Fix incorrect documentation on -error_output_stdout

/spend 3m

Merge branch 'psanan/docs-sphinx-man-pages' into 'main'

Integrate Man Pages into Sphinx Docs

Closes #1132 and #1015

See merge request petsc/petsc!4989

Docs: bulk add backticks to .seealso man page fields

```python
import os
import re
import fileinput

def _process_word(word):
comma = "," if word.endswith(",") else ""
return "`%s`%s" % (wor

Docs: bulk add backticks to .seealso man page fields

```python
import os
import re
import fileinput

def _process_word(word):
comma = "," if word.endswith(",") else ""
return "`%s`%s" % (word.rstrip(","), comma)

def _process_stripped_line(line):
return " ".join(map(_process_word, line.split()))

start_pattern = re.compile(r"^( *\.seealso:? )(.*$)")

def process_file(filename_full):
with fileinput.FileInput(filename_full, inplace=True) as f:
in_block = False
for line in f:
line_stripped = line.strip()
# end ".seealso blocks" on a blank line or C-style comment close
line_modified = None
if not line_stripped:
in_block = False
elif line_stripped.endswith("*/"):
in_block = False
else:
match = re.match(start_pattern,
line) # not stripped line
if match:
indent = " " * len(match.group(1))
in_block = True
line_modified = match.group(
1) + _process_stripped_line(
match.group(2).strip())
elif in_block:
line_modified = indent + _process_stripped_line(
line_stripped)
if line_modified:
print(line_modified) # prints to the file
else:
print(line, end="") # prints to the file

BASE_DIRS = ["src", "include"]
EXT = [".c", ".cxx", ".cpp", ".cu", ".h", ".hpp", ".hxx"]
EXCLUDE_DIRS = ["tests", "tutorials", "ftn-auto", "ftn-custom", "benchmarks"]

def main():
""" Process everything """
for base in BASE_DIRS:
for root, dirs, files in os.walk(base):
for filename in files:
if os.path.splitext(filename)[1] in EXT:
filename_full = os.path.join(root, filename)
print("FILE ---", filename_full)
process_file(filename_full)
for exclude_dir in EXCLUDE_DIRS:
if exclude_dir in dirs:
dirs.remove(exclude_dir)

if __name__ == "__main__":
main()
```

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Merge remote-tracking branch 'origin/release'

Merge branch 'balay/u2204-fixes' into 'release'

Some fixes for ubuntu-22.04

See merge request petsc/petsc!5159

gcov: newer versions of gcc use __gcov_dump() instead of __gcov_flush()

Merge branch 'barry/2022-03-30/turnoff-gpu-timing' into 'main'

Add support for -log_view with GPUs that does not time the kernels on the GPU

See merge request petsc/petsc!5056

Add support for -log_view with GPUs that does not time the kernels on the GPU

Adds -log_view_gpu_time

This is useful to get high-level times for the solvers without the overhead of
needing synchron

Add support for -log_view with GPUs that does not time the kernels on the GPU

Adds -log_view_gpu_time

This is useful to get high-level times for the solvers without the overhead of
needing synchronizations for GPU kernels

This means the times for any asynchronize operations, like most vector and matrix operations
in the -log_view will be incorrect.

Have -log_view display fields related to event time displayed appropriately with NaN when runn on the GPUs without synchronization to ensure correct times

Commit-type: timing
/spend 55m
Reported-by: Jed Brown <jed@jedbrown.org>

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Merge branch 'barry/2022-04-01/fix-petsc-options-begin-end/release' into 'main'

Remove bogus error returns from Begin/End() macros

See merge request petsc/petsc!5069

Cleanup of introduction of PetscCall()

* remove bogus error flags from XXXBegin()/End() macros such as PetscOptionsBegin()/End()

* rename for consistency certain XXXBegin()/End() macros such as Mat

Cleanup of introduction of PetscCall()

* remove bogus error flags from XXXBegin()/End() macros such as PetscOptionsBegin()/End()

* rename for consistency certain XXXBegin()/End() macros such as MatPreallocateInitialize()/Finalize()

* fix many lingering ierr = XXX that arose from multiline function calls

* sync slepc/hpddm - to use snapshots with the same changes

Commit-type: error-checking, style-fix
/spend 8h

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release: set petsc v3.17.0 strings

Merge branch 'barry/2022-03-30/fix-mpiu_allreduce' into 'main'

Fix mpiu_allreduce to always return PetscErrorCodes, never MPI error codes

See merge request petsc/petsc!5052

Fix mpiu_allreduce to always return PetscErrorCodes, never MPI error codes

Both for debug and optimized builds

Also removes shadow declaration errors from use of mpiu_allreduce

Commit-type: error-

Fix mpiu_allreduce to always return PetscErrorCodes, never MPI error codes

Both for debug and optimized builds

Also removes shadow declaration errors from use of mpiu_allreduce

Commit-type: error-checking
Reported-by: Lisandro Dalcin <dalcinl@gmail.com>

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Merge remote-tracking branch 'origin/release'

Merge branch 'prj--release-patch-68573' into 'release'

Update pinit.c

See merge request petsc/petsc!5027

Update pinit.c

Merge branch 'jacobf/2022-02-23/variadic-chkerr' into 'main'

Variadic CHKERRQ()

See merge request petsc/petsc!4889

The great renaming:

- CHKERRQ() -> PetscCall()
- CHKERRV() -> PetscCallVoid()
- CHKERRMPI() -> PetscCallMPI()
- CHKERRABORT() -> PetscCallAbort()
- CHKERRCONTINUE() -> PetscCallContinue()
- CHKERRXX

The great renaming:

- CHKERRQ() -> PetscCall()
- CHKERRV() -> PetscCallVoid()
- CHKERRMPI() -> PetscCallMPI()
- CHKERRABORT() -> PetscCallAbort()
- CHKERRCONTINUE() -> PetscCallContinue()
- CHKERRXX() -> PetscCallThrow()
- CHKERRCXX() -> PetscCallCXX()
- CHKERRCUDA() -> PetscCallCUDA()
- CHKERRCUBLAS() -> PetscCallCUBLAS()
- CHKERRCUSPARSE() -> PetscCallCUSPARSE()
- CHKERRCUSOLVER() -> PetscCallCUSOLVER()
- CHKERRCUFFT() -> PetscCallCUFFT()
- CHKERRCURAND() -> PetscCallCURAND()
- CHKERRHIP() -> PetscCallHIP()
- CHKERRHIPBLAS() -> PetscCallHIPBLAS()
- CHKERRHIPSOLVER() -> PetscCallHIPSOLVER()
- CHKERRQ_CEED() -> PetscCallCEED()
- CHKERR_FORTRAN_VOID_FUNCTION() -> PetscCallFortranVoidFunction()
- CHKERRMKL() -> PetscCallMKL()
- CHKERRMMG() -> PetscCallMMG()
- CHKERRMMG_NONSTANDARD() -> PetscCallMMG_NONSTANDARD()
- CHKERRCGNS() -> PetscCallCGNS()
- CHKERRPTSCOTCH() -> PetscCallPTSCOTCH()
- CHKERRSTR() -> PetscCallSTR()
- CHKERRTC() -> PetscCallTC()

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Make error handling when PetscErrorHandlingInitialized is not yet set more sane:

- set it at the top of PetscInitialize_Common()
- PetscError() now checks it before doing anything, if not initialize

Make error handling when PetscErrorHandlingInitialized is not yet set more sane:

- set it at the top of PetscInitialize_Common()
- PetscError() now checks it before doing anything, if not initialized, just return error
code
- CHKERRQ() and friends can now be used anywhere
- Use CHKERRQ() and in PetscOptions and friends

show more ...

pluck ~1000 low hanging PetscCheckFalse() -> PetscCheck() fruit

chkerr and friends wrapped

Merge branch 'jczhang/feature-remove-some-mpi2.1-checks' into 'main'

Remove some MPI-2.1 checks

See merge request petsc/petsc!4965

MPI: remove PETSC_HAVE_MPI_FINALIZED of MPI-2.1

Merge branch 'jacobf/2022-01-05/c99' into 'main'

Feature: C99 and C++11

See merge request petsc/petsc!4700

rename PetscAssert() -> PetscCheck() and PetscAssertDebug() -> PetscAssert()