segmentation fault (core dumped) when running predict.py in af2_binder_design

nrbennet / dl_binder_design

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segmentation fault (core dumped) when running predict.py in af2_binder_design #69

Closed MadelineMartin closed 7 months ago

MadelineMartin commented 7 months ago

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!

MadelineMartin commented 7 months ago

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.

Avidhoot26 commented 5 months ago

Hey, Could you clarify which older version of pyRosetta exactly, did you download to solve this.....

MadelineMartin commented 5 months ago

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!

Avidhoot26 commented 5 months ago

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.