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

Merge branch 'master' into knepley/feature-plex-adjoint-prelim

* master: (251 commits)
yaml: add a backup download URL
Fix documentation of MatSetRandom function
Ignore -malloc-hbw option if m

Merge branch 'master' into knepley/feature-plex-adjoint-prelim

* master: (251 commits)
yaml: add a backup download URL
Fix documentation of MatSetRandom function
Ignore -malloc-hbw option if malloc is already set
Plex: Fixed array initialization
pgi: compile fix
knl: update test to use memkind and remove option that worked arround a bug with intel 17
Check the return value for memkind_posix_memalign
Change the default behavour for -malloc_hbw
Bib: More refs
test: remove runex13f90 as its now converted to new test suite
fix win32 crash. This test was previously run with '-n 4' - so restoring it
Fix petscsfgetgraph_ to work for all Fortran compilers by directly using array of PetscSFNodes
bugfix for MatDuplicate_MPIAIJ_PtAP Reported-by: Samuel Lanthaler <s.lanthaler@gmail.com>
strip out dead sundials usage code; change sundials test to only run 5 timesteps to prevent different number of steps on different systems.
Remove extra lines of output file
Example uses C99 constructs so must mark with requires: c99
fix const missmatch for DMDAVecRestoreArrayRead()
remove conflict between function name in example and new PETSc TS function
builds: attempt to do maint/master/next test builds in separate clones
ex62: it turned out that CHACO partioning is not deterministic. Use a prescribed partition instead
...

Conflicts:
src/dm/interface/dm.c
src/snes/examples/tutorials/ex13.c

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Merge remote-tracking branch 'origin/hongzh/remove-bitarray-ell'

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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Merge commit 'd47bf9aaf1e5266cc3f0ff499f934c85788965a9' into jed/fix-matcreatempibaij/maint

Obtain changed (v3.5) handling of MatMPIBAIJSetPreallocationCSR to match
documentation.

Rename ELL to SELL

SELL is more accurate. It stands for sliced ELLPACK.

Funded-by:
Project: PETSc for Theta
Time: 2.5 hours
Reported-by:
Thanks-to:

Merge branch 'maint'

Merge remote-tracking branch 'origin/balay/fix-mkl-sparse/maint' into maint

mkl: add mkl_sparse.py as a separate package [as the interface code is organized this way]
and use PETSC_HAVE_MKL_SPARSE to enable/disable this interface code [so that this flag
represents functional

mkl: add mkl_sparse.py as a separate package [as the interface code is organized this way]
and use PETSC_HAVE_MKL_SPARSE to enable/disable this interface code [so that this flag
represents functionality that is more than PETSC_HAVE_MKL flag].

Also disable mkl_sparse, mkl_sparse_optimize for 64-bit-incides

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

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Merge remote-tracking branch 'origin/hongzh/add-ell-format'

MPIELL seems to work

Funded-by:
Project: PETSc for Theta
Time: 14 hours
Reported-by:
Thanks-to:

Add seqell format and its matmul kernel

-Make memkind error out when HBW is not usable

Funded-by:
Project: PETSc for Theta
Time: 52 hours
Reported-by:
Thanks-to:

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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Added new matrix classes to include files
Added define MKL_SUPPORTS_BAIJ_ZERO_BASED to suuport different versions
of MKL (older verions support only one based indexing for column major
blocks in baij

Added new matrix classes to include files
Added define MKL_SUPPORTS_BAIJ_ZERO_BASED to suuport different versions
of MKL (older verions support only one based indexing for column major
blocks in baij format)

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Merge branch 'rmills/add-aijmkl'

* rmills/add-aijmkl:
Adds AIJMKL matrix class to facilitate use of MKL sparse BLAS routines
BitBucket Pull Request 737
This is the initial version of the AIJMKL matr

Merge branch 'rmills/add-aijmkl'

* rmills/add-aijmkl:
Adds AIJMKL matrix class to facilitate use of MKL sparse BLAS routines
BitBucket Pull Request 737
This is the initial version of the AIJMKL matrix class,
a subclass of AIJ that has the goal of using MKL sparse BLAS routines whenever practicable.
If the MKL version is new enough, the sparse inspector-executor
("SpMV2" -- terrible name, but that's what the MKL team called it) routines are used by default.
Currently only MatMult, MatMultAdd, MatMultTranspose, and MatMultTransposeAdd operations are supported,
but more will be added once this initial attempt is at a point
that it provides an acceptable framework for adding additional further functionality.

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Fixed AIJMKL code breaking things when PETSc is built without Intel MKL.

Added MATMPIAIJMKL and fixed errors in MatMultAdd_SeqAIJMKL() and
MatMultTransposeAdd_SeqAIJMKL().

Initial skeleton for MATSEQAIJMKL matrix type that uses MKL sparse BLAS
routines. Currently only implements mult and multadd operations, but
ready to be expanded.

Merge branch 'master' into stefano_zampini/feature-gmsh-periodic

* master: (1016 commits)
metis: setself.downloaddirnames for change in 6d90219d8fa4f8b2fd242cc6ff9008358d87c26f
fix compile warni

Merge branch 'master' into stefano_zampini/feature-gmsh-periodic

* master: (1016 commits)
metis: setself.downloaddirnames for change in 6d90219d8fa4f8b2fd242cc6ff9008358d87c26f
fix compile warning: /sandbox/petsc/petsc.clone/src/snes/examples/tests/ex2.c:250:8: warning: ‘pointsAllProcs’ may be used uninitialized in this function [-Wmaybe-uninitialized] ierr = DMInterpolationSetUp(interpolator, dm, pointsAllProcs);CHKERRQ(ierr);
migrate 'build requires: !mpiuni' to new format
migrate 'build requires: !complex' to new format
workarround 'division by zero' compiler warning on windows C:\cygwin64\home\petsc\PETSC~3.CLO\src\ts\examples\TUTORI~1\ex11.c(416): warning #39: division by zero if (uL->h < 0 || uR->h < 0) {for (i=0; i<1+dim; i++) flux[i] = 0./0.; return;} /* SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Reconstructed thickness is negative"); */
dos2unix to prevent warnings on opensolaris "/export/home/petsc/petsc.clone/src/ksp/ksp/examples/tests/ex53.c", line 6: warning: invalid white space character in directive
fix output file - corresponding to code changes in efd4aadf157bf1ba2d80c2be092fcf4247860003
disable test on windows
update log from opensolaris so that the diff is clean on linux aswell
update grep in sync with change in efd4aadf157bf1ba2d80c2be092fcf4247860003
Fixed code that did not correctly set current color for block insertion
Update output files that did not get fixed after previous merges
Change MPIUni to not immediately abort on operations it cannot perform, instead return error code
Add filter for example that can produce 1 different iteration count
Example add system calloc, bad formating of %d in print, commented out code
Always use (void) for functions that take no arguments, never ()
always need to caste PetscReal variables to (double) in print statements
updates to manual page for clarity
update help menu for MatRARt() -- MatRARt_mpiaij_mpiaij is supported now, but not efficient.
fix nightlybuild error with c1cbb1def3f8ddca04c3998b9c06618fd1ffef35 on arch-linux-IPL64 src/ksp/pc/examples/tests ex5_1
...

Conflicts:
include/petscdm.h
src/dm/impls/plex/plexcreate.c
src/dm/impls/plex/plexgmsh.c
src/dm/impls/plex/plexhdf5.c

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Merge branch 'master' into knepley/feature-plex-sphere-mesh

* master: (2633 commits)
Bib: Added ref
SNES ex56: Update test output
add a citation to petsc.bib
Plex: Initialize variables
ini

Merge branch 'master' into knepley/feature-plex-sphere-mesh

* master: (2633 commits)
Bib: Added ref
SNES ex56: Update test output
add a citation to petsc.bib
Plex: Initialize variables
initialize ap as complained by the nightly tests
Plex ex3: Update to new point function API
initialize some variables as complained by nightly tests
SNES ex12: Mix misnaming Nf --> Nc
update tests
add tests
add MatView_SeqXAIJ_ASCII_structonly(); enable A->structure_only in MatSetValuesBlocked_SeqBAIJ
typo
fill-in some references
Bib: Fixed ref
Plex: Added PLY to file support
Plex: Adding PLY support
PetscDS: Turn off Fortran bindings for Constants
Plex tests: Updated to new point function API
SNES ex56: Moved tests to new format
DM: Allow field projection functions to take an array of scalars - This will allow us to pass in user data to kernels without void *, more efficiency than aux fields
...

Conflicts:
config/builder.py
include/petscdmplex.h
src/dm/impls/plex/examples/tests/ex1.c
src/dm/impls/plex/plexcreate.c
src/dm/impls/plex/plexgmsh.c
src/snes/examples/tutorials/ex63.c

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Merge branch 'master' into knepley/feature-plex-torus

* master: (174 commits)
Bib: Another ref
Increase patchlevel to 3.7.6
Explicitly listing the LTO library causes difficulties on MacOS so a

Merge branch 'master' into knepley/feature-plex-torus

* master: (174 commits)
Bib: Another ref
Increase patchlevel to 3.7.6
Explicitly listing the LTO library causes difficulties on MacOS so avoid it
TSBDF: Update changes/dev.html
Added Fortran TaoType and TaoLineSearchType definitions
Add Fortran TaoType and TaoLineSearchType definitions
setblocksize for iscol_sub
TSBDF: Use standard TS API and options to control adaptivity
Bib: More refs and a correction
SNESTest: Bug-fix in SNESTest when threshold printing option is turned on.
fix warning and valgrind complains reported by the nightly tests
Section+Doc: Small doc fix
pflotran: switch to using the new upstream git repo
DMPlex: Error if attempt to partition a distributed graph with Chaco
fix complex build error
fix complex build
PetscError() did not properly copy over the specific error message when error type was PETSC_ERROR_INITIAL
TSAdapt: Refactor handling of the always_accept flag
Additional clarification for MatMeshToCellGraph() manual page
optimize MatCreateSubMatrix_MPIAIJ() by merging check of sameXXXDist() into one MPI_AllReduce
...

Conflicts:
config/BuildSystem/config/packages/med.py

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Merge branch 'master' into knepley/feature-plex-tests-new

* master: (108 commits)
Bib: Added ref
Bib: Updated reference
Bib: Updated reference
Work around problems with Apple Xcode 8.3 and h

Merge branch 'master' into knepley/feature-plex-tests-new

* master: (108 commits)
Bib: Added ref
Bib: Updated reference
Bib: Updated reference
Work around problems with Apple Xcode 8.3 and handling of rpath argument with gfortran
help menu update for MatCreateSubMatrices() Reported-by: Brad Aagaard <baagaard@usgs.gov>
fix flops for PCApply_PBJacobi_1 and PCApply_PBJacobi_7 Reported-by: Pierre Jolivet <pierre.jolivet@enseeiht.fr>
TSRK: Fix FSAL optimization to not skip update and check or stages.
Travis-CI: Workaround too long TMPDIR in macOS with Open MPI
test: Fix type mismatch in KSP test.
test: Fix warnings from gfortran -Wconversion (OS X, Homebrew build)
MPIUNI: Silence GCC -Wconversion warnings
Fortran: Add error checking for incorrect PETSC_NULL_XXX argument when expecting function
fix test output per changes in 517c9301b2e9239931bfd644803fd6bb859387ea
MUMPS: update to version 5.1.1 with opensolaris compile fixes
TSRK: Mention 5BS in the changelog.
TSRK: Mention the new 5BS scheme in the manual.
fix 'unused variable' warning
Remove unused code
added hbw_realloc
fixed undefined ptr
...

Conflicts:
config/BuildSystem/config/packages/med.py

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Merge remote-tracking branch 'origin/balay/fix-redundant-decls-warnings-master'

Merge branch 'knepley/fix-plex-example-logging' into knepley/feature-plex-torus

* knepley/fix-plex-example-logging: (151 commits)
Plex ex12: Added logging stages
Plex ex1: Added logging stages

Merge branch 'knepley/fix-plex-example-logging' into knepley/feature-plex-torus

* knepley/fix-plex-example-logging: (151 commits)
Plex ex12: Added logging stages
Plex ex1: Added logging stages
update to latest hypre tag on github
fix 'inf' vs 'Inf' diff wrt vec_vec_utils_tagger_tutorials-ex1_8,9,18,19
MatSetOption(mat,MAT_IGNORE_ZERO_ENTRIES,PETSC_TRUE) no longer applies to zero values set or added to the matrix diagonal, they are now not ignored and are included in the matrix nonzero structure. This is useful for Jacobians passed to TS.
replace use/mention of depreciated -log_summary in many places
add extchem.py which was written years ago but never put in the distribution (hence it is broken).
petsc4py: update to snapshot with MatGetSubMatrices -> MatCreateSubMatrices etc API changes
Minor fixes for tchem examples due to changes in PETSc infrastructure
update webpage about API changes
add help menu for MatCreateSubMatricesMPI()
PetscCMPLX: assume type punning is safe
rename struct Mat_SubMat -> Mat_SubSppt
add a little information to the manual about using tchem
rename MatCreateSubMatrixComposite -> MatCreateSubMatrixVirtual; Mat_SubMatrix -> Mat_SubVirtual
need to protect the \ passed on the makefile on my Mac
Bib: Updated ref
update src/mat/examples/tests/output/ex23_#.out
rename MatGetSubMat -> MatCreateSubMat
Mark MatCreateMPIAIJWithSplitArrays() and MatMPIAIJSetPreallocationCSR() with MAT_NO_OFF_PROC_ENTRIES
...

Conflicts:
src/dm/impls/plex/examples/tests/ex1.c
src/dm/impls/plex/examples/tests/ex12.c

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Merge branch 'knepley/fix-plex-example-logging' into knepley/feature-plex-tests-new

* knepley/fix-plex-example-logging: (151 commits)
Plex ex12: Added logging stages
Plex ex1: Added logging stag

Merge branch 'knepley/fix-plex-example-logging' into knepley/feature-plex-tests-new

* knepley/fix-plex-example-logging: (151 commits)
Plex ex12: Added logging stages
Plex ex1: Added logging stages
update to latest hypre tag on github
fix 'inf' vs 'Inf' diff wrt vec_vec_utils_tagger_tutorials-ex1_8,9,18,19
MatSetOption(mat,MAT_IGNORE_ZERO_ENTRIES,PETSC_TRUE) no longer applies to zero values set or added to the matrix diagonal, they are now not ignored and are included in the matrix nonzero structure. This is useful for Jacobians passed to TS.
replace use/mention of depreciated -log_summary in many places
add extchem.py which was written years ago but never put in the distribution (hence it is broken).
petsc4py: update to snapshot with MatGetSubMatrices -> MatCreateSubMatrices etc API changes
Minor fixes for tchem examples due to changes in PETSc infrastructure
update webpage about API changes
add help menu for MatCreateSubMatricesMPI()
PetscCMPLX: assume type punning is safe
rename struct Mat_SubMat -> Mat_SubSppt
add a little information to the manual about using tchem
rename MatCreateSubMatrixComposite -> MatCreateSubMatrixVirtual; Mat_SubMatrix -> Mat_SubVirtual
need to protect the \ passed on the makefile on my Mac
Bib: Updated ref
update src/mat/examples/tests/output/ex23_#.out
rename MatGetSubMat -> MatCreateSubMat
Mark MatCreateMPIAIJWithSplitArrays() and MatMPIAIJSetPreallocationCSR() with MAT_NO_OFF_PROC_ENTRIES
...

Conflicts:
src/dm/impls/plex/examples/tests/ex12.c

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