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Multi-Stage Builds

Reference to the documentation

One might want to install software that requires external libraries that are not available with the distribution or to recompile existing with different options. Usually, this will require installing common building tools and compilers that are not needed for running the executables...

Similar to Docker multi-stage builds, Singularity also offers a multi-stage builds that allows for copying files between stages (Singularity can copy only from previous to current stage). Below is an example definition file that compiles the ARPIP (Ancestral sequence Reconstruction under the Poisson Indel Process) tool. The recipe is following the local installation for the static binary build. 

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Bootstrap: docker
From: ubuntu:20.04
Stage: devel

%post
  export LC_ALL=C
  export DEBIAN_FRONTEND=noninteractive

  # Package cache in /tmp
  mkdir -p /tmp/apt20 &&  echo "Dir::Cache "/tmp/apt20";" > /etc/apt/apt.conf.d/singularity-cache.conf

  apt-get update && apt-get -y dist-upgrade && \
  apt-get install -y wget git cmake build-essential zlib1g-dev

  # Download
  export TMPD=/tmp/downloads &&   mkdir -p $TMPD
  mkdir -p /installs 

  # bpp-core http://biopp.univ-montp2.fr/
  cd /installs
  git clone https://github.com/BioPP/bpp-core
  cd bpp-core
  git checkout tags/v2.4.1 -b v241
  mkdir build 
  cd build
  cmake ..
  make -j 16 install

  # bpp-seq http://biopp.univ-montp2.fr/
  cd /installs
  git clone https://github.com/BioPP/bpp-seq
  cd bpp-seq
  git checkout tags/v2.4.1 -b v241
  mkdir build
  cd build
  cmake ..
  make -j 16 install

  # bpp-phyl http://biopp.univ-montp2.fr/
  cd /installs
  git clone https://github.com/BioPP/bpp-phyl
  cd bpp-phyl
  git checkout tags/v2.4.1 -b v241
  mkdir build
  cd build
  cmake  ..
  make -j 16 install

  # boost - C++ Libraries http://www.boost.org/
  cd /installs
  wget -P $TMPD -c https://boostorg.jfrog.io/artifactory/main/release/1.79.0/source/boost_1_79_0.tar.gz 
  tar xvf $TMPD/boost_1_79_0.tar.gz
  cd boost_1_79_0
  ./bootstrap.sh --prefix=/usr/
  ./b2 
  ./b2 install 

  # glog - Google Logging Library https://github.com/google/glog/
  cd /installs
  git clone -b v0.5.0 https://github.com/google/glog
  cd glog
  cmake -H. -Bbuild -G "Unix Makefiles"
  cmake --build build --target install

  # gtest - Google Test Library https://github.com/google/googletest/
  cd /installs
  git clone https://github.com/google/googletest.git -b release-1.11.0
  cd googletest
  mkdir build
  cd build
  cmake ..
  make -j 4 install

  # ARPIP
  cd /opt
  git clone https://github.com/acg-team/bpp-arpip/
  cd bpp-arpip
  cmake --target ARPIP -- -DCMAKE_BUILD_TYPE=Release-static CMakeLists.txt
  make -j 8 

  clean 
  cd / && rm -rf /installs

#########################################################

Bootstrap: docker
From: ubuntu:20.04
Stage: final

%files from devel
  /opt/bpp-arpip                       /opt/
  /usr/local/lib/libbpp-core.so.4      /usr/local/lib/libbpp-core.so.4  
  /usr/local/lib/libbpp-seq.so.12      /usr/local/lib/libbpp-seq.so.12
  /usr/local/lib/libbpp-phyl.so.12     /usr/local/lib/libbpp-phyl.so.12
  /usr/local/lib/libglog.so.0          /usr/local/lib/libglog.so.0

%environment
  export LC_ALL=C
  export PYTHONNOUSERSITE=True

%post
  export LC_ALL=C
  export PYTHONNOUSERSITE=True
  export DEBIAN_FRONTEND=noninteractive

  # Package cache in /tmp
  mkdir -p /tmp/apt20 &&  echo "Dir::Cache "/tmp/apt20";" > /etc/apt/apt.conf.d/singularity-cache.conf

  apt-get update && apt-get -y dist-upgrade && \
  apt-get install -y wget git libc6 libstdc++6 libgcc-s1 

%runscript
  /opt/bpp-arpip/ARPIP "$@"

Stage: devel lines 1-82 are compiling all the required libraries and tools to compile the ARPIP code. This stage can be used in a container that will run perfectly fine and with a bit more luck, if the final executable was fully static, one can even try to copy the file outside the container and run it as it is. Unfortunately, extracting the executable on Rackham shows these disappointing results.

Under Ubuntu 20.04 GLIBC... problems are resolved but libbpp-core.so.4, libbpp-seq.so.12, libbpp-seq.so.12, and libglog.so.0 we just compiled remain missing.

ldd ARPIP 
./ARPIP: /lib64/libm.so.6: version `GLIBC_2.29' not found (required by ./ARPIP)
./ARPIP: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.26' not found (required by ./ARPIP)
./ARPIP: /lib64/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by ./ARPIP)
./ARPIP: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by ./ARPIP)
./ARPIP: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by ./ARPIP)
        linux-vdso.so.1 =>  (0x00007ffe9257f000)
        libbpp-core.so.4 => not found
        libbpp-seq.so.12 => not found
        libbpp-phyl.so.12 => not found
        libglog.so.0 => not found
        libpthread.so.0 => /lib64/libpthread.so.0 (0x00002b529980d000)
        libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00002b5299a29000)
        libm.so.6 => /lib64/libm.so.6 (0x00002b5299d31000)
        libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00002b529a033000)
        libc.so.6 => /lib64/libc.so.6 (0x00002b529a249000)
        /lib64/ld-linux-x86-64.so.2 (0x00002b52995e9000)
And that is what we are doing in Stage: final - we copy the compiled libraries from Stage: devel in to a minimum Ubuntu 20.04 (could be other flavor as well) (lines: 90-95). In this case we avoid "stuffing" the container with unnecessary packages needed for compiling - cmake build-essential zlib1g-dev. There are no shortcuts - one needs to check you have everything you need in the new container - in this case apt-get install -y libc6 libstdc++6 libgcc-s1 which will make sure we have the remaining libraries in /lib64/....