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Re: configure stalling on MacOSX

Hi Matthew and Barry,

I tried again after installing intel fortran 10.0.020 but I still get the hanging. I copy below the output from configure.log that exhibits the timeout. When I remove the test related to '-rpath ' then the scripts does not hang. No problems either if I disable fortran with -- with-fc=0

uname -a gives:

Darwin dolfin.local 8.10.1 Darwin Kernel Version 8.10.1: Wed May 23 16:33:00 PDT 2007; root:xnu-792.22.5~1/RELEASE_I386 i386 i386

Regards,
Bernard.



======================================================================== ========
TEST checkSharedLinkerPaths from config.setCompilers(/Users/bknaepen/ Desktop/petsc-2.3.3-p6/python/BuildSystem/config/setCompilers.py:1107)
TESTING: checkSharedLinkerPaths from config.setCompilers(python/ BuildSystem/config/setCompilers.py:1107)
Determine the shared linker path options
- IRIX: -rpath
- Linux, OSF: -Wl,-rpath,
- Solaris: -R
- FreeBSD: -Wl,-R,
Pushing language C
sh: mpicc -flags
Executing: mpicc -flags
sh:
Trying C linker flag -Wl,-rpath,
sh: mpicc -c -o conftest.o -fPIC conftest.c
Executing: mpicc -c -o conftest.o -fPIC conftest.c
sh:
Pushing language C
Popping language C
sh: mpicc -o conftest -Wl,-rpath,/Users/bknaepen/Desktop/ petsc-2.3.3-p6 -Wl,-multiply_defined,suppress -Wl,-multiply_defined - Wl,suppress -Wl,-multiply_defined,suppress -Wl,-multiply_defined - Wl,suppress -fPIC conftest.o
Executing: mpicc -o conftest -Wl,-rpath,/Users/bknaepen/Desktop/ petsc-2.3.3-p6 -Wl,-multiply_defined,suppress -Wl,-multiply_defined - Wl,suppress -Wl,-multiply_defined,suppress -Wl,-multiply_defined - Wl,suppress -fPIC conftest.o
sh:
Possible ERROR while running linker: /usr/bin/ld: unknown flag: -rpath
collect2: ld returned 1 exit status
output: ret = 256
error message = {/usr/bin/ld: unknown flag: -rpath
collect2: ld returned 1 exit status
}
Pushing language C
Popping language C
in mpicc -o conftest -Wl,-rpath,/Users/bknaepen/Desktop/ petsc-2.3.3-p6 -Wl,-multiply_defined,suppress -Wl,-multiply_defined - Wl,suppress -Wl,-multiply_defined,suppress -Wl,-multiply_defined - Wl,suppress -fPIC conftest.o
Source:
#include "confdefs.h"
#include "conffix.h"

int main() {
;
return 0;
}
Rejecting linker flag -Wl,-rpath,/Users/bknaepen/Desktop/ petsc-2.3.3-p6 due to nonzero status from link
Rejecting C linker flag -Wl,-rpath,/Users/bknaepen/Desktop/ petsc-2.3.3-p6 due to
/usr/bin/ld: unknown flag: -rpath
collect2: ld returned 1 exit status

Rejected C linker flag -Wl,-rpath,
Trying C linker flag -R
sh: mpicc -c -o conftest.o -fPIC conftest.c
Executing: mpicc -c -o conftest.o -fPIC conftest.c
sh:
Pushing language C
Popping language C
sh: mpicc -o conftest -R/Users/bknaepen/Desktop/petsc-2.3.3-p6 -Wl,- multiply_defined,suppress -Wl,-multiply_defined -Wl,suppress -Wl,- multiply_defined,suppress -Wl,-multiply_defined -Wl,suppress -fPIC conftest.o
Executing: mpicc -o conftest -R/Users/bknaepen/Desktop/petsc-2.3.3- p6 -Wl,-multiply_defined,suppress -Wl,-multiply_defined -Wl,suppress - Wl,-multiply_defined,suppress -Wl,-multiply_defined -Wl,suppress - fPIC conftest.o
sh:
Possible ERROR while running linker: i686-apple-darwin8-gcc-4.0.1: unrecognized option '-R/Users/bknaepen/Desktop/petsc-2.3.3-p6'
output: error message = {i686-apple-darwin8-gcc-4.0.1: unrecognized option '-R/Users/bknaepen/Desktop/petsc-2.3.3-p6'
}
Pushing language C
Popping language C
in mpicc -o conftest -R/Users/bknaepen/Desktop/petsc-2.3.3-p6 - Wl,-multiply_defined,suppress -Wl,-multiply_defined -Wl,suppress -Wl,- multiply_defined,suppress -Wl,-multiply_defined -Wl,suppress -fPIC conftest.o
Source:
#include "confdefs.h"
#include "conffix.h"

int main() {
;
return 0;
}
Rejecting C linker flag -R/Users/bknaepen/Desktop/ petsc-2.3.3-p6 due to
i686-apple-darwin8-gcc-4.0.1: unrecognized option '-R/Users/bknaepen/ Desktop/petsc-2.3.3-p6'

Rejected C linker flag -R
Trying C linker flag -rpath
sh: mpicc -c -o conftest.o -fPIC conftest.c
Executing: mpicc -c -o conftest.o -fPIC conftest.c
sh:
Pushing language C
Popping language C
sh: mpicc -o conftest -rpath /Users/bknaepen/Desktop/petsc-2.3.3-p6 -Wl,-multiply_defined,suppress -Wl,-multiply_defined -Wl,suppress - Wl,-multiply_defined,suppress -Wl,-multiply_defined -Wl,suppress - fPIC conftest.o
Executing: mpicc -o conftest -rpath /Users/bknaepen/Desktop/ petsc-2.3.3-p6 -Wl,-multiply_defined,suppress -Wl,-multiply_defined - Wl,suppress -Wl,-multiply_defined,suppress -Wl,-multiply_defined - Wl,suppress -fPIC conftest.o
sh:
Possible ERROR while running linker: i686-apple-darwin8-gcc-4.0.1: unrecognized option '-rpath'
/usr/bin/ld: can't map file: /Users/bknaepen/Desktop/petsc-2.3.3-p6 ((os/kern) invalid argument)
collect2: ld returned 1 exit status
output: ret = 256
error message = {i686-apple-darwin8-gcc-4.0.1: unrecognized option '- rpath'
/usr/bin/ld: can't map file: /Users/bknaepen/Desktop/petsc-2.3.3-p6 ((os/kern) invalid argument)
collect2: ld returned 1 exit status
}
Pushing language C
Popping language C
in mpicc -o conftest -rpath /Users/bknaepen/Desktop/petsc-2.3.3- p6 -Wl,-multiply_defined,suppress -Wl,-multiply_defined -Wl,suppress - Wl,-multiply_defined,suppress -Wl,-multiply_defined -Wl,suppress - fPIC conftest.o
Source:
#include "confdefs.h"
#include "conffix.h"

int main() {
;
return 0;
}
Rejecting linker flag -rpath /Users/bknaepen/Desktop/ petsc-2.3.3-p6 due to nonzero status from link
Rejecting C linker flag -rpath /Users/bknaepen/Desktop/ petsc-2.3.3-p6 due to
i686-apple-darwin8-gcc-4.0.1: unrecognized option '-rpath'
/usr/bin/ld: can't map file: /Users/bknaepen/Desktop/petsc-2.3.3-p6 ((os/kern) invalid argument)
collect2: ld returned 1 exit status

Rejected C linker flag -rpath
Trying C linker flag -Wl,-R,
sh: mpicc -c -o conftest.o -fPIC conftest.c
Executing: mpicc -c -o conftest.o -fPIC conftest.c
sh:
Pushing language C
Popping language C
sh: mpicc -o conftest -Wl,-R,/Users/bknaepen/Desktop/petsc-2.3.3-p6 -Wl,-multiply_defined,suppress -Wl,-multiply_defined -Wl,suppress - Wl,-multiply_defined,suppress -Wl,-multiply_defined -Wl,suppress - fPIC conftest.o
Executing: mpicc -o conftest -Wl,-R,/Users/bknaepen/Desktop/ petsc-2.3.3-p6 -Wl,-multiply_defined,suppress -Wl,-multiply_defined - Wl,suppress -Wl,-multiply_defined,suppress -Wl,-multiply_defined - Wl,suppress -fPIC conftest.o
sh:
Possible ERROR while running linker: /usr/bin/ld: unknown flag: -R
collect2: ld returned 1 exit status
output: ret = 256
error message = {/usr/bin/ld: unknown flag: -R
collect2: ld returned 1 exit status
}
Pushing language C
Popping language C
in mpicc -o conftest -Wl,-R,/Users/bknaepen/Desktop/petsc-2.3.3- p6 -Wl,-multiply_defined,suppress -Wl,-multiply_defined -Wl,suppress - Wl,-multiply_defined,suppress -Wl,-multiply_defined -Wl,suppress - fPIC conftest.o
Source:
#include "confdefs.h"
#include "conffix.h"

int main() {
;
return 0;
}
Rejecting linker flag -Wl,-R,/Users/bknaepen/Desktop/ petsc-2.3.3-p6 due to nonzero status from link
Rejecting C linker flag -Wl,-R,/Users/bknaepen/Desktop/ petsc-2.3.3-p6 due to
/usr/bin/ld: unknown flag: -R
collect2: ld returned 1 exit status

Rejected C linker flag -Wl,-R,
Popping language C
Pushing language FC
sh: mpicc -flags
Executing: mpicc -flags
sh:
Trying FC linker flag -Wl,-rpath,
sh: mpif90 -c -o conftest.o -I. -fPIC conftest.F
Executing: mpif90 -c -o conftest.o -I. -fPIC conftest.F
sh:
Pushing language C
Popping language C
sh: mpif90 -o conftest -Wl,-rpath,/Users/bknaepen/Desktop/ petsc-2.3.3-p6 -I. -fPIC conftest.o
Executing: mpif90 -o conftest -Wl,-rpath,/Users/bknaepen/Desktop/ petsc-2.3.3-p6 -I. -fPIC conftest.o
sh:
Possible ERROR while running linker: ipo: error #11019: OBJREAD Error: Could not create mapping for /Users/bknaepen/Desktop/ petsc-2.3.3-p6
ifort: error #10014: problem during multi-file optimization compilation (code 1)
output: ret = 256
error message = {ipo: error #11019: OBJREAD Error: Could not create mapping for /Users/bknaepen/Desktop/petsc-2.3.3-p6
ifort: error #10014: problem during multi-file optimization compilation (code 1)
}
Pushing language C
Popping language C
in mpif90 -o conftest -Wl,-rpath,/Users/bknaepen/Desktop/ petsc-2.3.3-p6 -I. -fPIC conftest.o
Source:
program main

end
Rejecting linker flag -Wl,-rpath,/Users/bknaepen/Desktop/ petsc-2.3.3-p6 due to nonzero status from link
Valid FC linker flag -Wl,-rpath,/Users/bknaepen/Desktop/ petsc-2.3.3-p6
Rejected FC linker flag -Wl,-rpath,
Trying FC linker flag -R
sh: mpif90 -c -o conftest.o -I. -fPIC conftest.F
Executing: mpif90 -c -o conftest.o -I. -fPIC conftest.F
sh:
Pushing language C
Popping language C
sh: mpif90 -o conftest -R/Users/bknaepen/Desktop/petsc-2.3.3-p6 - I. -fPIC conftest.o
Executing: mpif90 -o conftest -R/Users/bknaepen/Desktop/petsc-2.3.3- p6 -I. -fPIC conftest.o
sh:
Possible ERROR while running linker: ifort: command line warning #10006: ignoring unknown option '-R/Users/bknaepen/Desktop/ petsc-2.3.3-p6'
output: error message = {ifort: command line warning #10006: ignoring unknown option '-R/Users/bknaepen/Desktop/petsc-2.3.3-p6'
}
Pushing language C
Popping language C
in mpif90 -o conftest -R/Users/bknaepen/Desktop/petsc-2.3.3-p6 - I. -fPIC conftest.o
Source:
program main

end
Rejecting FC linker flag -R/Users/bknaepen/Desktop/ petsc-2.3.3-p6 due to
ifort: command line warning #10006: ignoring unknown option '-R/Users/ bknaepen/Desktop/petsc-2.3.3-p6'

Rejected FC linker flag -R
Trying FC linker flag -rpath
sh: mpif90 -c -o conftest.o -I. -fPIC conftest.F
Executing: mpif90 -c -o conftest.o -I. -fPIC conftest.F
sh:
Pushing language C
Popping language C
sh: mpif90 -o conftest -rpath /Users/bknaepen/Desktop/petsc-2.3.3- p6 -I. -fPIC conftest.o
Executing: mpif90 -o conftest -rpath /Users/bknaepen/Desktop/ petsc-2.3.3-p6 -I. -fPIC conftest.o
Runaway process exceeded time limit of 600.0s
Possible ERROR while running linker: Runaway process exceeded time limit of 600.0s
output: Runaway processret = -1
error message = {Runaway process exceeded time limit of 600.0s
}
Pushing language C
Popping language C
in mpif90 -o conftest -rpath /Users/bknaepen/Desktop/petsc-2.3.3- p6 -I. -fPIC conftest.o
Source:
program main

end
Rejecting linker flag -rpath /Users/bknaepen/Desktop/ petsc-2.3.3-p6 due to nonzero status from link
Valid FC linker flag -rpath /Users/bknaepen/Desktop/ petsc-2.3.3-p6
Rejected FC linker flag -rpath
Trying FC linker flag -Wl,-R,
sh: mpif90 -c -o conftest.o -I. -fPIC conftest.F
Executing: mpif90 -c -o conftest.o -I. -fPIC conftest.F
sh:
Pushing language C
Popping language C
sh: mpif90 -o conftest -Wl,-R,/Users/bknaepen/Desktop/petsc-2.3.3- p6 -I. -fPIC conftest.o
Executing: mpif90 -o conftest -Wl,-R,/Users/bknaepen/Desktop/ petsc-2.3.3-p6 -I. -fPIC conftest.o
sh:
Possible ERROR while running linker: IPO link: Warning unknown option '-R'.
ipo: error #11019: OBJREAD Error: Could not create mapping for /Users/ bknaepen/Desktop/petsc-2.3.3-p6
ifort: error #10014: problem during multi-file optimization compilation (code 1)
output: ret = 256
error message = {IPO link: Warning unknown option '-R'.
ipo: error #11019: OBJREAD Error: Could not create mapping for /Users/ bknaepen/Desktop/petsc-2.3.3-p6
ifort: error #10014: problem during multi-file optimization compilation (code 1)
}
Pushing language C
Popping language C
in mpif90 -o conftest -Wl,-R,/Users/bknaepen/Desktop/petsc-2.3.3- p6 -I. -fPIC conftest.o
Source:
program main

end
Rejecting linker flag -Wl,-R,/Users/bknaepen/Desktop/ petsc-2.3.3-p6 due to nonzero status from link
Rejecting FC linker flag -Wl,-R,/Users/bknaepen/Desktop/ petsc-2.3.3-p6 due to
IPO link: Warning unknown option '-R'.
ipo: error #11019: OBJREAD Error: Could not create mapping for /Users/ bknaepen/Desktop/petsc-2.3.3-p6
ifort: error #10014: problem during multi-file optimization compilation (code 1)

Rejected FC linker flag -Wl,-R,
Popping language FC
======================================================================== ========
On 12 Oct 2007, at 23:26, Barry Smith wrote:


I have run with 10.0.0.20 on the Mac with no difficulties using the options
below with petsc-2.3.3-6 and have no hanging. config/configure.py just takes a
couple of minutes.

[bsmith:~/Src/petsc-release-2.3.3] bsmith% uname -a
Darwin bsmith.mcs.anl.gov 8.10.1 Darwin Kernel Version 8.10.1: Wed May 23
16:33:00 PDT 2007; root:xnu-792.22.5~1/RELEASE_I386 i386 i386


   Barry


On Fri, 12 Oct 2007, Knaepen Bernard wrote:

Hello,

is it normal that the ./config/configure.py stalls for a long time when building petsc-2.3.3-p6 on MacOSX? The step at which it stays stuck is:

TESTING: checkSharedLinkerPaths from config.setCompilers(python/ BuildSystem/config/setCompilers.py:1107)

It remains there for around five minutes then continues the configure process without problem. Except that it leaves a fortran process alive that I have to manually kill later on. This process looks like:

17623 fortcom 60.8% 5:06.44 1 13 60 364K 12.1M 2.23M 57.8M
17614 ifortia32 0.0% 0:00.02 1 14 19 392K 1.96M 1.86M 29.0M
17613 ifortbin 0.0% 0:00.01 1 13 16 148K 992K 876K 28.6M

when I use the top command.

I am configuring with the following options:

/config/configure.py --with-cc=mpicc --with-fc=mpif90 --with- hypre=1 --download-hypre=1 --with-debugging=0 COPTFLAGS=-O3 FOPTFLAGS=-O3 --with-cxx=mpicxx --with-x=0 --with-sudo=sudo

The system is MacOSX 10.4.9 (latest) running on a MacPro (or Macbook Pro) and the fortran compiler is ifort 10.0.17.

Regards,
Bernard.