To follow (tangently) on Klaus' message, I've released a book last year on some
advanced topics in R programming and development:
https://hal.ird.fr/ird-03850685
Chapter 9 is on parallelization and HPC. There are a few (detailed) examples
showing when multi-core is benefitial and when it is
Hello, Emmanuel,
I overlooked that repo, sorry. OK, so I opened
https://github.com/emmanuelparadis/ape/issues/72
and https://github.com/emmanuelparadis/ape/pull/71
Sincerely,
V.
Dne úterý 7. března 2023 12:13:49 CET, Emmanuel Paradis napsal(a):
> Hi Vojtěch,
> The GH repos for ape is:
>
on, 06 Mar 2023 14:43:04 +0100
> > From: =?utf-8?B?Vm9qdMSbY2g=?= Zeisek
> > To: mailinglist R
> > Subject: [R-sig-phylo] Parallelization in ape::dist.topo
> > Message-ID: <3551602.QO7bkq4lFn@veles>
> > Content-Type: text/plain; charset="utf-8"
> &g
Hello,
thank You for Your comments, dear Klaus.
Dne úterý 7. března 2023 13:01:07 CET, Klaus Schliep napsal(a):
> Dear Vojtěch,
> nice work. Just a few random comments:
> Parallelization is often not straightforward as it
> depends on the hardware and the operating system.
Yes. E.g. it typically
Dear Vojtěch,
nice work. Just a few random comments:
Parallelization is often not straightforward as it depends on the hardware
and the operating system. My preference is using the future package for
parallelization as it does some nice abstraction for the different R
packages, so you can try
=?utf-8?B?Vm9qdMSbY2g=?= Zeisek)
>
> --
>
> Message: 1
> Date: Mon, 06 Mar 2023 14:43:04 +0100
> From: =?utf-8?B?Vm9qdMSbY2g=?= Zeisek
> To: mailinglist R
> Subject: [R-sig-phylo] Parallelization in ape::dist.topo
> Message-ID: <3551602.QO7bkq4lFn@vele
Hi Vojtěch,
The GH repos for ape is:
https://github.com/emmanuelparadis/ape
I had a quick look at your code and these are interesting improvements. It
seems also possible to improve the basic code of dist.topo() (e.g., using
bitsplits) so it is worth opening an issue.
Cheers,
Emmanuel
Hello dear colleagues,
I use often ape::dist.topo (see here dist.topo.r), which is doing the
calculations sequentially, which is very slow for large data sets. I'm sorry,
I haven't found any relevant Git repository or so, so I hope Emmanuel won't
mind if I discuss it here.
I discussed various
