madduri/singularity-freesurfer-gpu:latest

$ singularity pull shub://madduri/singularity-freesurfer-gpu:latest

Singularity Recipe

Bootstrap: docker
From: ubuntu:16.04
%files
    license.txt
%post
    # Links
    GET_PIP=https://bootstrap.pypa.io/get-pip.py
    TESLA=http://us.download.nvidia.com/tesla/396.44/NVIDIA-Linux-x86_64-396.44.run
    CUDA5=http://developer.download.nvidia.com/compute/cuda/5_0/rel-update-1/installers/cuda_5.0.35_linux_64_ubuntu11.10-1.run
    CUDA8=https://developer.nvidia.com/compute/cuda/8.0/Prod2/local_installers/cuda_8.0.61_375.26_linux-run
    FREESURFER=ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz
    BEDPOSTX_GPU=http://users.fmrib.ox.ac.uk/~moisesf/Bedpostx_GPU/CUDA_8.0/bedpostx_gpu.zip
    mkdir /share
    apt-get -y update
    apt-get install -y apt-transport-https
    apt-get install -y software-properties-common
    add-apt-repository -y universe
    apt-get -y update
    apt-get -y install wget tcsh build-essential python3 python3-dev curl libtool unzip kmod initramfs-tools locales vim-tiny dkms
    locale-gen en_US.UTF-8
    rm /bin/sh
    ln -s /bin/bash /bin/sh
    # Python3 and Parsl
    curl -Ok $GET_PIP
    python3 get-pip.py
    python3 -m pip install parsl
    # Nvidia Drivers
    apt-get -y install linux-headers-`uname -r`
    echo "blacklist nouveau" >> /etc/modprobe.d/blacklist-nouveau.conf
    echo "options nouveau modeset=0" >> /etc/modprobe.d/blacklist-nouveau.conf
    update-initramfs -u
    TESLA_RUN=$(basename $TESLA)
    wget --no-check-certificate $TESLA
    sh $TESLA_RUN --dkms -s --no-drm
    # CUDA 5.0
    CUDA5_RUN=$(basename $CUDA5)
    wget --no-check-certificate $CUDA5
    sh $CUDA5_RUN -silent -override -toolkit
    # CUDA 8.0
    CUDA8_RUN=$(basename $CUDA8)
    wget --no-check-certificate $CUDA8
    sh $CUDA8_RUN -silent -override -toolkit
    # FSL
    gpg --keyserver hkp://keyserver.ubuntu.com:80 --recv 9BDB3D89CE49EC21
    wget -O- http://neuro.debian.net/lists/xenial.us-nh.full | tee /etc/apt/sources.list.d/neurodebian.sources.list
    apt-key adv --recv-keys --keyserver hkp://pool.sks-keyservers.net:80 0xA5D32F012649A5A9
    apt-get -y update
    apt-get -y install fsl-5.0-complete
    # Bedpostx GPU
    BEDPOSTX_GPU_ZIP=$(basename $BEDPOSTX_GPU)
    wget --no-check-certificate $BEDPOSTX_GPU
    unzip -o -d /usr/share/fsl/5.0 $BEDPOSTX_GPU_ZIP
    cp /usr/share/fsl/5.0/bin/*.so /usr/share/fsl/5.0/lib/
    # Freesurfer
    FREESURFER_GZ=$(basename $FREESURFER)
    wget --no-check-certificate $FREESURFER
    tar -xzf $FREESURFER_GZ -C /opt
    # Fake License - should be replaced by a real one
    touch license.txt
    cp license.txt /opt/freesurfer/license.txt
    # Cleanup
    rm -rf get-pip.py
    rm -rf $TESLA_RUN
    rm -rf $CUDA5_RUN
    rm -rf $CUDA8_RUN
    rm -rf $FREESURFER_GZ
    rm -rf $BEDPOSTX_GPU_ZIP
    rm -rf /license.txt
    apt-get -y clean
%environment
    export FSLDIR=/usr/share/fsl/5.0
    FSL_DIR=$FSLDIR
    FSLOUTPUTTYPE=NIFTI_GZ
    FSLMULTIFILEQUIT=TRUE
    FSLTCLSH=${FSLDIR}/bin/fsltclsh
    FSLWISH=${FSLDIR}/bin/fslwish
    FSLGECUDAQ="cuda.q"
    FSL_BIN=${FSLDIR}/bin
    FS_OVERRIDE=0
    COMPILE_GPU=1
    export FSL_DIR FSLOUTPUTTYPE FSLMULTIFILEQUIT FSLTCLSH FSLWISH FSLGECUDAQ FSL_BIN FS_OVERRIDE COMPILE_GPU
    export FREESURFER_HOME=/opt/freesurfer
    LOCAL_DIR=${FREESURFER_HOME}/local
    PERL5LIB=${FREESURFER_HOME}/mni/share/perl5
    FSFAST_HOME=${FREESURFER_HOME}/fsfast
    FMRI_ANALYSIS_DIR=${FREESURFER_HOME}/fsfast
    FSF_OUTPUT_FORMAT="nii.gz"
    MNI_DIR=${FREESURFER_HOME}/mni
    MNI_DATAPATH=${FREESURFER_HOME}/mni/data
    MNI_PERL5LIB=${FREESURFER_HOME}/mni/share/perl5
    MINC_BIN_DIR=${FREESURFER_HOME}/mni/bin
    MINC_LIB_DIR=${FREESURFER_HOME}/mni/lib
    SUBJECTS_DIR=/share
    FUNCTIONALS_DIR=${FREESURFER_HOME}/sessions
    export LOCAL_DIR PERL5LIB FSFAST_HOME FMRI_ANALYSIS_DIR FSF_OUTPUT_FORMAT MNI_DIR MNI_DATAPATH MNI_PERL5LIB MINC_BIN_DIR MINC_LIB_DIR SUBJECTS_DIR FUNCTIONALS_DIR
    export CUDA_5_LIB_DIR=/usr/local/cuda-5.0/lib64
    export CUDA_8_LIB_DIR=/usr/local/cuda-8.0/lib64
    export PATH="${FREESURFER_HOME}/bin:${MNI_DIR}/bin:${FSLDIR}/bin:$PATH"
    export LD_LIBRARY_PATH="${FSLDIR}/lib:$LD_LIBRARY_PATH"
    export OS=LINUX

Collection

• Name: madduri/singularity-freesurfer-gpu
• License: Apache License 2.0

Metrics

Feedback

Was this page helpful?

Glad to hear it! Please tell us how we can improve.

Sorry to hear that. Please tell us how we can improve.