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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 Fri, Mar 10, 2017 at 12:34 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote: > Reproduced with gcc 5.3.1 and cuda 7.5 on different machine. Confirmed that > the issue was solved by the addition of -lstdc++ during linking. > Alternatively you can use g++ to link with the -lgfortran flag. Not tested > with other compilers yet. > > -Dan > > On Fri, Mar 10, 2017 at 3:07 PM Daniel Roe <daniel.r.roe.gmail.com> wrote: > >> What version gcc out of curiosity? >> >> On Fri, Mar 10, 2017 at 3:00 PM Gerald Monard < >> Gerald.Monard.univ-lorraine.fr> wrote: >> >> Hello, >> >> It builds for me now (gcc + cuda 8.0). >> >> Gerald. >> >> On 03/10/2017 07:34 PM, Ray Luo wrote: >> > Gerald, >> > >> > After I "git add" these files by force, looks like they are in. Could >> > you check whether you can see these files? >> > >> > I'm compiling a "git clean -xfd"-ed version. >> > >> > 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 Fri, Mar 10, 2017 at 8:30 AM, Gerald Monard >> > <Gerald.Monard.univ-lorraine.fr> wrote: >> >> Hello, >> >> >> >> When I compare the "original" (=downloaded) version of >> >> cusplibrary-0.5.1, I can see the following files missing in the amber >> >> git tree: >> >> ./build >> >> ./build/build-env.py >> >> ./build/g++.py >> >> ./build/nvcc.py >> >> ./cusp >> >> ./cusp/detail >> >> ./cusp/detail/config.h >> >> >> >> All the best, >> >> >> >> Gerald. >> >> >> >> On 03/10/2017 02:39 PM, Jason Swails wrote: >> >>> On Fri, Mar 10, 2017 at 8:12 AM, Daniel Roe <daniel.r.roe.gmail.com> >> wrote: >> >>> >> >>>> As of commit 372e01050807ea56cfe36e8164a4f8b4d59b9d1b, still broken. >> Same >> >>>> error. >> >>>> >> >>>> ``` >> >>>> /usr/local/cuda-7.5/bin/nvcc -gencode arch=compute_20,code=sm_20 >> >>>> -gencode arch=compute_30,code=sm_30 -gencode >> >>>> arch=compute_50,code=sm_50 -gencode arch=compute_52,code=sm_52 >> >>>> -gencode arch=compute_53,code=sm_53 -use_fast_math -O3 -ccbin g++ >> >>>> -I../cusplibrary-0.5.1 -o cuda_cg_wrapper.o -c cuda_cg_wrapper.cu >> >>>> -DCUSP -DPCG -DJacobi -DDIA >> >>>> In file included from cuda_cg_wrapper.cu:832:0: >> >>>> ../cusplibrary-0.5.1/cusp/csr_matrix.h:23:32: fatal error: >> >>>> cusp/detail/config.h: No such file or directory >> >>>> #include <cusp/detail/config.h> >> >>>> ``` >> >>> >> >>> >> >>>> File is indeed missing: >> >>>> >> >>>> ``` >> >>>> $ cd $AMBERHOME/AmberTools/src/pbsa >> >>>> $ ls ../cusplibrary-0.5.1/cusp/detail/config.h >> >>>> ls: cannot access ../cusplibrary-0.5.1/cusp/detail/config.h: No such >> >>>> file or directory >> >>>> ``` >> >>> >> >>> >> >>>> There is no config.h anywhere in the cusp directory. Have you tested >> >>>> by pulling a fresh copy into a new directory and then attempting to >> >>>> configure/install? Am I the only one seeing this? >> >>>> >> >>> >> >>> config.h is in .gitignore (since we don't want to track *our* >> config.h). >> >>> This is preventing Ray from adding it and "git status" from finding it. >> >>> >> >>> I've fixed this so it should ignore *only* the config.h files that our >> >>> configure script generates.. >> >>> >> >>> .Ray, try adding it again. And after you do, please try a fresh clone >> and >> >>> build (which would have caught this missing file) and make sure that >> works >> >>> first. >> >>> >> >>> All the best, >> >>> Jason >> >>> >> >> >> >> -- >> >> >> ____________________________________________________________________________ >> >> >> >> Prof. Gerald MONARD >> >> Directeur du mésocentre EXPLOR >> >> Université de Lorraine >> >> Boulevard des Aiguillettes B.P. 70239 >> >> F-54506 Vandoeuvre-les-Nancy, FRANCE >> >> >> >> e-mail : Gerald.Monard.univ-lorraine.fr >> >> phone : +33 (0)372.745.279 >> >> web : http://www.monard.info >> >> >> >> >> ____________________________________________________________________________ >> >> >> >> >> >> _______________________________________________ >> >> 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 >> > >> >> -- >> >> ____________________________________________________________________________ >> >> Prof. Gerald MONARD >> Directeur du mésocentre EXPLOR >> Université de Lorraine >> Boulevard des Aiguillettes B.P. 70239 >> F-54506 Vandoeuvre-les-Nancy, FRANCE >> >> e-mail : Gerald.Monard.univ-lorraine.fr >> phone : +33 (0)372.745.279 >> web : http://www.monard.info >> >> >> ____________________________________________________________________________ >> >> >> _______________________________________________ >> 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 >> > -- > ------------------------- > 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 Fri Mar 10 2017 - 13:00:03 PST