lapacke.h in CentOS 5

Question

I'm trying to create a Python wheel that makes use of the BLAS and LAPACK C extensions. Compiling such package under Ubuntu requires of the following system packages:

libopenblas-dev: (Open)BLAS development libraries
liblapack-dev: LAPACK development libraries
liblapacke-dev: C headers for LAPACK

This works nicely, but now I need to repeat the process under CentOS 5. The reason being I'm trying to create a manylinux wheel, and a recommended way seems to be using an old CentOS toolchain to guarantee it will work under different linux distributions.

The problem is, while libopenblas-dev and liblapack-dev have equivalences in CentOS 5 (openblas-devel and lapack-devel), there is no equivalent package for liblapacke-dev. This makes some sense considering the LAPACK version provided in those packages is very old (3.0), which doesn't seem to support lapacke. But because of that I'm unable to compile my software, as gcc complains about missing lapacke.h headers.

Things I have tried:

Manually downloading and compiling a newer LAPACK version (3.8.0 and 3.6.0). I get compilation errors.
Directly copying the lapacke.h header from one of the LAPACK versions above to /usr/include. Didn't work, probably because of the difference in LAPACK versions.
Adding Intel MKL repositories following the official instructions and replace BLAS/LAPACK by MKL. Unfortunately CentOS 5 does not include the --add-repo option in yum-config-manager, so I'm a bit at a loss here.

You can convert your Ubuntu-generated wheels to manylinux using [auditwheel](https://pypi.org/project/auditwheel/). See [how I use it](https://github.com/CheetahTemplate3/cheetah3/blob/24475a148b303da781ced12105f231e5c0579981/devscripts/release#L20) when releasing Cheetah3 at Debian. — phd, Aug 05 '18 at 23:33
@phd I'm afraid that doesn't work for me, at least under Ubuntu Xenial, because of the "presence of too-recent versioned symbols". That is why the [recommended way](https://github.com/pypa/manylinux) to use auditwheel is under CentOS 5. — albarji, Aug 06 '18 at 15:13

score 0 · Accepted Answer · answered Nov 24 '18 at 13:10

lapacke is not supported in CentOS 5.0, so the C interface is not available, but you can still do the trick by calling the fortran symbols.

First, install CentOS packages for BLAS and LAPACK

yum install -y blas-devel lapack-devel

and add these libraries to the linker path

export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:/usr/lib64"

Now you should be able to use BLAS and LAPACK functions in your C/C++ extensions code by importing the fortran symbols. For instance, to use the LAPACK function dpttrs in the C++ source you would need to declare it as an external C symbol

extern "C" {
    void dpttrs_(lapack_int* n, lapack_int* nrhs, const double* d, const double* e, 
                 double* b, lapack_int* ldb, lapack_int *info );
}

and then it can be used normally by calling the dpttrs_ function.

Finally, when bundling the python package make sure to include the blas and lapack libraries and headers. For instance, when using cffi you should configure your sources in the following pattern

ffi.set_source(
    'YOUR MODULE NAME',
    "BASE SOURCES",
    sources=sources,
    source_extension='.cpp',
    libraries=['blas', 'lapack'],
    include_dirs=['/usr/include']
)

lapacke.h in CentOS 5

1 Answers1