[gmx-users] Compiling 4.0.7 parallel fails

Matthew L. Danielson mldaniel at purdue.edu
Fri Feb 5 21:29:47 CET 2010


I am having a problem installing version 4.0.7, specifically the 
parallel version.  Searching the mailing archives i came across several 
posts related to my problem but none seemed to offered a solution to the 
error message i am seeing (tried all suggestions).  I have root access 
to my machine (installing in /usr/local) so there should not be any 
permission problems.

Here is exactly what i have done (tried to follow the instructions on 
the website but i find this section not as well put together on the new 
1.  fftw-3.3.1: ./configure --enable-float, make -j 4, make install
2.  openmpi-1.2.8: ./configure, make -j 4, make install
3.  gromacs-4.0.7: ./configure --enable-mpi

Compiling fftw and openmpi seems to finish successfully.  The serial 
version of gromacs installed correctly, just when i issue --enable-mpi i 
am seeing this error message (i can attached the config.log if it would 
"checking size of int... configure: error: cannot compute sizeof (int)"

 From what i can get out of the mail-archive, I think this is  problem 
with the mpi installation or not finding the correct files etc.  I have 
tried re-installing openmpi (always removing the old version) using yum 
(installed version 1.3.2) and installing openmpi from their website 
(1.4.1).  Both seem to install correctly, yet the same error message 
arises when i do ./configure --enable-mpi for gromacs.

I have also tried to set in my bash shell:  export 
Same problem still as above.

Anyone had this problem and solved it?  Or can anyone possible offer a 
solution?  I am to the point where i do not know where to look next & I 
would appreciate any feedback.

Matt Danielson


Matthew L. Danielson

Graduate Student of Medicinal Chemistry & Molecular Pharmacology
College of Pharmacy, Nursing, and Health Sciences
Purdue University
575 Stadium Mall Drive
West Lafayette, IN 47907-2091

(765)496-6643 office 

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