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schrodinger / pymol-open-source

Open-source foundation of the user-sponsored PyMOL molecular visualization system.
https://pymol.org/
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Pymol crashes when i am trying to split states on M3 chip #327

Closed venzera closed 10 months ago

venzera commented 10 months ago

I've got PyMOL installed via "brew install pymol" on MacBook on M3 chip OS Sonoma. And when i load (this step is fine) structure with multiple states and try to split states it immediately crushes with "segmentation fault". What should i do to solve that kind of issue? I did try to reinstall it multiple times. And seems like no one hasn't experienced such a problem.

samuelhoover commented 10 months ago

I had a similar issue where loading a GROMACS coordinate file (2.2 MB) caused my Homebrew-installed PyMOL to crash with a segmentation fault. I had no problem loading a 107 KB PDB file though.

M1 MacBook Pro on macOS Sonoma 14.2.1.

image
JarrettSJohnson commented 10 months ago

Is there a sample file that I can try to reproduce this with

Couldn't reproduce with

fetch 1nmr
split_states 1nmr
venzera commented 10 months ago

@samuelhoover did you find any solution?

venzera commented 10 months ago

@JarrettSJohnson it does with any structures with multiple states inluding 1nmr

JarrettSJohnson commented 10 months ago

Thanks for confirming; I've checked with homebrew on an older Intel Mac, I think I only have an M1 around--I'll check with that.

JarrettSJohnson commented 10 months ago

I was able to confirm the issue on an M2. Seems like this was fixed via https://github.com/schrodinger/pymol-open-source/pull/324 . Maintainers of homebrew package should update.

samuelhoover commented 10 months ago

@venzera I haven't found a solution, it seems to work with smaller files and fails on bigger files. My only guess is it's some memory issue. My friend on a Linux machine was able to open both files without problem, but their Intel Mac did crash with the coordinates file. They used pacman to install PyMOL.

@JarrettSJohnson fetch 1nmr works for me too. I'll link the coordinates file (which causes a segmentation fault) and the PDB file (which does not cause an issue) here. .gro file: https://github.com/samuelhoover/gromacs-tutorials/blob/main/lysozyme-in-water/MD/md_0_1.gro PDB file: https://github.com/samuelhoover/gromacs-tutorials/blob/main/lysozyme-in-water/1AKI_clean.pdb

EDIT: I should have added that we both have no issue with the licensed PyMOL version. The only issue has been with the open-source PyMOL on Homebrew.

samuelhoover commented 10 months ago

@venzera Looks like Homebrew maintainers updated the formula. Uninstall PyMOL and then reinstall with the--HEAD option for it to work. If you just do brew install pymol like I did initially, it will crash as before.

@JarrettSJohnson In case you notified the Homebrew maintainers, thanks!

JarrettSJohnson commented 10 months ago

I haven't contacted the maintainers yet. I'm guessing --HEAD just pulls the head commit and builds it itself?

samuelhoover commented 10 months ago

Correct, I noticed when I did brew install pymol that it had the same warnings from #321.

venzera commented 10 months ago

@samuelhoover @JarrettSJohnson that indeed worked very well except fetch takes a little bit longer, but it doesnt cause any problem. Thank you very much for help.

P.S. I almost started to use ChimeraX instead 😄 It was quite unusual