Typos

Merge branch 'jolivet/fix-more-typos' into 'master'

Fix more typos and add missing examples

See merge request petsc/petsc!2511

Fix more typos and add missing examples

Merge remote-tracking branch 'origin/maint'

Merge branch 'barry/2020-02-04/fix-log-view-memory' into 'maint'

Fixed broken -log_view_memory and added a test

See merge request petsc/petsc!2504

Fixed broken -log_view_memory and added a test

Commit-type: bug-fix, testing-fix

Merge branch 'master' into 'barry/2019-08-22/fix-fblaslapack-for-nag'

# Conflicts:
# lib/petsc/conf/test

Merge branch 'barry/2019-09-04/feature-nan-malloc' into 'master'

Add code to initialize PetscMalloc() memory with Nan. Simplify and clarify the...

See merge request petsc/petsc!2017

Fixed spelling mistakes, removed out-dated references to PetscMalloc() options and functions, added PetscMalloc() changes to dev.html

Commit-type: style-fix, documentation
Reported-by: Jed Brown <je

Fixed spelling mistakes, removed out-dated references to PetscMalloc() options and functions, added PetscMalloc() changes to dev.html

Commit-type: style-fix, documentation
Reported-by: Jed Brown <jed@jedbrown.org>

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Remove extra 0x in front of hexadecimal number

Commit-type: bug-fix
Reported-by: gitlab-ci

Add code to initialize PetscMalloc() memory with Nan. Simplify and clarify the options for controlling PetscMalloc() debugging.

This now trivially detects an error that lay undetected in ts/examples

Add code to initialize PetscMalloc() memory with Nan. Simplify and clarify the options for controlling PetscMalloc() debugging.

This now trivially detects an error that lay undetected in ts/examples/tutorials/multistage/ex5.c for months

Commit-type: style-fix, feature, documentation

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Merge branch 'barry/2019-07-21/fix-petscmallocvalidate-checkmumpshermetian' [PR #1899]

* barry/2019-07-21/fix-petscmallocvalidate-checkmumpshermetian:
Mumps no Cholesky with Hermitian, no PetscMallo

Merge branch 'barry/2019-07-21/fix-petscmallocvalidate-checkmumpshermetian' [PR #1899]

* barry/2019-07-21/fix-petscmallocvalidate-checkmumpshermetian:
Mumps no Cholesky with Hermitian, no PetscMallocValidate() unless -malloc_*, example used PetscAbsScalar() on real
Mumps has no support for Cholesky for Hermitian matrix so document and error check Documentation says CHKMEMQ() and PetscMallocValidate() with -malloc_debug or -malloc_test but in fact it still checked memory even without those being set (slowing code)
Example used PetscAbsScalar() on real values, also had incorrect indentation formating

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Mumps no Cholesky with Hermitian, no PetscMallocValidate() unless -malloc_*, example used PetscAbsScalar() on real

Mumps has no support for Cholesky for Hermitian matrix so document and error check

Mumps no Cholesky with Hermitian, no PetscMallocValidate() unless -malloc_*, example used PetscAbsScalar() on real

Mumps has no support for Cholesky for Hermitian matrix so document and error check
Documentation says CHKMEMQ() and PetscMallocValidate() with -malloc_debug or -malloc_test but in fact
it still checked memory even without those being set (slowing code)
Example used PetscAbsScalar() on real values, also had incorrect indentation formating

Commit-type: testing-fix, style-fix, documentation, example

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Merged in barry/optimize-aij-da (pull request #1762)

Non-numeric optimizations focused on AIJ, MatFDColoring, and DMCreateMatrix_DA_*AIJ, looking to improve performance in GPU environments

Non-numeric optimizations focused on AIJ, MatFDColoring, and DMCreateMatrix_DA_*AIJ, looking to improve performance in GPU environments

1) PetscCalloc*() now uses system calloc()
2) Merged some Pets

Non-numeric optimizations focused on AIJ, MatFDColoring, and DMCreateMatrix_DA_*AIJ, looking to improve performance in GPU environments

1) PetscCalloc*() now uses system calloc()
2) Merged some PetscMalloc*()
3) Eliminated unneeded PetscCalloc*()
4) Removed some memory allocations and copies in MatFDColoringSetUp(), added local variables for better compiler optimization
5) Added MatSetValues_SeqAIJ_SortedFull(), added MatSetOption(MAT_SORTED_FULL)
6) Optimized DMCreateMatrix_DA_*AIJ for nonperiodic case to automatically have sorted columns (faster MatSetValues() times)
7) Eliminated call to PetscMemzero() in PetscFree()

Commit-type: style-fix, feature

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Merge remote-tracking branch 'origin/psanan/docs-remove-manconcepts' [PR #1733]

Man pages: remove Concepts: fields

These fields were previously stripped from the man pages by logic removed in
21a59cba2737d49dc2f0bd12c08db0d2a3f3f209

Remove these fields from all man pages (but

Man pages: remove Concepts: fields

These fields were previously stripped from the man pages by logic removed in
21a59cba2737d49dc2f0bd12c08db0d2a3f3f209

Remove these fields from all man pages (but not from examples).

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 -not -path "*/examples/*" -not -name "*.html" -not -name "*.bib" -exec gsed -i '/Concepts:/ {N; /\n\s*$/d}' {} +
find src -type f -not -path "*/examples/*" -not -name "*.html" -not -name "*.bib" -exec gsed -i '/Concepts:/d' {} +
find include -type f -not -path "*/examples/*" -not -name "*.html" -not -name "*.bib" -exec gsed -i '/Concepts:/ {N; /\n\s*$/d}' {} +
find include -type f -not -path "*/examples/*" -not -name "*.html" -not -name "*.bib" -exec gsed -i '/Concepts:/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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Merged in barry/log-memory (pull request #1677)

Introduce logging of memory usage to the PETSc event logging infrastructure.

Introduce logging of memory usage to the PETSc event logging infrastructure.

The logging can be turned on and viewed with the options -log_view -log_view_memory

The logging requires the use of the

Introduce logging of memory usage to the PETSc event logging infrastructure.

The logging can be turned on and viewed with the options -log_view -log_view_memory

The logging requires the use of the PETSc malloc so may slow the runs slightly but since it is not
doing error checking of the memory it should not slow down the computations significently.

Four pieces of information about memory are logged and display in four additional columns in the table.
They are documented in the output above the table. Each column provides a particular "view" of the
memory usage in the event and they complement each other.

This should make it much easier for developers focusing on memory usage in their implementations
to understand the usage in the code, where the memory is being utilized, how it scales with problem size and number of processes etc.

Commit-type: feature

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Merge branch 'master' into wence/feature-patch-all-at-once

Merge branch 'dalcinl/plex-gmsh-v4' [PR #1348]

* dalcinl/plex-gmsh-v4:
Adds DMPlex Gmsh v4 file format support

Sys: Fix PetscTrReallocDefault() to handle NULL pointers

Merged petsc/petsc into master

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

* master: (984 commits)
netcdf: set zlib as optional dependency corretly [wrt --enable-netcdf-4] - otherwise netcdf configure errors out

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

* master: (984 commits)
netcdf: set zlib as optional dependency corretly [wrt --enable-netcdf-4] - otherwise netcdf configure errors out
fix gcov obj path
-options_table was changed to options_view in 2014 but documentation was not updated to reflect it
configure: fix F2003 test
Dev manual: remove duplicate entry
Plex test ex5: Removed "future" test, as it resulted in issues in the nightly tests.
Some minor typos in TS
Add ADIOS2.py which I forgot to git add in the past
Plex ex5: Disable test
Doc: Added note for interface change
KSPLSQRMonitorDefault fixed for quad precision
Tao: Added alternative output for chwirut2 test.
TS ex45,ex46: Removed overly refined tests for faster nightly tests.
KSP ex72: Fixed needlessly long-running PCTFS tests.
SNES ex56: Reduced test size to speed up nightly test suite.
KSPSolve_LSQR: don't compute unused norm of rhs
SNES ex13: Reduced problem sizes for nightly tests.
PetscOptionsDeprecated(): fix for NULL prefix
PetscOptionsDeprecated(): add option to print additional info
SNES ex12: Reduced sizes for BDDC tests.
...

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Merge branch 'master' into knepley/feature-plex-elasticity-test

* master: (1553 commits)
-options_table was changed to options_view in 2014 but documentation was not updated to reflect it
config

Merge branch 'master' into knepley/feature-plex-elasticity-test

* master: (1553 commits)
-options_table was changed to options_view in 2014 but documentation was not updated to reflect it
configure: fix F2003 test
Plex test ex5: Removed "future" test, as it resulted in issues in the nightly tests.
Some minor typos in TS
Add ADIOS2.py which I forgot to git add in the past
Plex ex5: Disable test
Doc: Added note for interface change
KSPLSQRMonitorDefault fixed for quad precision
Tao: Added alternative output for chwirut2 test.
TS ex45,ex46: Removed overly refined tests for faster nightly tests.
KSP ex72: Fixed needlessly long-running PCTFS tests.
SNES ex56: Reduced test size to speed up nightly test suite.
KSPSolve_LSQR: don't compute unused norm of rhs
SNES ex13: Reduced problem sizes for nightly tests.
PetscOptionsDeprecated(): fix for NULL prefix
PetscOptionsDeprecated(): add option to print additional info
SNES ex12: Reduced sizes for BDDC tests.
PetscFileRetrieve(): Suppress output to STDERR when downloading a file.
MatMatMult: Fixed unused variable pN.
DMDestroy: Guard call to dm->ops->destroy * Similar guards are in place in many other methods (IS,Vec,Mat) and permit the DM to be destroyed even if DMSetType() was never called.
...

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