Frequently asked questions or encountered issues in OpenFold Setup and training.
Frequently asked questions or encountered issues when running OpenFold.
## Setup
## Setup
-In the unittests, I see an error such as
-When running unit tests (e.g. [`./scripts/run_unit_tests.sh`](https://github.com/aqlaboratory/openfold/blob/main/scripts/run_unit_tests.sh)), I see an error such as
@@ -145,14 +145,3 @@ If MPI is configured on your system, and you would like to use MPI to train Open
...
@@ -145,14 +145,3 @@ If MPI is configured on your system, and you would like to use MPI to train Open
1. Add the `mpi4py` package, which are available through pip and conda. Please see [mpi4py documentation](https://pypi.org/project/mpi4py/) for more instructions on installation.
1. Add the `mpi4py` package, which are available through pip and conda. Please see [mpi4py documentation](https://pypi.org/project/mpi4py/) for more instructions on installation.
2. Add the `--mpi_plugin` flag to your training command.
2. Add the `--mpi_plugin` flag to your training command.
## Troubleshooting FAQ
My model training is hanging on the data loading step:
While each system is different, a few general suggestions:
Check your `$KMP_AFFINITY` environment setting
Adjust the number of data workers used to prepare data with the `--num_workers` setting. Increasing the number could help with dataset processing speed. However, to many workers could cause an OOM issue.
When I reload my pretrained model weights or checkpoints, I get `RuntimeError: Error(s) in loading state_dict for OpenFoldWrapper: Unexpected key(s) in state_dict:`
This suggests that your checkpoint / model weights are in OpenFold v1 format with outdated model layer names. Convert your weights/checkpoints following [this guide](convert_of_v1_weights.md).