Re: configure stalling on MacOSX

[Bernard Knaepen <bknaepen@xxxxxxxxx>]

Hi,

If I try to compile with ifort a (helloworld) program directly from  
the command line with the rpath option I get:

dolfin:~/Desktop bknaepen$ ifort -o test -rpath /Users/bknaepen/ 
Desktop/petsc-2.3.3-p6  -I. -fPIC test.o
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)

Same result with mpif90 (my version of mpi is mpich2-106):

dolfin:~/Desktop bknaepen$ mpif90 -o test -rpath /Users/bknaepen/ 
Desktop/petsc-2.3.3-p6  -I. -fPIC test.o
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)

In other words, the compiler complains and exits immediately without  
getting stuck.



Regards,
Bernard.



On 13 Oct 2007, at 22:13, 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.