[Bioc-devel] Check time on macOS (MIRit)

[Mike Smith]

Hi Martin,

A very short summary is that on kjohnson3 a build/check on package launched
by cron takes significantly longer than if one runs the same command
manually in a terminal.

There's some further discussion on this at
https://community-bioc.slack.com/archives/CEQ04GKEC/p1706816310942079 and
and Jen has some nice documentation of their investigation at
https://github.com/Bioconductor/BBS/issues/387

However since the original inquiry in this thread is about a package in
submission, and so the relevant tests are run by the single package builder
on merida1, I'm not sure it's pertinent to this particular issue.

Cheers,
Mike

On Wed, 7 Feb 2024 at 16:34, Martin Grigorov <martin.grigorov using gmail.com>
wrote:

> Hi Kasper,
>
> According to
>
> https://github.com/Bioconductor/BBS/blob/9ebb2cf20e70e4bebf24a2a824a67193de821b08/3.19/bioc-mac-arm64/kjohnson3/config.sh#L17-L20
> the machine has 24 vCPUs.
> The automatic/weekly build utilizes 12-16 out of those at any given time!
> With the respective RAM and disk usage.
>
> By "by hand" do you mean to run the build/check of a given package on a
> "calm" machine ?
> It would be expected that it will be faster if it has all/most resources
> just for it.
>
> Martin
>
> On Wed, Feb 7, 2024 at 5:12 PM Kasper Daniel Hansen <
> kasperdanielhansen using gmail.com> wrote:
>
> > To be a bit more clear and vague at the same time: currently, some of our
> > macOS builders exhibit weird slowdowns when the build system is run
> > automatically compared to running builds "by hand". This is pretty weird,
> > and hopefully we can figure out the cause and fix it. Specifically,
> builds
> > on kjohnson3 is (at the moment) weirdly slow.
> >
> > Best,
> > Kasper
> >
> > On Wed, Feb 7, 2024 at 7:24 AM Jacopo Ronchi <jacopo.ronchi using unimib.it>
> > wrote:
> >
> > > Ok, understood. Thanks
> > >
> > > Il mer 7 feb 2024, 12:46 Vincent Carey <stvjc using channing.harvard.edu> ha
> > > scritto:
> > >
> > > > We need a bit of internal discussion before committing to this
> > notion.  I
> > > > will get back to the list on this.
> > > >
> > > > On Wed, Feb 7, 2024 at 6:34 AM Jacopo Ronchi <
> jacopo.ronchi using unimib.it>
> > > > wrote:
> > > >
> > > >> Dear Vincent, thanks for your answer. So, at least for now, can I
> > ignore
> > > >> the warning on macOS for the submission of MIRit?
> > > >>
> > > >> Il mer 7 feb 2024, 12:26 Vincent Carey <stvjc using channing.harvard.edu>
> > ha
> > > >> scritto:
> > > >>
> > > >>> Thanks Jacopo.  You shouldn't have to struggle.  We are aware of
> > > >>> disparities of platform
> > > >>> performance and are working to improve the build process.  It will
> > take
> > > >>> time.  I believe that
> > > >>> achievement of acceptable timings on the linux platform should be
> the
> > > >>> key goal at
> > > >>> this time.
> > > >>>
> > > >>> On Wed, Feb 7, 2024 at 5:18 AM Jacopo Ronchi <
> > jacopo.ronchi using unimib.it>
> > > >>> wrote:
> > > >>>
> > > >>>> Dear developers,
> > > >>>>
> > > >>>> I am struggling to reduce R CMD check times for my package, MIRit,
> > on
> > > >>>> macOS. The check on linux takes 4 minutes, while on macOS it needs
> > > 9/10
> > > >>>> minutes. I have severely reduced the size of examples and tests,
> > which
> > > >>>> now
> > > >>>> use smaller datasets and cached resources.
> > > >>>>
> > > >>>> On linux, unit tests require 30 seconds more or less, and examples
> > 40
> > > >>>> seconds. On the other hand, macOS tests take 100 seconds, and 75
> for
> > > the
> > > >>>> examples. The issue is that sometimes the check runs in less than
> 10
> > > >>>> minutes, sometimes it needs a little bit more.
> > > >>>>
> > > >>>> However I am out of ideas on how to further reduce examples and
> > > tests...
> > > >>>> The vignette is really extensive, but since SPB uses the
> > > "--no-vignette"
> > > >>>> option this should not influence heavily on this behavior, at
> least
> > to
> > > >>>> my
> > > >>>> understanding.
> > > >>>>
> > > >>>> Sorry for bothering you,
> > > >>>> Best regards,
> > > >>>> Jacopo
> > > >>>>
> > > >>>>         [[alternative HTML version deleted]]
> > > >>>>
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> >
> > --
> > Best,
> > Kasper
> >
> >         [[alternative HTML version deleted]]
> >
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