What options are you passing to configure besides -cuda gnu?
On Fri, Mar 10, 2017 at 5:16 PM, Gerald Monard
<Gerald.Monard.univ-lorraine.fr> wrote:
> I've redone it after a 'git clean -fdx'.
> It still compiles.
> I'm going to test other gcc and cuda version.
>
> Gerald.
>
> On 03/10/2017 10:37 PM, Daniel Roe wrote:
>> And was this from a clean directory? All of the times I have gotten
>> the error have been from clean or freshly cloned GIT trees.
>>
>> On a third machine with gcc 4.8.4, cuda 8.0, ubuntu 14.04, same error.
>>
>> -Dan
>>
>> On Fri, Mar 10, 2017 at 4:17 PM, Gerald Monard
>> <Gerald.Monard.univ-lorraine.fr> wrote:
>>> Oups. I forgot: gcc-4.4.7 on Red Hat 6.3
>>>
>>> Gerald.
>>>
>>> On 03/10/2017 09:07 PM, Daniel Roe wrote:
>>>> What version gcc out of curiosity?
>>>>
>>>> On Fri, Mar 10, 2017 at 3:00 PM Gerald Monard <
>>>> Gerald.Monard.univ-lorraine.fr> wrote:
>>>>
>>>>> Hello,
>>>>>
>>>>> It builds for me now (gcc + cuda 8.0).
>>>>>
>>>>> Gerald.
>>>>>
>>>>> On 03/10/2017 07:34 PM, Ray Luo wrote:
>>>>>> Gerald,
>>>>>>
>>>>>> After I "git add" these files by force, looks like they are in. Could
>>>>>> you check whether you can see these files?
>>>>>>
>>>>>> I'm compiling a "git clean -xfd"-ed version.
>>>>>>
>>>>>> 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 Fri, Mar 10, 2017 at 8:30 AM, Gerald Monard
>>>>>> <Gerald.Monard.univ-lorraine.fr> wrote:
>>>>>>> Hello,
>>>>>>>
>>>>>>> When I compare the "original" (=downloaded) version of
>>>>>>> cusplibrary-0.5.1, I can see the following files missing in the amber
>>>>>>> git tree:
>>>>>>> ./build
>>>>>>> ./build/build-env.py
>>>>>>> ./build/g++.py
>>>>>>> ./build/nvcc.py
>>>>>>> ./cusp
>>>>>>> ./cusp/detail
>>>>>>> ./cusp/detail/config.h
>>>>>>>
>>>>>>> All the best,
>>>>>>>
>>>>>>> Gerald.
>>>>>>>
>>>>>>> On 03/10/2017 02:39 PM, Jason Swails wrote:
>>>>>>>> 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?
>>>>>>>>>
>>>>>>>>
>>>>>>>> config.h is in .gitignore (since we don't want to track *our*
>>>>> config.h).
>>>>>>>> This is preventing Ray from adding it and "git status" from finding it.
>>>>>>>>
>>>>>>>> I've fixed this so it should ignore *only* the config.h files that our
>>>>>>>> configure script generates..
>>>>>>>>
>>>>>>>> .Ray, try adding it again. And after you do, please try a fresh clone
>>>>> and
>>>>>>>> build (which would have caught this missing file) and make sure that
>>>>> works
>>>>>>>> first.
>>>>>>>>
>>>>>>>> All the best,
>>>>>>>> Jason
>>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>>
>>>>> ____________________________________________________________________________
>>>>>>>
>>>>>>> Prof. Gerald MONARD
>>>>>>> Directeur du mésocentre EXPLOR
>>>>>>> Université de Lorraine
>>>>>>> Boulevard des Aiguillettes B.P. 70239
>>>>>>> F-54506 Vandoeuvre-les-Nancy, FRANCE
>>>>>>>
>>>>>>> e-mail : Gerald.Monard.univ-lorraine.fr
>>>>>>> phone : +33 (0)372.745.279
>>>>>>> web : http://www.monard.info
>>>>>>>
>>>>>>>
>>>>> ____________________________________________________________________________
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> AMBER-Developers mailing list
>>>>>>> AMBER-Developers.ambermd.org
>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber-developers
>>>>>>
>>>>>> _______________________________________________
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>>>>>> http://lists.ambermd.org/mailman/listinfo/amber-developers
>>>>>>
>>>>>
>>>>> --
>>>>>
>>>>> ____________________________________________________________________________
>>>>>
>>>>> Prof. Gerald MONARD
>>>>> Directeur du mésocentre EXPLOR
>>>>> Université de Lorraine
>>>>> Boulevard des Aiguillettes B.P. 70239
>>>>> F-54506 Vandoeuvre-les-Nancy, FRANCE
>>>>>
>>>>> e-mail : Gerald.Monard.univ-lorraine.fr
>>>>> phone : +33 (0)372.745.279
>>>>> web : http://www.monard.info
>>>>>
>>>>>
>>>>> ____________________________________________________________________________
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> AMBER-Developers mailing list
>>>>> AMBER-Developers.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber-developers
>>>>>
>>>
>>> --
>>> ____________________________________________________________________________
>>>
>>> Prof. Gerald MONARD
>>> Directeur du mésocentre EXPLOR
>>> Université de Lorraine
>>> Boulevard des Aiguillettes B.P. 70239
>>> F-54506 Vandoeuvre-les-Nancy, FRANCE
>>>
>>> e-mail : Gerald.Monard.univ-lorraine.fr
>>> phone : +33 (0)372.745.279
>>> web : http://www.monard.info
>>>
>>> ____________________________________________________________________________
>>>
>>>
>>> _______________________________________________
>>> AMBER-Developers mailing list
>>> AMBER-Developers.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber-developers
>>
>>
>>
>>
>>
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>
> --
> ____________________________________________________________________________
>
> Prof. Gerald MONARD
> Directeur du mésocentre EXPLOR
> Université de Lorraine
> Boulevard des Aiguillettes B.P. 70239
> F-54506 Vandoeuvre-les-Nancy, FRANCE
>
> e-mail : Gerald.Monard.univ-lorraine.fr
> phone : +33 (0)372.745.279
> web : http://www.monard.info
>
> ____________________________________________________________________________
>
>
> _______________________________________________
> 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 - 15:30:02 PST
