# Installing the AMICI Python package¶

## Short guide¶

Installation of the AMICI Python package has the following prerequisites:

• Python>=3.7

• >=3.0

• CBLAS compatible BLAS library (e.g., OpenBLAS, CBLAS, Atlas, Accelerate, Intel MKL)

• a C++14 compatible C++ compiler and a C compiler (e.g., g++, clang, 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 20.04¶

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


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


## 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


Install AMICI:

pip3 install amici


## Installation on Windows¶

Some general remarks:

• 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.

### Using the MinGW compilers¶

• Install MinGW-W64 (the 32bit version will succeed to compile, but fail during linking).

MinGW-W64 GCC-8.1.0 for x86_64-posix-sjlj (direct link) has been shown to work on Windows 7 and 10 test systems.

• Add the following directory to your PATH: C:\mingw-w64\x86_64-8.1.0-posix-sjlj-rt_v6-rev0\mingw64\bin

• Make sure that this is the compiler that is found by the system (e.g. where gcc in a cmd should point to this installation).

Set the following environment variables:

• BLAS_CFLAGS=-IC:/OpenBLAS-v0.2.19-Win64-int32/include

• BLAS_LIBS=-Wl,-Bstatic -LC:/OpenBLAS-v0.2.19-Win64-int32/lib -lopenblas -Wl,-Bdynamic

• Install SWIG and add the SWIG directory to PATH (e.g. C:\swigwin-3.0.12 for version 3.0.12)

• Install AMICI using:

pip install --global-option="build_clib" \
--global-option="--compiler=mingw32" \
--global-option="build_ext" \
--global-option="--compiler=mingw32" \
amici --no-cache-dir --verbose


Note

Possible sources of errors:

• On recent Windows versions, anaconda3\Lib\distutils\cygwinccompiler.py fails linking msvcr140.dll with [...] x86_64-w64-mingw32/bin/ld.exe: cannot find -lmsvcr140. This is not required for amici, so in cygwinccompiler.py return ['msvcr140'] can be changed to return [].

• If you use a python version where python/cpython#880 has not been fixed yet, you need to disable define hypot _hypot in anaconda3\include/pyconfig.h yourself.

• import amici in Python resulting in the very informative

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

means that some amici module dependencies were not found (not the AMICI module itself). DependencyWalker can show you which ones.

### Using the Microsoft Visual Studio¶

Note

Support for MSVC is experimental.

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.

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

C: \Users\travis\build\AMICI\scripts\compileBLAS.cmd

C:\BLASlib\openblas.lib C:\BLAS\bin\openblas.dll

You will also need to define two environment variables:

BLAS_LIBS="/LIBPATH:C:\BLAS\lib openblas.lib"
BLAS_CFLAGS="/IC:\BLAS\OpenBLAS-v0.3.10\OpenBLAS-0.3.10"


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

[System.Environment]::SetEnvironmentVariable("BLAS_LIBS", "/LIBPATH:C:\BLAS\lib openblas.lib", [System.EnvironmentVariableTarget]::User)
[System.Environment]::SetEnvironmentVariable("BLAS_LIBS", "/LIBPATH:C:\BLAS\lib openblas.lib", [System.EnvironmentVariableTarget]::Process)
[System.Environment]::SetEnvironmentVariable("BLAS_CFLAGS", "-IC:\BLAS\OpenBLAS-v0.3.10\OpenBLAS-0.3.10", [System.EnvironmentVariableTarget]::User)
[System.Environment]::SetEnvironmentVariable("BLAS_CFLAGS", "-IC:\BLAS\OpenBLAS-v0.3.10\OpenBLAS-0.3.10", [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\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.

This can be tested using the “where” command. For example

where openblas.dll

should return

C:\BLAS\bin\openblas.dll

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.

## 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 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

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

### Installation under Anaconda¶

To use an Anaconda installation of Python https://www.anaconda.com/distribution/, Python>=3.7), proceed as follows:

Since Anaconda provides own versions of some packages which might not work with AMICI (in particular the gcc compiler), create a minimal virtual 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).

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 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

Anaconda 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)

### 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.