JP-3698: Fixed Memory Leak in Ramp Fitting C-Extension

[kmacdonald-stsci]

…eturned too early, so never decremented reference counts for python objects.

Resolves JP-3698

Closes jwst/#8680
Closes #276

This PR addresses a memory leak found in the ramp fitting C-extension. Added decrement reference counters to objects referenced that were passed from the python code. These missing decrements meant that reference counts were not properly garbage collected.

Attached is a screen shot of the memory usage from memray demonstrating there is no memory leak.

Checklist

• added entry in CHANGES.rst (either in Bug Fixes or Changes to API)
• updated relevant tests
• updated relevant documentation
• updated relevant milestone(s)
• added relevant label(s)

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 84.38%. Comparing base (2112773) to head (cd47dc6).
Report is 179 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #281      +/-   ##
==========================================
+ Coverage   84.32%   84.38%   +0.05%     
==========================================
  Files          41       41              
  Lines        7529     7557      +28     
==========================================
+ Hits         6349     6377      +28     
  Misses       1180     1180              

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[drlaw1558]

I can't speak to the details of the C changes, but empirically it looks like this has fixed the memory leak in my tests as well. Previously I saw the memory used grow by about 6-7 GB over the course of processing about 25 files from PID 1523, and with this branch that number is more like 1 GB (which I'd consider within uncertainty given how I've been measuring usage).

[braingram]

Thanks for the responses.

Changes look good to me. Is there a link to jwst regression tests with this PR?

Do you think it's worth adding a unit test to check for the re-introduction of this problem? Running main the extra references fixed in this PR can be seen (with sys.getrefcount) for data, err, pixeldq groupdq and averagedarkcurrent after a call to ramp_fit_data. I looked for a close unit test that might be modifiable but I'm not seeing any that use OLS_C. Do the unit tests only cover the python version?

[kmacdonald-stsci]

Thanks for the responses.

Changes look good to me. Is there a link to jwst regression tests with this PR?

Do you think it's worth adding a unit test to check for the re-introduction of this problem? Running main the extra references fixed in this PR can be seen (with sys.getrefcount) for data, err, pixeldq groupdq and averagedarkcurrent after a call to ramp_fit_data. I looked for a close unit test that might be modifiable but I'm not seeing any that use OLS_C. Do the unit tests only cover the python version?

I'll think of a unit test that can check the reference counts. I am working on a PR now to change all unit tests to test OLS_C, since it is now the default.

[braingram]

Thanks for finding and fixing the bug!

[kmacdonald-stsci]

Thanks for the responses.

Changes look good to me. Is there a link to jwst regression tests with this PR?

Do you think it's worth adding a unit test to check for the re-introduction of this problem? Running main the extra references fixed in this PR can be seen (with sys.getrefcount) for data, err, pixeldq groupdq and averagedarkcurrent after a call to ramp_fit_data. I looked for a close unit test that might be modifiable but I'm not seeing any that use OLS_C. Do the unit tests only cover the python version?

I developed a unit test for this. Take a look. It creates a basic RampData class, along with some other necessary objects, then runs only the C-extension, examining the reference count before and after the call for objects of interest, then asserts they must be the same.

[braingram]

Thanks for the responses.
Changes look good to me. Is there a link to jwst regression tests with this PR?
Do you think it's worth adding a unit test to check for the re-introduction of this problem? Running main the extra references fixed in this PR can be seen (with sys.getrefcount) for data, err, pixeldq groupdq and averagedarkcurrent after a call to ramp_fit_data. I looked for a close unit test that might be modifiable but I'm not seeing any that use OLS_C. Do the unit tests only cover the python version?

I developed a unit test for this. Take a look. It creates a basic RampData class, along with some other necessary objects, then runs only the C-extension, examining the reference count before and after the call for objects of interest, then asserts they must be the same.

Thanks! Does the unit test use OLS_C? I'm not seeing where it overwrites the python default.

EDIT: nevermind... I see where it imports the c extension directly. Looks great!

[tapastro]

LGTM. Ran regression tests just to ensure no unforeseen bugs, which passed (all failures known to be from other issues): https://plwishmaster.stsci.edu:8081/job/RT/job/JWST-Developers-Pull-Requests/1669/

@nden do we need to request review from a Roman rep to get this merged?

[nden]

@tapastro This doesn't need Roman approval. Feel free to merge when good.