[gmx-users] compilation of gmx-4.0.2

Mark Abraham Mark.Abraham at anu.edu.au
Wed Nov 12 01:20:22 CET 2008

Xavier Periole wrote:
> Dears,
> my turn to ask a stupid question:
> I am trying to install gmx402 on a IBM pSeries 575
> CPUs: dual core IBM Power6
> when running the command:
> ./configure --enable-mpi --prefix==/home/XXXXX/gmx402/
> I run very into the error:
> .....
> .....
> checking size of int... configure: error: cannot compute sizeof (int)
> See config.log for more details.
> config.log did not help much.
> Is this a known issue? I had never seen it.

Yep there's at least one known cause. By default, configure assumes that 
you are building on the same architecture on which your target will run. 
So when testing for machine properties it can use either successful 
compilation or successful execution. However in a cross-compilation 
environment, the latter will fail.

There are several work-arounds. There's a tool called yodconfigure that 
I understand takes care of much of such issues, but I'm not sure how. Or 
you can trick configure into running code on the target machine somehow 
- this is tricky with GROMACS, because in src/gmxlib/nonbonded/nb_kernel 
you need to make and run on the build machine to create the generic 
kernels. Or you can tell configure you are cross-compiling with the 
--build and --host flag, so that it uses only successful compilation as 
a diagnostic tool.

I'm surprised that lack of mpicc caused such a problem and didn't cause 
a problem when testing mpicc.


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