initial upload

2025-12-17 10:53:43 +08:00
commit f3f1778f77
308 changed files with 129940 additions and 0 deletions
--- a/singularity/Dockerfile
+++ b/singularity/Dockerfile
@@ -0,0 +1,45 @@
+FROM ubuntu:latest AS spython-base
+ADD ../../TomoATT /opt/TomoATT
+LABEL Maintainer MasaruNagaso
+LABEL Version v1.0
+
+ENV PKG_DIR=/opt/ompi
+ENV SINGULARITY_PKG_DIR=$PKG_DIR
+ENV SINGULARITYENV_APPEND_PATH=$PKG_DIR/bin
+ENV SINGULAIRTYENV_APPEND_LD_LIBRARY_PATH=$PKG_DIR/lib
+ENV PATH=$PKG_DIR/bin:$PATH
+ENV PATH=/opt/TomoATT/build/bin:$PATH
+
+RUN echo "Installing required packages..."
+RUN apt-get update && apt-get install -y wget git bash gcc gfortran g++ make file cmake
+RUN export PKG_DIR=/opt/packages
+RUN export NPROC=4
+
+RUN echo "Installing Open MPI"
+RUN export OMPI_VERSOIN_MAJOR=3.0
+RUN export OMPI_VERSION_FULL=3.0.1
+RUN export OMPI_URL="https://download.open-mpi.org/release/open-mpi/v$OMPI_VERSOIN_MAJOR/openmpi-$OMPI_VERSION_FULL.tar.gz"
+RUN mkdir -p /tmp/ompi
+RUN mkdir -p /opt
+RUN cd /tmp/ompi && wget -O openmpi-$OMPI_VERSION_FULL.tar.gz $OMPI_URL && tar -xvf openmpi-$OMPI_VERSION_FULL.tar.gz
+RUN cd /tmp/ompi/openmpi-$OMPI_VERSION_FULL && ./configure --prefix=$PKG_DIR && make -j$NPROC && make install
+RUN export PATH=$PKG_DIR/bin:$PATH
+RUN export LD_LIBRARY_PATH=$PKG_DIR/lib:$LD_LIBRARY_PATH
+RUN export MANPATH=$PKG_DIR/share/man:$MANPATH
+RUN echo "openmpi installed."
+
+RUN echo "Compiling hdf5"
+RUN export HDF5_VERSION_MAJOR=1.13
+RUN export HDF5_VERSION_FULL=1.13.2
+RUN export HDF5_URL="https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-$HDF5_VERSION_MAJOR/hdf5-$HDF5_VERSION_FULL/src/hdf5-$HDF5_VERSION_FULL.tar.gz"
+RUN mkdir -p /tmp/hdf5
+RUN cd /tmp/hdf5 && wget -O hdf5-$HDF5_VERSION_FULL.tar.gz $HDF5_URL && tar -xvf hdf5-$HDF5_VERSION_FULL.tar.gz && cd hdf5-$HDF5_VERSION_FULL
+RUN tar -xvf hdf5-$HDF5_VERSION_FULL.tar.gz && cd hdf5-$HDF5_VERSION_FULL
+RUN CC=mpicc CXX=mpic++ ./configure --enable-parallel --enable-unsupported --enable-shared --enable-cxx --prefix=$PKG_DIR && make -j$NPROC && make install
+RUN echo "hdf5 installed."
+
+RUN cd /opt/TomoATT
+RUN mkdir -p build && cd build && rm -rf ./*
+RUN cmake .. -DCMAKE_PREFIX_PATH=$PKG_DIR
+RUN make -j$NPROC
+RUN echo "TomoATT installed."
--- a/singularity/Dockerfile_singularity_on_centos6
+++ b/singularity/Dockerfile_singularity_on_centos6
@@ -0,0 +1,47 @@
+FROM centos:6
+
+# install wget without yum
+RUN mv /etc/yum.repos.d/CentOS-Base.repo /etc/yum.repos.d/CentOS-Base.repo.bak && \
+    curl https://www.host-stage.net/hsmirrors/centos6repofix >/etc/yum.repos.d/CentOS-Base.repo && \
+    yum clean all
+
+RUN yum update ca-certificates -y
+
+# install dependencies
+RUN yum update -y && \
+     yum groupinstall -y 'Development Tools' && \
+     yum install -y \
+     openssl-devel \
+     libuuid-devel \
+     libseccomp-devel \
+     wget \
+     squashfs-tools \
+     cryptsetup
+
+
+
+# install go
+ENV VERSION=1.16.2 OS=linux ARCH=amd64
+RUN wget https://dl.google.com/go/go$VERSION.$OS-$ARCH.tar.gz && \
+    tar -C /usr/local -xzvf go$VERSION.$OS-$ARCH.tar.gz && \
+    rm go$VERSION.$OS-$ARCH.tar.gz
+ENV PATH="${PATH}:/usr/local/go/bin"
+
+# install singularity of 3.6.4
+RUN wget https://github.com/apptainer/singularity/releases/download/v3.6.4/singularity-3.6.4.tar.gz && \
+    tar -xvf singularity-3.6.4.tar.gz && \
+    rm singularity-3.6.4.tar.gz && \
+    cd singularity && \
+    ./mconfig && \
+    make -C builddir && \
+    make -C builddir install
+
+# install singularity of 3.9
+#ENV VERSION=3.9.5
+#RUN wget https://github.com/sylabs/singularity/releases/download/v${VERSION}/singularity-ce-${VERSION}.tar.gz && \
+#    tar -xzf singularity-ce-${VERSION}.tar.gz && \
+#    cd singularity-ce-${VERSION} && \
+#    ./mconfig && \
+#    make -C builddir && \
+#    make -C builddir install
+
--- a/singularity/Dockerfile_singularity_on_centos6_cuda10.1
+++ b/singularity/Dockerfile_singularity_on_centos6_cuda10.1
@@ -0,0 +1,47 @@
+FROM nvidia/cuda:10.2-devel-centos6
+
+# install wget without yum
+RUN mv /etc/yum.repos.d/CentOS-Base.repo /etc/yum.repos.d/CentOS-Base.repo.bak && \
+    curl https://www.host-stage.net/hsmirrors/centos6repofix >/etc/yum.repos.d/CentOS-Base.repo && \
+    yum clean all
+
+RUN yum update ca-certificates -y
+
+# install dependencies
+RUN yum update -y && \
+     yum groupinstall -y 'Development Tools' && \
+     yum install -y \
+     openssl-devel \
+     libuuid-devel \
+     libseccomp-devel \
+     wget \
+     squashfs-tools \
+     cryptsetup
+
+
+
+# install go
+ENV VERSION=1.16.2 OS=linux ARCH=amd64
+RUN wget https://dl.google.com/go/go$VERSION.$OS-$ARCH.tar.gz && \
+    tar -C /usr/local -xzvf go$VERSION.$OS-$ARCH.tar.gz && \
+    rm go$VERSION.$OS-$ARCH.tar.gz
+ENV PATH="${PATH}:/usr/local/go/bin"
+
+# install singularity of 3.6.4
+RUN wget https://github.com/apptainer/singularity/releases/download/v3.6.4/singularity-3.6.4.tar.gz && \
+    tar -xvf singularity-3.6.4.tar.gz && \
+    rm singularity-3.6.4.tar.gz && \
+    cd singularity && \
+    ./mconfig && \
+    make -C builddir && \
+    make -C builddir install
+
+# install singularity of 3.9
+#ENV VERSION=3.9.5
+#RUN wget https://github.com/sylabs/singularity/releases/download/v${VERSION}/singularity-ce-${VERSION}.tar.gz && \
+#    tar -xzf singularity-ce-${VERSION}.tar.gz && \
+#    cd singularity-ce-${VERSION} && \
+#    ./mconfig && \
+#    make -C builddir && \
+#    make -C builddir install
+
--- a/singularity/README.md
+++ b/singularity/README.md
@@ -0,0 +1,51 @@
+# Singularity image of TomoATT project
+
+[Singularity](https://docs.sylabs.io/guides/3.10/user-guide/introduction.html) is a container technology that prepare a pre-compiled project's executable with an environment required dependencies (this is called a container image).
+This is very useful for the users who are not familiar with the process of compiling the project's executable and installing the required dependencies, and also for the users who are not allowed to install the required dependencies on their system.
+
+Once the container image is prepared, this image can be uploaded on singularity-hub.org, and the users can download the image and run the project's executable on their system instantly.
+
+[Docker](https://www.docker.com/) is another container technology similar to Singularity, which is rather popular in the Information Technology (IT) community. However, Docker may not access the MPI library on the native system, which Singularity can do, and this cause degradation of the performance of the application.
+
+Therefore, Singularity is more popular and suitable in scientific computing community and often used in the HPC environment.
+
+
+This directry includes a singularity receipe file (*.def) to build a container image of TomoATT project.
+To build the container image,
+``` bash
+sudo singularity build tomoatt.sif tomoatt.def
+```
+
+To run the TomoATT executable on the container image,
+``` bash
+singularity run tomoatt.sif TOMOATT
+```
+
+To run the TomoATT executable on the container image with native MPI library,
+``` bash
+mpirun -n 8 singularity run tomoatt.sif TOMOATT -i input_params.yml
+```
+For utilizing the native MPI library, the version number of OpenMPI should be the same between the native system and the container image.
+The two variables in tomoatt.def file need to be modified for this purpose.
+``` bash
+    export OMPI_VERSOIN_MAJOR=3.0
+    export OMPI_VERSION_FULL=3.0.1
+```
+
+
+# For running the container image on the HPC with old kernel environment
+
+Some HPC systems have old kernel environment, e.g. CentOS 6, RHEL 6, and Ubuntu 16.04.
+In this case, the container image cannot be run on the HPC system. (The error message is "FATAL: kernel too old")
+To create a container image that can be run on the HPC system, this image needs to be built on the old kernel environment as well.
+For this purpose, we use [docker](https://www.docker.com/) for virtualy creating an old kernel environment, and then build the container image on it.
+
+To build the container image on the old kernel environment,
+``` bash
+docker build -t singularity_on_centos6 -f Dockerfile_singularity_on_centos6 .
+```
+
+To build the container image on the old kernel environment,
+``` bash
+docker run --privileged -v "(full path to)/TomoATT:/TomoATT" singularity_on_centos6 singularity build /TomoATT/singularity/tomoatt.sif /TomoATT/singularity/tomoatt.def
+```
--- a/singularity/tomoatt.def
+++ b/singularity/tomoatt.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$NPROC && make install
+
+    echo "hdf5 installed."
+
+    cd /opt/TomoATT
+    mkdir -p build && cd build && rm -rf ./*
+    cmake .. -DCMAKE_PREFIX_PATH=$PKG_DIR
+    make -j$NPROC
+
+    echo "TomoATT installed."
+
+%labels
+
+    Maintainer MasaruNagaso
+
+    Version v1.0
--- a/singularity/tomoatt_cuda.def
+++ b/singularity/tomoatt_cuda.def
@@ -0,0 +1,87 @@
+Bootstrap: docker
+From: ubuntu:16.04
+
+%help
+This is a test container.
+
+%files
+    ../../TomoATT /opt/TomoATT
+
+%environment
+    export PKG_DIR=/opt/packages
+    export SINGULARITY_PKG_DIR=$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