[Bioc-devel] OpenMP on Mac OS "Mavericks" build server morelia

Dan Tenenbaum dtenenba at fredhutch.org
Mon Apr 13 20:26:47 CEST 2015

----- Original Message -----
> From: "Ulrich Bodenhofer" <bodenhofer at bioinf.jku.at>
> To: "Dan Tenenbaum" <dtenenba at fredhutch.org>
> Cc: "Hervé Pagès" <hpages at fhcrc.org>, msa at bioinf.jku.at, "Johannes Palme" <jpalme at aon.at>, bioc-devel at r-project.org
> Sent: Monday, April 13, 2015 11:22:11 AM
> Subject: Re: [Bioc-devel] OpenMP on Mac OS "Mavericks" build server morelia
> Hi Dan,
> Thanks for your reply!
> On our Mavericks machine (10.9.5 with XCode 6.1), there was no OpenMP
> installed at all. The configure script correctly found that out and
> compiled our package without OpenMP support. On morelia, however, the
> configure script seems to enforce OpenMP or at least thinks there is
> some OpenMP installed. And then, during compilation, the include file
> omp.h is not found. Maybe omp.h has to be prefixed with some
> directory,
> I don't know. Do you know of any other Bioconductor package that
> supports OpenMP on the Mavericks platform - to check out how this
> package does it?

Openmp is not installed on the mavericks machines. That's why I asked how you had installed it.

> For the time being, the workaround of switching off OpenMP entirely
> on
> Mac platforms seems to solve the problem: our version 0.99.5 at last
> builds smoothly on all four platforms.

> One more question: is it generally a good idea to build binary
> packages
> using OpenMP? What if somebody tries to install and run a package
> built
> with OpenMP on a Mac or Windows machine that has no OpenMP? I would
> rather expect the Mac and Windows binary packages to be built for
> maximum compatibility with standard systems. If a more experienced
> user
> wants to optimize the package for his/her platform, he/she can
> compile
> the source package him-/herself.

I agree. This is why openmp is not installed on our mavericks build machines. I'm not sure why you're seeing the behavior you report on morelia. I will look into it.


> Thanks and best regards,
> Ulrich
> Am 13.04.15 um 19:22 schrieb Dan Tenenbaum:
> > Hi Ulrich,
> >
> > [...
> > How did you set up OpenMP on your Mavericks machine?
> > Dan
> >

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