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

KACHMAR Ali kachmar_ali at hotmail.fr
Fri Jul 23 09:32:30 CEST 2010 

Hi,
 I had already installed xcode. 
I would like to be sure if it is correct my .bash_profile concerning the gcc and mpicc

# Setting PATH for Python 2.7# The orginal version is saved in .bash_profile.pysavePATH="/Library/Frameworks/Python.framework/Versions/2.7/bin:${PATH}"export PATH
# Setting PATH for MacPython 2.6# The orginal version is saved in .bash_profile.pysavePATH="/Library/Frameworks/Python.framework/Versions/2.6/bin:${PATH}"export PATH
export PATH=/usr/local/bin:$PATHexport PATH=$PATH:/usr/bin/gccexport PATH=$PATH:/usr/bin/mpicc

Ali



Date: Fri, 23 Jul 2010 09:13:44 +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,



  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

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

> > > Please search the archive at http://www.gromacs.org/search
before posting!

> > > Please don't post (un)subscribe requests to the list.
Use the 

> > > www interface or send it to gmx-users-request at gromacs.org.

> > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php

> > 

> > De nouvelles Emoticones sur Messenger ? Téléchargez
gratuitement les émoticônes Summer !

> 

> -- 

> 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

> Please search the archive at http://www.gromacs.org/search
before
posting!

> Please don't post (un)subscribe requests to the list. Use the 

> www interface or send it to gmx-users-request at gromacs.org.

> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

      
> > 

      

      Le nouveau Messenger arrive ! Téléchargez-le
gratuitement et découvrez ses nouvelles fonctionnalités
    

    

    -- 
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

!! PGP-ENCODED emails preferred !!
    
    

    De nouvelles Emoticones sur Messenger ? Téléchargez
gratuitement les émoticônes Summer !
  

  

  -- 
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

!! PGP-ENCODED emails preferred !!
  
  

  De nouvelles Emoticones sur Messenger ? Téléchargez
gratuitement les émoticônes Summer !




-- 
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

!! PGP-ENCODED emails preferred !! 		 	   		  
_________________________________________________________________
Découvrez Microsoft Security Essentials, l'antivirus gratuit par Microsoft
http://clk.atdmt.com/FRM/go/212688364/direct/01/
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100723/bc7b291a/attachment.html>

More information about the gromacs.org_gmx-users mailing list