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

[Dommert Florian]

On Sun, 2012-04-01 at 19:19 +1000, Mark Abraham wrote: 
> On 1/04/2012 6:55 PM, Dommert Florian wrote:
> > On Sun, 2012-04-01 at 03:50 +0000, 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?
> >>
> > I have a similar problem, but it is related to building with OpenMPI on
> > Ubuntu. For the releases so far, my MPI Compiler was found without any
> > problems. For the 4-6-release I have to explicitly declare the C and CXX
> > compilers as mpicc and mpic++, respectively. I am using gcc4.4.3 and
> > OpenMPI 1.4.3 on a 64bit Ubuntu 10.4 machine.
> >
> > I would also be interest why this happens now ?
> 
> I changed the way MPI is detected and used in commit hash 417d0affff. In 
> the commit message there I said:
> 
> commit 417d0affff5485d10f905aa3581f14602aca873a
> Author: Mark Abraham <mark.j.abraham at gmail.com>
> Date:   Mon Jan 9 20:38:33 2012 +1100
> 
>      Remove use of FindMPI.cmake
> 
>      The functionality of FindMPI.cmake should not be needed for GROMACS,
>      since the wrapper compiler will do the complete job. This already
>      worked for Cray and BlueGene, and so far this new version is known
>      to work for OpenMPI wrapping icc and gcc.
> 
>      CMake now warns the user about possible unsuitable versions of
>      OpenMPI and MVAPICH2.
> 
>      The process of managing MPI is more modular than it used to be.
> 
>      To use:
> 
>      cmake .. -DGMX_MPI=ON -DCMAKE_C_COMPILER=`which mpicc`
> 
>      or with bash
> 
>      CC=mpicc cmake .. -DGMX_MPI=ON
> 
>      and whatever else suits your setup.
> 
>      Fixes #851 and #636.
> 
>      Change-Id: Ibe41206bed8b70b83a25da1e4e29dd87b61ea17d
> 
> I have no idea whether this has any bearing on Michael's problem - what 
> is libgomp anyway?
> 
> Mark

Thank you very much for the insight. Next time I will check the git logs
first.

Regarding libgomp, it sounds like a G library for OpenMP, but this is
just a guess.

/Flo


-- 
Florian Dommert
Dipl. - Phys.

Institute for Computational Physics
University Stuttgart

Pfaffenwaldring 27
70569 Stuttgart

EMail: dommert at icp.uni-stuttgart.de
Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert

Tel.: +49 - (0)711 - 68563613
Fax.: +49 - (0)711 - 68563658
-------------- next part --------------
A non-text attachment was scrubbed...
Name: signature.asc
Type: application/pgp-signature
Size: 198 bytes
Desc: This is a digitally signed message part
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-developers/attachments/20120401/3760cae7/attachment.sig>