chmod 777 -R /workspace/bionemo2/

uv pip install h11==0.16.0

/usr/local/rustup /usr/local/rustup

/usr/local/cargo /usr/local/cargo

./docs ./docs

./ci/scripts ./ci/scripts

./README.md ./

VERSION .

mkdir -p /workspace/bionemo2/.cache/

RUN |4 TARGETARCH=amd64 TE_TAG=9d4e11eaa508383e35b510dc338e58b09c30be73 CAUSAL_CONV_TAG=52e06e3d5ca10af0c7eb94a520d768c48ef36f1f NEMU_RUN_TAG=v0.3.0 /bin/sh -c set -eo pipefail uv pip install maturin --no-build-isolation # install nvidia-resiliency-ext separately because it doesn't yet have ARM wheels
git clone https://github.com/NVIDIA/nvidia-resiliency-ext
uv pip install nvidia-resiliency-ext/
rm -rf nvidia-resiliency-ext/
# ngcsdk causes strange dependency conflicts (ngcsdk requires protobuf<4, but nemo_toolkit requires protobuf==4.24.4, deleting it from the uv pip install prevents installation conflicts)
sed -i "/ngcsdk/d" ./sub-packages/bionemo-core/pyproject.toml
# Remove llama-index because bionemo doesn't use it and it adds CVEs to container sed -i "/llama-index/d" ./3rdparty/NeMo/requirements/requirements_nlp.txt # Pin 'nvidia-modelopt' to 0.27.1 due to an API incompatibility of version 0.25.0 sed -i -E "s|nvidia-modelopt\[torch\]>=[^,]+,<=([^ ;]+)|nvidia-modelopt[torch]==\1|" ./3rdparty/NeMo/requirements/requirements_nlp.txt uv pip install --no-build-isolation \
./3rdparty/* \
./sub-packages/bionemo-* \
-r /requirements-cve.txt \
-r /requirements-test.txt # Install back ngcsdk, as a WAR for the protobuf version conflict with nemo_toolkit. uv pip install ngcsdk==3.64.3 # Temporary fix for changed filename, see https://nvidia.slack.com/archives/C074Z808N05/p1746231345981209 # Install >=0.46.1 bitsandbytes specifically because it has CUDA>12.9 support. # TODO(trvachov) remove this once it stops conflicting with strange NeMo requirements.txt files uv pip uninstall bitsandbytes && uv pip install bitsandbytes==0.46.1 # Addressing security scan issue - CVE vulnerability https://github.com/advisories/GHSA-g4r7-86gm-pgqc The package is a # dependency of lm_eval from NeMo requirements_eval.txt. We also remove zstandard, another dependency of lm_eval, which # seems to be causing issues with NGC downloads. See https://nvbugspro.nvidia.com/bug/5149698 uv pip uninstall sqlitedict zstandard rm -rf ./3rdparty rm -rf /tmp/* rm -rf ./sub-packages/bionemo-noodles/target # buildkit