[Bioc-devel] Support for Linux ARM64

Fri Jan 6 01:08:26 CET 2023

On Thu, Jan 5, 2023 at 1:44 PM Hervé Pagès <hpages.on.github using gmail.com>
wrote:

> Hi Martin,
>
> Linux runs on many architectures, ARM64 is just one of them.
>
> Our daily builds have traditionally focused on 3 platforms: Intel-based
> Linux (Ubuntu 22.04), Windows, and Intel-based Mac. Note that we
> recently added ARM64-based Mac to our daily builds.
>
> One big difference between Linux and the other platforms is that we only
> produce binary packages for the latter. More precisely:
>
> - on the Linux builders: the daily builds only run 'R CMD INSTALL', 'R
> CMD build', and 'R CMD check', on each Bioconductor package,
>
> - on the Windows and Mac builders: the daily builds run all the above
> plus an additional step that we call the BUILD BIN step that produces a
> binary for each Bioconductor package.
>
> This means that on Linux, as well as on any other Unix-like OS that is
> not macOS (e.g. FreeBSD, OpenBSD, Solaris, HP-UX, etc...), users will
> install all their packages (Bioconductor and CRAN) **from source**. This
> should work as long as they are on a platform where R is supported and
> have the required compilers (C, C++, and Fortran).
>
> Note that if officially supporting a given platform means running the
> daily builds on that particular platform, then there's no way for us to
> do that because platform == OS + architecture, and the list of
> combinations of Unix-like OS's (Linux, FreeBSD, Solaris, etc...) +
> architectures (Intel, ARM64, Sparc, powerpc) is endless. Even if we
> narrow this list to Intel-based Linux, there are hundreds of Linux
> distributions around that use different kernel, compilers, package
> managers, etc...
>
> All this to say that, as far as the daily builds are concerned, we had
> to make choices, and those choices are based on the most commonly used
> platforms. Since all Bioconductor packages are tested daily on
> Intel-based Linux (Ubuntu 22.04), Windows, Intel-based Mac, and
> ARM64-based Mac, we have some reasonable confidence that they will work
> properly on these 4 platforms (still not a 100% guarantee of course,
> there's nothing like that).
>
> My understanding is that ARM64-based Linux is still a marginally used
> platform so probably not worth for us to allocate resources on adding it
> to our daily builds at the moment. If it ever becomes more mainstream in
> the future, then we will certainly reconsider. That does not mean that
> you can't use Bioconductor on a ARM64-based Linux machine **now**. I see
> no reason a priori why you couldn't install (from source) Bioconductor
> packages on this platform, and use them, as long as:
>
>
Thanks Hervé for a good overview of the issues.  I think there are a couple
of reasons to keep this dialogue going (and there is now a community slack
channel
for further discussion: #arm-linux at community-bioc.slack.com.)

The first reason is Martin's offer of resources to accomplish the support
aim.  What
exactly that support aim is remains to be made precise.  As you note, a
properly
configured system with R can use BiocManager::install to build from source,
but
there are a few additional things that can be done to produce binaries, and
perhaps
some of our software in BBS or some of the binary repo generation tools
could be
useful for Martin's group to make a relevant binary repo.  The
package-management
oriented process of Dirk Eddelbuettel's r2u
<https://github.com/eddelbuettel/r2u> also seems potentially relevant.  We
also
have tooling to build all the CRAN dependencies that Bioc packages
declare.  This
is all in the open and it would be interesting to see how much work is
needed to
get solutions for ARM64 linux.  It could lead to some robustification of
the existing
build machinery.  I am not offering to do it, but the fact that all the
tooling is out in
the open may not be fully clear and I am just mentioning this.

The second reason to stay engaged is the nature of the ARM platform, which
is
said to require lower power consumption for equivalent throughput.  It may
be
environmentally beneficial to be ahead of the curve in being able to work
with
this platform.  Earlier I linked to a github issue indicating that rocker
now has a dual
platform container image including arm64 support but I don't know if that
really
addresses the issue at hand. Maybe I need to go onto a graviton machine to
find out.

In any case it is not so often that we get a request for enhancements that
includes
an offer of VMs and person power so I want to be sure we don't lose the
thread
prematurely.

> - R is supported on your ARM64-based Linux machine
>
> - you have compilers that are supported by R
>
> - you have the external libraries that are required by some CRAN and/or
> Bioconductor packages.
>
> Hope this helps,
>
> H.
>
> On 05/01/2023 02:01, Martin Grigorov wrote:
> > Dear community,
> >
> > Happy and successful new year!
> >
> > Appologies if this has been discussed before but
> > https://stat.ethz.ch/pipermail/bioc-devel/ does not provide search
> > facilities and my googling didn't help much!
> >
> > I'd like to ask whether Linux ARM64 is officially supported ?
> > I know that Mac ARM64 is supported since 3.16 [1] [2].
> > I cannot find such test results for Linux ARM64 and the site search [3]
> > also mentions "arm64" only in context of "macOS".
> > In addition the Docker images are also single-platform [4] (linux/amd64).
> >
> > How can we help to add support for Linux ARM64 ?
> > My employer is willing to donate VMs and man power if the community is
> > interested in adding support for Linux ARM64!
> >
> >
> > Regards,
> > Martin
> >
> > 1. https://bioconductor.org/news/bioc_3_16_release/
> > 2. https://bioconductor.org/checkResults/3.17/bioc-mac-arm64-LATEST/
> > 3. https://bioconductor.org/help/search/index.html?q=arm64/
> > 4. https://hub.docker.com/r/bioconductor/bioconductor_docker/tags
> >
> >       [[alternative HTML version deleted]]
> >
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>
> --
> Hervé Pagès
>
> Bioconductor Core Team
> hpages.on.github using gmail.com
>
> _______________________________________________
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>

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