configure stalling on MacOSX
Barry Smith
bsmith at mcs.anl.gov
Sun Oct 14 10:24:25 CDT 2007
Ok.
It never hangs for me, for several different versions of icc/ifort.
Must be a hardware problem :-)
Barry
On Sat, 13 Oct 2007, Satish Balay wrote:
> Just a note: I've noticed similar hang with 'icc' on Dinesh's Mac.
> The thing that hangs is some component within the compiler -not
> compile wrapper. This is noticeable with graphical process listing
> utility from OSX' [I managed to kill it from this tool for configure
> to continue].
>
> I didn't spend enough time debugging this. However I'm pretty sure [in
> case of icc] its a compiler bug - not any MPI wrapper [I was using
> --with-mpi=0 for this test]
>
> Will try to dig more when I get a chance. [perhaps sometime nextweek].
>
> Satish
>
> On Sat, 13 Oct 2007, Barry Smith wrote:
>
> >
> > 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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