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

Hi Ulrich,

----- Original Message -----
From: "Ulrich Bodenhofer" <bodenhofer at bioinf.jku.at>
To: bioc-devel at r-project.org
Cc: "Herv? Pag?s" <hpages at fhcrc.org>, msa at bioinf.jku.at, "Johannes Palme" <jpalme at aon.at>
Sent: Monday, April 13, 2015 3:37:37 AM
Subject: [Bioc-devel] OpenMP on Mac OS "Mavericks" build server morelia

Dear BioC Core Team members,

As you know, we have submitted a package 'msa' for Bioconductor 3.1
which has been accepted last week. After having fixed some other
cross-platform problems, we are still having issues on the Mavericks
build server morelia (see
http://bioconductor.org/checkResults/3.1/bioc-LATEST/msa/morelia-buildsrc.html).
Version 0.99.4 of our package throws an error that the OpenMP include
file omp.h is not found. Our configure script actually checks for
OpenMP
and our package builds without any errors on all Mac OS systems we
have
tested so far (Yosemite and Mavericks, and it also works on the Snow
Leopard build server petty). I suppose there are two possible sources
of
How did you set up OpenMP on your Mavericks machine?
Dan
the problem: that something is still wrong with our code or that
OpenMP
is ill-configured on morelia. In the meantime, we have checked in
Version 0.99.5 which explicitly turns off OpenMP for all Mac OS
platforms, but we would prefer to remove this suboptimal workaround
if
possible. Any help is gratefully appreciated!

Thanks in advance and best regards,
Ulrich

P.S.: If this is a question that should not be discussed on this
list,
but elsewhere, please let us know.
P.P.S.: That the Makefile says "Compilation successful" despite the
compilation error, has been fixed in 0.99.5.

_______________________________________________
Bioc-devel at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

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?

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.

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

----- Original Message -----
From: "Ulrich Bodenhofer" <bodenhofer at bioinf.jku.at>
To: "Dan Tenenbaum" <dtenenba at fredhutch.org>
Cc: "Herv? Pag?s" <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.

Dan
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