[gmx-users] MPI configure "cannot compute sizeof (int)"

[Mark Abraham]

Chris Borchert wrote:
> Hello. I'm trying to get a MPI GROMACS 3.3.2 build for a Cray XT3 (AMD Opteron cluster). The compute pool runs a linux microkernel called Catamount. You compile for Catamount with "cc" or 'ftn", and launch a job with "yod". I'm getting a "cannot compute sizeof int" error from configure. Here is what I've done:

What do you mean by "launch a job"?

> module load fftw/3.1.1
> setenv CC linux-pgcc
> setenv F77 linux-pgf77
> setenv MPICC cc
> setenv CFLAGS "-tp k8-64 -fast -Mscalarsse"
> setenv FFLAGS "-tp k8-64 -fast -Mscalarsse"
> setenv CPPFLAGS -I${FFTW_INC}
> setenv LDFLAGS -L${FFTW_DIR}
> ./configure --enable-mpi --program-suffix="_mpi" --prefix=/usr/local/usp/gromacs
> 
> Configure errors here:
> checking for int... yes
> checking size of int... configure: error: cannot compute sizeof (int)
> 
> Config.log output:
> configure:7267: checking size of int
> configure:7617: cc -o conftest -tp k8-64 -fast -Mscalarsse -I/opt/fftw/3.1.1/cnos/include -L/opt/fftw/3.1.1/cnos/lib conftest.c  >&5

This is not an MPI compilation, unless your cc magically makes all 
targets MPI targets.

> /opt/xt-pe/1.5.52/bin/snos64/cc: INFO: catamount target is being used
> conftest.c:
> configure:7620: $? = 0
> configure:7626: ./conftest
> ./configure: line 1:  5147 Segmentation fault      ./conftest$ac_exeext
> configure:7629: $? = 139
> configure: program exited with status 139
> 
> It appears configure is trying to run the MPI job with just
> "./conftest" which doesn't work here (or on many other architectures).

What makes you think it's an MPI binary? How do you mean it doesn't work 
on many other architectures?

> Is there another variable I should set to tell it to use "yod" to launch the binary? 

Not that I'm aware of.

> Or is there a way to skip the int check?

configure does scores of such compile-and-test things, so you need to 
solve the underlying problem.

Mark