Date: Fri, 10 Mar 2017 22:43:14 -0500
very minor point: pbsa code(s) has lots of whitespace trailing (see the
attached image)
cheers
Hai
On Fri, Mar 10, 2017 at 7:22 PM, Ray Luo <rluo.uci.edu> wrote:
> It's great that it also works with intel ...
>
> 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 3:28 PM, Gerald Monard
> <Gerald.Monard.univ-lorraine.fr> wrote:
> > 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
>
> _______________________________________________
> AMBER-Developers mailing list
> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
>
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(image/png attachment: pb_minor.png)
