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-- Ray Luo, Ph.D. Professor of Structural Biology/Biochemistry/Biophysics, Chemical Physics, Biomedical Engineering, and Chemical Engineering Department of Molecular Biology and Biochemistry University of California, Irvine, CA 92697-3900 On Mon, Mar 13, 2017 at 2:49 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote: > PBSA in general still doesn't build with the cray compilers, so I'll > disable pbsa for the CUDA build with cray compilers. Working on it > now. > > -Dan > > On Mon, Mar 13, 2017 at 5:38 PM, Ray Luo <rluo.uci.edu> wrote: >> Thanks! >> >> Ray >> -- >> Ray Luo, Ph.D. >> Professor of Structural Biology/Biochemistry/Biophysics, >> Chemical Physics, Biomedical Engineering, and Chemical Engineering >> Department of Molecular Biology and Biochemistry >> University of California, Irvine, CA 92697-3900 >> >> >> On Mon, Mar 13, 2017 at 12:03 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote: >>> I will test for cray. >>> >>> -Dan >>> >>> On Mon, Mar 13, 2017 at 2:46 PM, Ray Luo <rluo.uci.edu> wrote: >>>> Cool! Ruxi is testing it ... I think we can at least make sure it >>>> works under gfortran, clang, and intel compilers before release. We >>>> don't have access to cray machines so can't test it. >>>> >>>> Ray >>>> -- >>>> Ray Luo, Ph.D. >>>> Professor of Structural Biology/Biochemistry/Biophysics, >>>> Chemical Physics, Biomedical Engineering, and Chemical Engineering >>>> Department of Molecular Biology and Biochemistry >>>> University of California, Irvine, CA 92697-3900 >>>> >>>> >>>> On Mon, Mar 13, 2017 at 6:16 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote: >>>>> I just pushed a potential fix. Seems to work well for me. Let me know >>>>> if anyone sees something break. >>>>> >>>>> -Dan >>>>> >>>>> On Sat, Mar 11, 2017 at 4:03 PM, Ruxi Qi <ruxiq.uci.edu> wrote: >>>>>> Hi Jason, >>>>>> >>>>>> I'll test pmemd CUDA flags with PBSA. >>>>>> >>>>>> Best, >>>>>> >>>>>> Ruxi >>>>>> >>>>>> >>>>>> On 3/11/17 12:49, Jason Swails wrote: >>>>>>> I saw the same thing as Dan. I needed to add -lstdc++ to the linker line >>>>>>> to resolve this. >>>>>>> >>>>>>> It seems either your gfortran build links the C++ libraries on its own or >>>>>>> it doesn't. If it does, then everything will work. If it doesn't, you get >>>>>>> the error unless you explicitly link libstdc++. We saw exactly the same >>>>>>> problem with pmemd.cuda in the early days and spent a fair bit of effort >>>>>>> iterating over the available compilers and options and such before we >>>>>>> finally got something that works. Look at line 1406 of configure2 and >>>>>>> you'll see fc_cxx_link_flag being added to the CUDA library. Note that not >>>>>>> all compilers use libstdc++, though (which is why fc_cxx_link_flag exists >>>>>>> and changes based on your compiler choice). >>>>>>> >>>>>>> I *highly* recommend specifying flags in configure rather than hardcoding >>>>>>> them in the Makefile. In fact, I would recommend just trying the pmemd >>>>>>> CUDA flags and see if that works. If not, you may need to add another >>>>>>> variable for PBSA's CUDA libraries. >>>>>>> >>>>>>> All the best, >>>>>>> Jason >>>>>>> >>>>>>> On Sat, Mar 11, 2017 at 3:20 PM, Ray Luo <rluo.uci.edu> wrote: >>>>>>> >>>>>>>> From Ruxi ... >>>>>>>> It's strange our gnu 4.8.2 with cuda-7.5 on gpu-1-1 passed the tests, >>>>>>>> even I >>>>>>>> didn't use -lstdc++. >>>>>>>> Best, >>>>>>>> Ruxi >>>>>>>> >>>>>>>> On Mar 11, 2017 11:59 AM, Ray Luo <rluo.uci.edu> wrote: >>>>>>>> >>>>>>>> Thanks for spotting this! Will fix it soon. >>>>>>>> Ray >>>>>>>> _______________________________________________ >>>>>>>> AMBER-Developers mailing list >>>>>>>> AMBER-Developers.ambermd.org >>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber-developers >>>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> AMBER-Developers mailing list >>>>>> AMBER-Developers.ambermd.org >>>>>> http://lists.ambermd.org/mailman/listinfo/amber-developers >>>>> >>>>> >>>>> >>>>> -- >>>>> ------------------------- >>>>> Daniel R. Roe >>>>> Laboratory of Computational Biology >>>>> National Institutes of Health, NHLBI >>>>> 5635 Fishers Ln, Rm T900 >>>>> Rockville MD, 20852 >>>>> https://www.lobos.nih.gov/lcb >>>>> >>>>> _______________________________________________ >>>>> AMBER-Developers mailing list >>>>> AMBER-Developers.ambermd.org >>>>> http://lists.ambermd.org/mailman/listinfo/amber-developers >>>> >>>> _______________________________________________ >>>> AMBER-Developers mailing list >>>> AMBER-Developers.ambermd.org >>>> http://lists.ambermd.org/mailman/listinfo/amber-developers >>> >>> >>> >>> -- >>> ------------------------- >>> Daniel R. Roe >>> Laboratory of Computational Biology >>> National Institutes of Health, NHLBI >>> 5635 Fishers Ln, Rm T900 >>> Rockville MD, 20852 >>> https://www.lobos.nih.gov/lcb >>> >>> _______________________________________________ >>> AMBER-Developers mailing list >>> AMBER-Developers.ambermd.org >>> http://lists.ambermd.org/mailman/listinfo/amber-developers >> >> _______________________________________________ >> AMBER-Developers mailing list >> AMBER-Developers.ambermd.org >> http://lists.ambermd.org/mailman/listinfo/amber-developers > > > > -- > ------------------------- > Daniel R. Roe > Laboratory of Computational Biology > National Institutes of Health, NHLBI > 5635 Fishers Ln, Rm T900 > Rockville MD, 20852 > https://www.lobos.nih.gov/lcb > > _______________________________________________ > AMBER-Developers mailing list > AMBER-Developers.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber-developers _______________________________________________ AMBER-Developers mailing list AMBER-Developers.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber-developersReceived on Mon Mar 13 2017 - 17:30:03 PDT