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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 Thu, Mar 9, 2017 at 1:44 PM, Hai Nguyen <nhai.qn.gmail.com> wrote: > I dont see the "detail" sub-folder in git log > > Hai > > On Thu, Mar 9, 2017 at 4:35 PM Ray Luo <rluo.uci.edu> wrote: > >> Dan, >> >> Okay, please try again ... >> >> 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 Thu, Mar 9, 2017 at 9:17 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote: >> > The problem is that there is an include directive specifying >> > 'cusp/detail/config.h', but the CUSP directory cusplibrary-0.5.1 does >> > not have a 'detail' subdirectory. Perhaps that was not committed? >> > >> > -Dan >> > >> > On Thu, Mar 9, 2017 at 11:58 AM, Ray Luo <rluo.uci.edu> wrote: >> >> I suppose this is for ./configure -cuda gnu with cuda7.5? >> >> >> >> We tested both cuda 7.5 and 8.0 with gnu before pushing. We'll test >> >> the current version again ... >> >> >> >> 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 Thu, Mar 9, 2017 at 5:57 AM, Daniel Roe <daniel.r.roe.gmail.com> >> wrote: >> >>> Still fails for me: >> >>> >> >>> ``` >> >>> make[3]: Leaving directory >> >>> `/mnt/raid0/droe/Amber/GIT/amber-test/AmberTools/src/arpack' >> >>> /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> >> >>> ^ >> >>> compilation terminated. >> >>> ``` >> >>> >> >>> -Dan >> >>> >> >>> >> >>> On Wed, Mar 8, 2017 at 4:36 PM, Ray Luo <rluo.uci.edu> wrote: >> >>>> Dan, >> >>>> >> >>>> I just added the cusp library to AmberTools/src/. Could you try again >> >>>> to see whether it compiles this time? We tested both cuda 8.0 and 7.5 >> >>>> on rocks and both worked. >> >>>> >> >>>> All the best, >> >>>> 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 Tue, Mar 7, 2017 at 9:48 AM, Daniel Roe <daniel.r.roe.gmail.com> >> wrote: >> >>>>> Clean GIT master: 0494517ae737e465fdd737684454526f7ad14d26 >> >>>>> >> >>>>> ./configure --with-python `which python` -cuda gnu >> >>>>> >> >>>>> ``` >> >>>>> make[2]: Entering directory >> >>>>> `/mnt/raid0/droe/Amber/GIT/amber-test/AmberTools/src/pbsa' >> >>>>> Error: CUSP_HOME is not properly set. This must point to your CUSP >> >>>>> library installation. >> >>>>> make[2]: *** [.cuda_precheck] Error 2 >> >>>>> make[2]: Leaving directory >> >>>>> `/mnt/raid0/droe/Amber/GIT/amber-test/AmberTools/src/pbsa' >> >>>>> make[1]: *** [cuda_serial] Error 2 >> >>>>> ``` >> >>>>> >> >>>>> The message offers no clues as to what CUSP_HOME is supposed to refer >> >>>>> to but I assume it's this: https://developer.nvidia.com/cusp >> >>>>> >> >>>>> CUSP appears to come with CUDA 8.0 (at least there is a >> libcusparse.so >> >>>>> in the lib64 subdir). However, some fiddling around shows PBSA >> expects >> >>>>> CUSP_HOME to point to something that has a /cusp subdirectory. I'm >> >>>>> guessing previously this was an add-on install for CUDA? >> >>>>> >> >>>>> Bottom line is that currently it seems that CUDA-enabled PBSA depends >> >>>>> on this, but it is not properly checked for during configure. >> Probably >> >>>>> configure should search for CUSP and set a config.h variable pointing >> >>>>> to it, or leave it blank if not found. The entire CUDA install >> >>>>> shouldn't fail just because this one piece isn't there. >> >>>>> >> >>>>> -Dan >> >>>>> >> >>>>> _______________________________________________ >> >>>>> 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 >> > _______________________________________________ > 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 Thu Mar 09 2017 - 14:30:03 PST