For a full AMUSE installation, you will need to install some further dependencies that can be installed via your package manager - e.g. apt or yum on Linux; macports or homebrew on macOS.
You can choose between openmpi and mpich as desired, both work with AMUSE. Please do not install both!
For openmpi:
sudo apt-get install build-essential gfortran python3-dev \
libopenmpi-dev openmpi-bin \
libgsl-dev cmake libfftw3-3 libfftw3-dev \
libgmp3-dev libmpfr6 libmpfr-dev \
libhdf5-serial-dev hdf5-tools \
libblas-dev liblapack-dev \
python3-venv python3-pip git
For mpich:
sudo apt-get install build-essential gfortran python3-dev \
mpich libmpich-dev \
libgsl-dev cmake libfftw3-3 libfftw3-dev \
libgmp3-dev libmpfr6 libmpfr-dev \
libhdf5-serial-dev hdf5-tools \
libblas-dev liblapack-dev \
python3-venv python3-pip git
On macOS, you will first need to install Xcode. You can do so via the app store. In the examples below we choose GCC-11 as the compiler. Older versions may not work on recent versions of macOS. In macOS Big Sur and later, you may have to add the following line to your .bashrc or .zshrc profile:
export SDKROOT=/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
In this section we assume a default macOS installation (up to Monterey) with MacPorts, but other methods (such as Homebrew) will also work. Please do not install packages using more than one package manager (MacPorts, Homebrew and/or Conda), as this will almost certainly lead to problems! On a Mac with an Apple Silicon chip (M1 and later) please use gcc12 (or later), earlier versions of gcc may not always work.
You can choose between openmpi and mpich as desired, both work with AMUSE. Please make sure to set the compilers installed here as default, as it will greatly simplify things later on.
For openmpi:
sudo port install gcc12 openmpi-gcc12 hdf5 gsl cmake gmp mpfr fftw-3 +gcc12 openblas lapack
sudo port install python39
sudo port select --set mpi openmpi-gcc12-fortran
sudo port select --set gcc mp-gcc12
sudo port select --set python3 python39
For mpich:
sudo port install gcc12 mpich-gcc12 hdf5 gsl cmake gmp mpfr fftw-3 +gcc12 openblas lapack
sudo port install python39
sudo port select --set mpi mpich-gcc12
sudo port select --set gcc mp-gcc12
sudo port select --set python3 python39
After installing the prerequisites, you can install AMUSE. Optionally, first create a virtual environment to install AMUSE and other desired Python packages in. This ensures that you don’t need root privileges and that your AMUSE environment is isolated from other system-installed packages.
To create the virtual environment, do (from a desired directory):
python3 -m venv Amuse-env
When the environment is created, you can activate it with:
. Amuse-env/bin/activate
You may want to make an alias for this, e.g.:
alias amuse-env='. ~/virtualenvironments/Amuse-env/bin/activate'
From this point, your prompt will have ‘Amuse-env’ in front of it, so you will always know when you’re in this virtual environment.
Now you can use pip to install the prerequisite python modules for AMUSE:
pip install --upgrade pip
pip install numpy docutils mpi4py h5py wheel
Probably, you’ll want to install these Python modules too:
pip install scipy astropy jupyter pandas seaborn matplotlib
Now we can finally install AMUSE itself. This is done easiest via pip, installing first the framework and then any of the required packages:
pip install amuse-framework
pip install amuse-$(community_code_name)
Alternatively, you may try to install all of AMUSE in one go:
pip install amuse
However, this may fail if any of the packages fail to build. Installing the packages separately is generally a faster and more successful method.
The packages installed with pip are distributed as source packages that must be compiled against the libraries
installed on your local machine. After compilation pip saves a binary package version in its cache.
In case of problems with the AMUSE installation using pip or if the environment changes it may be necessary to clean the pip cache (e.g. at `~/.cache/pip`). In addition, the cache can be disabled using the `--no-cache-dir` option. the `--no-build-isolation` may also be tried in case the virtualenv has all the prerequisites, but the build still fails.
The `--no-clean` pip install option preserves the build directory for debugging purposes (The actual directory is reported
in verbose mode `-v`).
Alternatively, you can install amuse as a development build, which allows you to modify the source code. It is potentially also more convenient when encountering issues with installation of specific codes as the build.log file in the root directory of the repository contains the error logs of the installation process.
Installation can also be handled through pip by executing (in the root of a clone of the repository)
pip install -e .
after this the codes need to be build:
python setup.py develop_build
individual codes can be build with:
make {code}.code
with {code} the name of the code in lower case.
Note that the modules on your local HPC system may be differently named.
module load 2022
module load foss/2022a
Load python.
module load Python/3.10.4-GCCcore-11.3.0 # or another version of python, 3.7 or higher
Following AMUSE documentation (see above), download/upgrade the python package: (–user is required by Snellius)
mkdir MY_PROJECT_DIR
cd MY_PROJECT_DIR
python3 -m venv env # initialise a Python virtual environment, which will contain all the packages we install
source env/bin/activate # activate the virtual environment - this must be repeated every time you log in
pip install --upgrade pip
cd AMUSE_DIR # change to where you downloaded AMUSE
pip install -r requirements.txt --upgrade # install/upgrade all required packages
pip install matplotlib # not required but highly recommended
pip install -e .
Now you can build the AMUSE framework with
make framework
Finally, build AMUSE individual codes by running from the AMUSE directory:
make {code}.code
When you log in again (and in your SLURM scripts), you will need to load the same modules and activate the same environment:
module load 2022
module load foss/2022a
module load Python/3.10.4-GCCcore-11.3.0 # or another version of python, 3.7 or higher
cd MY_PROJECT_DIR
source env/bin/activate