On Thu, Mar 9, 2017 at 5:27 PM, Ray Luo <rluo.uci.edu> wrote:
> The git behavior is very strange ... I put a fresh copy there. When I
> "git status", nothing new got picked up so it's not in the log, but I
> can now compile with this fresh copy.
>
>
> Do you see the sub-folder physically under
> AmberTools/src/cusplibrary-0.5.1/cusp after git pull?
>
I do too.
Hai
>
> 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 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
> >>
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> >>
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Received on Thu Mar 09 2017 - 18:30:03 PST
