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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 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-developersReceived on Thu Mar 09 2017 - 10:30:03 PST