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Improve instrumentation support #4747

Merged
merged 10 commits into from
Jul 14, 2023
Merged

Improve instrumentation support #4747

merged 10 commits into from
Jul 14, 2023

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jngrad
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@jngrad jngrad commented Jun 28, 2023

Fixes #4740, fixes #2509

Description of changes:

  • third-party tools:
    • fix the broken Caliper integration and write an integration test
    • use standard Caliper macros instead of macro aliases
    • build Caliper as a CMake subproject to inherit options (e.g. CUDA and MPI support) and facilitate linking
    • add native support for CUDA-GDB (a few compiler flags were missing from Debug builds)
    • add native support for kernprof (new flag added to pypresso)
  • documentation:
    • centralize scattered information about debuggers into a self-contained section of the user guide
    • document all supported debuggers and profilers: Caliper, Valgrind, GDB, CUDA-GDB, kernprof, perf, sanitizers
    • make the Doxygen docs more consistent with the Sphinx user guide (same fonts) and website (same logo)

@jngrad
docs: Modernize visual identity
a76f62a 
Re-use Sphinx font families in Doxygen to fix kerning issues.
Use the modern ESPResSo logo in Doxygen. Cleanup BibTeX records.
@jngrad
docs: Centralize information about debuggers
28bd800
@jngrad
Rewrite Valgrind integration
33894d4
@jngrad
Rewrite Caliper integration
201abee 
* replace its Cython interface by a Python interface
* fix bug in the begin/end markers script interface
* use the original Caliper annotation macros
* build Caliper as a CMake subproject
* add integration tests
@jngrad
Add support for CUDA-GDB
0dde046
@jngrad
Add support for kernprof
2916f90
@jngrad
docs: Document all debuggers and profilers
3b516b4
@jngrad
docs: Cite third-party software
ad708fb
@jngrad jngrad force-pushed the instrumentation branch 4 times, most recently from cb95309 to ad708fb Compare June 28, 2023 15:40
@jngrad jngrad marked this pull request as ready for review June 28, 2023 16:21
@jngrad jngrad added this to the ESPResSo 4.3.0 milestone Jun 28, 2023
@jngrad jngrad requested a review from reinaual June 28, 2023 16:22
@jngrad
docs: Improve support for BibTeX containing macros
017ccbc 
Pybtex offers minimal support for LaTeX syntax in BibTeX records.
Using the plugin API, inject a visitor that expands LaTeX macros
that take only one argument. Doxygen doesn't support plugins, so
sed expressions are used to post-process the final bibliography.
@jngrad jngrad requested a review from RudolfWeeber July 11, 2023 07:55
RudolfWeeber
RudolfWeeber previously approved these changes Jul 13, 2023
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Thank you. In particular, the very extensive documentation will be helpful to developers sorting out performance issues.

@jngrad jngrad added the automerge Merge with kodiak label Jul 13, 2023
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kodiakhq bot commented Jul 13, 2023

This PR currently has a merge conflict. Please resolve this and then re-add the automerge label.

@kodiakhq kodiakhq bot removed the automerge Merge with kodiak label Jul 13, 2023
@jngrad jngrad added the automerge Merge with kodiak label Jul 13, 2023
@jngrad jngrad requested a review from RudolfWeeber July 13, 2023 18:56
reinaual
reinaual approved these changes Jul 14, 2023
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reviewed the merge commit only

@kodiakhq kodiakhq bot merged commit 4c03ac4 into espressomd:python Jul 14, 2023
5 checks passed
@jngrad jngrad deleted the instrumentation branch July 14, 2023 08:26
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@reinaual reinaual reinaual approved these changes

@RudolfWeeber RudolfWeeber Awaiting requested review from RudolfWeeber

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automerge Merge with kodiak BugFix CMake Documentation New Feature Testcase
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Successfully merging this pull request may close these issues.

Caliper bindings are broken Add documentation for Caliper
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@jngrad @RudolfWeeber @reinaual