No longer initialize PetscDevice greedily with -log_view (to front load handle costs), instead have separate log events for them

Merge branch 'barry/2022-06-28/rm-view-object-memory' into 'main'

Remove the view of object memory in -log_view since it is usually very wrong !3143

See merge request petsc/petsc!5378

Remove the view of object memory in -log_view since it is usually very wrong !3143

Also add comments in the code where object memory information is stored and collecting indicating
for developers it

Remove the view of object memory in -log_view since it is usually very wrong !3143

Also add comments in the code where object memory information is stored and collecting indicating
for developers it is unreliable. We cannot rely on developer's personal memory for this type of knowledge.

Commit-type: bug-fix, housekeeping
/spend 15m
Reported-by: Patrick Sanan <patrick.sanan@gmail.com>

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Merge branch 'barry/2022-05-03/cleanup-makefiles' into 'main'

remove unneeded stuff from makefiles

See merge request petsc/petsc!5211

Get values of makefile SOURCE etc from the file system instead of makefiles

Use SUBMANSEC from include files for manual sections instead of the makefile

Unfortunately this has to be one large commi

Get values of makefile SOURCE etc from the file system instead of makefiles

Use SUBMANSEC from include files for manual sections instead of the makefile

Unfortunately this has to be one large commit since the changes all have to be done at once

Commit-type: docs
/spend 10m

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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 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 '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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rewrote the PetscLL macros as functions to let the linter understand them. Also helps
reduce the staggering amount of code duplication in Mat

chkerr and friends wrapped

Merge branch 'wence/fix/log-is-active' into 'main'

Fix PetscLogIsActive for !PETSC_USE_LOG case

See merge request petsc/petsc!4985

Fix PetscLogIsActive for !PETSC_USE_LOG case

If !PETSC_USE_LOG then PetscLogIsActive should set the flag argument
to PETSC_FALSE, rather than leaving it unset, since it is an output
argument.

Merge branch 'connorjward/petsc4py-addlogisactive' into 'main'

petsc4py: Add Log.getActive function

See merge request petsc/petsc!4847

Add PetscLogIsActive

Merge branch 'dalcinl/fix-PetscInfo3' into 'main'

Fix definition of PetscInfo3

See merge request petsc/petsc!4846

Fix definition of PetscInfo3

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()

deprecate PETSC_STATIC_INLINE

apply PetscAssertFalse() -> PetscAssert() transformation to headers

add PetscAssert() and PetscAssertFalse()

make PetscInfo() variadic