0.17.1 install fails

[Mjvolk3]

What did you expect to happen?

I am using a conda environment on a linux machine to install amici. Amici install fails with the #include error (First Q in the FAQ)

What has happened instead?

I expected a proper installation of Amici. The reproduction code below works with v0.16.1.

To Reproduce

conda create --yes -n env pip python=3.10
conda activate env
conda install --yes -c conda-forge swig hdf5 openblas
export BLAS_LIBS=-lopenblas
pip install --no-cache-dir amici==0.17.1 # also fails with 0.17.0

Note: This works with v0.16.1

AMICI version and system environment

• OS and version: [e.g. Ubuntu, iOS, Windows]

%lsb_release -a
LSB Version:    :core-4.1-amd64:core-4.1-noarch:cxx-4.1-amd64:cxx-4.1-noarch:desktop-4.1-amd64:desktop-4.1-noarch:languages-4.1-amd64:languages-4.1-noarch:printing-4.1-amd64:printing-4.1-noarch
Distributor ID: RedHatEnterprise
Description:    Red Hat Enterprise Linux release 8.6 (Ootpa)
Release:        8.6
Codename:       Ootpa

• AMICI interface: [e.g. Python, Matlab, C++]
  python

• AMICI version:
  0.17.1

• Additional information: Compiler name and version used, Python/Matlab version, ...

GCC 11.2.0 compiler + OpenMPI
More information about the machine can be found here NCSA Delta.

How to fix
Do you know how to resolve the problem?

No. I reverted to the previous version that works

Can you submit a pull request?

No. I don't know the solution.

[dweindl]

Hi @Mjvolk3, in v0.17.0 we reorganized how the AMICI extension is built. This involved changing/removing some of the dependency handling. Before, we had some hard-coded paths to look for BLAS headers, but this is not very sustainable, and potentially incompatible with conda environments.

That means, you will now have to set BLAS_CFLAGS=-I/absolute/path/of/cblas.h/containing/directory (in addition to BLAS_LIBS). You can get that path either from searching cblas.h inside your conda environment, or if you have a running amici<0.17.0 installation, from python -c "from amici.setuptools import get_blas_config; print(get_blas_config()['include_dirs'])" .

I will consider using CMake to try to find some BLAS automatically, but last time I tried, this had other issues...

[dweindl]

P.S.: Does pip3 install -ve git+https://github.com/AMICI-dev/amici.git@develop#egg=amici\&subdirectory=python/sdist work for you, after unsetting both BLAS_LIBS and BLAS_CFLAGS? (#2104)