openfold

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Unable to achieve the expected training accuracy

1

Hi, thank you very much for your work. Now I want to training openfold, and download the corresponding dataset(RODA dataset), and then use the following script for training. `python3 train_openfold.py...

llwx593

download_roda_pdbs.sh doesn't download any files from server

2

The download script download_roda_pdbs.sh has this rsync command: https://github.com/aqlaboratory/openfold/blob/84659c93ba6f06b8a0a2646d1cf27646c003a0c6/scripts/download_roda_pdbs.sh#L35 It doesn't download anything, perhaps because there aren't any files at the given path on the server. I'm following the README...

awaelchli

I've found that I'm unable to load the provided openfold model parameters when using `--resume_model_weights_only=True` in `train_openfold.py` . An error arises because the keys corresponding the model parameters are prefixed...

jonathanking

Hi and thanks for your amazing model! I would like to grab the gradient of the model before the optimizer.step. According to the definition, this can be fetched through the...

sgyersula

Only the first timing is recorded in timings.json. Furthermore, it would be nice to include also the MSA (maybe even with timings of the substeps), next to the inference and...

carlmensch

Flash Attention seems broken

4

Hello, Thanks for a very useful and well documented package. Great effort! I have tried to train the model with flash attention enabled, and ran into the following error: ```...

tanhevg

Run OpenFold on CPU

3

Hello, I have issues when running openfold on a CPU. When I execute the `run_pretrained_openfold.py` script with the `--model_device cpu` argument set, I get the following error: ```shell Traceback (most...

Old-Shatterhand

Hello, I think I install all the dependencies except the flash-attention. I ran the unit test using the script, and the test_model failed. ``` ====================================================================== FAIL: test_dry_run (tests.test_model.TestModel) ---------------------------------------------------------------------- Traceback...

SingL3

Dockerfile that has mmseq2 installed

2

I saw [#71](https://github.com/aqlaboratory/openfold/pull/71) that built a docker image. However, if I wanted mmseq2 installed within my image, has anyone already done this?

rrw1007

No error but also no output ("Successfully loaded params ...")

4

I've been trying to set up Openfold to test it out this week. It's been somewhat of a struggle but I am sooo close right now. Everything is installed and...

ecfischer