configure stalling on MacOSX
Barry Smith
bsmith at mcs.anl.gov
Sat Oct 13 15:13:00 CDT 2007
You get
> 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
I get (not using mpif90, whose is it anyways MPICH1, MPICH2, Lam, OpenMPI?)
sh: ifort -o conftest -rpath /Users/bsmith/Src/petsc-dev -fPIC conftest.o
Executing: ifort -o conftest -rpath /Users/bsmith/Src/petsc-dev -fPIC conftest.o
sh:
Possible ERROR while running linker: ifort: command line warning #10156: ignoring option '-r'; no argument required
ifort: error #10106: Fatal error in /opt/intel/fc/10.0.020/bin/fortcom, terminated by bus error
ifort: error #10014: problem during multi-file optimization compilation (code 1)
output: ret = 256
My guess is that your underlying ifort is crashing with a bus error just like
mine, but your mpif90 is not properly handling this and so doesn't end and return like it should.
Can you try running the compile line that hangs directly from the shell with both ifort
directly and then your mpif90; what happens in each case? (Just make a tiny Fortran program in a file).
Perhaps yet another reason for hating the absurd "MPI compiler wrappers"; like MPI is SO-so-so special
(because it needs to link against a couple of MPI libraries and maybe a couple of system libraries?)
that it cannot be be compiled and linked like EVERY OTHER F*&& Unix package ever written but needs
its own special compiler wrappers, make me sick.
Barry
On Sat, 13 Oct 2007, Bernard Knaepen wrote:
> 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.
> > >
> > >
> > >
> > >
>
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