Mat: MAT_INPLACE_MATRIX can be used for transposition with rectangular matrices

Added a couple of tests

Merge branch 'master' into knepley/feature-snes-ex13-spectral

* master: (2350 commits)
migrate warning fix from next-tmp
Revert "Remove dead code."
clarifying comment in the code
Remove dead

Merge branch 'master' into knepley/feature-snes-ex13-spectral

* master: (2350 commits)
migrate warning fix from next-tmp
Revert "Remove dead code."
clarifying comment in the code
Remove dead code.
Add JuMP citation
Copyedits and updates to developers manual
Add more protection to intrinsics
MPI: protect arguments in MPI macros
Add the missing conditionals for 64-bit build
Plex+VTK: Fix field type determination
Fix bug in name cleanup
Bib: Added ref
Plex+VTK: Fix field type determination
Plex: Updated test output - I am now hating this shit
forgot to save file after moving prototypes to petscsys.h
update Apple example project settings per Xcode
Two functions should actually be public, used, for example from Apple MacOS and iOS programs
includes should always be included relative to include directory
Apple removed old locations of docsets
SNES ex12: Updated test output
...

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

show more ...

Merge branch 'master' into knepley/feature-pc-patch

* master: (440 commits)
revert sources to dev - reset PETSC_VERSION_RELEASE - reset changes/dev.html
release: set v3.9 strings
fix grep us

Merge branch 'master' into knepley/feature-pc-patch

* master: (440 commits)
revert sources to dev - reset PETSC_VERSION_RELEASE - reset changes/dev.html
release: set v3.9 strings
fix grep usage on solaris [use egrep]
opensolaris: fix errors
Update timer reporting and minor reporting fix
Remove redundant if statement. Found by @jedbrown
Fixed problem with order of developer photos on website.
superlu_dist: use correct flag in example [PETSC_HAVE_SUPERLU -> PETSC_HAVE_SUPERLU_DIST]
Bib: PERMON ref
fix for osx
doc: more author fixes
doc: more author fixes
Italicized "orderings" in MPI process placement discussion.
Added Richard to the user manual author list.
Added Richard to the list of active developers on the website.
add string check for MS-MPI and IMPI timeout errors
opensolaris does not have multiple grep utils - but default one does not support -F. So use fgrep instead
Standardizing timeout checks
Report wall clock time of total tests
Use time instead of date %s
...

Conflicts:
include/petscpc.h
src/ksp/ksp/interface/itfunc.c

show more ...

Merge branch 'stefano_zampini/fix-matis-dmda-l2g'

Merge branch 'pr902/jkruzik/feature-MatCreateMPIMatConcatenateSeqMat_Dense/master'

* pr902/jkruzik/feature-MatCreateMPIMatConcatenateSeqMat_Dense/master:
adds MatCreateMPIMatConcatenateSeqMat implem

Merge branch 'pr902/jkruzik/feature-MatCreateMPIMatConcatenateSeqMat_Dense/master'

* pr902/jkruzik/feature-MatCreateMPIMatConcatenateSeqMat_Dense/master:
adds MatCreateMPIMatConcatenateSeqMat implementation for MATDENSE

show more ...

MatCreateMPIMatConcatenateSeqMat_SeqDense impl

Merge remote-tracking branch 'origin/knepley/fix-snes-ex69' into tisaac/feature-dmfield

* origin/knepley/fix-snes-ex69: (311 commits)
PetscFECreateDefault: fix custom Fortran interface to use MPI_

Merge remote-tracking branch 'origin/knepley/fix-snes-ex69' into tisaac/feature-dmfield

* origin/knepley/fix-snes-ex69: (311 commits)
PetscFECreateDefault: fix custom Fortran interface to use MPI_Comm
SNES ex69: Updated test output
SNES ex69: Removed all mantle stuff and change fields to constants - Also use dsymutil for executables
SNES ex69: Removed special partition
SNES ex69: Fixed null space creation - Null space locks its vectors
PetscFE: PetscFECreateDefault() now takes MPI_Comm instead of DM
cleanup very ugly PCGAMG manual page
minor clarifications for VecScatterCreate() manual page
gcov: PETSC_ARCH is required onlyfor -run_gcov - and not for -merge_gcov [where it doesn't exist]
make clearer in help statements what --with-external-packages-dir is for.
Website: Added news entry for PETSc User Meeting 2018 on main page.
CUDA: Further test output fixes for mat_tests-ex2
Turn off elemental test for parmetis running since this does not work on batch systems.
3.8 Changes: KSPCHEBYSHEV
CUDA: Fixed most test errors due to MatMultTranspose*
website: update urls
website: fix Jason's name to match pic. Also add Todd's pic
Dev manual: copyedit
DMPlexDistributeLabels: Propagate the output flag
cuda/cusp: update minimum supported versions of cuda to 7.5 and cusp to 0.5.0
...

show more ...

Merge branch 'hongzh/change-vecarray-to-mat-tlm'

* hongzh/change-vecarray-to-mat-tlm:
Uses a dense array instead of multiple vectors to store TLM sensitivity
and removes TSForwardSetRHSJacobianP (us

Merge branch 'hongzh/change-vecarray-to-mat-tlm'

* hongzh/change-vecarray-to-mat-tlm:
Uses a dense array instead of multiple vectors to store TLM sensitivity
and removes TSForwardSetRHSJacobianP (use TSAdjointSetRHSJacobian instead).

show more ...

Improve naming and doc

Funded-by:
Project: FASTMATH
Time: 0.5 hours
Reported-by:
Thanks-to:

MATSEQDENSE: extend support for MatTransposeSolve

fix POTR case, add HETR

Added test

Add MatDenseGetColumn and MatDenseRestoreColumn

This allows one to modify a column of a dense matrix.

Funded-by:
Project: PETSc for Theta
Time: 4.0 hours
Reported-by:
Thanks-to:

Merge branch 'barry/fix-matdensegetarray'

Merge branch 'maint'

Error in SOR for dense matrices, BLASdot() uses the complex-conjugate transpose

This is not appropriate for applying lower triangular rows of the matrix to the current partial solution

Commit-type:

Error in SOR for dense matrices, BLASdot() uses the complex-conjugate transpose

This is not appropriate for applying lower triangular rows of the matrix to the current partial solution

Commit-type: bug-fix
Reported-by: Vinh Pham-Xuan <vinh.phamxuan2@mail.dcu.ie>

show more ...

Introduce MatDenseGetArrayRead(), add object state update to MatDenseGetArray(), adding missing MatDenseRestoreArray() to MKL_CPardiso

Commit-type: bug-fix, feature
Reported-by: Pierre Jolivet <Pier

Introduce MatDenseGetArrayRead(), add object state update to MatDenseGetArray(), adding missing MatDenseRestoreArray() to MKL_CPardiso

Commit-type: bug-fix, feature
Reported-by: Pierre Jolivet <Pierre.Jolivet@enseeiht.fr>

show more ...

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
...

show more ...

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

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

Merge branch 'maint'

Merge remote-tracking branch 'origin/barry/fix-matmult-seqdense-cherrypick/maint' into maint

Fix bug in sequential dense multiply and transpose multiply with zero rows or columns

Routines just returned instead of zeroing output vector

Commit-type: bug-fix
Reported-by: Florian Lindner <mail

Fix bug in sequential dense multiply and transpose multiply with zero rows or columns

Routines just returned instead of zeroing output vector

Commit-type: bug-fix
Reported-by: Florian Lindner <mailinglists@xgm.de>

show more ...

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.

show more ...

Associated seqaijmkl_seqdense_C functions.

Merge remote-tracking branch 'origin/barry/feature-aij-subtypes'

Add subtype concept to SeqAIJ matrices

Introduced -mat_seqaij_type <seqaijperm, ...> MatSeqAIJSetType() to allow running code written for AIJ to work
with any subtype. See MatSeqAIJRegister() and Ma

Add subtype concept to SeqAIJ matrices

Introduced -mat_seqaij_type <seqaijperm, ...> MatSeqAIJSetType() to allow running code written for AIJ to work
with any subtype. See MatSeqAIJRegister() and MatSeqAIJRegisterAll() for registering new subtypes

Use

export PETSC_OPTIONS="-mat_seqaij_type seqaijperm -malloc_test"
make alltests

to run the entire test suite using an alternative subclass, in this case seqaijperm. This will produce output regarding the different name for
the matrix class but otherwise should produce no errors.

This was implemented to 1) allow easy testing of an MKL subtype and 2) to allow users to easily use the MKL subtype
without changing their code.

Also fixes several bugs in seqaijperm, if it isn't tested its broken.

Commit-type: testing-fix,style-fix, feature
Funded-by: ECP
Project: MKL
Time: 32 hours
Reported-by: Irina Sokolova <irina.sokolova@intel.com>

show more ...

Merge branch 'master' into knepley/fix-fe-default

* master: (297 commits)
Bib: Added refs and fixed one
Doc: Fixed formatting problems for MatCreateAIJ() manual page.
Add to PCSOR manual page

Merge branch 'master' into knepley/fix-fe-default

* master: (297 commits)
Bib: Added refs and fixed one
Doc: Fixed formatting problems for MatCreateAIJ() manual page.
Add to PCSOR manual page information about convergence testing when using KSPRICHARDSON
SNES ex5: Restore old output since this breaks an example I have
Noted that some Cray XC systems will use 'aprun' instead of 'srun'. Thanks to Herr Doktor Hong Zhang for this suggestion.
Added example configure script for Cray XC40 with KNL processors (e.g., NERSC Cori).
Fix possible sprintf -Wformat-overflow
PetscMalloc2-7: fix -Wint-in-bool-context for GCC 7
SNES ex5: make boundary condition handling consistent for symmetry
SNES ex5: use L2 norm and *_monitor_short for output
SNES ex5: the L^2 norm scales with the l^2 norm over sqrt(N)
SNES ex5: refactor MMS capability to avoid extreme code duplication
Documentation fix: typo in PetscLogStageRegister manual page.
nodes -> vertices
rename DMNetworkGetComponentTypeOffset -> DMNetworkGetComponentKeyOffset
rename DMNetworkGetConnectedNodes() -> DMNetworkGetConnectedVertices()
Jacobians for adjoints for explicit methods and constant Jacobians never got initialized
fix complex build error
fix build failure with fortran interface
fix compile error with cdc753b64c658d532d7813e942002e67025667a6
...

Conflicts:
src/snes/examples/tutorials/ex13.c
src/snes/examples/tutorials/ex62.c
src/snes/examples/tutorials/ex69.c

show more ...