openfold issues

Inference with mixed precision

1

Hello, I am wondering if the inference code can run at mixed precision? For example, if I modify `run_pretrained_openfold.py` line 254 from `out = run_model(model, processed_feature_dict, tag, args.output_dir)` to ```...

soumyadipghosh

Running inference using MultiGPU

6

Hi everyone, I am trying to run inference using multiGPU. I am currently able to run it on a single gpu which is by default using parser.add_argument( "--model_device", type=str, default="cpu",...

chinmayraneQ

WARNING:root:Failed to run alignments for 6kal_A. Skipping

Hey everyone, I am trying to compute alignments for training of openfold. But I am getting stuck at the first step. I am running the following code `python3 scripts/precompute_alignments.py /workspace/dataset/pdb_mmcif/mmcif_files/...

chinmayraneQ

Which Python versions this package supports? Only Python 3.7?

4

Python 3.7 is approaching its EOL in 5 months. Are there plans or blockers to bump the supported Python version from 3.7 (if it's the only one now supported) to...

rfilgueiras

code uses np.object, which is deprecated in numpy version 1.24

1

I received the following nested exception: File "/dccstor/mm_hcls/usr/ozery/miniconda/envs/fuse_2/lib/python3.8/site-packages/openfold/data/data_pipeline.py", line 23, in from openfold.data import templates, parsers, mmcif_parsing File "/dccstor/mm_hcls/usr/ozery/miniconda/envs/fuse_2/lib/python3.8/site-packages/openfold/data/templates.py", line 88, in "template_domain_names": np.object, File "/dccstor/mm_hcls/usr/ozery/miniconda/envs/fuse_2/lib/python3.8/site-packages/numpy/__init__.py", line 305, in __getattr__...

michalozeryflato

installation issues - scripts/install_third_party_dependencies.sh

3

I face multiple errors during installation on an ubuntu workstation: Ubuntu 22.04.1 LTS 5.15.0-58-generic #64-Ubuntu SMP Thu Jan 5 11:43:13 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux NVIDIA-SMI 520.61.05 Driver Version:...

chewyalvin