[gmx-users] installation: gromacs on Mac.10.5.8 leopard
Florian Dommert
dommert at icp.uni-stuttgart.de
Fri Jul 23 09:13:44 CEST 2010
Hi,
no just download the Apple Developer Tools from the Apple Developer
page. This will provide the latest version Apple builds of XCode, gcc,
and OpenMPI. Here is the link:
http://developer.apple.com/technologies/tools/
Hope this helps.
Cheers,
Flo
On 22.07.10 20:13, KACHMAR Ali wrote:
> Hi Florian,
>
> I download cudatoolkit_3.1_macos.pkg.
>
> I am confused, what I should change now in my .bash_profile.
>
> Ali
>
> ------------------------------------------------------------------------
> Date: Thu, 22 Jul 2010 19:28:22 +0200
> From: dommert at icp.uni-stuttgart.de
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] installation: gromacs on Mac.10.5.8 leopard
>
> Hi,
>
> I would download the latest developer toolkit, install it and all
> should be correct to install an MPI - Version of GROMACS. Everything
> works fine and I realize no trouble with compilation.
>
> Cheers,
>
> Flo
>
> On 22.07.10 18:58, KACHMAR Ali wrote:
>
> Hi Florian,
>
> Thanks for your answer. You're right, I found I don't have lam in
> my usr/local/. Where I should download this package?
>
> It is not coming on the developer. What I install, it is just this
> OpenMPI
>
> The latest OpenMPI source
> from http://www.open-mpi.org/software/ompi/v1.2/downloads/openmpi-1.2.8.tar.bz2
>
> Could you please give the link for this OpenMPI/LAM.
>
> As you advised me I disable this command export
> CPPFLAGS=-I/usr/local/openmpi/include, and I tried again, still
> the same error.
>
> Thanks.
>
> Ali
> ------------------------------------------------------------------------
> Date: Thu, 22 Jul 2010 12:51:53 +0200
> From: dommert at icp.uni-stuttgart.de
> <mailto:dommert at icp.uni-stuttgart.de>
> To: gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
> Subject: Re: [gmx-users] installation: gromacs on Mac.10.5.8 leopard
>
> Hello Ali,
>
> starting with OS X 10.5 the Developer tools included also a
> nicely working distribution of OpenMPI. So as soon as the
> Developer Tools have been installed on the Mac following the steps
> on the GROMACS website allowed to compile parallel binaries.
> Taking a look at your bash_profile open several questions. Have
> you installed a self compiled version of OpenMPI and LAM, because
> you define corresponding environment variables ? It is also
> somehow uncommon that you find binaries in a directory usually
> dedicated for libraries like /usr/local/lib.
>
> On 22.07.10 11:00, KACHMAR Ali wrote:
>
> > > export PATH=$PATH:/usr/local/lib
> > > export PATH=$PATH: /usr/bin/mpicc
> > > export PATH=$PATH:/usr/local/lam/bin/
> > >
>
> In this three lines it seems you try to define the compilers, but
> take a look at your environment variable PATH. Somewhere at the
> beginning you should find the directory /usr/bin as set by the
> system wide bash_profile. So the configure scripts usually
> chooses the compilers contained in this directory. In your case
> it will be the gcc and mpicc compilers and linkers supplied by the
> Developer tools.
>
> > >
> > > export CPPFLAGS=-I/usr/local/openmpi/include
> > >
>
>
> Why do you involve now this header files, perhaps they do not suit
> to the used version of OpenMPI ?
>
> Disable this lines in your .bash_profile open a new terminal and
> try again, perhaps this solves the problem. Then we know that just
> the path of the different installed MPI distributions were messed up.
>
> Cheers,
>
> Flo
>
> > > PS: the gcc is under the directory: /usr/local/lib or /usr/lib.
>
> > >
> > > Thanks.
> > >
> > > Ali
> > >
> > >
> > >
> > > > From: Ansgar.Esztermann at mpi-bpc.mpg.de
> <mailto:Ansgar.Esztermann at mpi-bpc.mpg.de>
> > > > To: gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
> > > > Date: Wed, 21 Jul 2010 12:15:25 +0200
> > > > Subject: Re: [gmx-users] installation: gromacs on
> Mac.10.5.8 leopard
> > > >
> > > >
> > > > On Jul 21, 2010, at 11:07 , KACHMAR Ali wrote:
> > > >
> > > > > checking whether the MPI cc command works...
> configure: error: Cannot compile and link MPI code with mpicc
> > > >
> > > >
> > > > This is the immediate problem: something goes wrong when
> compiling a test program with mpicc. If you look into the
> configure log, you should find a more detailed explanation of
> what went wrong (somewhere near the end).
> > > >
> > > > Regards,
> > > >
> > > > A.
> > > > --
> > > > Ansgar Esztermann
> > > > DV-Systemadministration
> > > > Max-Planck-Institut für biophysikalische Chemie,
> Abteilung 105
> > > >
> > > > --
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> <mailto:gmx-users at gromacs.org>
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> > --
> > Ansgar Esztermann
> > DV-Systemadministration
> > Max-Planck-Institut für biophysikalische Chemie, Abteilung 105
> >
> > --
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> --
> Florian Dommert
> Dipl. Phys.
>
> Institute for Computational Physics
> University Stuttgart
>
> Pfaffenwaldring 27
> 70565 Stuttgart
>
> Germany
>
> Tel: +49 - 711 / 6856-3613
> Fax: +49 - 711 / 6856-3658
>
> EMail: dommert at icp.uni-stuttgart.de <mailto:dommert at icp.uni-stuttgart.de>
> Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert <http://www.icp.uni-stuttgart.de/%7Eicp/Florian_Dommert>
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>
> --
> Florian Dommert
> Dipl. Phys.
>
> Institute for Computational Physics
> University Stuttgart
>
> Pfaffenwaldring 27
> 70565 Stuttgart
>
> Germany
>
> Tel: +49 - 711 / 6856-3613
> Fax: +49 - 711 / 6856-3658
>
> EMail: dommert at icp.uni-stuttgart.de <mailto:dommert at icp.uni-stuttgart.de>
> Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert <http://www.icp.uni-stuttgart.de/%7Eicp/Florian_Dommert>
>
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--
Florian Dommert
Dipl. Phys.
Institute for Computational Physics
University Stuttgart
Pfaffenwaldring 27
70565 Stuttgart
Germany
Tel: +49 - 711 / 6856-3613
Fax: +49 - 711 / 6856-3658
EMail: dommert at icp.uni-stuttgart.de
Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert
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