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drmeisterdrmeister
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update apptainer
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‎apptainer/amber.def‎

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BootStrap: docker
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From: debian:latest
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%files
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$HOME/Downloads/AmberTools23.tar.bz2 /downloads/AmberTools23.tar.bz2
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%post
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apt upgrade
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apt update
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apt -y install tcsh make \
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gcc gfortran g++ \
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flex bison patch bc \
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libbz2-dev libzip-dev \
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xorg-dev wget cmake \
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mpich openssh-client linux-perf
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apt install --yes bzip2
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cd /opt
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bunzip2 -c /downloads/AmberTools23.tar.bz2 | tar xvf -
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cd /opt/amber22_src/build
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mkdir /opt/amber22
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cmake /opt/amber22_src \
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-DCMAKE_INSTALL_PREFIX=/opt/amber22 \
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-DCOMPILER=GNU \
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-DBUILD_GUI=FALSE \
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-DMPI=FALSE -DCUDA=FALSE -DINSTALL_TESTS=FALSE \
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-DDOWNLOAD_MINICONDA=FALSE \
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-DBUILD_PYTHON=FALSE \
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2>&1 | tee cmake.log
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make -j20 install
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ln -s /opt/amber22 /opt/amber
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apt install --yes binutils libboost-all-dev clang-18 libclang-cpp18-dev libclang-18-dev libgmp-dev libfmt-dev libunwind-dev llvm-18 llvm-18-dev ninja-build sbcl jupyterlab emacs openssh-client openssh-server libnetcdf-dev expat gocryptfs nodejs npm strace emacs libelf-dev wget
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wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-aarch64.sh
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bash Miniconda3-latest-Linux-aarch64.sh -b -p /home/cando/miniconda3
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rm -rf Miniconda3-latest-Linux-aarch64.sh
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export PATH="/home/cando/miniconda3/bin:${PATH}"
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conda tos accept --override-channels --channel https://repo.anaconda.com/pkgs/main
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conda tos accept --override-channels --channel https://repo.anaconda.com/pkgs/r
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conda install -y -c conda-forge jupyterlab sidecar # ambertools not available
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jupyter-lab build
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# cd /mnt
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# ./koga --reproducible-build --extensions=cando --build-mode=bytecode-faso --llvm-config="/usr/bin/llvm-config-18" --build-path=build-apptainer/
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# ninja -C build-apptainer
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# ninja -C build-apptainer install
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# mkdir -p /home/cando/
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# chmod ugo+rwx /home/cando/
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# tar -xvf /mnt/systems.tar -C /home/cando
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# whoami
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# ls /home/
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# chmod -R ugo+rw /home/cando/
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%environment
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export AMBERHOME=/opt/amber
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# export LD_LIBRARY_PATH=/usr/local/lib
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# export XDG_CACHE_HOME=/home/cando/.cache
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‎apptainer/build-cando-debian‎

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#! /bin/bash
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#
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# In the clasp toplevel directory use...
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# make -f apptainer/makefile
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#
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rm -rf build-apptainer/*
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tar --exclude-vcs -cvf systems.tar -C $HOME ./common-lisp
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apptainer build -F --bind $PWD:/mnt cando.sif apptainer/cando-debian.def

‎apptainer/cando-debian.def‎

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BootStrap: localimage
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From: /home/drmeister/Development/cando/amber.sif
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# From: debian:latest
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%post
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# apt upgrade
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# apt update
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apt install --yes libzmq3-dev
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cd /mnt
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./koga --reproducible-build --extensions=cando --build-mode=bytecode-faso --llvm-config="/usr/bin/llvm-config-18" --build-path=build-apptainer/
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ninja -C build-apptainer
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ninja -C build-apptainer install
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mkdir -p /home/cando/
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chmod ugo+rwx /home/cando/
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tar -xvf /mnt/systems.tar -C /home/cando
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# wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-aarch64.sh
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# bash Miniconda3-latest-Linux-aarch64.sh -b -p /home/cando/miniconda3
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# rm -rf Miniconda3-latest-Linux-aarch64.sh
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# export PATH="/home/cando/miniconda3/bin:${PATH}"
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# conda tos accept --override-channels --channel https://repo.anaconda.com/pkgs/main
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# conda tos accept --override-channels --channel https://repo.anaconda.com/pkgs/r
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# conda install -y -c conda-forge jupyterlab sidecar # ambertools not available
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# jupyter-lab build
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whoami
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ls /home/
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chmod -R ugo+rw /home/cando/
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%environment
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export PATH="/home/cando/miniconda3/bin:${PATH}"
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export LD_LIBRARY_PATH=/usr/local/lib
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# export XDG_CACHE_HOME=/home/cando/.cache
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‎apptainer/makefile‎

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all:
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ninja -C build
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extensions/cando/scando-zeus-install
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amber.sif: ./apptainer/amber.def
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apptainer build --fakeroot ./amber.sif apptainer/amber.def
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cando.sif: amber.sif apptainer/cando-debian.def
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./apptainer/build-cando-debian
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app:
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make cando.sif
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send:
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scp cando.sif owlsnest:work/bin/
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# time ssh owlsnest-update
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app-send:
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make app
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make send

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