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Singularity: Update Singularity recipe for eddy_cuda9.1 support #2388

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Singularity: Update Singularity recipe for eddy_cuda9.1 support #2388

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25 changes: 22 additions & 3 deletions Singularity
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Original file line number Diff line number Diff line change
Expand Up @@ -26,8 +26,8 @@ Include: apt
export FSLDIR FSLOUTPUTTYPE FSLMULTIFILEQUIT FSLTCLSH FSLWISH

# All
LD_LIBRARY_PATH="/usr/local/cuda/lib64:/usr/local/cuda/bin:/.singularity.d/libs:/usr/lib:/opt/fsl/lib:$LD_LIBRARY_PATH"
PATH="/opt/mrtrix3/bin:/opt/ants/bin:/opt/art/bin:/opt/fsl/bin:/usr/local/cuda/bin:$PATH"
LD_LIBRARY_PATH="/usr/local/cuda-9.1/lib64:/usr/local/cuda-9.1/bin:/.singularity.d/libs:/usr/lib:/opt/fsl/lib:$LD_LIBRARY_PATH"
PATH="/opt/mrtrix3/bin:/opt/ants/bin:/opt/art/bin:/opt/fsl/bin:/usr/local/cuda-9.1/bin:$PATH"
export LD_LIBRARY_PATH PATH

%post
Expand All @@ -44,6 +44,25 @@ Include: apt
# Build requirements
apt-get update && apt-get install -y --no-install-recommends build-essential ca-certificates curl git libeigen3-dev libfftw3-dev libgl1-mesa-dev libpng-dev libqt5opengl5-dev libqt5svg5-dev libtiff5-dev qt5-qmake qtbase5-dev-tools wget zlib1g-dev

# Add CUDA 9.1 support for eddy (based on https://gist.github.com/DaneGardner/accd6fd330348543167719002a661bd5#install-cuda-toolkit)
# Create tmp directory for CUDA installers
mkdir /cuda_tmp && cd /cuda_tmp
curl -LO https://developer.nvidia.com/compute/cuda/9.1/Prod/local_installers/cuda_9.1.85_387.26_linux
curl -LO https://developer.nvidia.com/compute/cuda/9.1/Prod/patches/1/cuda_9.1.85.1_linux
curl -LO https://developer.nvidia.com/compute/cuda/9.1/Prod/patches/2/cuda_9.1.85.2_linux
curl -LO https://developer.nvidia.com/compute/cuda/9.1/Prod/patches/3/cuda_9.1.85.3_linux

# Only install CUDA 9.1 toolkit
sh cuda_9.1.85_387.26_linux --silent --override --toolkit

# Install patches
sh cuda_9.1.85.1_linux --silent --accept-eula
sh cuda_9.1.85.2_linux --silent --accept-eula
sh cuda_9.1.85.3_linux --silent --accept-eula

# Clean up
cd && rm -r /cuda_tmp

# Neuroimaging software / data dependencies
# Download minified ART ACPCdetect (V2.0).
mkdir -p /opt/art && curl -fsSL https://osf.io/73h5s/download | tar xz -C /opt/art --strip-components 1
Expand All @@ -62,7 +81,7 @@ Include: apt
cd /opt/mrtrix3 && ./configure && ./build -persistent -nopaginate && rm -rf testing/ tmp/ && cd ../../

# apt cleanup to recover as much space as possible
apt-get remove -y build-essential ca-certificates curl git libeigen3-dev libfftw3-dev libgl1-mesa-dev libpng-dev libqt5opengl5-dev libqt5svg5-dev libtiff5-dev qt5-qmake qtbase5-dev-tools wget zlib1g-dev && apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
apt-get remove -y build-essential ca-certificates curl git libeigen3-dev libfftw3-dev libgl1-mesa-dev libpng-dev libqt5opengl5-dev libqt5svg5-dev libtiff5-dev qt5-qmake qtbase5-dev-tools wget zlib1g-dev && apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* #/tmp/* #/var/tmp/*
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@Lestropie Lestropie Apr 5, 2022

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@araikes Do you have any recollection of whether it was necessary to no longer wipe the contents of these directories, or whether this is just residual from testing?

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@Lestropie Lestropie Apr 7, 2022

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Note: This was originally addressed in comment in #2383.


%runscript
exec /usr/bin/bash -c "$@"