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

Mark Adams mfadams at lbl.gov
Fri Dec 13 12:19:58 CST 2019 

There is a MR winding its way in. I think it is ready to go. There is
confusion with branches but it is something like
barry/12-01-19-pc-feature-amgx.

It is a PC, but it is so fragile. I could only get AMGx to work with
classical AMG (preferred) by using its Krylov solver also. So the test sets
-ksp_preonly.

There is an example in snes/ex13.

On Fri, Dec 13, 2019 at 12:09 PM Fande Kong <fdkong.jd at gmail.com> wrote:

> 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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