[gmx-users] installation: gromacs on Mac.10.5.8 leopard

Thu Jul 22 20:13:18 CEST 2010

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

To: 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

> > > To: 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

> > > 

> > > -- 

> > > gmx-users mailing list gmx-users at gromacs.org

> > > http://lists.gromacs.org/mailman/listinfo/gmx-users

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> > 

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> -- 

> Ansgar Esztermann

> DV-Systemadministration

> Max-Planck-Institut für biophysikalische Chemie, Abteilung 105

> 

> -- 

> gmx-users mailing list gmx-users at gromacs.org

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University Stuttgart

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Germany

Tel: +49 - 711 / 6856-3613
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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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