Custom Search
-- 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-developersReceived on Mon Mar 13 2017 - 12:00:03 PDT