sokrypton / sokrypton/ColabFold
local installation error
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Description
Hi, I am trying to install colabfold locally (ubunutu 20.04, NVIDIA-SMI 470.161.03 Driver Version: 470.161.03 CUDA Version: 11.4 ) so that I can use our 3090RTX cards. I followed the instructions given on this site and this .whl file for jaxlib:
jaxlib-0.3.25+cuda11.cudnn82-cp37-cp37m-manylinux2014_x86_64.whl
The colabfold_batch command runs for a while (trying to predict a ~1000 AA sequence) and then produces these errors:
2023-02-16 14:05:16,653 Setting max_seq=512, max_extra_seq=1076
2023-02-16 14:05:17.665658: E external/org_tensorflow/tensorflow/compiler/xla/stream_executor/gpu/asm_compiler.cc:114] *** WARNING *** You are using ptxas 10.1.243, which is older than 11.1. ptxas before 11.1 is known to miscompile XLA code, leading to incorrect results or invalid-address errors.
2023-02-16 14:05:17.668585: W external/org_tensorflow/tensorflow/compiler/xla/stream_executor/gpu/asm_compiler.cc:231] Falling back to the CUDA driver for PTX compilation; ptxas does not support CC 8.6
2023-02-16 14:05:17.668641: W external/org_tensorflow/tensorflow/compiler/xla/stream_executor/gpu/asm_compiler.cc:234] Used ptxas at ptxas
2023-02-16 14:05:17.672166: E external/org_tensorflow/tensorflow/compiler/xla/stream_executor/cuda/cuda_driver.cc:628] failed to get PTX kernel "concatenate" from module: CUDA_ERROR_NOT_FOUND: named symbol not found
2023-02-16 14:05:17.672239: E external/org_tensorflow/tensorflow/compiler/xla/pjrt/pjrt_stream_executor_client.cc:2153] Execution of replica 0 failed: INTERNAL: Could not find the corresponding function
2023-02-16 14:05:17,672 Could not predict martin1. Not Enough GPU memory? INTERNAL: Could not find the corresponding function
2023-02-16 14:05:17,674 Done
Any suggestions on what to do?
Thank you!
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with the installation instructions and the colabfold_batch command, then compare the reported Python, JAX, CUDA, driver, and ptxas versions. The issue is resolved when a local prediction of the reported long sequence completes without the CUDA/XLA errors.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- linux, python, ubuntu
- Domain
- bioinformatics, devops, machine-learning
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100