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
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> >>>> 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
> >>>
> >>> _______________________________________________
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> >>> http://lists.ambermd.org/mailman/listinfo/amber-developers
> >>
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> >> 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
>
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Received on Thu Mar 09 2017 - 14:00:02 PST
