[gmx-developers] Problems building for OS X with threads
erikm at xray.bmc.uu.se
Sun Apr 1 22:02:26 CEST 2012
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
>> 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.
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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
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