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
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Received on Fri Mar 10 2017 - 05:30:04 PST
