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 = $CC for the configure and then modify the Makefile(s) manually?
Thanks, Chris ----- Original Message ---- From: Mark Abraham <[EMAIL PROTECTED]> To: Discussion list for GROMACS users <[email protected]> Sent: Monday, November 19, 2007 5:02:49 PM Subject: Re: [gmx-users] MPI configure "cannot compute sizeof (int)" Chris Borchert wrote: > Hello. I'm trying to get a MPI GROMACS 3.3.2 build for a Cray XT3 (AMD > Opteron cluster). The compute pool runs a linux microkernel called > Catamount. You compile for Catamount with "cc" or 'ftn", and launch a job > with "yod". I'm getting a "cannot compute sizeof int" error from configure. > Here is what I've done: What do you mean by "launch a job"? > module load fftw/3.1.1 > setenv CC linux-pgcc > setenv F77 linux-pgf77 > setenv MPICC cc > setenv CFLAGS "-tp k8-64 -fast -Mscalarsse" > setenv FFLAGS "-tp k8-64 -fast -Mscalarsse" > setenv CPPFLAGS -I${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 _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ____________________________________________________________________________________ Never miss a thing. Make Yahoo your home page. http://www.yahoo.com/r/hs _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
