Skip to content

Commit

Permalink
working from updated README and added documentation and release info
Browse files Browse the repository at this point in the history
  • Loading branch information
sirelkhatim committed Nov 18, 2024
1 parent 7add0a0 commit da3bfbc
Showing 1 changed file with 2 additions and 9 deletions.
11 changes: 2 additions & 9 deletions README.md
Original file line number Diff line number Diff line change
@@ -1,6 +1,5 @@
# BioNeMo Framework (v2.0)


NVIDIA BioNeMo Framework is a collection of programming tools, libraries, and models for computational drug discovery. It accelerates the most time-consuming and costly stages of building and adapting biomolecular AI models by providing domain-specific, optimized models and tooling that are easily integrated into GPU-based computational resources for the fastest performance on the market. You can access BioNeMo Framework as a free community resource here in this repository or learn more at https://www.nvidia.com/en-us/clara/bionemo/ about getting an enterprise license for improved expert-level support.


Expand Down Expand Up @@ -194,13 +193,10 @@ export MY_DATA_SOURCE="pbss"

```bash
# The fastest transformer engine environment variables in testing were the following two
export NVTE_FUSED_ATTN=1
export NVTE_FLASH_ATTN=0

TEST_DATA_DIR=$(download_bionemo_data esm2/testdata_esm2_pretrain:2.0 --source $MY_DATA_SOURCE); \
ESM2_650M_CKPT=$(download_bionemo_data esm2/650m:2.0 --source $MY_DATA_SOURCE); \
python \
scripts/protein/esm2/esm2_pretrain.py \

train_esm2 \
--train-cluster-path ${TEST_DATA_DIR}/2024_03_sanity/train_clusters_sanity.parquet \
--train-database-path ${TEST_DATA_DIR}/2024_03_sanity/train_sanity.db \
--valid-cluster-path ${TEST_DATA_DIR}/2024_03_sanity/valid_clusters.parquet \
Expand Down Expand Up @@ -256,9 +252,6 @@ and DataModule types.
> ⚠️ **Warning:** This setup does NO configuration of Weights and Biases. Edit your config JSON and populate it with your WandB details.
```
export NVTE_FUSED_ATTN=1
export NVTE_FLASH_ATTN=0
bionemo-esm2-train \
--data-config-t bionemo.esm2.run.config_models.ESM2DataConfig \
--model-config-t bionemo.esm2.run.config_models.ExposedESM2PretrainConfig \
Expand Down

0 comments on commit da3bfbc

Please sign in to comment.