On Thu, Jan 5, 2023 at 1:44 PM Hervé Pagès <hpages.on.git...@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]] > > > > _______________________________________________ > > Bioc-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > -- > Hervé Pagès > > Bioconductor Core Team > hpages.on.git...@gmail.com > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- The information in this e-mail is intended only for the ...{{dropped:18}} _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
