[gmx-developers] Problems building for OS X with threads

[Roland Schulz]

On Sun, Apr 1, 2012 at 9:09 AM, David van der Spoel <spoel at xray.bmc.uu.se>wrote:

> On 2012-04-01 15:05, Roland Schulz wrote:
> >
> >
> > On Sun, Apr 1, 2012 at 6:20 AM, David van der Spoel
> > <spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>> wrote:
> >
> >     On 2012-04-01 05:50, Shirts, Michael (mrs5pt) wrote:
> >      > Hi, all-
> >      >
> >      > I'm very recently (with 4.6 updates in the last couple of weeks)
> >     having
> >      > issues with building gromacs with threads on OS X.  When I try to
> >     compile
> >      > with shared libraries, I get:
> >      >
> >      > ld: warning: in /usr/local/lib/libgomp.dylib, file was built for
> >     i386 which
> >      > is not the architecture being linked (x86_64)
> >      >
> >      > When I build without shared libraries, it compiles, but crashes
> >     when run
> >      > with -nt more than 1.
> >      >
> >      > Currently using OS X 10.6.8, gcc 4.1.2 to compile.
> >      >
> >      > Everything works fine with 4.5.5, and with earlier versions of
> 4.6.
> >      >
> >      > Anyone else having similar problems, or know what changes could
> >     have caused
> >      > this?
> >
> >     There is a redmine for this (900).
> >
> >
> > Michael's issue is a different because it is gcc 4.1.2 and because it is
> > not a segfault but the linker errorr.
> > I'm surprised that you get a linker error. gcc 4.1 doesn't support
> > OpenMP and if run cmake with gcc 4.1 on Linux I get:
> > Could NOT find OpenMP (missing: OpenMP_C_FLAGS OpenMP_CXX_FLAGS)
>
> He does mention a crash with -nt > 1, and it is only recently, he also
> links to libgomp, so it must be the same error.
>

True. I overlooked that part. Yes that part is the same. I'm still puzzled
why cmake doesn't detect that gcc 4.1 doesn't have OpenMP.
@Michael: Or was your compiler version a typo and you are also using gcc
4.2?

Roland



> >
> > If you rerun cmake (without a cache), do you still not get any error
> > during cmake?
> >
> > BTW: We probably should automatic disable OpenMP if the flags can't be
> > found (e.g. for clang and gcc <4.2)
>
> At least on Macs for now.
>
> >
> > Roland
> >
> >
> >     Your simplest solution is cmake -DGMX_OPENMP:BOOL=OFF
> >
> >      >
> >      > Thanks!
> >      > ~~~~~~~~~~~~
> >      > Michael Shirts
> >      > Assistant Professor
> >      > Department of Chemical Engineering
> >      > University of Virginia
> >      > michael.shirts at virginia.edu <mailto:michael.shirts at virginia.edu>
> >      > (434)-243-1821 <tel:%28434%29-243-1821>
> >      >
> >
> >
> >     --
> >     David van der Spoel, Ph.D., Professor of Biology
> >     Dept. of Cell & Molec. Biol., Uppsala University.
> >     Box 596, 75124 Uppsala, Sweden. Phone: +46184714205
> >     <tel:%2B46184714205>.
> >     spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>
> >     http://folding.bmc.uu.se
> >     --
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> >
> >
> >
> >
> >
> >
> > --
> > ORNL/UT Center for Molecular Biophysics cmb.ornl.gov <
> http://cmb.ornl.gov>
> > 865-241-1537, ORNL PO BOX 2008 MS6309
> >
> >
>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
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-- 
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
865-241-1537, ORNL PO BOX 2008 MS6309
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