tests: get latest datafiles before starting builds

msys2: fix link error with incorrect library order - when /c/PROGRA~2/MICROS~2/MPI/Lib/x64/msmpi.lib is used

wrong:
gcc -g3 -g3 -I/home/balay/petsc/include -I/home/balay/petsc/arch-msys-c-debug/in

msys2: fix link error with incorrect library order - when /c/PROGRA~2/MICROS~2/MPI/Lib/x64/msmpi.lib is used

wrong:
gcc -g3 -g3 -I/home/balay/petsc/include -I/home/balay/petsc/arch-msys-c-debug/include -I/c/PROGRA~2/MICROS~2/MPI/Include -Wl,-rpath,/home/balay/petsc/arch-msys-c-debug/lib -L/home/balay/petsc/arch-msys-c-debug/lib /c/PROGRA~2/MICROS~2/MPI/Lib/x64/msmpi.lib ex2.c -lpetsctao -lpetscts -lpetscsnes -lpetscksp -lpetscdm -lpetscmat -lpetscvec -lpetscsys -llapack -lblas -lgdi32 -luser32 -ladvapi32 -lkernel32 -lquadmath -o ex2
C:/msys64/home/balay/petsc/arch-msys-c-debug/lib/libpetscksp.a(itcl.o): In function `PetscMPIParallelComm':
C:/msys64/home/balay/petsc/include/petsclog.h:428: undefined reference to `MPI_Comm_size'

fixed:
gcc -g3 -g3 -I/home/balay/petsc/include -I/home/balay/petsc/arch-msys-c-debug/include -I/c/PROGRA~2/MICROS~2/MPI/Include -Wl,-rpath,/home/balay/petsc/arch-msys-c-debug/lib -L/home/balay/petsc/arch-msys-c-debug/lib ex2.c -lpetsctao -lpetscts -lpetscsnes -lpetscksp -lpetscdm -lpetscmat -lpetscvec -lpetscsys /c/PROGRA~2/MICROS~2/MPI/Lib/x64/msmpi.lib -llapack -lblas -lgdi32 -luser32 -ladvapi32 -lkernel32 -lquadmath -o ex2

Reported-by: Pierre Jolivet <pierre.jolivet@enseeiht.fr>

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Merge branch 'pr1819/jkruzik/feature-pcdeflation/master' [PR #1819]

* pr1819/jkruzik/feature-pcdeflation/master:
PCDeflation.
Implements multilevel deflation preconditioner that can shift part of th

Merge branch 'pr1819/jkruzik/feature-pcdeflation/master' [PR #1819]

* pr1819/jkruzik/feature-pcdeflation/master:
PCDeflation.
Implements multilevel deflation preconditioner that can shift part of the spectrum to a predefined value.

Given a full rank deflation matrix W, the deflation preconditioner uses projections Q = W*(W'*A*W)^{-1}*W' and P = I - Q*A.
It computes computes initial guess x0 = x_{-1} - Q*r_{-1} which is the solution on the deflation space.
The preconditioner application consists of P*M^{-1} + factor*Q, where M^{-1} is an additional preconditioner.

See the documentation for PCDEFLATION above PCCreate_Deflation for more detailed description.

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Makefiles: remove TARGET_ARCH

TARGET_ARCH is predefined in these rules (see make -p -f/dev/null) and
is intended to be used with options like -march=armv8.5-a, but Cygwin
environments apparently def

Makefiles: remove TARGET_ARCH

TARGET_ARCH is predefined in these rules (see make -p -f/dev/null) and
is intended to be used with options like -march=armv8.5-a, but Cygwin
environments apparently define TARGET_ARCH in a way that is
syntactically incorrect when used this way.

Reported-by: Barry Smith <bsmith@mcs.anl.gov>

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Merged in barry/cleanup-petscconf-h (pull request #1834)

Remove testing and inserting into petscconf.h items that are not actually used by PETSc

Remove testing and inserting into petscconf.h items that are not actually used by PETSc

1) PETSC_HAVE_LIBXXXX - which was rarely used
be careful with the package libpng and libjpeg since they hav

Remove testing and inserting into petscconf.h items that are not actually used by PETSc

1) PETSC_HAVE_LIBXXXX - which was rarely used
be careful with the package libpng and libjpeg since they have lib in the name of the package
2) various system include files that are never used or always exist: for example stdlib.h
3) various system functions that are never used or always exist
4) fixes for requires for MUMPS and SuperLU_DIST when dependent packages are installed or not installed (unrelated to the rest of this pull request)
5) packages that always exist such as PETSC_HAVE_BLASLAPACK, or are not used by PETSc such as PETSC_HAVE_NETCFD
6) remove a couple of uses of HAVE_LIB* in the code that were not needed by adjusting the configure code slightly
7) remove all the #if guards for each entry in petscconf.h since petscconf.h already has a guard and
the values are never defined else where the extra guards just make the file cluttered

For a build with about 10 external packages this reduced the size of petscconf.h from 1236 lines to 828/4 around 220 entries.

Commit-type: style-fix, cleanup

Reported-by: Jed Brown <jed@jedbrown.org

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fix fortran

Merge from doc-fixes branch

Merged in psanan/manimplementations-ignore-private-functions (pull request #1745)

Man pages: ignore _Private functions in Implementations sections

Fixes for doctext update

Merged in barry/cuda-multigrid-test (pull request #1763)

Various improvements for GPUs (mostly for performance and CUDA)

Various improvements for GPUs (mostly for performance and CUDA)

1) Add VecPinToCPU() for CUDA vector and matrices
2) Move initialization of cuBLAS to PetscInitialize() since it takes 1/2 second and

Various improvements for GPUs (mostly for performance and CUDA)

1) Add VecPinToCPU() for CUDA vector and matrices
2) Move initialization of cuBLAS to PetscInitialize() since it takes 1/2 second and distorts timing with -log_view
3) Add logging for DMCreateMatrix (for large meshes this is very large)
4) Add VecGet/RestoreArrayWrite() to prevent unneeded copies from GPU (only implemented so far for CUDA);
added a small number of usages in the source so that snes tutorials ex19 does not do unneeded communication from the GPU
5) Automatically convert MAIJ matrices to AIJ for CUDA since they are not yet supported natively in PETSc's CUDA matrix implementation
6) Pinned objects should still use the CUDA/ViennaCL versions of Destroy to clean up the GPU stuff

Commit-type: feature

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Remove no longer needed buildmod rules for building Fortran libraries from various directories

Commit-type: cleanup
Reported-by: Jose E. Roman <jroman@dsic.upv.es>

Merged in barry/rm-cmake-legacy (pull request #1714)

Remove legacy and cmake compile systems

Approved-by: BarryFSmith <bsmith@mcs.anl.gov>

Merge branch 'pr1783/jgiordani/add-py3-xdmf/master' [PR #1783]

* pr1783/jgiordani/add-py3-xdmf/master:
petsc_gen_xdmf.py is now py2/3 compatible

petsc_gen_xdmf.py is now py2/3 compatible

Under py3 h5py attributes are byte strings, unlike py2. See https://github.com/h5py/h5py/issues/379
The added conditional handles both py2/3 environments.

PetscBinaryIO.py: fix default precision to double

Commit-type: bug-fix
Reported-by: Patrick Sanan <patrick.sanan@gmail.com>

PetscBinaryIO.py: make module executable to convert MatrixMarket files

I was tired of remembering a couple lines of code in Python for
converting files. Now you can

python -m PetscBinaryIO conve

PetscBinaryIO.py: make module executable to convert MatrixMarket files

I was tired of remembering a couple lines of code in Python for
converting files. Now you can

python -m PetscBinaryIO convert matrix.mtx

and you'll get matrix.petsc ready to be used by PETSc.

Commit-type: feature

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Man pages: ignore _Private functions in Implementations sections

Assuming that there is never an implementation called "Private" (e.g.
KSPPrivate), this ignores potentially-confusing matches, which

Man pages: ignore _Private functions in Implementations sections

Assuming that there is never an implementation called "Private" (e.g.
KSPPrivate), this ignores potentially-confusing matches, which could
- lead to someone missing implementaton logic (e.g. KSPFoo_Bar() calls
KSPFoo_Bar_Special_Case_Private())
- create some spurious links (e.g. the current link from
DMPlexGetConeRecursive() to DMPlexGetConeRecursive_Private())

Minor formatting/cleanup of the description of manimplementations logic,
to attempt to better describe the often-hard-to-decode logic of this
sort of scripting.

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