Merge branch 'barry/add-ftn-linfinity-conv-test' of bitbucket.org:petsc/petsc into barry/add-ftn-linfinity-conv-test

Merge branch 'jose/lapack-ungqr'

petscblaslapack.h: rename LAPACKungqr_ to LAPACKorgqr_

The intention is to be consistent with other subroutines like
LAPACKsyev_ where the 'real' name is used for both the 'real' subroutine
(_syev)

petscblaslapack.h: rename LAPACKungqr_ to LAPACKorgqr_

The intention is to be consistent with other subroutines like
LAPACKsyev_ where the 'real' name is used for both the 'real' subroutine
(_syev) and the 'complex' subroutine (_heev) depending on scalar-type

show more ...

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

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

try to fix error in eigen estimator

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/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

show more ...

Merge branch 'master' into knepley/feature-plex-pragmatic-parallel

* master: (1379 commits)
Minor fixes for tchem examples due to changes in PETSc infrastructure
update webpage about API changes

Merge branch 'master' into knepley/feature-plex-pragmatic-parallel

* master: (1379 commits)
Minor fixes for tchem examples due to changes in PETSc infrastructure
update webpage about API changes
add help menu for MatCreateSubMatricesMPI()
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
superlu: libray is installed in PREFIX/lib64 - fix this to use PREFIX/lib
backport fixes cc105cc3 2b35c90a - required for 3bf428d - that was backported from master - 80c96bb
'echo -n' fails on opensolaris/osx - so avoid using it.
fix diffs in nightlybuilds due to options in ~/.petscrc
add Kelley03 to src/docs/tex/petsc.bib
build: determine moudles, mpi.h used during buildtime and print in 'info'
fix analyzer warnings
fix build failure on opensolaris - where -lm from flibs is removed due to -lm in cxxlibs. But then - only flib gets used for some configure tests [blaslapack, parms]
config: prefer __restrict over C99 restrict keyword
...

show more ...

Merge branch 'barry/remove-funct'

Remove the use and definition of __FUNCT__ throughout the code

Since all modern C/C++ compilers provide this functionality we no longer need to provide it manually in PETSc
Time: 1.5 hours
Thanks-t

Remove the use and definition of __FUNCT__ throughout the code

Since all modern C/C++ compilers provide this functionality we no longer need to provide it manually in PETSc
Time: 1.5 hours
Thanks-to: Andreas Mang <andreas@ices.utexas.edu>

show more ...

Merge branch 'master' into stefano_zampini/feature-pcbddc-saddlepoint

This is needed to deal with some changes in MatNullSpace from commit 9d2471e

Merge branch 'master' into tisaac/dmplex-feature-real-to-ref

I need updated PetscFE interfaces in what I'm going to do

* master: (603 commits)
parmetis: fix typo in testsuite
Added PETSC_HAVE_A

Merge branch 'master' into tisaac/dmplex-feature-real-to-ref

I need updated PetscFE interfaces in what I'm going to do

* master: (603 commits)
parmetis: fix typo in testsuite
Added PETSC_HAVE_ATTRIBUTEALIGNED flag to makefile
PCSetUp_SVD() used incorrect matrix for matrix size in parallel, also need to skip LAPACK call if matrix size is zero
strumpack: update to latest version 1.0.4
Remove valgrind warning about MPI_Allreduce() with uninitialized data
sed for test output that has atol convergence with quad precision
updated ex1_nest tests
fixed incorrect key value
fix: bad merge a69d34a
test: move runex78 to TESTEXAMPLES_C_NOTSINGLE
build: fix warnings
sys: update test to produce same result - irrespective of debug/opt build - and presence of ~/.petscrc
sys: src/sys/examples/tests/ex30.c -> src/sys/examples/tests/ex32.c to avoid conflict in master
Sed output, since quad precision reduces below atol on these tests
remove automatically generated matrix names from test output files since can be different
Fixes for MatMPIXXXSetPreallocation(), they were not reentrant, since they kept the information used for matrix-vector products
GAMG: fix PCView_GAMG() format - and update output/ex56_0.out
superlu_dist: 64-bit-indices fix https://github.com/xiaoyeli/superlu_dist/issues/4
Add SNESSetDivergenceTolerance / -snes_divergence_tolerance.
fixed unit read in Plex
...

show more ...

Merge remote-tracking branch 'origin/mark/snes-ex56-b'

made threshold an array, fixed up ex56 convergence test (have a Plex/FEM bug)

Merge branch 'stefano_zampini/feature-convert-matnest-matis' into stefano_zampini/feature-pcbddc-saddlepoint

I have to merge it here, since there's an API addition for MatIS in stefano_zampini/featu

Merge branch 'stefano_zampini/feature-convert-matnest-matis' into stefano_zampini/feature-pcbddc-saddlepoint

I have to merge it here, since there's an API addition for MatIS in stefano_zampini/feature-pcbddc-saddlepoint
that prevents me to smoothly merge stefano_zampini/feature-convert-matnest-matis into next.

This will also facilitate merging stefano_zampini/feature-pcbddc-saddlepoint into master

Conflicts:
src/docs/website/documentation/changes/dev.html

show more ...

When suggesting options database items in error messages you must include the appropriate options prefix

Time: .05 hours
Reported-by: Sophie Blondel <sblondel@utk.edu>

Merge branch 'mark/gamg-aijtest'

added guards for AIJ requirement in GAMG

Merge branch 'tisaac/sys-fix-realloc' into tisaac/petscfe-matching-quadrature-order

* tisaac/sys-fix-realloc: (71 commits)
Sys: fix PetscTrReallocDefault() and PetscReallocAlign()
clearify when

Merge branch 'tisaac/sys-fix-realloc' into tisaac/petscfe-matching-quadrature-order

* tisaac/sys-fix-realloc: (71 commits)
Sys: fix PetscTrReallocDefault() and PetscReallocAlign()
clearify when MatMkl_CPardisoSetCntl() can be used in the manual pages
Fixed manual page for -snes_anderson_beta
Update zfftf.c
remove Hermitian information from output since it is only produced in complex case and thus produces different test output
fixes for 64 bit integers in test example, fix uninitialized variable in test example
tests: move runex49 to TESTEXAMPLES_C_NOTSINGLE
add a PCView_SVD to show parameters
-petscpartitioner_type simple was not being picked up by options thus generating test error
missing CHKERRQ(ierr) on PetscPrintf() statements in newly added test example
PetscViewerVTK: Move DM reference increment into the VTK viewer and out of the DM implementation, as suggested by Jed Brown
missing crosslinks between manual pages
Updated 3.7 release notes to clearly indicate how to update usage of KSP/SNES/TS/SetMonitor(xxx,XXXMonitorDefault,NULL,NULL);
Fix for commit b6480e041dd2293a65f96222772d68cdb4ed6306 that broke this example
Example of factorization of a singular matrix may actually work due to round off
removed unused variables
matshell: clean up and add some new MATOPs to Fortran.
Remove unneeded checks for use of the compressed row for diagonal block of matrices in GAMG
ptscotch: update to version 6.0.4
ptscotch: fix buggy pthread detection code on Mac/Linux
...

show more ...

Merge branch 'mark/snes-ex56'

Merged in mark/gamg-unused-vars (pull request #528)

removed unused variables

removed unused variables

Remove unneeded checks for use of the compressed row for diagonal block of matrices in GAMG

I cannot understand why these checks where not always triggered.

Time: .5 hours
Reported-by: Artur Safin

Remove unneeded checks for use of the compressed row for diagonal block of matrices in GAMG

I cannot understand why these checks where not always triggered.

Time: .5 hours
Reported-by: Artur Safin <aks084000@utdallas.edu>

show more ...

Merge branch 'tisaac/dmplex-fix-nonaffine-geom' into tisaac/petscfe-matching-quadrature-order

* tisaac/dmplex-fix-nonaffine-geom:
fixing Toby's fix
DMPlexComputeGeometryFEM(): clarify what is ex

Merge branch 'tisaac/dmplex-fix-nonaffine-geom' into tisaac/petscfe-matching-quadrature-order

* tisaac/dmplex-fix-nonaffine-geom:
fixing Toby's fix
DMPlexComputeGeometryFEM(): clarify what is expected if fe != NULL and correct computations accordingly
added checks for AIJ in MIS and GAMG
Bib: Added refs
loop upper bound was one too high
force runex22_4 to produce same output in __float128 precision where it wants to do one more timestep
remove duplicate .bib item, fix typos in .bib items
Fortran wrapper for DMGetType (copy-pasted from src/mat/interface/ftn-custom/zmatregf.c).
Variants of example also need to handle atol convergence with quad precision in test
Add rtol and atol to output of TSView ASCII
Fortran wrapper for MatNullSpaceGetVecs
MATIS: fix compiling error from nightly builds
MATIS: set block size if it is greater than zero
MATIS: added MatTranspose_IS
Quadrature: Fix creation init
Plex: Fix output optimization - We obviously have no test for this logic

show more ...