[Openmd-users] Question regarding gcc4.2

[Dan Gezelter]

Dr. Akabani,

  You don't need the gcc 4.4 variants, but they do install a fortran compiler (which is not installed by default under Mac OS X with Xcode.  You can indeed use the +gcc42 variant for both fftw-3 and openmpi. 

This is also likely the cause of your problem with atom2md.  That particular program is linked against the openbabel dynamic library, and the dynamic loading code is not portable from gcc 4.2 to gcc 4.4.  So, it would probably be advisable to step back the compiler to version 4.2. 

Thank you for pointing this out.  It looks like we need to change the install instructions on the site to specify the gcc42 variants.

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
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> 
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