[Openmd-users] Question regarding gcc4.2

[Dan Gezelter]

Gamal,

  I just updated the install instructions and tested on my Mac (OS X 10.6.4, Xcode 3.2.2, MacPorts 1.9.1).  Since the atom2md code links against the openbabel dynamic libraries, you need to use a compiler that is link compatible with the one that was used to build openbabel (which is usually gcc 4.2).  Also, the stock Xcode development environment does not come with a fortran compiler, so we need to build one to compile OpenMD.

The current version of MacPorts has a broken gcc42 port, but the gcc43 port does work well, so these commands will generate a build environment that will work:

sudo /opt/local/bin/port install subversion openbabel qhull zlib fftw-3
sudo /opt/local/bin/port install openmpi +gcc43

If you have versions of these tools already installed with other variants, you might want to clean up your ports a bit before running those two install commands:

sudo /opt/local/bin/port uninstall subversion openbabel qhull zlib fftw-3 openmpi gcc44
sudo /opt/local/bin/port clean subversion openbabel qhull zlib fftw-3 openmpi gcc44

Once the prerequisites are installed, you can follow the instructions here to get OpenMD built:

http://openmd.net/?p=83

Let me know if you run into any other problems.

Best regards,

 --Dan Gezelter


On Jun 27, 2010, at 1:48 PM, Gamal Akabani wrote:

> Hello there:
> 
> First of all I am no genius. So I am sorry to post simple question but your help will be very much appreciated.
> I am new and I am trying to install openmd. So far I have no success.
> I followed very carefully the instructions for installing the “prerequisites”  at http://openmd.net/?p=56
> My computer is using gcc version 4.2.1 (Apple Inc. build 5659).
> However, the instruction state that MacPorts are “directed” at gcc version 4.4 as indicated below.
> 
> sudo /opt/local/bin/port install subversion openbabel qhull zlib
> sudo /opt/local/bin/port install fftw-3 +gcc44
> sudo /opt/local/bin/port install openmpi +gcc44
> 
> Do I need gcc version 4.4 installed in my computer?
> 
> Also, when I try to follow the example provided at http://openmd.net/?cat=4 I invoke 
> 
> atom2md -ixyz methanol.xyz
> 
> It crashes with the following output
> 
> atom2md(25909) malloc: *** error for object 0x10087d6c0: pointer being freed was not allocated
> *** set a breakpoint in malloc_error_break to debug
> Abort
> 
> Your help will be very much appreciated.
> 
> Gamal Akabani, PhD.
> Associate Professor
> Department of Nuclear Engineering
> Texas A&M University
> 129 Zachry Bldg
> 3133 TAMU
> College Station, TX 77843-3133
> (979) 458-1699 Phone
> (979) 676-0695 Mobile
> (979) 845-6443 FAX
> <image.png>
> 
> _______________________________________________
> Openmd-users mailing list
> Openmd-users at maul.chem.nd.edu
> http://maul.chem.nd.edu/mailman/listinfo/openmd-users

***********************************************
  J. Daniel Gezelter
  Associate Professor of Chemistry
  Director of Graduate Admissions
  Department of Chemistry and Biochemistry
  251 Nieuwland Science Hall
  University of Notre Dame
  Notre Dame, IN 46556-5670

  phone:  +1 (574) 631-7595
  fax:    +1 (574) 631-6652
  e-mail: gezelter at nd.edu
  web:    http://www.nd.edu/~gezelter
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