segmentation fault (core dumped) when running predict.py in af2_binder_design
MadelineMartin opened this issue · 4 comments
I ran the importtest for af2_binder_design and it passed, but when I run predict.py, I get a segmentation fault. I narrowed it down to it being that I am running out of memory when importing packages, specifically jax.numpy and pyrosetta, but I am on a 40gb GPU and I have tried as high as 128G of memory on my university's HPC. How do I overcome this memory issue?
My jax version is 0.4.23 build pypi_0, channel pypi
jaxlib 0.4.23+cuda12.cudann89, pypi_0, pypi
jmp 0.0.4 pypi_0, pypi
pyrosetta 2024.01+release.00b7914, py311_0, graylab
Thanks in advance for your help!
I fixed this problem. I had to download an older version of PyRosetta. I downloaded version 2023.49+release.9891f2c59fb.
I downloaded the proper tar.bz2 file from the coast mirror on pyrosetta.org, unpacked it in the af2_binder_design conda environment, and installed it using "python setup.py install" inside the af2_binder_design environment.
Hey,
Could you clarify which older version of pyRosetta exactly, did you download to solve this.....
Hey, Could you clarify which older version of pyRosetta exactly, did you download to solve this.....
Version: 2023.49+release.9891f2c59fb
Let me know if you need more info!
I managed to download it using conda install pyrosetta=2023.49+release.9891f2c
However the segmentation fault still persists. Any suggestions on how I could solve it.