Blas-lapack-switch

GSoC2019/Gentoo: BLAS/LAPACK Runtime Switch
The BLAS/LAPACK switching mechanism was created in a GSoC2019 project. It is based on an ld.so feature and produces similar result to Debian's update-alternatives. Classical numerical linear algebra libraries, BLAS and LA-PACK play important roles in the scientific computing field. Various demands on these libraries pose non-trivial challenges on system management and Linux distribution development. By leveraging this mechanism which enables user to switch BLAS and LAPACK libraries smoothly and painlessly, the problems could be properly and decently addressed. This project aims at introducing the mechanism into Gentoo’s eselect framework to manage BLAS and LA-PACK, providing equivalent or better functionality of Debian’s update-alternatives.

Disabling The Feature
This feature is disabled by default, which means users who don’t care about it could simply ignore the  USE flag as if it doesn’t exist and install things under the default settings like before. Users who don’t read any documentation at all won’t fall into trouble with this default setting.

Enabling The Feature
First install the skeleton of the mechanism:

These virtual packages will pull in the reference BLAS/LAPACK implementation and the customized eselect modules for BLAS and LAPACK, i.e. . After finishing the installation, the user should be able to check the status of BLAS/LAPACK selections:

That means all binaries linked against or  will use the reference BLAS implementation; those linked against  will use the reference LAPACK implementation.

The reference implementation is very slow, and for some users (e.g. scientific computing users) this is unacceptable. In Gentoo’s main repository, there are several typical optimized BLAS/LAPACK implementations available, for example BLIS and OpenBLAS. They could be automatically registered in the mechanism as long as the  USE flag is toggled during installation. For example:

Note that without the flag, these packages won’t be registered in the mechanism and won’t install extra libraries at all. After installation with the feature enabled, we could switch the BLAS/LAPACK implementation like so:

Directly run your program again and see if it’s running faster. No any re-compilation is required thanks to this mechanism. For more details about the or  usage please look up the manual page or the help messages.

In Gentoo's main repository, BLAS/LAPACK providers that support this  mechanism are:, , , and. The most recommended choice is. If non-free software is acceptable to you,  is also a decent choice. Advanced users could explore the rest possible combinations, but note the  combination is discouraged.

If you are in the transition from the old BLAS/LAPACK packages and encountered package confliction, keep in mind to keep,  , and. The old  packages should be removed.

BLAS/LAPACK Providers
It must be pointed out that for any BLAS/LAPACK implementation, providing extra shared object with proper SONAMEs is necessary. For example, do not use (SONAME=) as the BLAS/CBLAS provider by simply symlinking it into  and  because any program to be linked against BLAS  or CBLAS  will be eventually linked against  (verify this with ), which will clearly break the runtime switching mechanism. The current solution is to patch upstream build systems and build customized shared objects with proper SONAMEs.

To package a BLAS/LAPACK provider with the runtime switching feature enabled, the maintainer should pay attention to the following points:


 * Patch upstream build systems and provide extra shared objects in a private library directory. Specifically, a new BLAS/CBLAS implementation, say "myblas", should install 4 files to the directory:
 * (ELF shared object, providing the fortran BLAS ABI, SONAME=)
 * (symlink pointing to );
 * (ELF shared object, providing the C BLAS ABI, SONAME=)
 * (symlink pointing to ).
 * Similarly, a new LAPACK implementation, say "mylapack" should install 2 files to the directory:
 * (ELF shared object, providing the fortran LAPACK ABI, SONAME=);
 * (symlink pointing to ).
 * Register an alternative with during postinst.
 * Remove an alternative with during postrm.
 * Guard the code associated with all the above points with the  USE flag.

For real example please see the latest ebuild files for, , or.

BLAS/LAPACK Reverse Dependencies
If a package needs to be linked against the reference (aka. netlib) BLAS and LAPACK, it should declare virtual packages dependency, i.e.  instead of a specific implementation. In this case the package must assume a standard (reference) API and ABI from the virtual package. Otherwise, please write a specific implementation in the dependency list and avoid linking against  or.

Implementation Details
The core part of the implementation involves,   and  , where the former one controls both (fortran) BLAS and CBLAS alternatives at the same time.

The is the code base of the reference (or standard) BLAS, CBLAS, LAPACK, and LAPACKE. BLAS and LAPACK are a set of stable Fortran API / ABI. CBLAS and LAPACKE are thin wrappers around BLAS and LAPACK respectively, providing the C API / ABI. In our BLAS/LAPACK runtime switching mechanism, every candidate must provide every API / ABI that the reference implementation provides. Taking advantage of the API/ABI stability, we can change the backend libraries (e.g. ) without recompiling applications as long as the new one provides a compatible set of ABI.

The users could easily switch the libraries by adjusting the LD_LIBRARY_PATH environment variables as a temporary solution. For system level library switching, two custom eselect modules are provided. They manipulates configuration files under the directory, hinting  on the places to find the BLAS/LAPACK libraries.

As a side effect, this solution depends on the support from the system C standard library. Besides, it is recommended to read the code if you need even more details.

Code:

Frequently Asked Questions
'''Q: I disabled this feature when installing a bunch of packages, but now I regret and want to enable the runtime switching feature. How to accomplish this?'''

A: Simply reinstall the virtual packages and your favorate BLAS/LAPACK providers with the  flag toggled. The whole dependency tree doesn’t need to be rebuilt as a rebuild is expected to make no difference.

'''Q: Some BLAS/LAPACK implementations support 64-bit array indexing, which provides functions such as. How does this mechanism deal with such feature?'''

A: The “BLAS64” or “BLAS-ILP64” ABI is different from the “BLAS32” or “BLAS-LP64” ABI. Mixing them together will lead to unpredictable results, hence the “BLAS64” feature is not integrated into the mechanism. Currently we only provide this feature in the package for Julia’s use. Besides, the generic switching mechanism for BLAS64/LAPACK64 is still being experimented in Debian. When the demand on “BLAS64” is common enough or the experiment in Debian was successful, we could start to provide it in Gentoo.

Q: How to add a customized implementation into this mechanism?

A: Taking MKL as an example. We first install MKL to, and symlink to. Then register it with. Note that building programs when MKL is selected is discouraged. The reason could be found in the developer guide part.

A real example about adding and setting Intel MKL as the backend library:

To remove the MKL candidate, or any other customized library, just remove the corresponding files under and  directories, then select some other candidates. Note, the package can do all the above steps for you.

Reference

 * 1) GSoC Project Link
 * 2) [gentoo-science] GSoC Proposal: Improvements to the BLAS / LAPACK and their reverse-dependencies https://archives.gentoo.org/gentoo-science/message/4d0186acdce6df538a2740e0f1146ae6
 * 3) [gentoo-dev] RFC: BLAS and LAPACK runtime switching https://archives.gentoo.org/gentoo-dev/message/d917547f7a9e1226fca63632a1e02026
 * 4) [gentoo-dev] [PATCH 0/2] RFC: Introducing ldso switching to BLAS/LAPACK https://archives.gentoo.org/gentoo-dev/message/95beba3dc1c0f684ce1ec82d51988fc8
 * 5) [gentoo-science] On BLAS and LAPACK int64 ABI https://archives.gentoo.org/gentoo-science/message/8e3b9567297de5a1809feb28c62be633
 * 6) Hasan ÇALIŞIR (Gentoo Proxy Maintainer) wrote an “openblas” script for similar switching purpose. However the implementation is neither generic nor simple enough. See https://github.com/gentoo/gentoo/pull/11700/files
 * 7) Zongyu Zhang fixed a bug in numpy ebuild so that numpy could make use of the switching mechanism correctly.
 * 8) Some positive user feedbacks: https://github.com/gentoo/sci/issues/805#issuecomment-510469206 https://github.com/gentoo/sci/issues/805#issuecomment-512097570

Related pull requests:
 * 1) https://github.com/gentoo/gentoo/pull/12316
 * 2) https://github.com/gentoo/gentoo/pull/12318
 * 3) https://github.com/gentoo/gentoo/pull/12319
 * 4) https://github.com/gentoo/gentoo/pull/12322
 * 5) https://github.com/gentoo/gentoo/pull/12323
 * 6) https://github.com/gentoo/gentoo/pull/12356
 * 7) https://github.com/gentoo/gentoo/pull/12357
 * 8) https://github.com/gentoo/gentoo/pull/12358
 * 9) https://github.com/gentoo/gentoo/pull/12381
 * 10) https://github.com/gentoo/gentoo/pull/12382
 * 11) https://github.com/gentoo/gentoo/pull/12405
 * 12) https://github.com/gentoo/gentoo/pull/12409
 * 13) https://github.com/gentoo/gentoo/pull/12420
 * 14) https://github.com/gentoo/gentoo/pull/12422
 * 15) https://github.com/gentoo/gentoo/pull/12423
 * 16) https://github.com/gentoo/gentoo/pull/12475
 * 17) https://github.com/gentoo/gentoo/pull/12742

Maintainers
Author: Mo Zhou [mailto:lumin@debian.org lumin@debian.org] GSoC Mentor: Benda Xu [mailto:heroxbd@gentoo.org heroxbd@gentoo.org]