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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 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-developersReceived on Thu Mar 09 2017 - 09:00:03 PST