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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 3:28 PM, Gerald Monard <Gerald.Monard.univ-lorraine.fr> wrote: > I do > - git clean -fdx > - ./configure -cuda gnu > - cd AmberTools/src && make -j8 install > > That's all > > This is what I have on my side: > - gcc 4.4.7 & cuda 8.0: OK > - gcc 4.4.7 & cuda 7.5: OK > - gcc 5.1.0 & cuda 8.0: OK > - gcc 5.1.0 & cuda 7.5: NO > > /apps/cuda/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 /apps/cuda/cuda-7.5/include/cuda_runtime.h:76:0, > from <command-line>:0: > /apps/cuda/cuda-7.5/include/host_config.h:115:2: error: #error -- > unsupported GNU version! gcc versions later than 4.9 are not supported! > #error -- unsupported GNU version! gcc versions later than 4.9 are not > supported! > ^ > make[1]: *** [cuda_cg_wrapper.o] Error 1 > make[1]: Leaving directory > `/home/gmonard/amber-git-master/AmberTools/src/pbsa' > > That may be system dependent. I don't know. > > - intel 16 & cuda 8.0: OK > - intel 15 & cuda 7.5: OK > > On that machine, I cannot test any other flavor of gcc. I'll try > tomorrow on another machine with more flavors. > > G. > > On 03/11/2017 12:04 AM, Daniel Roe wrote: >> What options are you passing to configure besides -cuda gnu? >> >> On Fri, Mar 10, 2017 at 5:16 PM, Gerald Monard >> <Gerald.Monard.univ-lorraine.fr> wrote: >>> I've redone it after a 'git clean -fdx'. >>> It still compiles. >>> I'm going to test other gcc and cuda version. >>> >>> Gerald. >>> >>> On 03/10/2017 10:37 PM, Daniel Roe wrote: >>>> And was this from a clean directory? All of the times I have gotten >>>> the error have been from clean or freshly cloned GIT trees. >>>> >>>> On a third machine with gcc 4.8.4, cuda 8.0, ubuntu 14.04, same error. >>>> >>>> -Dan >>>> >>>> On Fri, Mar 10, 2017 at 4:17 PM, Gerald Monard >>>> <Gerald.Monard.univ-lorraine.fr> wrote: >>>>> Oups. I forgot: gcc-4.4.7 on Red Hat 6.3 >>>>> >>>>> Gerald. >>>>> >>>>> On 03/10/2017 09:07 PM, Daniel Roe 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 >>>>>>> >>>>> >>>>> -- >>>>> ____________________________________________________________________________ >>>>> >>>>> 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 >> >> >> > > -- > ____________________________________________________________________________ > > 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-developersReceived on Fri Mar 10 2017 - 16:30:02 PST