Also, note that cusp is distributed under the Apache 2.0 license,
which appears to be incompatible with the gnu LGPL 2.1 that Amber is
distributed under:
https://www.gnu.org/licenses/license-list.html#apache2
-Dan
On Fri, Mar 10, 2017 at 8:12 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> As of commit 372e01050807ea56cfe36e8164a4f8b4d59b9d1b, still broken. Same error.
>
> ```
> /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>
> ```
>
> File is indeed missing:
>
> ```
> $ cd $AMBERHOME/AmberTools/src/pbsa
> $ ls ../cusplibrary-0.5.1/cusp/detail/config.h
> ls: cannot access ../cusplibrary-0.5.1/cusp/detail/config.h: No such
> file or directory
> ```
>
> There is no config.h anywhere in the cusp directory. Have you tested
> by pulling a fresh copy into a new directory and then attempting to
> configure/install? Am I the only one seeing this?
>
> -Dan
>
>
> On Thu, Mar 9, 2017 at 9:03 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
>> 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
>>> >>
>>> >> _______________________________________________
>>> >> 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-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
--
-------------------------
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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Received on Fri Mar 10 2017 - 06:00:05 PST
