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
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