I do
- git clean -fdx
- ./configure -cuda gnu
- cd AmberTools/src && make -j8 install
That's all
This is what I have on my side:
- gcc 4.4.7 & cuda 8.0: OK
- gcc 4.4.7 & cuda 7.5: OK
- gcc 5.1.0 & cuda 8.0: OK
- gcc 5.1.0 & cuda 7.5: NO
/apps/cuda/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 /apps/cuda/cuda-7.5/include/cuda_runtime.h:76:0,
from <command-line>:0:
/apps/cuda/cuda-7.5/include/host_config.h:115:2: error: #error --
unsupported GNU version! gcc versions later than 4.9 are not supported!
#error -- unsupported GNU version! gcc versions later than 4.9 are not
supported!
^
make[1]: *** [cuda_cg_wrapper.o] Error 1
make[1]: Leaving directory
`/home/gmonard/amber-git-master/AmberTools/src/pbsa'
That may be system dependent. I don't know.
- intel 16 & cuda 8.0: OK
- intel 15 & cuda 7.5: OK
On that machine, I cannot test any other flavor of gcc. I'll try
tomorrow on another machine with more flavors.
G.
On 03/11/2017 12:04 AM, Daniel Roe wrote:
> 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
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> 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
>>>>>>
>>>>
>>>> --
>>>> ____________________________________________________________________________
>>>>
>>>> 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
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> 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
>
>
>
--
____________________________________________________________________________
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
Received on Fri Mar 10 2017 - 15:30:03 PST
