Re: [gmx-users] MPI configure cannot compute sizeof (int)
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 = $CC for the
configure and then modify the Makefile(s) manually?
Thanks,
Chris
- Original Message
From: Mark Abraham [EMAIL PROTECTED]
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Monday, November 19, 2007 5:02:49 PM
Subject: Re: [gmx-users] MPI configure cannot compute sizeof (int)
Chris Borchert wrote:
Hello. I'm trying to get a MPI GROMACS 3.3.2 build for a Cray XT3 (AMD
Opteron cluster). The compute pool runs a linux microkernel called
Catamount. You compile for Catamount with cc or 'ftn, and launch a job
with yod. I'm getting a cannot compute sizeof int error from configure.
Here is what I've done:
What do you mean by launch a job?
module load fftw/3.1.1
setenv CC linux-pgcc
setenv F77 linux-pgf77
setenv MPICC cc
setenv CFLAGS -tp k8-64 -fast -Mscalarsse
setenv FFLAGS -tp k8-64 -fast -Mscalarsse
setenv CPPFLAGS -I${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: $? = 139
configure: program exited with status 139
It appears configure is trying to run the MPI job with just
./conftest which doesn't work here (or on many other architectures).
What makes you think it's an MPI binary? How do you mean it doesn't work
on many other architectures?
Is there another variable I should set to tell it to use yod to launch the
binary?
Not that I'm aware of.
Or is there a way to skip the int check?
configure does scores of such compile-and-test things, so you need to
solve the underlying problem.
Mark
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[gmx-users] MPI configure cannot compute sizeof (int)
Hello. I'm trying to get a MPI GROMACS 3.3.2 build for a Cray XT3 (AMD Opteron
cluster). The compute pool runs a linux microkernel called Catamount. You
compile for Catamount with cc or 'ftn, and launch a job with yod. I'm
getting a cannot compute sizeof int error from configure. Here is what I've
done:
module load fftw/3.1.1
setenv CC linux-pgcc
setenv F77 linux-pgf77
setenv MPICC cc
setenv CFLAGS -tp k8-64 -fast -Mscalarsse
setenv FFLAGS -tp k8-64 -fast -Mscalarsse
setenv CPPFLAGS -I${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
/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: $? = 139
configure: program exited with status 139
It appears configure is trying to run the MPI job with just
./conftest which doesn't work here (or on many other architectures). Is there
another variable I should set to tell it to use yod to launch the binary? Or
is there a way to skip the int check?
Thanks,
Chris
Never miss a thing. Make Yahoo your home page.
http://www.yahoo.com/r/hs
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Re: [gmx-users] MPI configure cannot compute sizeof (int)
Chris Borchert wrote:
Hello. I'm trying to get a MPI GROMACS 3.3.2 build for a Cray XT3 (AMD Opteron cluster). The compute pool runs a
linux microkernel called Catamount. You compile for Catamount with cc or 'ftn, and launch a job
with yod. I'm getting a cannot compute sizeof int error from configure. Here is what I've
done:
What do you mean by launch a job?
module load fftw/3.1.1
setenv CC linux-pgcc
setenv F77 linux-pgf77
setenv MPICC cc
setenv CFLAGS -tp k8-64 -fast -Mscalarsse
setenv FFLAGS -tp k8-64 -fast -Mscalarsse
setenv CPPFLAGS -I${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
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