Kernel Die in FastRelax

[MichaelLaw2003]

Problem

When I run 1.4. Step 1. Prepare the starting structure with FastRelax() of 06.08-Point-Mutation-Scan.ipynb in Jupyter lab, I encontered the following error:

The kernel for student-notebooks/06.08-Point-Mutation-Scan.ipynb appears to have died. It will restart automatically.
The error is reproduced each time I run the corresponding cell in Jupyter lab.
The error is reproduced in Google Colab, too. The cause is unknown.

Environment

WSL2 Ubuntu 22.04.5 LTS, on Windows 10, on my PC

[MichaelLaw2003]

I'm attemping to reply to this issue myself. This issue is likely to be caused by inappropriate instantiation of the FastRelax object.

Original code in cell [15] ( 1.4. Step 1. Prepare the starting structure with FastRelax() )

from pyrosetta.rosetta.protocols.relax import FastRelax

relax = FastRelax()
scorefxn = get_fa_scorefxn()
relax.set_scorefxn(scorefxn)
relax = rosetta.protocols.relax.FastRelax()
relax.constrain_relax_to_start_coords(True)
print(relax)
#relax.apply(testPose)
#testPose.dump_pdb('test.relax.pdb')

Modified code.

from pyrosetta.rosetta.protocols.relax import FastRelax

my_relax = FastRelax()
scorefxn = get_fa_scorefxn()
my_relax.set_scorefxn(scorefxn)
#my_relax = rosetta.protocols.relax.FastRelax()
my_relax.constrain_relax_to_start_coords(True)
print(my_relax)
my_relax.apply(testPose)
testPose.dump_pdb('./test.relax.pdb')
pmm.apply(testPose)
# It works

[roccomoretti]

Doing relax = rosetta.protocols.relax.FastRelax() completely resets the relax object, making the preceding relax = FastRelax(); relax.set_scorefxn(scorefxn) pointless. (This isn't anything PyRosetta-related, it's just how the Python object model works.)

Looking at the code, it does appear that trying to run FastRelax without setting the scorefunction will result in a segfault and a kernel crash. (We probably should be better about checking for that case.)