> They're packages for a header-only system, not libraries, hence my confusion. Hi Dave, okay. > Who's pushing this, and how do I present an HPC performance engineering perspective? I appreciate your interest in the bioinformatics in HPC. The simde Fedora package: Me The simde Debian package: Michael (You can see his account in the simde project. The author of the Common Workflow Language). If you want to discuss something related to simde, opening the ticket on the upstream might be good. https://github.com/nemequ/simde My target is to enable the set of bio tools RPMs used in COVID-19 analysis on ppc64le and aarch64 based HPC use cases. As you know there are ppc64le and aarch64 based HPC where it's hard to run some of the bio-tools. > Well, what I've already said from some experience and research. Where's > the POWER and S390 support? All I saw is x86 and arm. We've heard > there's ppc64le compatibility support anyhow, which is rising up my list > to investigate for work. Who's going to do bioinformatics on Blue > Boxes? Bioinf causes enough trouble on x86... bowtie2 * POWER: supported from version 2.4.0. > Added preliminary support for ppc64le architectures with the help of SIMDE project https://github.com/BenLangmead/bowtie2/blob/b8c13c0401885873a99b229fca668deecde08749/NEWS#L46-L47 Travis CI ppc64le job: https://github.com/BenLangmead/bowtie2/blob/master/.travis.yml#L75 * s390x: Not supported yet. Some tests failed. https://github.com/BenLangmead/bowtie2/issues/286 minimap2 https://github.com/lh3/minimap2 There is no official support yet. But a little discussion about it. You see Makefile.simde is added on the latest commits. That means we can try to build it as potentially. I am planning to contribute to the upstream for that. > Who's going to do bioinformatics on Blue Boxes? Bioinf causes enough trouble on x86... What is Blue Boxes and Bioinf? > There's been an issue for bowtie2 for years, and I've long had it in > copr, though it probably needs updating there. Has someone done the > unresponsive maintainer thing for Adam Huffman (who is, or was, back > more in that area)? You can pick up the bowtie2 latest version x86 and arm on my copr repository here. Copr does not have a ppc64le build root right now. https://copr.fedorainfracloud.org/coprs/jaruga/staging/packages/ Or from my scratch build to pick up the ppc64le version. https://koji.fedoraproject.org/koji/taskinfo?taskID=43660524 As I said, bowtie2 is in review status for the Fedora dist-git from last Friday. I sometimes work with Adam for bioinformatics tools. He is busy with his main job to respond. I have been co-maintainer of some of his RPM packages such as samtools, bwa, bowtie, working on it instead of him. If you are interested in bioinformatics, DNA/RNA sequencing in Fedora, Fedora medical-sig is the place. We can talk there. You may see some information that you are interested in there. https://fedoraproject.org/wiki/SIGs/Medical Cheers, Jun -- Jun | He - His - Him _______________________________________________ devel mailing list -- devel@xxxxxxxxxxxxxxxxxxxxxxx To unsubscribe send an email to devel-leave@xxxxxxxxxxxxxxxxxxxxxxx Fedora Code of Conduct: https://docs.fedoraproject.org/en-US/project/code-of-conduct/ List Guidelines: https://fedoraproject.org/wiki/Mailing_list_guidelines List Archives: https://lists.fedoraproject.org/archives/list/devel@xxxxxxxxxxxxxxxxxxxxxxx
