7. Installation


NEMO is available on https://github.com/teuben/nemo

7.1. Installation from github

Installation is normally done by getting the source code via github.

7.1.1. The One Liners

Here is an example, just 3 lines in your (bash) shell, using a configurable helper script:

wget --backups=1 https://teuben.github.io/nemo/install_nemo.sh


curl -LO https://teuben.github.io/nemo/install_nemo.sh

after which installation can be done with something like

bash install_nemo.sh nemo=$HOME/opt/nemo yapp=pgplot bench5=1 python=1
source  $HOME/opt/nemo/nemo_start.sh

where the arguments to the install_nemo.sh script are optional, but a few are given to show some often use non-defaults. See that script for more details, or use the -h flag

7.1.2. A Fuller Example

A more manual install, bypassing this script, can be:

git clone https://github.com/teuben/nemo
cd nemo
./configure --with-yapp=pgplot
make build check bench5 python
source nemo_start.sh

On a Mac with SIP protection, enabled, the --disable-shared flag may need to be added.

git clone https://github.com/teuben/nemo
cd nemo
./configure --with-yapp=pgplot --disable-shared
make build check bench5
source nemo_start.sh

Disabling SIP is not recommended, so we’ve been told. On a Mac you will also need to have Xcode installed, and gfortran (e.g. via brew). We need a special section on this

7.2. Pre-conditions

For a minimal install a number of packages need to be present on your system. Compilers, the make utility, the csh shell, etc. For some systems (e.g. Ubuntu) we keep a list of minimum requirements of the packages that you will need for a minimal install.n

cd $NEMO
make install_apt
cat src/scripts/requirements/apt.txt
cat src/scripts/linux/ubuntu20.04

where the last ubuntu20.04 file is a more complete list of packages. See below for some expanded information on packing.

7.3. Rebuilding

If you have an existing installation, but many things have change, this is probably the preferred method:

cd $NEMO
git pull
make rebuild

this will also preserve the possibly peculiar options for configure that you passed the first time it was installed. Or more importantly, if you had edited the $NEMOLIB/makedefs file.

7.4. Advanced Installation

It’s a fact of life that you will not always be satisified with the compiler or libraries that your system provides. Add to this that if you don’t have admin privilages, and you might be in for a rude awakening.

No worries, NEMO has you covered (to some degree). We provide an environment (a poor man’s container) where most open source libraries can be installed with a supported $NEMO/opt prefix. This means you can configure packages using


or for cmake based packages


as NEMO generally adds the $NEMO/opt tree search for include and library files, as well as adding its binaries to the search path. Even if you would not use NEMO itself, building your other software with the $NEMO/opt could be useful.

For some packages this has been automated using the mknemo command, described in the next section.

7.5. mknemo

Although the mknemo script was intended to quickly compile a NEMO program (from any directory), and without the need to know where the source code lives, it is now also used to aid the installation of a number of supported libraries that can be used by NEMO. They are compiled within $NEMO/local, and will be installed in $NEMO/opt, as described in the previous section. The supporting scripts are generally located $NEMO/src/scripts/mknemo.d for you to examine.


mknemo cfitsio fftw gsl hdf4 hdf5 hypre netcdf4 wcslib

The Programmers Guide will give some advanced examples how to deal with other libraries, and writing your own programs or one of the plugins.

7.6. python

With so many useful python packages around, and so many different methods (anaconda, conda, venv etc.), we will not recommend a method, as this will likely depend on your own situation. The installation examples below should give you enough information how to adapt it for your python workflow.

However, if you install python from within NEMO, there will be a $NEMO/anaconda3 directory, that gets automatically activated once NEMO is loaded. Here is how you can install that version:

cd $NEMO
make python

This could also install a few python modules we often wind up using: amuse-framework, amuse-galactics, amuse-gadget2, amuse-bhtree, astromartini, gala, galpy, pynbody, python-unsio, python-unsiotools, and yt

For a number of these we have small test scripts to see if they are functional:

cd $NEMO/src/scripts/python
make tests

For the cases where you want some control and be in developer mode, we suggest the recommended practice of placing the code in $NEMO/local, as can be seen in the example below

cd $NEMO/local
git clone https://github.com/webbjj/clustertools
pip install -e clustertools

For a few packages, we have a few existing examples in the $NEMO/usr tree (e.g. amuse, martini, unsio and uns_projects)

7.7. Package Managers

Most operating systems will have some package manager that controls how software is installed. There is also a list in $NEMO/src/scripts/linux and $NEMO/src/scripts/brew, but here we list a few common ones:

Ubuntu: the package manager is called apt

sudo apt install ...



Fedora: the package manager is called dnf (formerly rpm)

sudo dnf install ...



Not tested, probably same as Fedora

sudo dnf install ...

The package manager is called brew, but installation is done via https://brew.sh

Normally installed in the users own space. Prepend with the usual “sudo” if need be. Can be used on both Linux and Mac. Recent versions have barred pgplot, because of Caltech licencing issues.

brew install ...