clean up shell commands ? about hpc-container-maker

[samcmill]

Hi @biocyberman - thank you for your interest in HPCCM.

The Singularity installation needs to be copied from the first stage into the second stage. Since Singularity is installed in /usr by default, cherry picking the Singularity files can be a challenge.

An alternative is to install Singularity in it's own directory; then you can simply copy the whole directory into the second stage. The --prefix option of mconfig can be used for this.

I also experiment with Singularity inside a container, so I can share 2 of my HPCCM recipes for Singularity.

Stage0 += baseimage(image='ubuntu:16.04')

# Build Dependencies
Stage0 += packages(apt=['build-essential', 'libssl-dev', 'uuid-dev',
                        'libgpgme11-dev', 'wget', 'git', 'ca-certificates',
                        'squashfs-tools', 'gcc'])

# Golang
Stage0 += shell(commands=[
    'cd /var/tmp',
    'wget https://dl.google.com/go/go1.11.linux-amd64.tar.gz',
    'tar -C /usr/local -xzf /var/tmp/go1.11.linux-amd64.tar.gz'])
Stage0 += environment(variables={'GOPATH': '/root/go',
                                 'PATH': '/usr/local/go/bin:$PATH:/root/go/bin'})

# Download Singularity sources
singularity_tag='v3.2.0-rc1'
Stage0 += shell(commands=[
    'mkdir -p /root/go/src/github.com/sylabs',
    'cd $GOPATH/src/github.com/sylabs',
    'git clone --depth=1 --branch {} https://github.com/sylabs/singularity.git'.format(singularity_tag)])

# Get dependencies
Stage0 += shell(commands=[
    'cd $GOPATH/src/github.com/sylabs/singularity',
    'go get -u -v github.com/golang/dep/cmd/dep'])

# Build and install Singularity
Stage0 += shell(commands=[
    'cd $GOPATH/src/github.com/sylabs/singularity',
    './mconfig --prefix={}'.format('/opt/singularity'),
    'cd builddir',
    'make',
    'make install'])

# Second stage
Stage1 += baseimage(image='ubuntu:16.04')

# Runtime dependencies
Stage1 += packages(ospackages=['ca-certificates', 'squashfs-tools'])

# Copy Singularity installation
Stage1 += copy(_from='0', src='/opt/singularity', dest='/opt/singularity')

# Set environment
Stage1 += environment(variables={'PATH': '/opt/singularity/bin:$PATH'})

I have split the Singularity build into a few steps. There's a trade-off between the number of layers and the re-use of the Docker build cache. There is no right answer, but it doesn't matter much in this case because we are essentially discarding the first stage. Generally I recommend making each component it's own layer, e.g., install Go in a separate layer than Singularity.

Singularity can also be built as an RPM. Here's a recipe for that:

Stage0 += baseimage(image='centos:7')

# Build dependencies
Stage0 += gnu(fortran=False)
Stage0 += packages(epel=True,
                   yum=['make', 'libarchive-devel',
                        'squashfs-tools', 'wget', 'ca-certificates',
                        'rpm-build', 'git', 'libuuid-devel',
                        'openssl-devel', 'libseccomp-devel', 'golang',
                        'which'])

# Build Singularity RPM
singularity_version='3.2.0'
singularity_version_full='3.2.0-rc1'
Stage0 += shell(commands=['cd /var/tmp',
                          'wget https://github.com/sylabs/singularity/releases/download/v{0}/singularity-{1}.tar.gz'.format(singularity_version_full, singularity_version),
                          'rpmbuild -tb /var/tmp/singularity-{}.tar.gz'.format(singularity_version)])

# Second stage
Stage1 += baseimage(image='centos:7')

# Runtime dependencies
Stage1 += packages(yum=['ca-certificates', 'libseccomp', 'squashfs-tools'])

# Copy Singularity RPM
Stage1 += copy(_from='0', src='/root/rpmbuild/RPMS/x86_64/singularity-{}.el7.x86_64.rpm'.format(singularity_version_full), dest='/tmp')

# Install Singularity
Stage1 += shell(commands=['rpm --install /tmp/singularity-{}.el7.x86_64.rpm'.format(singularity_version_full)])

P.S. Don't forget to start your Singularity Docker container with --privileged.

[biocyberman]

@samcmill Thank you for sharing the recipes. I was also wondering about cross-distribution build. The --privileged flag is indeed crucial.