your code (execution)

Stefano Moia

École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland;    physiopy (https://github.com/physiopy)

14.02.2023

apptainer exec docker://ghcr.io/apptainer/lolcow cowsay "Hello $USER, and happy B-day Carlo!"

Try it now on stiitsrv21/22/23!

Follow from your laptop:

https://slides.com/d/7mDp4d4/live

smoia
@SteMoia
s.moia.research@gmail.com
Stefano Moia, 2023

Where are we in Open Science/Development?

To be Open, Science should be publicly available, reusable,
and transparent¹. It should aim at reaching:

1. The Turing Way Community, 2019 (Zenodo). https://the-turing-way.netlify.app (CC-BY 4.0)

  • Open Data
  • Open Source Software
  • Open Hardware
  • Open Access (outreach)
  • Reproducible results
  • Usable artefacts, independently of setting.
  • Complete and clear process documentation

How do we do Open Science?

  1. Read literature, formulate hypotheses, decide methods, submit a Registered Report (~ Introduction, hypotheses, methods), get through first peer review round.
  2. Find open development projects, contribute if needed, check licences.
  3. Decide a (permissive) licence for the artefacts, start open developing code (share it!), use VCS, test and document code, create releases.
  4. Create containers.
  5. Collect data, curate them using community schemas (e.g. BIDS), upload them on public databases with embargo ("private time").
  6. Run analyses in containers, interpret results, write the second part of your Registered Report (~ Results, a posteriori analyses, discussion, conclusions)
  7. Publish open access.
  8. Remove embargoes.
  9. Rinse and repeat.

Replicable, Robust, Reproducible, Generalisable

The Turing Way Community, & Scriberia, 2022 (Zenodo). Illustrations from The Turing Way (CC-BY 4.0)

Guaranteeing reproducibility is important for "reusable, transparent" research.

Really Replicable?

Same hardware, two Freesurfer builds (different glibc version)
Difference in estimated cortical tickness.¹

Same hardware, same FSL version, two glibc versions
Difference in estimated tissue segmentation.²

Same hardware, two Freesurfer builds (two glibc versions)

Difference in estimated parcellation.²

1. Glatard, et al., 2015 (Front. Neuroinform.)    2. Ali, et al., 2021 (Gigascience)

Containerisation (vs VM)

Containers vs VM:

Pros:

  • Cost (less CPU, less memory)
  • Faster runtime = faster runs
  • Smaller sizes
  • More portable*

 

Cons:

  • Security (can be exploited)*
  • Graphic User Interface is secondary*

Docker vs Apptainer

Docker:

  • Targeting Laptops: better OS support (yes, you, mac/win peeps)
  • Hosts public hub to share built containers
  • Works with layer images to build containers
  • Docker images can be used as bases for Apptainer recipes

Apptainer:

  • Built for HPCs (Unix only), maintained by the Linux Foundation
  • Easier "recipe" syntax
  • Containers are a full root system folder that can be built as sandboxes
  • Supports Docker images as bases
  • It is safer than docker

Docker vs Apptainer

Bootstrap: docker
From: python:3.8.13-slim-buster

%files
.. /opt

%environment
export DEBIAN_FRONTEND=noninteractive
export TZ=Europe/Brussels

%post
# Set install variables, create tmp folder
export DEBIAN_FRONTEND=noninteractive
export TZ=Europe/Brussels
# Prepare repos and install dependencies
pip3 install /opt/.[all]

%runscript
nigsp

%labels
org.label-schema.name="NiGSP"
org.label-schema.description="NiGSP: python library for Graph Signal Processing on Neuroimaging data"
org.label-schema.url="https://github.com/miplabch/nigsp"
org.label-schema.vcs-url="https://github.com/miplabch/nigsp"
org.label-schema.schema-version="1.0"
FROM python:3.8.13-slim-buster AS nigspdock

WORKDIR /app

# Prepare environment
COPY .. .
RUN pip3 install .[all]

ENV LANG="en_US.UTF-8" \
    LC_ALL="en_US.UTF-8"

CMD nigsp

ARG BUILD_DATE
ARG VCS_REF
ARG VERSION
LABEL org.label-schema.build-date=$BUILD_DATE \
      org.label-schema.name="NiGSP" \
      org.label-schema.description="NiGSP: python library for Graph Signal Processing on Neuroimaging data" \
      org.label-schema.url="https://github.com/miplabch/nigsp" \
      org.label-schema.vcs-ref=$VCS_REF \
      org.label-schema.vcs-url="https://github.com/miplabch/nigsp" \
      org.label-schema.version=$VERSION \
      org.label-schema.schema-version="1.0"

Docker

Apptainer

Example container: NiGSP

Bootstrap: docker
From: python:3.8.13-slim-buster

%environment
export DEBIAN_FRONTEND=noninteractive
export TZ=Europe/Brussels

%post
# Set install variables, create tmp folder
export DEBIAN_FRONTEND=noninteractive
export TZ=Europe/Brussels
# Prepare repos and install dependencies
pip3 install nigsp[all]

%runscript
nigsp

FROM python:3.8.13-slim-buster

# Prepare environment
ENV DEBIAN_FRONTEND=noninteractive \
    TZ=Europe/Brussels

RUN pip3 install nigsp[all]

CMD nigsp

Docker

Apptainer

# Create a sandbox image from a python image on the Docker Hub
apptainer build --fakeroot --sandbox nigsp.img docker://python:3.8.13-slim-buster

# Start an interactive session to modify the sandbox (short and long flags)
apptainer shell -f -e -w --no-home nigsp.img
apptainer shell --fakeroot --cleanenvironment --writable --no-home nigsp.img

# Install nigsp in the container
pip3 install nigsp[all]
pip3 list

# Exit the container
exit

# Create an unmodifiable image from the previous sandbox
apptainer build -f nigsp.sif nigsp.img

# Execute a command in the new image, in this case call the help of nigsp
apptainer exec -e --no-home nigsp.sif nigsp --help

Example container

Bootstrap: docker
From: ubuntu:20.04

%environment
export DEBIAN_FRONTEND=noninteractive
export TZ=Europe/Brussels
export FSLDIR="/opt/fsl-6.0.6.2"
source ${FSLDIR}/etc/fslconf/fsl.sh
export FSLOUTPUTTYPE="NIFTI_GZ"
export FSLMULTIFILEQUIT="TRUE"
export FSLTCLSH="$FSLDIR/bin/fsltclsh"
export FSLWISH="$FSLDIR/bin/fslwish"
export FSLLOCKDIR=""
export FSLMACHINELIST=""
export FSLREMOTECALL=""
export FSLGECUDAQ="cuda.q"
export PATH="$FSLDIR/bin:$PATH"


%post
# Set install variables, create tmp folder
export DEBIAN_FRONTEND=noninteractive
export TZ=Europe/Brussels
# Prepare repos and install dependencies
apt update -qq
apt install -y -q --no-install-recommends \
    bc \
    build-essential \
    ca-certificates \
    curl \
    dc \
    dirmngr \
    file \
    g++ \
    gcc \
    git \
    less \
    make \
    nano \
    sudo \
    wget \
    python3-distutils \
    python3-pip \
    python3-rpy2 \
    python-is-python3

# Install FSL
mkdir -p ${TMPDIR}/fsl
cd ${TMPDIR}/fsl || exit 1
curl -fL https://fsl.fmrib.ox.ac.uk/fsldownloads/fslinstaller.py --output ./fslinstaller.py
chmod +x fslinstaller.py
python3 fslinstaller.py -d /opt/fsl-6.0.6.2 -V 6.0.6.2
# echo "Installing FSL conda environment ..."
# bash /opt/fsl-6.0.6.2/etc/fslconf/fslpython_install.sh -f /opt/fsl-6.0.6.2
cd ${TMPDIR} || exit 1
rm -rf ${TMPDIR}/fsl

# Install PYTHON things.
pip3 install pip==22.3.1 setuptools==65.5.1 wheel==0.38.4

# Install wxPython in a particular way.
pip3 install --no-cache -f https://extras.wxpython.org/wxPython4/extras/linux/gtk3/ubuntu-20.04 wxpython==4.2.0

# Install datalad, fsleyes, nilearn, peakdet, phys2cvr.
pip3 install \
    annexremote==1.6.0 \
    datalad==0.17.10 \
    fsleyes==1.5.0 \
    fsleyes-props==1.8.2 \
    fsleyes-widgets==0.12.3 \
    fslpy==3.10.0 \
    ipython \
    h5py==3.7.0 \
    matplotlib==3.6.2 \
    nibabel==4.0.2 \
    nilearn==0.10.0 \
    numpy==1.23.5 \
    pandas==1.5.2

# Final removal of lists and cleanup
rm -rf /var/lib/apt/lists/*

%runscript
fslmaths


FROM ubuntu:20.04 AS ubuntudock

# Prepare environment
ENV DEBIAN_FRONTEND=noninteractive \
    TZ=Europe/Brussels

ENV FSLDIR="/opt/fsl-6.0.5.1" \
    PATH="/opt/fsl-6.0.5.1/bin:$PATH" \
    FSLOUTPUTTYPE="NIFTI_GZ" \
    FSLMULTIFILEQUIT="TRUE" \
    FSLTCLSH="/opt/fsl-6.0.5.1/bin/fsltclsh" \
    FSLWISH="/opt/fsl-6.0.5.1/bin/fslwish" \
    FSLLOCKDIR="" \
    FSLMACHINELIST="" \
    FSLREMOTECALL="" \
    FSLGECUDAQ="cuda.q"

RUN apt-get update -qq \
    && apt-get install -y -q --no-install-recommends \
            bc \
            build-essential \
            ca-certificates \
            curl \
            dc \
            dirmngr \
            file \
            g++ \
            gcc \
            git \
            gnupg \
            libfontconfig1 \
            libfreetype6 \
            libgl1-mesa-dev \
            libgl1-mesa-dri \
            libglu1-mesa-dev \
            libgomp1 \
            libice6 \
            libopenblas-base \
            libxcursor1 \
            libxft2 \
            libxinerama1 \
            libxrandr2 \
            libxrender1 \
            libxt6 \
            less \
            make \
            nano \
            sudo \
            wget \
            python3-distutils \
            python3-pip \
            python3-rpy2 \
            python-is-python3 \
    && rm -rf /var/lib/apt/lists/* \
    && echo "Downloading FSL ..." \
    && mkdir -p /opt/fsl-6.0.5.1 \
    && curl -fL https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-6.0.5.1-centos7_64.tar.gz \
    | tar -xz -C /opt/fsl-6.0.5.1 --strip-components 1 \
    && echo "Installing FSL conda environment ..." \
    && bash /opt/fsl-6.0.5.1/etc/fslconf/fslpython_install.sh -f /opt/fsl-6.0.5.1

RUN pip3 install pip==22.3.1 setuptools==65.5.1 wheel==0.38.4

RUN pip3 install --no-cache -f https://extras.wxpython.org/wxPython4/extras/linux/gtk3/ubuntu-20.04 wxpython==4.2.0

RUN pip3 install annexremote==1.6.0 \
    datalad==0.17.10 \
    fsleyes==1.5.0 \
    fsleyes-props==1.8.2 \
    fsleyes-widgets==0.12.3 \
    fslpy==3.10.0 \
    ipython \
    h5py==3.7.0 \
    matplotlib==3.6.2 \
    nibabel==4.0.2 \
    nilearn==0.10.0 \
    numpy==1.23.5 \
    pandas==1.5.2

RUN ln -s /opt/fsl-6.0.5.1/bin/eddy_cuda9.1 /opt/fsl-6.0.5.1/bin/eddy_cuda

ENV FSLOUTPUTTYPE="NIFTI_GZ"

RUN apt-get update -qq \
           && apt-get install -y -q --no-install-recommends \
                  locales \
           && rm -rf /var/lib/apt/lists/*

RUN sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen && locale-gen

CMD source ${FSLDIR}/etc/fslconf/fsl.sh; fslmaths

Docker

Apptainer

Apptainer example: complete data analysis.

Bootstrap: docker
From: ubuntu:20.04

%environment
# export templateloc=/usr/share/afni/atlases
export AFNIPATH=/opt/afni-AFNI_22.3.07
export AFNI_PLUGINPATH="$AFNIPATH"
export templateloc=/usr/share/afni/atlases
export AFNI_AUTOGZIP=YES
export AFNI_COMPRESSOR=GZIP
export ANTSPATH="/opt/ants-2.4.2/bin"
export ANTSSCRIPTS="/opt/ants-2.4.2/Scripts"
export C3DPATH="/opt/convert3d-1.0.0"
export FSLDIR="/opt/fsl-6.0.6.2"
source ${FSLDIR}/etc/fslconf/fsl.sh
export FSLOUTPUTTYPE="NIFTI_GZ"
export FSLMULTIFILEQUIT="TRUE"
export FSLTCLSH="$FSLDIR/bin/fsltclsh"
export FSLWISH="$FSLDIR/bin/fslwish"
export FSLLOCKDIR=""
export FSLMACHINELIST=""
export FSLREMOTECALL=""
export FSLGECUDAQ="cuda.q"
export DEBIAN_FRONTEND=noninteractive
export TZ=Europe/Brussels
export R_LIBS="/usr/lib/R"
export LD_LIBRARY_PATH="/opt/ants-2.4.2/lib:$LD_LIBRARY_PATH"
export PREPROCPATH="/opt/preprocessing"
export PATH="$AFNIPATH:$ANTSPATH:$ANTSSCRIPTS:$C3DPATH/bin:$FSLDIR/bin:$PREPROCPATH:$PREPROCPATH/00.pipelines:$PATH"

%post
# Set install variables, create tmp folder
export TMPDIR="/tmp/general_preproc_build_$( date -u +"%F_%H-%M-%S" )"
[[ -d ${TMPDIR} ]] && rm -rf ${TMPDIR}
mkdir -p ${TMPDIR}
export DEBIAN_FRONTEND=noninteractive
export TZ=Europe/Brussels
apt update -qq
apt install -y -q --no-install-recommends ca-certificates dirmngr gnupg
# Prepare repos and install dependencies
apt-key adv --keyserver keyserver.ubuntu.com --recv-keys C9A7585B49D51698710F3A115E25F516B04C661B
apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 6E12762B81063D17BDDD3142F142A4D99F16EB04
echo "deb https://ppa.launchpadcontent.net/marutter/rrutter4.0/ubuntu focal main" | tee -a /etc/apt/sources.list
echo "deb-src https://ppa.launchpadcontent.net/marutter/rrutter4.0/ubuntu focal main" | tee -a /etc/apt/sources.list
echo "deb https://ppa.launchpadcontent.net/c2d4u.team/c2d4u4.0+/ubuntu focal main" | tee -a /etc/apt/sources.list
echo "deb-src https://ppa.launchpadcontent.net/c2d4u.team/c2d4u4.0+/ubuntu focal main" | tee -a /etc/apt/sources.list
apt update -qq
apt install -y -q --no-install-recommends \
    bc \
    build-essential \
    bzip2 \
    cmake \
    curl \
    dc \
    file \
    freeglut3-dev \
    g++ \
    gcc \
    git \
    less \
    libcurl4-openssl-dev \
    libeigen3-dev \
    libexpat1-dev \
    libf2c2-dev \
    libfftw3-3 \
    libfftw3-dev \
    libgdal-dev \
    libgfortran4 \
    libgfortran-8-dev \
    libglew-dev \
    libgl1-mesa-dev \
    libgl1-mesa-dri \
    libgl1-mesa-glx \
    libglib2.0-dev \
    libglu1-mesa-dev \
    libglw1-mesa \
    libgomp1 \
    libgsl-dev \
    libgts-dev \
    libjpeg8-dev \
    liblapack3 \
    libopenblas-dev \
    libmotif-dev \
    libnetpbm10-dev \
    libnode-dev \
    libpng16-16 \
    libpng-dev \
    libquadmath0 \
    libtiff5 \
    libtiff5-dev \
    libudunits2-dev \
    libxext-dev \
    libxi-dev \
    libxm4 \
    libxmhtml-dev \
    libxml2-dev \
    libxmu-dev \
    libxmu-headers \
    libxpm-dev \
    libxt-dev \
    m4 \
    make \
    mesa-common-dev \
    nano \
    r-base-dev \
    rsync \
    tcsh \
    python3-distutils \
    python3-pip \
    python3-rpy2 \
    python-is-python3 \
    qhull-bin \
    xvfb \
    zlib1g-dev
# Install AFNI
mkdir -p ${TMPDIR}/afni
cd ${TMPDIR}/afni || exit 1
ln -s /usr/lib/x86_64-linux-gnu/libgsl.so.23 /usr/lib/x86_64-linux-gnu/libgsl.so.19
ln -s /usr/lib/x86_64-linux-gnu/libXp.so.6 /usr/lib/x86_64-linux-gnu/libXp.so
git clone https://github.com/afni/afni.git source
cd source || exit 1
git fetch --tags
git -c advice.detachedHead=false checkout AFNI_22.3.07
cd src || exit 1
cp other_builds/Makefile.linux_ubuntu_16_64_glw_local_shared Makefile
make itall
mv linux_ubuntu_16_64_glw_local_shared /opt/afni-AFNI_22.3.07
export PATH="/opt/afni-AFNI_22.3.07:$PATH"
export R_LIBS="/usr/lib/R"
rPkgsInstall -pkgs ALL
cd ${TMPDIR} || exit 1
rm -rf ${TMPDIR}/afni
# Install ANTs
mkdir -p ${TMPDIR}/ants/build
git clone https://github.com/ANTsX/ANTs.git ${TMPDIR}/ants/source
cd ${TMPDIR}/ants/source || exit 1
git fetch --tags
git -c advice.detachedHead=false checkout v2.4.2
cd ${TMPDIR}/ants/build || exit 1
cmake -DCMAKE_INSTALL_PREFIX=/opt/ants-2.4.2 -DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF ${TMPDIR}/ants/source
make -j 10
mkdir -p /opt/ants-2.4.2
cd ANTS-build || exit 1
make install
mv ../../source/Scripts/ /opt/ants-2.4.2
cd ${TMPDIR} || exit 1
rm -rf ${TMPDIR}/ants
# Install C3D
echo "Downloading Convert3D ..."
mkdir -p /opt/convert3d-1.0.0
curl -fsSL https://sourceforge.net/projects/c3d/files/c3d/1.0.0/c3d-1.0.0-Linux-x86_64.tar.gz/download \
| tar -xz -C /opt/convert3d-1.0.0 --strip-components 1
# Install FSL
mkdir -p ${TMPDIR}/fsl
cd ${TMPDIR}/fsl || exit 1
curl -fL https://fsl.fmrib.ox.ac.uk/fsldownloads/fslinstaller.py --output ./fslinstaller.py
chmod +x fslinstaller.py
python3 fslinstaller.py -d /opt/fsl-6.0.6.2 -V 6.0.6.2
# echo "Installing FSL conda environment ..."
# bash /opt/fsl-6.0.6.2/etc/fslconf/fslpython_install.sh -f /opt/fsl-6.0.6.2
cd ${TMPDIR} || exit 1
rm -rf ${TMPDIR}/fsl

# Clone EuskalIBUR preprocessing.
git clone https://github.com/smoia/EuskalIBUR_preproc.git /opt/preprocessing

apt install -y -q csvtool

# Install PYTHON things.
pip3 install pip==22.3.1 setuptools==65.5.1 wheel==0.38.4

# Install wxPython in a particular way.
pip3 install --no-cache -f https://extras.wxpython.org/wxPython4/extras/linux/gtk3/ubuntu-20.04 wxpython==4.2.0

# Install datalad, fsleyes, nilearn, peakdet, phys2cvr.
pip3 install \
    annexremote==1.6.0 \
    boto==2.49.0 \
    certifi==2022.12.7 \
    cffi==1.15.1 \
    chardet==4.0.0 \
    charset-normalizer==2.1.1 \
    contourpy==1.0.6 \
    cryptography==38.0.4 \
    cycler==0.11.0 \
    datalad==0.17.10 \
    dill==0.3.6 \
    distro==1.8.0 \
    fasteners==0.18 \
    fonttools==4.38.0 \
    fsleyes==1.5.0 \
    fsleyes-props==1.8.2 \
    fsleyes-widgets==0.12.3 \
    fslpy==3.10.0 \
    h5py==3.7.0 \
    humanize==4.4.0 \
    idna==3.4 \
    importlib-metadata==5.1.0 \
    iso8601==1.1.0 \
    jaraco.classes==3.2.3 \
    jeepney==0.8.0 \
    Jinja2==3.1.2 \
    joblib==1.2.0 \
    keyring==23.11.0 \
    keyrings.alt==4.2.0 \
    kiwisolver==1.4.4 \
    lxml==4.9.2 \
    MarkupSafe==2.1.1 \
    matplotlib==3.6.2 \
    more-itertools==9.0.0 \
    msgpack==1.0.4 \
    nibabel==4.0.2 \
    nilearn==0.9.2 \
    numpy==1.23.5 \
    packaging==22.0 \
    pandas==1.5.2 \
    patool==1.12 \
    peakdet==0.2.0rc1 \
    phys2cvr==0.16.0 \
    Pillow==9.3.0 \
    platformdirs==2.6.0 \
    pycparser==2.21 \
    PyOpenGL==3.1.6 \
    pyparsing==2.4.7 \
    python-dateutil==2.8.2 \
    python-gitlab==3.12.0 \
    pytz==2022.6 \
    requests==2.28.1 \
    requests-toolbelt==0.10.1 \
    scikit-learn==1.2.0 \
    scipy==1.9.3 \
    SecretStorage==3.3.3 \
    simplejson==3.18.0 \
    six==1.16.0 \
    threadpoolctl==3.1.0 \
    tqdm==4.64.1 \
    urllib3==1.26.13 \
    Whoosh==2.7.4 \
    zipp==3.11.0

# Final removal of lists and cleanup
cd /tmp || exit 1
rm -rf ${TMPDIR}
rm -rf /var/lib/apt/lists/*

Containers in action (resources limitation)

apptainer run --cpus 1.3 --memory-reservation 10G nigsp.sif nigsp --help

mkdir -p mipcontainers/tmp && cd mipcontainers

cp -r /media/miplab-nas2/Data3/mipcontainers/phenotype .

git clone https://github.com/smoia/fuzzy-invention.git 
chmod +x fuzzy-invention/*.py

apptainer build -f sing2_apptainer.sif fuzzy-invention/sing2.def
cp /media/miplab-nas2/Data3/mipcontainers/sing2_apptainer.sif .

apptainer exec -e --no-home -B ./phenotype:/data -B ./fuzzy-invention:/scripts -B ./tmp:/tmp sing2_apptainer.sif \
/scripts/prepare_questionnaire.py /data/derivatives /data

BIDSapps: containers for BIDS pipelines

Easily build a neuroimaging container

Easily build a neuroimaging container

MATLAB container

That's all folks!

Thank you!

Stefano Moia, 2023

Any question [/opinions/objections/...]?

Stefano Moia, 2023