mirror of
https://github.com/RosettaCommons/foundry.git
synced 2026-06-04 13:24:22 +08:00
5a492032d5
* Initial commit of chiral changes Initial checkin of chiral feature code Add chiral metric * Update the way chiral features are incorporated into the model Move initialization to new func use default pytorch reset parameters fix initialization for chirals config rename argument of confidence head fix initialization for chirals * refactor: src nest, rename rf2aa to modelhub * refactor: initial commit without projects * Initial commit of chiral changes * Initial checkin of chiral feature code * Add chiral metric * Remove option for double residual connection. Add kq_norm oiptions to base (20250125) config. * Restoring flag * config * rename argument of confidence head * Update the way chiral features are incorporated into the model * config * rename argument of confidence head * Update the way chiral features are incorporated into the model * Initial commit of chiral changes Initial checkin of chiral feature code Add chiral metric * Update the way chiral features are incorporated into the model Move initialization to new func use default pytorch reset parameters fix initialization for chirals config rename argument of confidence head fix initialization for chirals * refactor: new modelhub --------- Co-authored-by: fdimaio <dimaio@uw.edu> Co-authored-by: HaotianZhangAI4Science <haotianzhang@zju.edu.cn>
134 lines
4.2 KiB
RPMSpec
134 lines
4.2 KiB
RPMSpec
Bootstrap: docker
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From: ubuntu:24.04
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IncludeCmd: yes
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# NOTE: This apptainer was written using apptainer version `1.1.6+2-g6808b5172-ipd`
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# To build this apptainer, use:
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# make apptainer
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%setup
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# Create a directory in the container to bind the host's current working directory
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mkdir ${APPTAINER_ROOTFS}/modelhub_host
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# ... for mounting `/projects` with --bind
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mkdir ${APPTAINER_ROOTFS}/projects
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# ... for mounting `/databases` with --bind
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mkdir ${APPTAINER_ROOTFS}/net
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# ... for mounting `/squash` with --bind
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mkdir ${APPTAINER_ROOTFS}/squash
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%files
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/etc/localtime
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/etc/hosts
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environment.yaml /opt/environment.yaml
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%post
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# get os name
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echo "Running on OS name $(lsb_release -i | awk '{ print $3 }')"
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# get os version
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echo "... in OS version $(lsb_release -r | awk '{ print $2 }')"
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## GENERAL SETUP
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# Switch shell to bash
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ln -sf /bin/bash /bin/sh
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# Common symlinks (within container)
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ln -s /net/databases /databases
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ln -s /net/software /software
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ln -s /home /mnt/home
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ln -s /projects /mnt/projects
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ln -s /net /mnt/net
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## PACKAGE INSTALLATION
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apt-get update
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# Install build essentials and other required packages (needed for compiling biotite cython files)
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apt-get install -y build-essential gcc g++
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# Install make (so we can run `make format`, `make clean`, etc.)
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apt-get install -y make git wget libaio-dev
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# required X libs
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apt-get install -y libx11-6 libxau6 libxext6 libxrender1
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apt-get clean
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# Clone CUTLASS (for DeepSpeed)
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git clone https://github.com/NVIDIA/cutlass.git /opt/cutlass
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# Clone DeepSpeed (so we can pre-install the wheel)
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git clone --branch v0.16.2 https://github.com/deepspeedai/DeepSpeed.git /opt/deepspeed
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## ENVIRONMENT CREATION & DEPENDENCY INSTALLATION
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# Download miniconda
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wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O /opt/miniconda.sh
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# Install conda
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bash /opt/miniconda.sh -b -u -p /usr
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# install everything
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# ... the environment in the container is at `/usr/envs/modelhub-apptainer`
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conda install -c conda-forge mamba
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mamba env create --file /opt/environment.yaml --name modelhub-apptainer
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# Set up conda
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conda init bash
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# Add conda environment to PATH
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export PATH=/usr/envs/modelhub-apptainer/bin:$PATH
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echo "Proceeding with DeepSpeed reinstallation."
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## PRE-COMPILE DEEPSPEED FROM WHEEL
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# (Overwrite deepspeed installation from the `environment.yaml`)
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pip uninstall deepspeed -y # Avoid interactive prompts
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# (Flags for building the Evoformer attention)
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export TORCH_CUDA_ARCH_LIST="7.0;7.5;8.0;8.6;8.9"
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export DS_BUILD_EVOFORMER_ATTN=1
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export CUTLASS_PATH=/opt/cutlass/
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# Reinstall DeepSpeed, pre-compiling the evoformer attentino kernel
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pip wheel /opt/deepspeed -w /opt/deepspeed
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pip install /opt/deepspeed/deepspeed-0.16.2+b344c04d-cp311-cp311-linux_x86_64.whl
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# Run the biotite setup command
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# (Temporary measure until we switch to released Biotite version)
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. /usr/etc/profile.d/conda.sh
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conda activate modelhub-apptainer
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python -m biotite.setup_ccd
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# clean up files to reduce size
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# ... remove conda
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mamba clean -a -y
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# ... remove other apt packages that are no longer needed
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apt-get -y purge build-essential wget
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apt-get -y autoremove
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apt-get clean
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rm /opt/miniconda.sh
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%environment
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source /usr/etc/profile.d/conda.sh
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conda activate modelhub-apptainer
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export PATH=$PATH:/usr/local/cuda/bin
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export CUTLASS_PATH=/opt/cutlass/
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%runscript
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# NOTE: The %runscript is invoked when the container is run without specifying a different command.
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exec python "$@"
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%help
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modelhub environment for running modelhub independently and for development
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To see this help message, use:
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apptainer run-help modelhub_apptainer.sif
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To build this apptainer, use:
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apptainer build --bind $PWD:/modelhub_host path/to/apptainer.sif apptainer.spec
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To run the container, use:
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apptainer exec /path/to/apptainer.sif <command>
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OR
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./path/to/apptainer.sif <command>
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To get an interactive shell in the container, use:
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apptainer shell /path/to/apptainer.sif
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%labels
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Version v1.0.0
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ApptainerVersion 1.1.6+2-g6808b5172-ipd
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