recipe.def

BootStrap: docker
From: fedora:38

%files
    SubPrecisionContactDetection.jl.zip /opt/SubPrecisionContactDetection.jl.zip

%post
    ## Get the tools we'll need
    #dnf install -y wget unzip python3 R python3-pip g++ openssh-clients curl
    dnf install -y wget unzip python3 g++ python3-pip which
    dnf groupinstall -y 'Development Tools'
    pip install kneed
    pip install scikit-image
    pip install scipy
    pip install pandas
    pip install argparse
    pip install scikit-learn
    export PYTHON=`which python3`
    echo $PYTHON

    ## Setup Julia
    export JLMJV=1.10
    export JLV=$JLMJV.5
    export JULIA_TGZ=julia-$JLV-linux-x86_64.tar.gz
    mkdir -p /opt/julia && cd /opt/julia
    wget https://julialang-s3.julialang.org/bin/linux/x64/$JLMJV/$JULIA_TGZ && tar -xf $JULIA_TGZ && rm $JULIA_TGZ
    export PATH=/opt/julia/julia-$JLV/bin:$PATH
    export JULIA_DEPOT_PATH=/opt/juliadepot
    mkdir -p $JULIA_DEPOT_PATH

    ## Setup local package
    export PKGNAME="SubPrecisionContactDetection"
    cd /opt && unzip $PKGNAME.jl.zip
    export LOCALPKG=/opt/$PKGNAME.jl
    cd $LOCALPKG
    julia --project=$LOCALPKG -e 'using Pkg; Pkg.update(); ENV["PYTHON"]="/usr/bin/python3"; Pkg.build(); Pkg.instantiate()'
    julia --project=$LOCALPKG -e 'using SubPrecisionContactDetection'
    echo "Setting up precompile"
    julia --project=$LOCALPKG --trace-compile=dc_precompile.jl scripts/precompile.jl
    echo "Creating test data"
    julia --project=$LOCALPKG scripts/setupdata.jl
    echo "Profiling API"
    julia --project=$LOCALPKG --trace-compile=dc_precompile2.jl scripts/ercontacts.jl --inpath /tmp/testdata -r "*[1,2].tif" -w 2 --sigmas 2.5-2.5-1.5 --outpath /tmp --nooutput --alpha 0.01 --beta 0.01 -c 1 -v 2000 --dimension 3 --mode=decon
    cat dc_precompile2.jl >> dc_precompile.jl
    #echo "Building precompiled image"
    julia --project=$LOCALPKG scripts/setupimage.jl
    rm -rf /opt/juliadepot/logs
    ln -s /dev/shm/ /opt/juliadepot/logs
    ln -s /dev/shm/ /opt/juliadepot/scratchspaces/
    chmod +x /opt/SubPrecisionContactDetection.jl/runjulia.sh
    chmod -R 777 /opt/SubPrecisionContactDetection.jl
    chmod -R 777 /opt/juliadepot
    chmod -R 777 /opt/julia  

    ## Cleanup
    dnf remove -y wget unzip

%environment
    export LC_ALL=C
    export LOCALPKG=/opt/SubPrecisionContactDetection.jl
    export JLMJV=1.10
    export JLV=$JLMJV.5
    export PATH=/opt/julia/julia-$JLV/bin:$PATH
    export JULIA_DEPOT_PATH=/opt/juliadepot
    export PYTHON="/usr/bin/python3"

%runscript
    echo "Executing runjulia.sh with args $@"
    /opt/SubPrecisionContactDetection.jl/runjulia.sh "$@"


%labels
    Author Ben Cardoen, bcardoen@sfu.ca
    Version v0.0.3

%help
    Usage (interactively):
    singularity shell image.sif
    Singularity> julia --project=/opt/SubPrecisionContactDetection.jl
    or
    singularity exec image.sif julia --project=/opt/SubPrecisionContactDetection.jl <yourcode>
    or for fastest execution
    singularity exec image.sif julia --project=/opt/SubPrecisionContactDetection.jl --sysimage=/opt/SubPrecisionContactDetection.jl/sys_img.so <yourcode.jl>