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

Chris Borchert cbborchert at yahoo.com
Tue Nov 20 15:22:13 CET 2007

Thanks Mark. OK I'll concede that the Cray XT3 is a strange bird -- "cc" and "ftn" build a binary for the compute pool only. That binary (serial or parallel) will not run on the front-end but only on the back-end with a "yod" to push it back there. If it checked the size of an int with $CC then it would work, but since it's building with $MPICC it needs a yod to run it. BTW, the serial version of GROMACS builds fine. So should I make $MPICC = $CC for the configure and then modify the Makefile(s) manually?


----- Original Message ----
From: Mark Abraham <Mark.Abraham at anu.edu.au>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Monday, November 19, 2007 5:02:49 PM
Subject: Re: [gmx-users] MPI configure "cannot compute sizeof (int)"

 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 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.

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