configure: fix 6365592377de12cd44b5476ba3049f4dd78c30f5

Merge remote-tracking branch 'origin/hzhang/vec_node/master-rebased-v2'

Merge remote-tracking branch 'origin/balay/fix-pkg-cflags'

petsc4py: update to snapshot with CUDA API change sync

zoltan: update to version v3.83
- this update fixes perl error:
'Can't use 'defined(@array)' (Maybe you should just omit the defined()?) at
../config/generate-makeoptions.pl line 13.

- cleanup dep

zoltan: update to version v3.83
- this update fixes perl error:
'Can't use 'defined(@array)' (Maybe you should just omit the defined()?) at
../config/generate-makeoptions.pl line 13.

- cleanup dependencies and [i.e mark parmetis, ptscotch as optional - required mathlib - and remove unused X]

- use LIBS, CPPFLAGS, FCFLAGS options to specify externalpackges to configure
[and avoid parsing these strings to construct and use -with-mpi-libs type options]

Reported-by: Victor Eijkhout <eijkhout@tacc.utexas.edu>

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hypre: update to version 2.14.0

Reported-by: Antonio Trande <anto.trande@gmail.com>

Merge branch 'karlrupp/feature-remove-cusp'

* karlrupp/feature-remove-cusp:
Removes VECCUSP vectors and AIJCUSP matrices, because they provide no added benefit over VECCUDA and AIJCUSPARSE.
Also rem

Merge branch 'karlrupp/feature-remove-cusp'

* karlrupp/feature-remove-cusp:
Removes VECCUSP vectors and AIJCUSP matrices, because they provide no added benefit over VECCUDA and AIJCUSPARSE.
Also removes the CUSP-based preconditioners for now.
SACUSP will be re-added later, after the new release is out.

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Merge branch 'jed/faster-pipelines' [PR #908]

* jed/faster-pipelines:
petsc_testrun: remove watchtime.sh in favor of ulimit -St
petsc_testrun: use exit code even when no job control
make: use

Merge branch 'jed/faster-pipelines' [PR #908]

* jed/faster-pipelines:
petsc_testrun: remove watchtime.sh in favor of ulimit -St
petsc_testrun: use exit code even when no job control
make: use and recommend "make check" instead of "make test" for the brief check
config make: MAKE_TEST_NP default to MAKE_NP for with-mpi=0
travis: update (deactivated) alltests for consistency with bitbucket-pipelines
pipelines: use COPTFLAGS=-O
pipelines: use -check_pointer_intensity 0 -malloc_test

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set flag 'HAVE_MPI_WIN_CREATE_FEATURE' only for newer MPICH that has HAVE_MPI_WIN_CREATE HAVE_MPI_WIN_ALLOCATE_SHARED and HAVE_MPI_WIN_SHARED_QUERY

old mpich-3.0.4 has buggy MPI_Win_shared_query()

set flag 'HAVE_MPI_WIN_CREATE_FEATURE' only for newer MPICH that has HAVE_MPI_WIN_CREATE HAVE_MPI_WIN_ALLOCATE_SHARED and HAVE_MPI_WIN_SHARED_QUERY

old mpich-3.0.4 has buggy MPI_Win_shared_query() - does not return correct values

update vecscatter code to use PETSC_HAVE_MPI_WIN_CREATE_FEATURE flag [and remove code that handled
for PETSC_HAVE_MPI_WIN_ALLOCATE_SHARED and PETSC_HAVE_MPI_WIN_SHARED_QUERY flags - this was not clean anyway]

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GPUs: Allow ViennaCL and VECCUDA to be used concurrently.

This also gets rid of the weird veccuda.py.

externalpackages: built with cmake should use user provided flags. This fixes issues with metis and strumpack

Reported-by: Jin Chen <jchen@pppl.gov>

config make: MAKE_TEST_NP default to MAKE_NP for with-mpi=0

Added test for mkl_sparse_sp2m().

Configure: Fixed the MED configure (I hope)

Merge branch 'maint'

configure: print warning if WITH_MPI_DIR/bin does not exist [when looking for WITH_MPI_DIR/bin/mpicc]

Reported-by: "Klaij, Christiaan" <C.Klaij@marin.nl>

Doc+Configure: Spelling error

prefix: always save PREFIXDIR even for non-prefix install - this way ctetgen can use this info

make clearer in help statements what --with-external-packages-dir is for.

Commit-type: documentation

Merge remote-tracking branch 'origin/balay/remove-cuda-arch'

Turn off elemental test for parmetis running since this does not work on batch systems.

Commit-type: portability-fix
Reported-by: Francois Pechereau <francois.pechereau@onera.fr>
Thanks-to: Jed Brow

Turn off elemental test for parmetis running since this does not work on batch systems.

Commit-type: portability-fix
Reported-by: Francois Pechereau <francois.pechereau@onera.fr>
Thanks-to: Jed Brown <jed@jedbrown.org>
Development Tools: Vim, Emacs, Eclipse

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cuda/cusp: update minimum supported versions of cuda to 7.5 and cusp to 0.5.0

Now we can remove the separate cuda requirement for complex build.

[we don't actively test with older versions anyway]

cuda: remove configure option -with-cuda-arch. [use CUDAFLAGS instead]

- configure defaults are not necessarily better then nvcc defaults
- List of cuda-arch flags required updating with each releas

cuda: remove configure option -with-cuda-arch. [use CUDAFLAGS instead]

- configure defaults are not necessarily better then nvcc defaults
- List of cuda-arch flags required updating with each release of nvcc
- we needed different default for single vs double precision for early cuda versions [not anymore]

Also use '-Wno-deprecated-gpu-targets' as default CUDAPPFLAGS [and avoid using --arch with CUDAPP]

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cusp: update --download-cusp to usecusp/cuda9 branch for cuda-9.0 and higher and v0.5.1 for older versions
And switch a test to use this option --download-cusp

cusp: cleanup version detection code.
- remove compile test and replace with preprocess test [similar to MPICH version check] so no need for batch mode code
- i.e remove option:--known-cusp-version
-

cusp: cleanup version detection code.
- remove compile test and replace with preprocess test [similar to MPICH version check] so no need for batch mode code
- i.e remove option:--known-cusp-version
- use CUSPMinVersion as the name for min version. And CUSPVersion for detected version

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