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

Chris Borchert cbborchert at yahoo.com
Mon Nov 19 21:23:51 CET 2007

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:

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"
./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
/opt/xt-pe/1.5.52/bin/snos64/cc: INFO: catamount target is being used
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). Is there another variable I should set to tell it to use "yod" to launch the binary? Or is there a way to skip the int check?


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