Merge branch 'barry/more-to-new-test-harness' into barry/all-new-test-harness-branches

Merge branch 'barry/vec-to-test-harness' into barry/all-new-test-harness-branches

Merge branch 'jed/tests-cxx-linker' into barry/more-to-new-test-harness

Merge branch 'rmills/fix-aijmkl-style'

Fix several minor code issues in AIJMKL and BAIJMKL code.

Remove improper returning of error codes from PetscFunctionReturn();
remove unused variable; fix some code formatting.

Commit-type: style-f

Fix several minor code issues in AIJMKL and BAIJMKL code.

Remove improper returning of error codes from PetscFunctionReturn();
remove unused variable; fix some code formatting.

Commit-type: style-fix
Reported-by: Barry Smith <bsmith@mcs.anl.gov>

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AIJMKL now uses PetscObjectState to determine if MKL matrix handle must be rebuilt.

Merge branch 'master' into knepley/fix-plex-bc-multiple

* master: (347 commits)
tests: add 'PETSC_HAVE_C99' flag - so that 'requires: c99' can be used in the test suite
PGI: fix build error with

Merge branch 'master' into knepley/fix-plex-bc-multiple

* master: (347 commits)
tests: add 'PETSC_HAVE_C99' flag - so that 'requires: c99' can be used in the test suite
PGI: fix build error with updated 17.10 compilers
Fix for test dirs that are not tutorials/tests
fix use of double in PetscAbsReal() which produces compiler warnings with single precision build
elemental: remove info on conflict of -with-cxx-dialect=C++11 on osx - it works now.
Cleanup .bib files
Fix allfortranstubs rule to rm generated files from correct directory, not outdated location
ierr set but not checked
Remove initial refine so test runs faster and does not time out on some machines
Gail's copyedits for bibtex items
Docs: manual: add further description of 3 different current testing options
DM: check for ops->localtolocalbegin/end before calling
PetscSF: fix typo in tutorial ex1
Vec+HDF5: Fix output for complex - Need to check for empty group name
SNES: SNESDestroy() can be called with snes->dm == NULL
SNES: SNESDestroy() can be called with snes->dm == NULL
Vec+HDF5: Fix output for complex - Need to check for empty group name
Docs: Manual: Update tests section
gmakegentest: also exclude .#filenames created by emacs
DMPlex: Fix output of test ex1 after changes to Gmsh reader
...

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mkl: fix compiler warning with --with-mkl_sparse_optimize=0

Reported-by: Eric Chamberland <Eric.Chamberland@giref.ulaval.ca>

mkl: fix breakage with --with-mkl_sparse_optimize=0

Also change one the tests using MKL to use the above option

Reported-by: Jose E. Roman <jroman@dsic.upv.es>
Reported-by: Eric Chamberland <Eric.C

mkl: fix breakage with --with-mkl_sparse_optimize=0

Also change one the tests using MKL to use the above option

Reported-by: Jose E. Roman <jroman@dsic.upv.es>
Reported-by: Eric Chamberland <Eric.Chamberland@giref.ulaval.ca>

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Merge remote-tracking branch 'origin/rmills/feature-aijmkl-matmatmult'

Document -mat_aijmkl_eager_inspection option and update formatting for SeqAIJMKL manual page.

Updated SeqAIJMKL documentation: MatMatMult() and MatTransposeMatMult() are now supported.

MatSeqAIJMKL_create_from_mkl_handle() now simply destroys the old matrix if MAT_REUSE_MATRIX is specified.

Previously, we attempted to save some expense by directly copying exported
CSR arrays from

MatSeqAIJMKL_create_from_mkl_handle() now simply destroys the old matrix if MAT_REUSE_MATRIX is specified.

Previously, we attempted to save some expense by directly copying exported
CSR arrays from MKL, but this causes problems because the MKL and PETSc
representations differ in small ways (e.g., more explicit nonzeros in the
PETSc representation due to preallocation.)

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Fixed wrong operation being set for SeqAIJMKL MatTransposeMatMult.

Fixed missing ')' in comment.

Destroy existing optimized MKL matrix handle in SeqAIJMK assembly end if using lazy inspection.

Fixed missing setup of aijmkl->descr in MatSeqAIJMKL_create_from_mkl_handle().

Added MatTransposeMatMult_SeqAIJMKL_SeqAIJMKL_SpMV2().

Added code to handle MAT_REUSE_MATRIX when constructing SEQAIJMKL matrix from MKL matrix handle.

Added initial MatMatMult_SeqAIJMKL_SeqAIJMKL_SpMV2() implementation.

Added routine to create sequential AIJMKL matrix from an MKL sparse matrix handle.

Merge branch 'rmills/aijmkl-lazy-inspection'

Can now choose between lazy or eager inspection for AIJMKL matrices; the default is lazy (i.e., does not happen until an operation like MatMult() is requested).

Commit-type: feature
Funded-by: ECP
T

Can now choose between lazy or eager inspection for AIJMKL matrices; the default is lazy (i.e., does not happen until an operation like MatMult() is requested).

Commit-type: feature
Funded-by: ECP
Time: 1.5 hours

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Merge branch 'pr746/irinasok/feature-baijmkl/master'

* pr746/irinasok/feature-baijmkl/master:
Implementation of BAIJMKL matrix type similar to AIJMKL.
Supports MKL calls for MatMult (add and transpo

Merge branch 'pr746/irinasok/feature-baijmkl/master'

* pr746/irinasok/feature-baijmkl/master:
Implementation of BAIJMKL matrix type similar to AIJMKL.
Supports MKL calls for MatMult (add and transposed).
In case if used MKL version does not support mkl_sparse_optimize() (MKL 11.2 and earlier) PETSc default kernels are used.
Test added on configuration step to check if used version of MKL supports column major layout with zero based indexing.
All released versions of MKL do not support such cross case and MatSeqBAIJMKL_create_mkl_handle() converts matrix arrays to one based indexing before passing them to mkl routines.

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Bug fixes
Fix for test 107_2. To prevent MKL routine returning error in case when MatSetOption(mat,MAT_STRUCTURE_ONLY,PETSC_TRUE) is called. In this case matrix will be optimized before call to mkl_s

Bug fixes
Fix for test 107_2. To prevent MKL routine returning error in case when MatSetOption(mat,MAT_STRUCTURE_ONLY,PETSC_TRUE) is called. In this case matrix will be optimized before call to mkl_sparse_x_mv.
The same problem will appear in AIJMKl case.
Also added MatCreateBAIJMKL and MatCreateSeqBAIJMKL to external include to call them from examples

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