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

[Erik Marklund]

1 apr 2012 kl. 11.19 skrev Mark Abraham:

> 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?

That's the gnu implementation of OpenMP.

> 
> Mark
> -- 
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-----------------------------------------------
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 6688        fax: +46 18 511 755
erikm at xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html

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