Getting Started

Installation

EpiHiper code is available from GitHub

Obtain Code

git clone https://github.com/NSSAC/EpiHiper.git

Building a single threaded executable

From the root directory of the repository execute:

mkdir build
cd build
cmake -G "Unix Makefiles" -DENABLE_MPI=OFF -DENABLE_OMP=OFF -DENABLE_LOCATION_ID=OFF ..
make -j4

Building an MPI (multi-process) executable

Additional dependencies:

From the root directory of the repository execute:

mkdir build
cd build
cmake -G "Unix Makefiles" -DENABLE_MPI=ON -DENABLE_OMP=OFF -DENABLE_LOCATION_ID=OFF ..
make -j4

Building an OpenMP (multi-threaded) executable

Additional dependencies:

  • OpenMP is provided by the compiler and optionally additional run time libraries (provided by package: libgomp1)

  • Microsoft Visual C++ support of OpenMP is outdated please see Getting started with OpenMP on Windows for help.

From the root directory of the repository execute:

mkdir build
cd build
cmake -G "Unix Makefiles" -DENABLE_MPI=OFF -DENABLE_OMP=ON -DENABLE_LOCATION_ID=OFF ..
make -j4

Note: It is possible to combine OpenMP and MPI

Dependencies

Installation of dependencies may require platform and system dependent tools such as zypper, yum or aptitude on Linux. Since specifics of such tools and package version may change with versions, we refer the user to the documentation accompanying these tools. All other dependencies are provided through git submodules, which are automatically retrieved during configuration and compiled during make.

Requirements for building EpiHiper:

  • C++ 11 compatible compiler (Clang, or gcc)

  • Cmake version 3.11 or above

  • PostgreSQL library and header (provided by packages: libpq5, postgresql-devel)

Ubuntu (22.04) or Debian (bullseye)

# required
sudo apt-get update
sudo apt-get install build-essential git
sudo apt-get install cmake libpq5 libpq-dev
# OpenMPI
sudo apt-get install libopenmpi-dev
# OpenMP
sudo apt-get install libgomp1

openSUSE (Leap latest)

# required
sudo zypper refresh
sudo zypper install patterns-devel-base-devel_basis
sudo zypper install patterns-devel-C-C++-devel_C_C++
sudo zypper install gcc-c++ git
sudo zypper install cmake libpq5 postgresql-devel
# OpenMPI (optional)
sudo zypper install openmpi4-devel
# OpenMP (optional)
sudo zypper install libgomp1

Arch Linux

# required
sudo pacman -S git cmake postgresql-libs
# OpenMPI (optional)
sudo pacman -S openmpi
# OpenMP (optional)
# no additional requirements

Rocky Linux (9)

# required
sudo dnf groupinstall 'Development Tools'
sudo dnf -y install cmake libpq-devel
# OpenMPI (optional)
sudo dnf install openmpi openmpi-devel
# Add MPI executables to your path, e.g.
echo export PATH=\"/usr/lib64/openmpi/bin/:\$PATH\" >> ~/.profile
# OpenMP (optional)
sudo dnf install libgomp

MacOS X

# required
brew install cmake git libpq
# OpenMPI (optional)
brew install open-mpi
# OpenMP (optional)
brew install libomp
All other dependencies are provided through git submodules, which are automatically retrieved during configuration and compiled during make. These dependencies are:

Configuration options:

Table 1 Configuration options.
Option
Values
Default
Description
-DCMAKE_BUILD_TYPE
Debug
Release
Release
Enable debug build.
-DENABLE_LOCATION_ID
ON
OFF
ON
Enable location Id support for networks.
-DENABLE_MPI
ON
OFF
ON
Enable MPI parallelization.
-DENABLE_OMP
ON
OFF
ON
Enable OpenMP parallelization.
-DENABLE_LOGLEVEL_TRACE
ON
OFF
OFF
Enable support for log level trace.