Installing the AMICI Python package
Short guide
Installation of the AMICI Python package has the following prerequisites:
Python>=3.8
SWIG>=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.
See also [#425](https://github.com/AMICI-dev/amici/issues/425) for further discussion.
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 acmd
should point to this installation).Download CBLAS headers and libraries, e.g. OpenBLAS, binary distribution 0.2.19.
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 linkingmsvcr140.dll
with[...] x86_64-w64-mingw32/bin/ld.exe: cannot find -lmsvcr140
. This is not required for amici, so incygwinccompiler.py
return ['msvcr140']
can be changed toreturn []
.If you use a python version where python/cpython#880 has not been fixed yet, you need to disable
define hypot _hypot
inanaconda3\include/pyconfig.h
yourself.import amici
in Python resulting in the very informativeImportError: 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.
To build OpenBLAS, download the following scripts from the AMICI repository:
https://github.com/AMICI-dev/AMICI/blob/master/scripts/installOpenBLAS.ps1
https://github.com/AMICI-dev/AMICI/blob/master/scripts/compileBLAS.cmd
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”
so that it matches your directory structure. This will download OpenBLAS and compile it, creating
C:\BLAS\lib\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-0.3.19/OpenBLAS-0.3.19"
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-0.3.19/OpenBLAS-0.3.19", [System.EnvironmentVariableTarget]::User)
[System.Environment]::SetEnvironmentVariable("BLAS_CFLAGS", "-IC:/BLAS/OpenBLAS-0.3.19/OpenBLAS-0.3.19", [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.
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\\bin")
import amici
or via the environment variable AMICI_DLL_DIRS
.
If Python returns the following error upon import amici
, try updating to the latest Python version.
OSError: [WinError 87] The parameter is incorrect: ‘’
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 |
---|---|---|
|
Path to the SWIG executable |
|
|
Setting the C(++) compiler |
|
|
Extra compiler flags used in every compiler invocation |
|
|
|
|
|
Flags for linking BLAS |
|
|
Set to build AMICI to generate code coverage information |
|
|
Set to build AMICI with debugging symbols |
|
|
Set to the number of parallel processes to be used for C(++) compilation (defaults to 1) |
|
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).
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
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.