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

[Martin Grigorov]

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]]
> > >>>>
> > >>>> _______________________________________________
> > >>>> Bioc-devel using r-project.org mailing list
> > >>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > >>>>
> > >>>
> > >>> The information in this e-mail is intended only for the person to
> whom
> > >>> it is
> > >>> addressed. If you believe this e-mail was sent to you in error and
> the
> > >>> e-mail
> > >>> contains patient information, please contact the Partners Compliance
> > HelpLine
> > >>> at
> > >>> http://www.partners.org/complianceline . If the e-mail was sent to
> you
> > >>> in error
> > >>> but does not contain patient information, please contact the sender
> and
> > >>> properly
> > >>> dispose of the e-mail.
> > >>
> > >>
> > > The information in this e-mail is intended only for th...{{dropped:16}}
> >
> > _______________________________________________
> > Bioc-devel using r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
>
> --
> Best,
> Kasper
>
>         [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

	[[alternative HTML version deleted]]