error 1 > > > CMakeFiles/Makefile2:1902: recipe for target > > > 'src/kernel/CMakeFiles/mdrun.dir/all' failed > > > make[1]: *** [src/kernel/CMakeFiles/mdrun.dir/all] Error 2 > > > Makefile:162: recipe for target 'all' failed > > > make: *** [all] Error 2 > > > > > > I have installed cuda 9.1, openmm, fftw, open-mpi and all other > necessary > > > software, so I'm at a loss. Please help me out. Google did not have > much > > > leads. > > > > > > Thank you. > > > > > > Regards, > > > Rajat > > > > > > -- > > > Dr. Rajat Desikan (Post Doctoral Fellow) > > > Prof. Narendra M Dixit's Lab (no 1), > > > Dept. of Chemical Engineering, > > > Indian Institute of Science, Bangalore > > > -- > > > 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.