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I think this is a problem with PETSc not converging. If you look at the logging information, the solver did not converge at all. So gradient computation will definitely be wrong.
I have a feeling that this is due to PETSc using 32-bit rather than 64-bit. If you have some time, please explore. Thanks.
This has to be fixed!
We may need to keep short gradient checks for each function to detect where the leak is happening.
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