cblas.h not found when installing on ubuntu 20.04.1

[TeaWolf]

I've had no problem installing amici on my OSX laptop, but no go on my Ubuntu desktop
Using the following commands as per the documentation.

sudo apt install libatlas-base-dev swig
sudo apt install libhdf5-serial-dev
pip install amici 

I get the following inclusion error.

 amici/src/cblas.cpp:16:13: fatal error: cblas.h: No such file or directory
     16 |    #include <cblas.h>
        |             ^~~~~~~~~
  compilation terminated.
  error: command '/home/llamagod/miniconda3/envs/rjmcmc_thesis/bin/x86_64-conda-linux-gnu-cc' failed with exit code 1
  ----------------------------------------
  ERROR: Failed building wheel for amici

I see that there's an issue open talking about making this more flexible.

Is there some kind of fix that I could apply at the moment however?

[dweindl]

Hi @TeaWolf, I am surprised AMICI doesn't find your cblas header files on Ubuntu.

Could you please post the output of locate /usr/*cblas*.h?

If there is no /usr/include/x86_64-linux-gnu/cblas.h but only /usr/include/x86_64-linux-gnu/cblas-atlas.h, you can create the missing symlink manually with sudo ln -s /usr/include/x86_64-linux-gnu/cblas-atlas.h /usr/include/x86_64-linux-gnu/cblas.h. This normally should have happened during the installation of libatlas-base-dev. After that, AMICI installation should succeed. Let me know if not.

[TeaWolf]

I'm unfamiliar with locate so I used find

find /usr -name '*blas*.h'
/usr/include/x86_64-linux-gnu/cblas.h
/usr/include/x86_64-linux-gnu/cblas-atlas.h
/usr/include/x86_64-linux-gnu/f77blas.h
/usr/include/x86_64-linux-gnu/cblas-openblas.h
/usr/include/x86_64-linux-gnu/openblas_config.h
/usr/include/x86_64-linux-gnu/openblas-pthread/cblas.h
/usr/include/x86_64-linux-gnu/openblas-pthread/f77blas.h
/usr/include/x86_64-linux-gnu/openblas-pthread/openblas_config.h

The file you mention does seem to be there though

[dweindl]

The file you mention does seem to be there though

That's funny. Could you please post the full output of pip install -v amici?

[dweindl]

Ah. I think the issue is that you are installing AMICI inside a conda environment. This does not use the regular include directories, and therefore, does not find /usr/include/x86_64-linux-gnu/cblas.h.

Does AMICI installation succeed after conda install -c anaconda openblas?

[dweindl]

Does AMICI installation succeed after conda install -c anaconda openblas?

You will probably have to set some additional environment variable during AMICI installation and when importing models:
export BLAS_LIBS=-lopenblas.

[TeaWolf]

Yes sorry it is a conda environment, forgot to mention it.

The combination of

conda install -c conda-forge openblas
export BLAS_LIBS=-lopenblas
pip install amici

Does the trick.

However my conda environment seemed to have an openblas in it before

# Present before conda install -c conda-forge openblas
libopenblas               0.3.18          pthreads_h8fe5266_0    conda-forge
# Present after conda install -c conda-forge openblas
openblas                  0.3.18          pthreads_h4748800_0    conda-forge

Not sure why the other one wasn't doing it.

[dweindl]

Does the trick.

Great.

Not sure why the other one wasn't doing it.

The issue was only the missing BLAS_LIBS=-lopenblas then. We will add that to the documentation.
Keep in mind, that you will have to have that set also when import any models.

[TeaWolf]

well I actually tried BLAS_LIBS=-lopenblas before installing the openblas from conda forge just to see if it would work, but it failed with the same error.

[dweindl]

Ah, yes, it seems libopenblas only contains the library, but not the header files.

[TeaWolf]

ah so that's it then!

[winkmal]

Sorry to reopen this again, but I got the same error message during installation with pip:
amici/src/cblas.cpp:16:13: fatal error: cblas.h: No such file or directory

It's an Alma Linux 8.7 system, and blas is installed. (I only have user access, no root privileges.)

$ yum list installed | grep blas
blas.x86_64                                       3.8.0-8.el8                              @appstream
blas-devel.x86_64                                 3.8.0-8.el8                              @powertools
openblas-openmp.x86_64                            0.3.15-4.el8                             @powertools
openblas-srpm-macros.noarch                       2-2.el8                                  @appstream

The output of the commands you mentioned give:

$ locate  /usr/*cblas*.h
$ find /usr -name '*blas*.h'
find: ‘/usr/share/polkit-1/rules.d’: No permission
find: ‘/usr/share/selinux/targeted/default/active’: No permission
/usr/include/cblas/cblas.h
/usr/include/cblas/cblas_f77.h
/usr/include/cblas/cblas_mangling.h
/usr/include/cblas/cblas_test.h
find: ‘/usr/libexec/initscripts/legacy-actions/auditd’: No permission
find: ‘/usr/libexec/warewulf/cgi-bin’: No permission

Any idea what else I could try?

[dweindl]

Hi @winkmal, does

BLAS_CFLAGS="$(pkg-config --cflags blas)" BLAS_LIBS="$(pkg-config --libs blas)" pip install amici 

work?

[winkmal]

Hi @winkmal, does

BLAS_CFLAGS="$(pkg-config --cflags blas)" BLAS_LIBS="$(pkg-config --libs blas)" pip install amici 

work?

Unfortunately not, I still get the same error message. As far as I understand, this writes the output of the commands in braces into two environment variables, which are then read by pip!?
The individual commands give the following output:

$ pkg-config --cflags blas

$ pkg-config --libs blas
-lblas

[dweindl]

Okay, according to that,

BLAS_CFLAGS="-I/usr/include/cblas/" BLAS_LIBS="-lblas" pip install amici 

might work.

Does locate /usr/*cblas.a show anything? If so, change the BLAS_LIBS part according to that:
e.g.

$ locate /usr/*cblas.a
/usr/lib/x86_64-linux-gnu/libcblas.a

->

BLAS_CFLAGS="-I/usr/include/cblas/" BLAS_LIBS="-L/usr/lib/x86_64-linux-gnu/ -lcblas" pip install amici 

[winkmal]

Does locate /usr/*cblas.a show anything?

No, nothing.

I tried:

BLAS_CFLAGS="-I/usr/include/cblas/" BLAS_LIBS="-lblas" pip3 install --user amici --upgrade

Now, I get a different error message:

amici/amici_wrap.cxx:174:11: fatal error:  Python.h: No such file or directory
# include <Python.h>
             ^~~~~~~~~~

As a sidenote, I could get AMICI to install and work on an Ubuntu 22.04 based Linux system (Python 3.10.6 via apt). The missing library error(s) are specific to this Alma Linux system.

[dweindl]

amici/amici_wrap.cxx:174:11: fatal error: Python.h: No such file or directory

It looks like python header files are not installed by default on your system (or at least not in a default location). On Ubuntu, they come in the python3-dev package, on CentOS python-devel. Are you able to install that?

If you can't use yum to install that, it's somewhat inconvient: You'll have to download that manually, unpack it, and set environment variable LDFLAGS to -L${absolute_path_to_directory_containing_Python.h}.