[petsc-dev] error with --download-amgx

Fande Kong fdkong.jd at gmail.com
Fri Dec 13 11:07:38 CST 2019 

I was wondering how we use AMGx? It is a PC? Do we have a native interface
to this package?  Any example?

Fande,

On Tue, Dec 3, 2019 at 9:10 PM Smith, Barry F. <bsmith at mcs.anl.gov> wrote:

>
>   Ok, since we are using a fork of the repository if it is causing grief
> we can remove it but otherwise best just to leave it since it put in by the
> AMGX developers.
>
>
>
> > On Dec 3, 2019, at 10:00 PM, Balay, Satish <balay at mcs.anl.gov> wrote:
> >
> > Its from the attached configure.log [from a prior e-mail on this
> > thread] - and this flag is not passed in from petsc configure to amgx
> > cmake - so it must be somehow set internally in this package.
> >
> > Satish
> >
> > On Wed, 4 Dec 2019, Smith, Barry F. wrote:
> >
> >>
> >>> Also - its best to avoid -Werror in externalpackage builds..
> >>
> >>  Hmm, my branch uses the CMake package to do the install  (it has no
> custom code) so is this a bug in package.py that it doesn't strip out the
> -Werror when passing stuff to cmake?
> >>
> >>  There is not enough information your email for me to determine where
> this message you printed below came from. Did it come from my branch?
> >>
> >>   Barry
> >>
> >>
> >>> On Dec 3, 2019, at 9:29 PM, Balay, Satish <balay at mcs.anl.gov> wrote:
> >>>
> >>>>>>>
> >>>
> autofs/nccs-svm1_sw/summit/.swci/0-core/opt/spack/20180914/linux-rhel7-ppc64le/gcc-4.8.5/cmake-3.15.2-xit2o3iepxvqbyku77lwcugufilztu7t/bin/cmake
> -E remove
> /autofs/nccs-svm1_home1/adams/petsc/arch-summit-opt64-gnu-cuda/externalpackages/git.amgx/petsc-build/core/CMakeFiles/amgx_core.dir/src/classical/interpolators/./
> amgx_core_generated_common.cu.o
> >>> /sw/summit/cuda/10.1.168/bin/nvcc -M -D__CUDACC__
> /autofs/nccs-svm1_home1/adams/petsc/arch-summit-opt64-gnu-cuda/externalpackages/git.amgx/
> plugin_config.cu -o
> /autofs/nccs-svm1_home1/adams/petsc/arch-summit-opt64-gnu-cuda/externalpackages/git.amgx/petsc-build/base/CMakeFiles/amgx_base.dir/__/amgx_base_generated_plugin_config.cu.o.NVCC-depend
> -m64 -Xcompiler
> ,\"-fstack-protector\",\"-g\",\"-O2\",\"-fPIC\",\"-Wno-terminate\",\"-static-libgcc\",\"-fopenmp\",\"-DRAPIDJSON_DEFINED\",\"-DAMGX_WITH_MPI\",\"-fstack-protector\",\"-g\",\"-O2\",\"-fPIC\"
> -ccbin mpicxx -gencode=arch=compute_35,code=\"sm_35,compute_35\"
> -gencode=arch=compute_52,code=\"sm_52,compute_52\"
> -gencode=arch=compute_60,code=\"sm_60,compute_60\"
> -gencode=arch=compute_70,code=\"sm_70,compute_70\" -O3 -DNDEBUG -std=c++11
> --Werror cross-execution-space-call -DNVCC
> -I/autofs/nccs-svm1_home1/adams/petsc/arch-summit-opt64-gnu-cuda/externalpackages/git.amgx/../../thrust
> -I/autofs/nccs-svm1_home1/adams/petsc/arch-summit-opt64-gnu-cuda/externalpackages/git..amgx/base/include
> -I/sw/summit/cuda/10.1.168/include
> -I/autofs/nccs-svm1_home1/adams/petsc/arch-summit-opt64-gnu-cuda/externalpackages/git.amgx/external/rapidjson/include
> >>> -- Removing
> /autofs/nccs-svm1_home1/adams/petsc/arch-summit-opt64-gnu-cuda/externalpackages/git.amgx/petsc-build/base/CMakeFiles/amgx_base.dir/src/./amgx_base_generated_device_properties.cu.o
> >>> <<<<<<
> >>>
> >>> Also - its best to avoid -Werror in externalpackage builds..
> >>>
> >>> Satish
> >>>
> >>> On Tue, 3 Dec 2019, Mark Adams wrote:
> >>>
> >>>> Barry,
> >>>>
> >>>> First, there is a fix that we need in the AMGx repo (appended).
> >>>>
> >>>> I've never had problems like this not being able to build. I will try
> to
> >>>> build my AMGx manually to check.
> >>>>
> >>>> 21:31 master *= ~/AMGX$ git diff
> >>>> diff --git a/base/include/amgx_c_wrappers.inl
> >>>> b/base/include/amgx_c_wrappers.inl
> >>>> index 42496f0..ed9f0e1 100644
> >>>> --- a/base/include/amgx_c_wrappers.inl
> >>>> +++ b/base/include/amgx_c_wrappers.inl
> >>>> @@ -643,7 +643,7 @@ inline AMGX_Mode get_mode_from(const Envelope
> &envl)
> >>>>    {
> >>>>        //throws...
> >>>>        //
> >>>> -        FatalError("Mode not found.\n", AMGX_ERR_BAD_MODE);
> >>>> +        // FatalError("Mode not found.\n", AMGX_ERR_BAD_MODE);
> >>>>    }
> >>>>
> >>>>    AMGX_Mode mode = static_cast<AMGX_Mode>(itFound->second);
> >>>> @@ -1125,4 +1125,4 @@ inline bool
> remove_managed_matrix(AMGX_matrix_handle
> >>>> envl)
> >>>> } //namespace unnamed
> >>>>
> >>>> On Tue, Dec 3, 2019 at 8:50 PM Smith, Barry F. <bsmith at mcs.anl.gov>
> wrote:
> >>>>
> >>>>>
> >>>>> The first error is
> >>>>>
> >>>>> nvcc error   : 'cicc' died due to signal 9 (Kill signal)
> >>>>> nvcc error   : 'cicc' died due to signal 9 (Kill signal)
> >>>>>
> >>>>> later
> >>>>>
> >>>>>
> >>>>>
> /autofs/nccs-svm1_home1/adams/petsc/arch-summit-opt64-gnu-cuda/externalpackages/git.amgx/base/src/
> >>>>> amgx_c_common.cu(77): catastrophic error: error while writing
> generated
> >>>>> C++ file: Cannot allocate memory
> >>>>>
> >>>>> 1 catastrophic error detected in the compilation of
> >>>>> "/tmp/tmpxft_000038d3_00000000-4_amgx_c_common.cpp4.ii".
> >>>>>
> >>>>> Whatever machine you are compiling on seems to be overloaded. What
> does
> >>>>> top show? Can you log into "different" compiler servers on Summit?
> >>>>>
> >>>>> I run the install on the utk system with no problems like this.
> >>>>>
> >>>>> PETSc configure is deciding
> >>>>>
> >>>>> TEST configureMakeNP from
> >>>>>
> config.packages.make(/autofs/nccs-svm1_home1/adams/petsc/config/BuildSystem/config/packages/make.py:168)
> >>>>> TESTING: configureMakeNP from
> >>>>> config.packages.make(config/BuildSystem/config/packages/make.py:168)
> >>>>> check no of cores on the build machine [perhaps to do make '-j
> ncores']
> >>>>>         module multiprocessing found 128 cores: using make_np = 59
> >>>>>           Defined make macro "MAKE_NP" to "59"
> >>>>>           Defined make macro "MAKE_TEST_NP" to "49"
> >>>>>           Defined make macro "MAKE_LOAD" to "166.4"
> >>>>>           Defined make macro "NPMAX" to "128"
> >>>>>
> >>>>> then somehow this gets passed down to the AMGX cmake. Perhaps you
> could
> >>>>> try less greedy numbers.
> >>>>>
> >>>>> Executing: /usr/bin/gmake -j59 -l166.4
> >>>>>
> >>>>> Perhaps try
> >>>>>
> >>>>> --with-make-np=20
> >>>>>
> >>>>> --with-make-load=20
> >>>>>
> >>>>> Barry
> >>>>>
> >>>>>
> >>>>>
> >>>>>> On Dec 3, 2019, at 4:17 PM, Mark Adams <mfadams at lbl.gov> wrote:
> >>>>>>
> >>>>>> That might have been from an old .nsf file. Here is a new one. I'm
> sure
> >>>>> I have the disk space.
> >>>>>>
> >>>>>> On Tue, Dec 3, 2019 at 4:51 PM Mark Adams <mfadams at lbl.gov> wrote:
> >>>>>> Humm, clean up and seem to have different error:
> >>>>>>
> >>>>>>
> >>>>>> On Tue, Dec 3, 2019 at 3:45 PM Matthew Knepley <knepley at gmail.com>
> >>>>> wrote:
> >>>>>> Could you have run out of disk space?
> >>>>>>
> >>>>>> /usr/bin/ranlib: libamgx_base.a: Input/output error
> >>>>>> gmake[2]: *** [base/libamgx_base.a] Error 1
> >>>>>> gmake[2]: *** Deleting file `base/libamgx_base.a'
> >>>>>> gmake[1]: *** [base/CMakeFiles/amgx_base.dir/all] Error 2
> >>>>>> gmake: *** [all] Error 2
> >>>>>>
> >>>>>>  Matt
> >>>>>>
> >>>>>> On Tue, Dec 3, 2019 at 1:44 PM Mark Adams <mfadams at lbl.gov> wrote:
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> --
> >>>>>> What most experimenters take for granted before they begin their
> >>>>> experiments is infinitely more interesting than any results to which
> their
> >>>>> experiments lead.
> >>>>>> -- Norbert Wiener
> >>>>>>
> >>>>>> https://www.cse.buffalo.edu/~knepley/
> >>>>>> <configure.log>
> >>>>>
> >>>>>
> >>>>
> >>
>
>
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