phase_linking.py does not exit for fatal error PATCH_0360 is not inverted

[falkamelung]

Hi @mirzaee
I mentioned previously that miaplpy does not always stops when an error occurs (#37). Here an example: run_03_miaplpy_concatenate_patches_0 ran for many hours and created a 137GB run_03_miaplpy_concatenate_patches_0__1.o file containing:

Error: PATCH_0360 is not inverted, run previous step (phase_linking) to complete
Error: PATCH_0360 is not inverted, run previous step (phase_linking) to complete

If we replace in

MiaplPy/miaplpy/phase_linking.py

Line 143 in 30fa971

print('Error: PATCH_{:04.0f} is not inverted, run previous step (phase_linking) to complete'.format(index))

print by raise RuntimeError, so that the line reads

raise RuntimeError('Error: PATCH_{:04.0f} is not inverted, run previous step (phase_linking) to complete'.format(index))

it will exit with an exception. Could you do this? My PRs don't seem to get through.

[mirzaees]

Hi @falkamelung,

The reason it does not exit with an error at this step is because it checks if a patch has not been processed for any reason and tries to process it again. If it exits with this exception, it won't reprocess and finish automatically

[falkamelung]

Hi @mirzaees ,
are you sure? This happened in the run_3 step (concatenation). It is in the concatenate_patches function which I'd think is only called in the concatenation step.

[mirzaees]

Hi @falkamelung
you are right, it is fixed now
Thank you