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Merged
merged 160 commits into from
Mar 13, 2025
Merged

Improve build and tests and add CI #36

merged 160 commits into from
Mar 13, 2025

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tdrwenski
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@tdrwenski tdrwenski commented Feb 25, 2025 •
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The goal of this PR is to improve the build process, tests, and add continuous integration (CI) so the build and tests can be automatically run on LC machines for each PR.

Build

  • uses CMake instead of make and BLT (RADIUSS project) to make CMake config easy
  • (optionally) Spack to make it easier to build Quandary with different architectures. Spack can install necessary libraries liek petsc and slepsc for you, and makes it easy to have multiple versions and variants of these. Spack can also build Quandary itself by using CMake. Spack is especially useful for running the CI.

Tests

  • run existing regression tests using pytest. This has nice built in options for running the tests. The comparison between output and expected output is done using a pandas comparison with a tolerance.

  • Updates to existing tests:

    • add quotes around column names and update output accordingly
    • Stefanie added/removed some tests to make sure all test cases were covered

CI

  • uses radiuss-spack-configs and uberenv (RADIUSS projects) to help set this up
  • Add continuous integration pipeline in GitLab (mirror of this repo) so that build and tests can be automatically run on different LC platforms.
  • This includes running with different compilers (clang, gcc), different architectures, and GPU versions of PETc for Rocm and cuda (may be useful in the future)
  • This pipeline will be run on every (non-draft) PR

Many files were changed (mostly related to the tests) so I realize it is a bit hard to review. I would especially appreciate feedback on the following:

  • README.md and tests/README.md
  • Testing the steps in the README such as building quandary, and running the tests, and running the python interface to see if the steps are clear

tdrwenski added 30 commits January 2, 2025 14:42
@tdrwenski
Add BLT as submodule
f9cc165
@tdrwenski
Use CMake for build
d6dc6c9
@tdrwenski
Add spack.yaml to project to define and install dependencies
219b442
@tdrwenski
Update gitignore rules
b6e39cf
@tdrwenski
Add spack develop and package.py
aa2b6e7
@tdrwenski
Ignore spack build files
3689e2b
@tdrwenski
Use BLT for MPI dependency
0727a0b
@tdrwenski
Use petsc in debug mode for development
f7b86c1
@tdrwenski
Add binary mirror to spack environment
734c6a6
@tdrwenski
Update README with more info about building with spack
e92485e
@tdrwenski
Add spack compiler step to readme
1757285
@tdrwenski
Update default quandary and petsc build settings in spack
b2d9ba1
@tdrwenski
Add BLT link to readme
b996189
@tdrwenski
Add info about spack build options to readme
6e0f150
@tdrwenski
Port bash test runner to pytest
0b37ef8
@tdrwenski
Add one gitignore for test dir and remove gitignores from data_out an…
37e3287 
…d result directories so its easier to clean these
@tdrwenski
Rebase optim_history.dat files as the column names and number have ch…
0daa06a 
…anged
@tdrwenski
Add pandas dataframe comparison instead of custom comparison
644ad1e
@tdrwenski
Add quotes to data header output files and update base files
4ceba85
@tdrwenski
Use constant for dir names
c7562eb
@tdrwenski
Remove bash and custom comparison version of tests
ffd0cd6
@tdrwenski
Move test cases to json and add a number of processing option to pass…
a0ee516 
… to mpirun
@tdrwenski
Add json schema to tests
8ad1dac
@tdrwenski
Improve test names
e223537
@tdrwenski
Update test readme
e1d1e37
@tdrwenski
Add bash script for rebasing tests
6251d69
@tdrwenski
Add pycache to gitignore
7f13bea
@tdrwenski
Sort imports
e546515
@tdrwenski
Improve constant names
c36dd8a
@tdrwenski
Use pydantic instead of jsonschema for test case validation
85ff43c
tdrwenski and others added 27 commits March 3, 2025 09:26
@tdrwenski
Re-enable /dev/shm/ on ruby and only use one node to avoid errors
c35babe
@tdrwenski
Allow matplotlib 3.9.0
29e097c
@tdrwenski
Remove no longer needed venv creation step (use spack venv)
11b6418
@tdrwenski
Update poetry.lock to reflect new matplotlib range
7888556
@tdrwenski
Move quandary spack package to radiuss-spack-configs
26e4b21
@steffi7574
Remodelling Readme.md overhaul.
c901b27 
* Removed all Slepsc mentions
* Improve introduction section
* Reorganize content building without spack.
@steffi7574
Another minor Readme.md update.
c721d80
@steffi7574
Another minor Readme.md update.
4df3bc0
@tdrwenski
Update radiuss-spack-configs to use main instead of master
3c0e05f
@tdrwenski
Add github workflow for mac os
3b3a755
@tdrwenski
Allow mpirun to oversubscribe so all test cases can be run on github …
d3d488e 
…actions
@tdrwenski
Fix typo
3963447
@tdrwenski
Remove commented out section
0611be3
@steffi7574
Mini fix for Readme typo.
458dfc9
@tdrwenski
Allow mpi options (like oversubscribe) to be passed in to the tests
299241a
@tdrwenski
Use oversubscribe in when running mpi in GitHub workflow tests
2171671
@tdrwenski
Use llnl namespace for ghcr for spack cache
f510d0d
@tdrwenski
Revert "Use llnl namespace for ghcr for spack cache"
c548ef2 
This reverts commit f510d0d.
@tdrwenski
Remove poetry lock file
18e0c32
@tdrwenski
Use version 4.1 in pyproject
00fc66c
@tdrwenski
Remove unit_tests until we write some useful ones
d15fb80
@tdrwenski
Rename test folder to regression_tests
26dda87
@tdrwenski
Update pytest command in CI
eb55640
@tdrwenski
Move scripts folder to .ci-scripts and update paths
770bf3f
@tdrwenski
Update compile and test instructions in documentation
a256080
@tdrwenski
Fix typo
0809264
@steffi7574
Updating python interface examples headers.
4ed9211
@tdrwenski tdrwenski merged commit 2ac75cd into main Mar 13, 2025
5 checks passed
@tdrwenski tdrwenski deleted the improve-build-test-ci branch March 13, 2025 23:31
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@adrienbernede adrienbernede adrienbernede left review comments

@steffi7574 steffi7574 steffi7574 approved these changes

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@tdrwenski @LostLittlePrince @steffi7574 @adrienbernede