Installing the AMICI Python package

Short guide

Installation of the AMICI Python package has the following prerequisites:

Python>=3.10
SWIG>=3.0
CBLAS compatible BLAS library (e.g., OpenBLAS, CBLAS, Atlas, Accelerate, Intel MKL)
a C++17 compatible C++ compiler and a C compiler (e.g., g++>=9.1, clang>=12, Intel C++ compiler, mingw)

If these requirements are fulfilled and all relevant paths are setup properly, AMICI can be installed using:

pip3 install amici

If this worked, you can now import the Python module via:

import amici

If this does not work for you, please follow the full instructions below.

Installation on Linux

Ubuntu 22.04 / 24.04

Install the AMICI dependencies via apt (this requires superuser privileges):

sudo apt install libatlas-base-dev swig

# optionally for HDF5 support:
sudo apt install libhdf5-serial-dev

# optionally for boost support (thread-specific CPU times, extended math functions, serialization)
libboost-chrono-dev libboost-math-dev libboost-serialization-dev

Install AMICI:

pip3 install amici

Fedora 32

Install the AMICI dependencies via apt (this requires superuser privileges):

sudo dnf install blas-devel swig

Install AMICI:

pip3 install amici

Arch Linux

Install the AMICI dependencies via pacman (this requires superuser privileges):

sudo pacman -S python swig openblas gcc hdf5 boost-libs

Export the bash variables BLAS_CFLAGS and BLAS_LIBS to point to where BLAS was installed, e.g.:

export BLAS_CFLAGS="-I/usr/include/openblas/"
export BLAS_LIBS="-lopenblas"

Install AMICI:

pip3 install amici

Alternatively:

Check if packages are already installed with the required versions for AMICI installation.

sudo pacman -Si python swig openblas gcc hdf5 boost-libs

Upgrade installed packages if required mininum versions are not satisfied for AMICI installation.

sudo pacman -Su python swig openblas gcc hdf5 boost-libs

Export the bash variables BLAS_CFLAGS and BLAS_LIBS to point to where BLAS was installed, e.g.:

export BLAS_CFLAGS="-I/usr/include/openblas/"
export BLAS_LIBS="-lopenblas"

Install AMICI:

pip3 install amici

Installation on OSX

Install the AMICI dependencies using homebrew:

brew install swig

# optionally for HDF5 support:
brew install hdf5

# optionally for parallel simulations:
brew install libomp
# followed by either `brew link openmp` once,
# or `export OpenMP_ROOT=$(brew --prefix)/opt/libomp"` where `OpenMP_ROOT` will have to be set during every re-installation of AMICI or any new model import

# optionally for boost support (thread-specific CPU times, extended math functions, serialization)
brew install boost && export BOOST_ROOT=$(brew --prefix)/opt/boost
# followed by either `brew link boost` once,
# or `export BOOST_ROOT=$(brew --prefix)/opt/boost"` where `BOOST_ROOT` will have to be set during every re-installation of AMICI or any new model import

Install AMICI:

pip3 install amici

Installation on Windows

Some general remarks:

Consider using the Windows Subsystem for Linux (WSL) and follow the instructions for installation on linux.
Install all libraries in a path not containing white spaces, e.g. directly under C:.
Replace the following paths according to your installation.
Slashes can be preferable to backslashes for some environment variables.
See also [#425](https://github.com/AMICI-dev/amici/issues/425) for further discussion.

Using the Microsoft Visual Studio

We assume that Visual Studio (not to be confused with Visual Studio Code) is already installed. Using Visual Studio Installer, the following components need to be included:

Microsoft Visual C++ (MSVC). This is part of multiple packages, including Desktop Development with C++.
Windows Universal C Runtime. This is an individual component and installs some DLLs that we need.

OpenBLAS

There are prebuilt OpenBLAS binaries available, but they did not seem to work well here. Therefore, we recommend building OpenBLAS from scratch. This requires an installation of CMake. CMake can be installed from https://cmake.org/download/ (system-wide), or via pip install cmake (in the current Python environment).

To build OpenBLAS, download the following scripts from the AMICI repository:

The first script needs to be called in Powershell, and it needs to call compileBLAS.cmd, so you will need to modify line 11:

cmd /c “scriptscompileBLAS.cmd $version”

Additionally, in compileBLAS.cmd make sure that you point to your Visual Studio installation on line 3. Newer installations could be located under C:\Program Files\Microsoft Visual Studio\...\VC\Auxiliary\Build\vcvars64.bat.

so that it matches your directory structure. This will download OpenBLAS and compile it, creating C:\\BLAS\\OpenBLAS\\lib\\openblas.lib and C:\\BLAS\\OpenBLAS\\bin\\openblas.dll.

You will also need to define two environment variables:

BLAS_LIBS="-LIBPATH:C:/BLAS/OpenBLAS/lib openblas.lib"
BLAS_CFLAGS="-IC:/BLAS/OpenBLAS"

One way to do that is to run a PowerShell script with the following commands:

[System.Environment]::SetEnvironmentVariable("BLAS_LIBS", "-LIBPATH:C:/BLAS/OpenBLAS/lib openblas.lib", [System.EnvironmentVariableTarget]::User)
[System.Environment]::SetEnvironmentVariable("BLAS_LIBS", "-LIBPATH:C:/BLAS/OpenBLAS/lib openblas.lib", [System.EnvironmentVariableTarget]::Process)
[System.Environment]::SetEnvironmentVariable("BLAS_CFLAGS", "-IC:/BLAS/OpenBLAS/include/openblas", [System.EnvironmentVariableTarget]::User)
[System.Environment]::SetEnvironmentVariable("BLAS_CFLAGS", "-IC:/BLAS/OpenBLAS/include/openblas", [System.EnvironmentVariableTarget]::Process)

The call ending in Process sets the environment variable in the current process, and it is no longer in effect in the next process. The call ending in User is permanent, and takes effect the next time the user logs on.

Now you need to make sure that all required DLLs are within the scope of the PATH variable. In particular, the following directories need to be included in PATH:

C:\BLAS\OpenBLAS\bin
C:\Program Files (x86)\Windows Kits\10\Redist\ucrt\DLLs\x64

The first one is needed for openblas.dll and the second is needed for the Windows Universal C Runtime.

If any DLLs are missing in the PATH variable, Python will return the following error upon import amici:

ImportError: DLL load failed: The specified module could not be found.

Almost all of the DLLs are standard Windows DLLs and should be included in either Windows or Visual Studio. But, in case it is necessary to test this, here is a list of some DLLs required by AMICI (when compiled with MSVC):

openblas.dll
python37.dll
MSVCP140.dll
KERNEL32.dll
VCRUNTIME140_1.dll
VCRUNTIME140.dll
api-ms-win-crt-convert-l1-1-0.dll
api-ms-win-crt-heap-l1-1-0.dll
api-ms-win-crt-stdio-l1-1-0.dll
api-ms-win-crt-string-l1-1-0.dll
api-ms-win-crt-runtime-l1-1-0.dll
api-ms-win-crt-time-l1-1-0.dll
api-ms-win-crt-math-l1-1-0.dll

MSVCP140.dll, VCRUNTIME140.dll, and VCRUNTIME140_1.dll are needed by MSVC (see Visual Studio above). KERNEL32.dll is part of Windows and in C:\Windows\System32. The api-ms-win-crt-XXX-l1-1-0.dll are needed by openblas.dll and are part of the Windows Universal C Runtime.

Note

Since Python 3.8, the library directory needs to be set either from Python:

import os
# directory containing `openblas.dll`
os.add_dll_directory("C:\\BLAS\\OpenBLAS\\bin")
import amici

or via the environment variable AMICI_DLL_DIRS="C:\BLAS\OpenBLAS\bin".

Further topics

Installation of development versions

To install development versions which have not been released to PyPI yet, you can install AMICI with pip directly from GitHub using:

pip3 install -e git+https://github.com/AMICI-dev/amici.git@develop#egg=amici\&subdirectory=python/sdist

Replace develop by the branch or commit you want to install.

Note that this will only work on Windows if you have enabled developer mode, because symlinks are not supported by default (more information).

Light installation

In case you only want to use the AMICI Python package for generating model code for use with Matlab or C++ and don’t want to bothered with any unnecessary dependencies, you can run

pip3 install --install-option --no-clibs amici

Note

Following this installation, you will not be able to simulate the imported models in Python.

Note

If you run into an error with above installation command, install all AMICI dependencies listed in setup.py manually, and try again. (This is because pip --install-option is applied to all installed packages, including dependencies.)

Custom installation

Installation of the AMICI Python package can be customized using a number of environment variables:

Variable	Purpose	Example
`SWIG`	Path to the SWIG executable	`SWIG=$HOME/bin/swig4.0`
`CC`	Setting the C(++) compiler	`CC=/usr/bin/g++`
`CFLAGS`	Extra compiler flags used in every compiler invocation
`BLAS_CFLAGS`	Compiler flags for, e.g. BLAS include directories
`BLAS_LIBS`	Flags for linking BLAS
`ENABLE_GCOV_COVERAGE`	Set to build AMICI to generate code coverage information	`ENABLE_GCOV_COVERAGE=TRUE`
`ENABLE_AMICI_DEBUGGING`	Set to build AMICI with debugging symbols	`ENABLE_AMICI_DEBUGGING=TRUE`
`AMICI_PARALLEL_COMPILE`	Set to the number of parallel processes to be used for C(++) compilation (defaults to 1)	`AMICI_PARALLEL_COMPILE=4`
`AMICI_TRY_ENABLE_HDF5`	Whether to build AMICI with HDF5-support if possible. Default: `ON`	`AMICI_TRY_ENABLE_HDF5=OFF`

Installation under conda

There is no amici conda recipe available yet. However, you can install AMICI using pip in a conda environment.

Note

It is possible, but we currently don’t recommend using conda for installing AMICI, as it commonly leads to conflicts with system installations of libraries and compilers.

Create a minimal conda environment via:

conda create --name ENV_NAME pip python

Here, replace ENV_NAME by some name for the environment.

To activate the environment, run:

source activate ENV_NAME

(and conda deactivate later to deactivate it again).

SWIG must be installed and available in your PATH, and a CBLAS-compatible BLAS must be available. You can also use conda to install the latter locally, using:

conda install -c conda-forge openblas

To make AMICI use openblas, set the following environment variable:

export BLAS_LIBS=-lopenblas

BLAS_LIBS needs to be set during installation of the AMICI package, as well as during any future model import.

To install AMICI, now run:

pip install amici

The pip option --no-cache may be helpful here to make sure the installation is done completely anew.

Now, you are ready to use AMICI in the virtual environment.

Note

conda on Mac

If the above installation does not work for you, try installing AMICI via:

CFLAGS="-stdlib=libc++" CC=clang CXX=clang pip3 install --verbose amici

This will use the clang compiler.

You will have to pass the same options when compiling any model later on. This can be done by inserting the following code before model import:

import os
os.environ['CC'] = 'clang'
os.environ['CXX'] = 'clang'
os.environ['CFLAGS'] = '-stdlib=libc++'

(For further discussion see https://github.com/AMICI-dev/AMICI/issues/357)

Known issues:

CMAKE_AR-NOTFOUND: not found: Try conda install binutils.

Optional Boost support

Boost is an optional C++ dependency only required for special functions (including e.g. gamma derivatives) in the Python interface. Boost can be installed via package managers via

apt-get install libboost-math-dev

or

brew install boost

As only headers are required, also a source code download suffices. The compiler must be able to find the module in the search path.