Merge branch 'jolivet/rm-explicit-empty-output_file' into 'main'

Remove 535 empty .out and consolidate the use of output/empty.out

See merge request petsc/petsc!8538

Remove explicitly listed empty files and switch to output/empty.out

Merge remote-tracking branch 'origin/release'

Merge branch 'tisaac/fix-log-view-multiple' into 'release'

Logging: Account for multiple log viewers in final checks (with new test)

See merge request petsc/petsc!8301

Logging: Account for multiple log viewers in final checks (with new test)

PetscLogHandlerView_Default_Info() wants to be sure that the only objects still in existence
at the end are the viewers for

Logging: Account for multiple log viewers in final checks (with new test)

PetscLogHandlerView_Default_Info() wants to be sure that the only objects still in existence
at the end are the viewers for the log handlers: this commit creates globals to keep track of
how many of these have been created and destroyed.

sys_tests-ex30_11 and sys_tests-ex30_12 test this functionality

Reported-by: Jed Brown <jed@jedbrown.org>
Co-authored-by: Jed Brown <jed@jedbrown.org>
Helped-by: Pierre Jolivet <pierre@joliv.et>

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Merge branch 'jolivet/remove-cast' into 'main'

Use NULL or nullptr instead of casted 0

See merge request petsc/petsc!7857

Use NULL or nullptr instead of casted 0

Merge branch 'tisaac/bugfix-sfwindow' into 'main'

Add PetscSFRegisterPersistent() and fix PETSCSFWINDOW for empty ranks

See merge request petsc/petsc!7786

Logging: tweak ex30 test to avoid reduce regressions due to time variabiity in CI

sys/tests/ex30_1 produces flamegraph output, which is sorted by (inclusive time)

It has two stages which should tak

Logging: tweak ex30 test to avoid reduce regressions due to time variabiity in CI

sys/tests/ex30_1 produces flamegraph output, which is sorted by (inclusive time)

It has two stages which should take 0.5 and 0.3 seconds, but in CI there is enough noise in the runtime that
the order of the stages will reverse. This lengthens the first stage to 0.7 seconds, which will reduce the
number of false positives that are created.

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Merge branch 'jolivet/rm-first-empty-line' into 'main'

Remove first and last empty lines

See merge request petsc/petsc!6892

Remove first and last empty lines

Merge branch 'tisaac/feature-log-nvtx' into 'main'

Profiling: Create PETSCLOGHANDLERNVTX (`-log_view` no longer required for Nsight ranges)

See merge request petsc/petsc!6884

Profiling: Create PETSCLOGHANDLERNVTX

Merge branch 'tisaac/feature-log-handler' into 'main'

Deglobalize logging into PetscLogHandler and PetscLogState

See merge request petsc/petsc!6709

Config: add configure test for PETSC_HAVE_LINUX

This would be redundant with __linux__ in a source file, but
is useful for allowing the test suite to have
'requires: linux'

Profiling: add flag for testing threadsafe data structures

We don't have coverage tests with PETSC_HAVE_THREADSAFETY, so
this flag allows us to test the data structures even without
it.

Profiling: Add tests of PetscLogHandler to sys/tests/ex30.c

- The pattern of events and stages is made more complicated
to test the fact that nested logging can represent nested
stages now.

- T

Profiling: Add tests of PetscLogHandler to sys/tests/ex30.c

- The pattern of events and stages is made more complicated
to test the fact that nested logging can represent nested
stages now.

- To test perfstubs without adding TAU as an optional dependency,
a dummy perfstubs tool implementation is tested.

New tests:

- 0: tests the fact that events and stages can be registered
in different orders for different processes (at least
for the default log handler: this is not true of all external tools
like MPE)

- 1: Test flamegraph (nested log handler)

- 2: Test trace log handler

- 3: Test PetscLogDump() output with actions and objects logging
Note that this test uses the "temporaries:" test key for the
dump file Log.0

- 4: Test CSV output

- 5: Test MPE log handler
MPE logging creates a .clog2 binary file. Without trying
to add a dependency to turn it into text, if we use
`strings` we can at least see if the names of the events
created in the test are in the file

- 6: Test perfstubs
Because this relies on dlsym(RTLD_DEFAULT, ...) dynamic linking, this
test can only be run on linux

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Merge branch 'jacobf/2022-09-21/2-bike-2-shed' into 'main'

Feature: Bicycle Storage Facility 2

See merge request petsc/petsc!5661

source code format changes due to .clang-format changes

Merge branch 'barry/2022-08-21/clang-format-source' into 'main'

format repository with clang-format

See merge request petsc/petsc!5541

clang-format: convert PETSc sources to comply with clang-format

Merge branch 'barry/2022-07-23/add-petscbeginuser' into 'main'

Add PetscFunctionBeginUser to all PETSc C/C++ examples

See merge request petsc/petsc!5470

Add PetscFunctionBeginUser to all PETSc C/C++ examples

Now the stack frames will contain the main program and the correct line numbers in them

git ls-files | egrep "(tutorials|tests)" | xargs sed -

Add PetscFunctionBeginUser to all PETSc C/C++ examples

Now the stack frames will contain the main program and the correct line numbers in them

git ls-files | egrep "(tutorials|tests)" | xargs sed -i "s?\(PetscCall(PetscInitialize(&argc\)?PetscFunctionBeginUser;\n \1?g"

Commit-type: error-checking, testing-fix
/spend 15m

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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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