configure stalling on MacOSX
Bernard Knaepen
bknaepen at ulb.ac.be
Sun Oct 14 12:56:53 CDT 2007
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.
>>>>
>>>>
>>>>
>>>>
>>
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