initial upload

2025-12-17 10:53:43 +08:00
commit f3f1778f77
308 changed files with 129940 additions and 0 deletions
--- a/singularity/tomoatt_cuda.def
+++ b/singularity/tomoatt_cuda.def
@@ -0,0 +1,87 @@
+Bootstrap: docker
+From: ubuntu:16.04
+
+%help
+This is a test container.
+
+%files
+    ../../TomoATT /opt/TomoATT
+
+%environment
+    export PKG_DIR=/opt/packages
+    export SINGULARITY_PKG_DIR=$PKG_DIR
+    export SINGULARITYENV_APPEND_PATH=$PKG_DIR/bin
+    export SINGULAIRTYENV_APPEND_LD_LIBRARY_PATH=$PKG_DIR/lib
+    export PATH=$PKG_DIR/bin:$PATH
+    export PATH=/opt/TomoATT/build/bin:$PATH
+    export LD_LIBRARY_PATH=$PKG_DIR/lib:$LD_LIBRARY_PATH
+
+%post
+    echo "Installing required packages..."
+    apt-get update && apt-get install -y wget git bash gcc gfortran g++ make file apt-transport-https ca-certificates
+
+    # install gcc-9 and g++-9
+    apt-get install -y software-properties-common && \
+    add-apt-repository ppa:ubuntu-toolchain-r/test -y && \
+    apt-get update -y && \
+    apt-get install -y gcc-9 g++-9 && \
+    update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-9 60 --slave /usr/bin/g++ g++ /usr/bin/g++-9
+
+    # install latest cmake
+    apt update && \
+    apt install -y software-properties-common lsb-release && \
+    apt clean all && \
+    wget -O - https://apt.kitware.com/keys/kitware-archive-latest.asc 2>/dev/null | gpg --dearmor - | tee /etc/apt/trusted.gpg.d/kitware.gpg >/dev/null && \
+    apt-add-repository "deb https://apt.kitware.com/ubuntu/ $(lsb_release -cs) main" && \
+    apt update && \
+    apt install kitware-archive-keyring && \
+    rm /etc/apt/trusted.gpg.d/kitware.gpg && \
+    apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 6AF7F09730B3F0A4 && \
+    apt update && \
+    apt install -y cmake && \
+    apt clean all
+
+    export PKG_DIR=/opt/packages
+    export NPROC=4
+
+    echo "Installing Open MPI"
+    export OMPI_VERSOIN_MAJOR=3.0
+    export OMPI_VERSION_FULL=3.0.1
+    export OMPI_URL="https://download.open-mpi.org/release/open-mpi/v$OMPI_VERSOIN_MAJOR/openmpi-$OMPI_VERSION_FULL.tar.gz"
+    mkdir -p /tmp/ompi
+    mkdir -p /opt
+    # Download
+    cd /tmp/ompi && wget -O openmpi-$OMPI_VERSION_FULL.tar.gz $OMPI_URL && tar -xvf openmpi-$OMPI_VERSION_FULL.tar.gz
+    # Compile and install
+    cd /tmp/ompi/openmpi-$OMPI_VERSION_FULL && ./configure --prefix=$PKG_DIR && make -j$NPROC && make install
+    # Set env variables so we can compile our application
+    export PATH=$PKG_DIR/bin:$PATH
+    export LD_LIBRARY_PATH=$PKG_DIR/lib:$LD_LIBRARY_PATH
+    export MANPATH=$PKG_DIR/share/man:$MANPATH
+
+    echo "openmpi installed."
+
+    echo "Compiling hdf5"
+
+    export HDF5_VERSION_MAJOR=1.13
+    export HDF5_VERSION_FULL=1.13.2
+    export HDF5_URL="https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-$HDF5_VERSION_MAJOR/hdf5-$HDF5_VERSION_FULL/src/hdf5-$HDF5_VERSION_FULL.tar.gz"
+    mkdir -p /tmp/hdf5
+    cd /tmp/hdf5 && wget -O hdf5-$HDF5_VERSION_FULL.tar.gz $HDF5_URL && tar -xvf hdf5-$HDF5_VERSION_FULL.tar.gz && cd hdf5-$HDF5_VERSION_FULL
+    tar -xvf hdf5-$HDF5_VERSION_FULL.tar.gz && cd hdf5-$HDF5_VERSION_FULL
+    CC=mpicc CXX=mpic++ ./configure --enable-parallel --enable-unsupported --enable-shared --enable-cxx --prefix=$PKG_DIR && make -j$NPROC && make install
+
+    echo "hdf5 installed."
+
+    cd /opt/TomoATT
+    mkdir -p build && cd build && rm -rf ./*
+    cmake .. -DUSE_CUDA=True -DCMAKE_PREFIX_PATH=$PKG_DIR
+    make -j$NPROC
+
+    echo "TomoATT installed."
+
+%labels
+
+    Maintainer MasaruNagaso
+
+    Version v1.0