Install Dependencies

The beta version is also available on devel branch of the repository. You can install it from source code by following the instructions below. TomoATT is a C++ library, developed for working efficiently with parallel computing and HDF5 with parallel IO option.

Dependencies

git
C++ compiler which supports C++17 (version 7.0 or higher for GNU compiler. version 19.0 or higher for Intel compiler. Clang is also supported.)
CMake (version 3.10 or higher)
MPI v3.0 or higher
HDF5 (parallel IO needs to be enabled)
(optional) PyTomoATT (used in pre/post processes examples)

Install compiler and CMake (with GNU compiler)

Conda/Mamba

Skip this step.

Ubuntu/Debian

bash sudo apt install build-essential cmake

CentOS/Fodera

bash sudo yum install gcc gcc-c++ cmake

MacOS

bash brew install gcc cmake

Windows (wsl)

bash sudo apt install build-essential cmake

Install MPI and HDF5 with parallel IO option

Conda/Mamba

Using Conda

Conda provides us a convenient way to install the dependencies, which is easier and faster than installing them from source codes.

Create a conda environment


conda create --name tomoatt --channel conda-forge

Then activate the virtual environment


source activate tomoatt

Install the required libraries in the created virtual environment


conda install cxx-compiler cmake yaml-cpp openmpi "hdf5=*=mpi_openmpi*" -c conda-forge

Ubuntu/Debian


sudo apt install libopenmpi-dev openmpi-bin libhdf5-openmpi-dev

CentOS/Fodera


sudo yum install openmpi-devel hdf5-openmpi-devel

MacOS


brew install openmpi hdf5

Windows (wsl)


sudo apt install libopenmpi-dev openmpi-bin libhdf5-openmpi-dev

From Source

Compile and instal the dependencies from source code

It is often necessary to compile and install the dependencies from source codes, for example, compiling TomoATT on HPCs where the required libraries are not installed in the system. The terminal commands below shows an example to download and build openmpi and hdf5 from source codes. The commands are tested on Ubuntu 22.04. The commands may vary on different operating systems.

Here we use a specific directory local_mpi_hdf5 to install the libraries. You can change it to any directory you like.

Install MPI (OpenMPI)


# create a directory to install the libraries
mkdir -p ./local_mpi_hdf5
 
# download source
wget https://download.open-mpi.org/release/open-mpi/v4.1/openmpi-4.1.3.tar.gz
 
# Extract it
tar -xvf openmpi-4.1.3.tar.gz
cd openmpi-4.1.3
 
# configure
./configure --prefix=$(pwd)/../local_mpi_hdf5
 
# make
make -j4 && make install

Install HDF5


# go back to the parent directory
cd ..
 
# download hdf5 source
wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.13/hdf5-1.13.3/src/hdf5-1.13.3.tar.gz
 
#Extract the downloaded directory
tar -xvf hdf5-1.13.3.tar.gz
cd hdf5-1.13.3/
 
# Configure the code. Note that we need to specify the path to the MPI commands we just installed.
CC=$(pwd)/../local_mpi_hdf5/bin/mpicc CXX=$(pwd)/../local_mpi_hdf5/bin/mpicxx ./configure --enable-parallel --enable-unsupported --enable-shared --enable-cxx --prefix=$(pwd)/../local_mpi_hdf5
 
# make
make -j4 && make install

Now you have installed the required libraries in the directory local_mpi_hdf5.