Linear Algebra Libraries

Introduction

BLAS (Basic Linear Algebra Subprograms) and LAPACK (Linear Algebra PACKage) are routines that provide standard building blocks for performing a wide range of linear algebra operations. There are stable reference implementations from Netlib written in Fortran, with C interfaces available (called CBLAS and LAPACKE respectively), as well as several optimized implementations providing fast subsets of these APIs.

Available implementations

  • blas, lapack - Netlib’s reference implementation of the Fortran and C interfaces.

  • atlas - Automatically Tuned Linear Algebra Software.

  • blis - BLAS-like Library Instantiation Software framework.

  • openblas - OpenBLAS, an optimized BLAS based on GotoBLAS2.

ATLAS, BLIS and OpenBLAS provide BLAS and a subset of LAPACK. Both BLIS and OpenBLAS provide several flavors: a sequential version, a threaded one, and another with OpenMP support (all of them with or without support for 64-bit integers).

Due to implementation differences, it is important that all components of a particular software stack link to the same BLAS/LAPACK implementation. Also, users may want to choose a particular implementation that works best for them at run time. This guideline gives a structure that can enforce the first while allowing the second, as well as providing a transparent fallback mechanism to Netlib’s reference implementation for those symbols not included in the selected backend via FlexiBLAS.

BLAS/LAPACK wrapper

FlexiBLAS is a framework that wraps both BLAS and LAPACK APIs in a single library. BLAS/LAPACK consumers must link against FlexiBLAS, and this wrapper is able to redirect calls to a selected optimized backend with negligible overhead. It also provides transparent fallback to Netlib’s reference implementation if a certain symbol is not present in the selected backend. These are the main features:

  • Provides a 100% BLAS and LAPACK compatible ABI/API, with interfaces for both 32- and 64-bit integers.

  • Runtime exchangeable BLAS and LAPACK backend without recompilation via an environment variable.

  • Integration of user-owned BLAS libraries without administrator privileges, even in system-wide installed programs.

  • Works with OpenBLAS, ATLAS and BLIS, as well as non-free alternatives such as Intel MKL, ACML…​

  • Flexible per-system/user/host configuration files.

  • Basic profiling support.

Fedora ships openblas-openmp as the system-wide default backend.

Packaging BLAS/LAPACK dependent packages

Consumers of any subset of BLAS and/or LAPACK MUST compile against FlexiBLAS (unless not supported; see below).

Exceptions

  • Although support for LAPACKE is planned, the few packages using this interface are not yet supported by FlexiBLAS as of v3.1.2. These packages MUST link against OpenBLAS instead, or lapack if the routines used are not supported by this backend. Current exceptions of this type include opencv, scamp and sextractor.

  • On rare occasions, a package may use an exceptional feature present in a particular backend and cannot be adapted to FlexiBLAS by any means. In such cases, the package MUST link against this backend. Current exceptions of this type include julia (linked against OpenBLAS) and psfex (linked against ATLAS).

Build requirements

First, only FlexiBLAS’s development package MUST be listed in BuildRequires:

BuildRequires: flexiblas-devel

which brings all the necessary development files, both for the 32-bit (the most common) and the 64-bit integer interface.

If the package only supports the interface for 64-bit integers, then 32-bit architectures MUST be excluded (see Arch-Specific Runtime and Build-Time Dependencies).

Configuration

The packager MUST specify flexiblas or flexiblas64 (for the 32-bit or 64-bit interface respectively) as both the BLAS and LAPACK library names where applicable, and packages using pkg-config will automatically obtain the proper flags for the headers and libraries. Similarly, CMake-based projects using FindBLAS will automatically detect and configure the proper flags for FlexiBLAS (since CMake v3.19), and no further action will be required from the packager.

Unfortunately, many upstream projects present heterogeneous ways of accessing these APIs. In a best-case scenario, the building framework may define specific options to explicitly set the BLAS and/or LAPACK libraries. More commonly, the packager MUST ensure that %{_includedir}/flexiblas and %{_libdir}/flexiblas (or %{_includedir}/flexiblas64 and %{_libdir}/flexiblas64) are injected as header and library locations in the proper flags and configuration files, and/or -lflexiblas (or -lflexiblas64) is provided to the linker. In rare occasions, hardcoded paths in source files MUST be modified, and patches MAY be required. The packager SHOULD work with upstream to standardize the way in which these libraries are detected and configured.

To ensure that the program has been properly linked against FlexiBLAS, the packager MUST check that the Requires are correct, i.e., libflexiblas is listed, but not libblas, liblapack or any other backend.

Tests

Optimized BLAS/LAPACK backends are much faster than Netlib’s reference implementation, but in return results may vary a little. Consequently, tests that are too tight (with too small tolerances) may fail. In these cases, the packager SHOULD enable the reference implementation in the %check section as follows:

export FLEXIBLAS=netlib

or, alternatively, via FLEXIBLAS64 for builds using 64-bit integers.

Backend selection

System-level selection

A package compiled against FlexiBLAS pulls out the corresponding flexiblas-netlib(64) subpackage, which in turn requires the default optimized backend (i.e., flexiblas-openblas-openmp(64)). This is set via the "default=IMPLEMENTATION-NAME" key (by default, default=openblas-openmp), present in the main configuration file shipped in the main subpackages, %{_sysconfdir}/flexiblasrc and %{_sysconfdir}/flexiblas64rc.

To allow system-level selection of other BLAS/LAPACK implementations, more backends must be installed in the first place (e.g., flexiblas-atlas, flexiblas-blis-serial…​), and then they can be swapped system-wide via the flexiblas CLI tool, or just by modifying the "default" key in the configuration file by hand.

User-level selection

Persistent user-level selection of system-provided BLAS/LAPACK implementations can be done via the CLI tool:

$ flexiblas set IMPLEMENTATION-NAME
$ flexiblas64 set IMPLEMENTATION-NAME

provided the sub-package for IMPLEMENTATION-NAME is installed.

Non-persistent user-level selection can be triggered via an environment variable:

$ FLEXIBLAS=IMPLEMENTATION-NAME ./yourapp
$ FLEXIBLAS64=IMPLEMENTATION-NAME ./yourapp64

User-level selection of user-owned BLAS/LAPACK libraries can be achieved just by changing IMPLEMENTATION-NAME with a path to any custom BLAS/LAPACK-compatible library in the examples above.

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