openfold

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OOM after reducing number of evoformer blocks

8

Just hoping someone has an idea of what might be going on, because I'm completely puzzled by this behavior. After reducing "no_blocks" from 48 to 12 I get an OOM...

lhatsk

Now that we have a dockerfile, we can push it somewhere. Dockerhub (https://hub.docker.com/) is probably a reasonable place since it's free for open source projects and the de facto standard....

decarboxy

Hello and so happy to see you use Pytorch-Lightning! :tada: Just wondering if you already heard about quite the new **Pytorch Lightning (PL) ecosystem CI** where we would like to...

pl-ghost

New entries in obsolete.dat will throw up errors.

15

```python Traceback (most recent call last): File "/ocean/projects/bio210060p/kadyan/openfold-release/scripts/precompute_te mplate_hits.py", line 224, in main(args, template_pipeline_runner) File "/ocean/projects/bio210060p/kadyan/openfold-release/scripts/precompute_te mplate_hits.py", line 116, in main feature_dict = template_pipeline_runner.run(a3m_dir, fasta_file_path) File "/ocean/projects/bio210060p/kadyan/openfold-release/scripts/precompute_te mplate_hits.py", line 80,...

sachinkadyan7

Some questions about running inference

1

When I use openfold to infer proteins, some of them can be inferred, but some of them will report errors. The reason for the error is probably: the template name...

wangleshuyang

training speed is about 2x slower than JAX trainable version (Uni-Fold)

44

device: 1 A100 with 40GB memory cuda: 11.3 Compared with https://github.com/dptech-corp/Uni-Fold, using `model_2` setting, and the same data (only use one sample, and use `DummyDataLoader` in openfold). And I follow...

guolinke

pdb files not exist in mmcif dir

3

Hi, Thank for the last time it helped me. However, now I have another error. After running the training from ProteinNet input: python /data/openfold/train_openfold.py /data/af_databases/pdb_mmcif/mmcif_files/ /home/ubuntu/ProteinNet_parsed/ProteinNet_lc/ /data/af_databases/pdb_mmcif/mmcif_files/ /home/ubuntu/OF_train_from_Protein_Net/try_1_Dec29_2021/ 2021-10-10 --template_release_dates_cache_path...

ozsolomon

About the evaluation in CASP14

2

Hello everyone. I am doing some evaluation jobs of the inference pipeline. I am wondering how to evaluate the result pdb file such like TM-score, for those proteins that CASP14...

YiningWang2

I've implemented low-memory attention (9670958) using an algorithm from a recent preprint (https://arxiv.org/pdf/2112.05682.pdf), enhanced a little bit with the ability to add multiple biases + batch dimensions. Lacking the JAX...

gahdritz

chunk_layer is memory-inefficient

1

The `chunk_layer` function in `openfold/utils/tensor_utils.py`, which implements the "chunking" procedure described in subsection 1.11.8 of the Alphafold 2 supplement, relies on a memory-expensive expand/reshape operation at the top to standardize...

gahdritz