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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 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-developersReceived on Mon Mar 13 2017 - 15:00:02 PDT