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wells-wood-research / de-stress

DE-STRESS is a model evaluation pipeline that aims to make protein design more reliable and accessible.
http://destressprotein.design
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EvoEF2 hangs for some PDB files #14

Closed MichaelJamesStam closed 3 years ago

MichaelJamesStam commented 3 years ago

EvoEF2 hangs for two PDB files, 2ht0.pdb and 4dyq.pdb. For 2ht0.pdb, some nan values are returned when running EvoEF2 from the command line. This could potentially be causing a problem as DE-STRESS hangs on "Job is running on server". On the other hand, running EvoEF2 on the file 4dyq.pdb from the command line, causes a segmentation fault. On DE-STRESS, it hangs on "Job submitted to server".

MichaelJamesStam commented 3 years ago

This issue is resolved by the two linked pull requests. The file 2ht0.pdb was hanging because EvoEF2 generated NaN values which had not been handled in the front-end/public/main.js. The issue with 4dyq.pdb was not specific to this file or EvoEF2. Some of the larger files were not being ran, because the event loop that checks for websocket activity was timing out. This has been addressed by moving the code for processing the message out of the timeout block.

MichaelJamesStam commented 3 years ago

The file 2ht0.pdb is still failing from ELM side. The elm object for EvoEF2 only has Float types for the energy values which need to be changed to Maybe Floats.