containerized development

development/README.md

+# Development Containers
+
+We are going to use spack to build a container with different libraries and headers inside and will produce different stages.
+
+
+## Define a spack configuration
+We can choose some libraries and version that we need and build it into a concise image.
+
+This needs to be in a file called spack.yaml 
+```yaml
+spack:
+  specs:
+  - hdf5@1.10.7+mpi target=skylake_avx512
+  - openmpi@3.1.6 target=skylake_avx512
+
+  container:
+    images:
+      os: "centos:8"
+      spack: 0.17.2
+
+    format: singularity
+
+    strip: true
+
+    os_packages:
+      final:
+      - gcc
+      - gcc-gfortran
+
+    labels:
+      app: "hdf5@1.10.7+mpi"
+      mpi: "openmpi@3.1.6"
+```
+
+micro architectures known to spack:
+
+```
+Generic architectures (families)
+    aarch64  arm  ppc  ppc64  ppc64le  ppcle  riscv64  sparc  sparc64  x86  x86_64  x86_64_v2  x86_64_v3  x86_64_v4
+
+GenuineIntel - x86
+    i686  pentium2  pentium3  pentium4  prescott
+
+GenuineIntel - x86_64
+    nocona  nehalem   sandybridge  haswell    skylake  cannonlake      cascadelake
+    core2   westmere  ivybridge    broadwell  mic_knl  skylake_avx512  icelake
+
+AuthenticAMD - x86_64
+    k10  bulldozer  piledriver  zen  steamroller  zen2  zen3  excavator
+
+IBM - ppc64
+    power7  power8  power9
+
+IBM - ppc64le
+    power8le  power9le
+
+Cavium - aarch64
+    thunderx2
+
+Fujitsu - aarch64
+    a64fx
+
+ARM - aarch64
+    graviton  graviton2
+
+Apple - aarch64
+    m1
+
+SiFive - riscv64
+    u74mc
+```
+
+convert this configuration into a singularity (apptainer) recipes
+
+```bash
+spack containerize > Singularity.hdf5.1.10.7
+```
+
+which has the following content
+
+```singularity
+Bootstrap: docker
+From: spack/centos7:0.16.3
+Stage: build
+
+%post
+  # Create the manifest file for the installation in /opt/spack-environment
+  mkdir /opt/spack-environment && cd /opt/spack-environment
+  cat << EOF > spack.yaml
+spack:
+  specs:
+  - hdf5@1.10.7+mpi
+  - openmpi@3.6.1
+  concretization: together
+  config:
+    install_tree: /opt/software
+  view: /opt/view
+EOF
+
+  # Install all the required software
+  . /opt/spack/share/spack/setup-env.sh
+  spack env activate .
+  spack install --fail-fast
+  spack gc -y
+  spack env deactivate
+  spack env activate --sh -d . >> /opt/spack-environment/environment_modifications.sh
+
+  # Strip the binaries to reduce the size of the image
+  find -L /opt/view/* -type f -exec readlink -f '{}' \; | \
+    xargs file -i | \
+    grep 'charset=binary' | \
+    grep 'x-executable\|x-archive\|x-sharedlib' | \
+    awk -F: '{print $1}' | xargs strip -s
+
+
+Bootstrap: docker
+From: centos:7
+Stage: final
+
+%files from build
+  /opt/spack-environment /opt
+  /opt/software /opt
+  /opt/view /opt
+  /opt/spack-environment/environment_modifications.sh /opt/spack-environment/environment_modifications.sh
+
+%post
+  # Update, install and cleanup of system packages needed at run-time
+  yum update -y && yum install -y epel-release && yum update -y
+  yum install -y gcc gcc-gfortran
+  rm -rf /var/cache/yum  && yum clean all
+  # Modify the environment without relying on sourcing shell specific files at startup
+  cat /opt/spack-environment/environment_modifications.sh >> $SINGULARITY_ENVIRONMENT
+
+%labels
+  app hdf5@1.10.7+mpi
+  mpi openmpi@3.6.1
+```
+
+Then we can use that recipes to build a singularity container:
+
+```bash
+singularity build hdf5.1.10.7.sif Singularity.hdf5.1.10.7
+```
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development/Singularity.hdf5.1.10.7

+Bootstrap: docker
+From: spack/ubuntu-bionic:0.16.3
+Stage: build
+
+%post
+  # Create the manifest file for the installation in /opt/spack-environment
+  mkdir /opt/spack-environment && cd /opt/spack-environment
+  cat << EOF > spack.yaml
+spack:
+  specs:
+  - hdf5@1.10.7+mpi
+  - openmpi@3.1.6
+  concretization: together
+  config:
+    install_tree: /opt/software
+  view: /opt/view
+EOF
+
+  # Install all the required software
+  . /opt/spack/share/spack/setup-env.sh
+  spack env activate .
+  spack install --fail-fast
+  spack gc -y
+  spack env deactivate
+  spack env activate --sh -d . >> /opt/spack-environment/environment_modifications.sh
+
+  # Strip the binaries to reduce the size of the image
+  find -L /opt/view/* -type f -exec readlink -f '{}' \; | \
+    xargs file -i | \
+    grep 'charset=binary' | \
+    grep 'x-executable\|x-archive\|x-sharedlib' | \
+    awk -F: '{print $1}' | xargs strip -s
+
+
+Bootstrap: docker
+From: ubuntu:18.04
+Stage: final
+
+%files from build
+  /opt/spack-environment /opt
+  /opt/software /opt
+  /opt/view /opt
+  /opt/spack-environment/environment_modifications.sh /opt/spack-environment/environment_modifications.sh
+
+%post
+  # Update, install and cleanup of system packages needed at run-time
+  apt-get -yqq update && apt-get -yqq upgrade
+  apt-get -yqq install gcc gfortran
+  rm -rf /var/lib/apt/lists/*
+  # Modify the environment without relying on sourcing shell specific files at startup
+  cat /opt/spack-environment/environment_modifications.sh >> $SINGULARITY_ENVIRONMENT
+
+%labels
+  app hdf5@1.10.7+mpi
+  mpi openmpi@3.1.6
+

development/spack.yaml

+spack:
+  specs:
+  - hdf5@1.10.7+mpi target=skylake
+  - openmpi@3.1.6 target=skylake
+
+  container:
+    images:
+      os: "ubuntu:18.04"
+      spack: 0.16.3
+
+    format: singularity
+
+    strip: true
+
+    os_packages:
+      final:
+      - gcc
+      - gcc-gfortran
+
+    labels:
+      app: "hdf5@1.10.7+mpi"
+      mpi: "openmpi@3.1.6"
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