batch solver in bjacobi allow batched solver w/o field major ordering, fixed up timers in Landau

Merge branch 'stefanozampini/hara-to-h2opus-rebased-v7' into 'main'

Update distributed hierarchical matrix package H2Opus

See merge request petsc/petsc!4347

Update H2 package

Merge branch 'tisaac/feature-spqr' into 'main'

Implement interface to SuiteSparseQR (SPQR) sparse direct QR factorization.

See merge request petsc/petsc!3976

Implement interface to SuiteSparseQR (SPQR) sparse direct QR factorization.

Merge branch 'jolivet/feature-bamg-hpddm-shared-libraries-0' into 'main'

configure: minor improvements for BAMG and HPDDM --with-shared-libraries=0

See merge request petsc/petsc!3744

PCHPDDM: no compilation --with-shared-libraries=0

Merge branch 'stefanozampini/feature-add-hpackages-rebased' into 'master'

Fixes to MatProduct + many bug fixes + new hierarchical matrix support

See merge request petsc/petsc!2800

PCHARA: class for preconditioners for H-matrices

Merge remote-tracking branch 'origin/maint'

Merge branch 'jolivet/fix-documentation' into 'maint'

Typos + nonexistent functions + "Not yet cataloged"

See merge request petsc/petsc!2527

Typos+nonexistent functions+"Not yet cataloged"

Merge branch 'master' into 'master'

Add --download-hpddm

See merge request petsc/petsc!1994

--download-hpddm for PCHPDDM and KSPHPDDM

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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init commit

Merged in Fande-Kong/feature_hmg (pull request #1682)

Hybrid of PETSc preconditioners (such as ASM, BJacobi, SOR, etc.) and Hypre BoomerAMG

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

HMG should work without hypre as well.

Implemented an AMG that uses Hypre to coarsen matrix

and generate a sequence of coarse matrices. These coarse
matrices are used to setup a PETSc PCMG.

There are two benefits:

(1) We can use any PE

Implemented an AMG that uses Hypre to coarsen matrix

and generate a sequence of coarse matrices. These coarse
matrices are used to setup a PETSc PCMG.

There are two benefits:

(1) We can use any PETSc preconditioners such as ASM, BJacobi as
level smoothers (solvers). For some applicaitons, the combination
of ASM and AMG works great while only AMG or AMS does not work at all.

(2) For multicomponent problems, we could just coarsen one submatrix
associated with one particular component. In this way, the setup of the
preconditioner is significantly improved. One typical use case is
neutron transport equations. There are many variables on each mesh
vertex due to the discretization of angle and energy. Each variable,
in fact, corresponds to the same PDEs but with different material
properties.

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Merged in psanan/man-pages-remove-keywords (pull request #1717)

Man pages: Remove .keywords fields

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

Man pages: remove .keywords: fields

This field is recognized by doctext from Sowing (http://wgropp.cs.illinois.edu/projects/software/sowing/doctext/node20.htm#Node20),
but it doesn't seem to be unif

Man pages: remove .keywords: fields

This field is recognized by doctext from Sowing (http://wgropp.cs.illinois.edu/projects/software/sowing/doctext/node20.htm#Node20),
but it doesn't seem to be uniformly used or maintained.

Thus, remove all .keywords: fields, and a following blank line, if present.

This is accomplished with GNU sed (gsed on OS X), with the following commands.
*Warning* that this type of command can corrupt a .git directory,
so be cautious in reusing or modifying these commands. They first look
for and delete matching lines with a following line consisting of only whitespace,
and then delete any remaining matching lines.

find src/ -type f -exec gsed -i '/keywords:/ {N; /\n\s*$/d}' {} +
find src/ -type f -exec gsed -i '/keywords:/d' {} +
find include/ -type f -exec gsed -i '/keywords:/ {N; /\n\s*$/d}' {} +
find include/ -type f -exec gsed -i '/keywords:/d' {} +

Hints on the sed command obtained from: https://unix.stackexchange.com/questions/100754/how-to-delete-a-specific-line-and-the-following-blank-line-using-gnu-sed

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Merge branch 'master' into jpusztay/feature-swarm-symplectic-example

Merge branch 'master' into jpustay/feature-swarm-example

Merged petsc/petsc into master

Merged petsc/petsc into master