sieve-dev error compiling PETSc-3.1 with Sieve on Blue Gene/L

Shi Jin jinzishuai at gmail.com
Sun Apr 4 17:12:48 CDT 2010 

I tried the wastson example. It has the same error as my code:
guntaka at fr0103en:~/src/petsc-dev/src/dm/mesh/examples/tutorials> make watson
mpicxx -o watson.o -c -Wall -Wwrite-strings -Wno-strict-aliasing -O
-I/home/guntaka/src/petsc-dev/linux-gnu-cxx-opt/include
-I/home/guntaka/src/petsc-dev/include
-I/home/guntaka/src/petsc-dev/include/sieve
-I/home/guntaka/src/petsc-dev/externalpackages/Boost/
-I/bgl/BlueLight/V1R3M4_300_2008-080728/ppc/bglsys/include -I/c++
-DDIMENSION=3 -DNUM_TERMS=10 -DNUM_COEFFICIENTS=10*10*3
-D__INSDIR__=src/dm/mesh/examples/tutorials/ watson.cxx
mpicxx -Wall -Wwrite-strings -Wno-strict-aliasing -O  -o watson watson.o
-Wl,-rpath,/home/guntaka/src/petsc-dev/linux-gnu-cxx-opt/lib
-L/home/guntaka/src/petsc-dev/linux-gnu-cxx-opt/lib -lpetsc
-Wl,-rpath,/home/guntaka/src/petsc-dev/linux-gnu-cxx-opt/lib
-L/home/guntaka/src/petsc-dev/linux-gnu-cxx-opt/lib -lchaco -lflapack
-lfblas -lm -L/bgl/BlueLight/V1R3M4_300_2008-080728/ppc/bglsys/lib
-L/bgl/BlueLight/V1R3M4_300_2008-080728/ppc/blrts-gnu/lib/gcc/powerpc-bgl-blrts-gnu/3.4.3
-L/bgl/BlueLight/V1R3M4_300_2008-080728/ppc/blrts-gnu/powerpc-bgl-blrts-gnu/lib
-lmpich.rts -lmsglayer.rts -ldevices.rts -lrts.rts -lg2c -lm -lm
-lcxxmpich.rts -lstdc++ -lmpich.rts -lmsglayer.rts -ldevices.rts -lrts.rts
collect2: ld terminated with signal 11 [Segmentation fault]
make: [watson] Error 1 (ignored)
/bin/rm -f -f watson.o

Does this mean anything to you?
Thanks.
Shi

On Sun, Apr 4, 2010 at 3:54 PM, Shi Jin <jinzishuai at gmail.com> wrote:

> Thanks a lot Matt.
> After switching to petsc-dev, I've successfully build petsc-dev-sieve with
> the same configuration options on the BlueGene/L.
> However, when I tried to build my code, I got the error at the final
> linking stage (all objects are compiled sucessfully):
> guntaka at fr0103en:~/src/fcpu> make
> mpicxx -Wall -Wwrite-strings -Wno-strict-aliasing -O  -o fcpu main.o
> Options.o USG.o Wall.o PlaneWall.o BC.o Quadrature.o Tetrahedron.o
> TetrahedronTaylorHood.o Cylinder.o Sphere.o CylinderWall.o CFD.o NSSolver.o
> ParticulateFlow.o BodyFitMeshPF.o CollisionBox.o GranularFlow.o
> -Wl,-rpath,/home/guntaka/src/petsc-dev/linux-gnu-cxx-opt/lib
> -L/home/guntaka/src/petsc-dev/linux-gnu-cxx-opt/lib -lpetsc
> -Wl,-rpath,/home/guntaka/src/petsc-dev/linux-gnu-cxx-opt/lib
> -L/home/guntaka/src/petsc-dev/linux-gnu-cxx-opt/lib -lchaco -lflapack
> -lfblas -lm -L/bgl/BlueLight/V1R3M4_300_2008-080728/ppc/bglsys/lib
> -L/bgl/BlueLight/V1R3M4_300_2008-080728/ppc/blrts-gnu/lib/gcc/powerpc-bgl-blrts-gnu/3.4.3
> -L/bgl/BlueLight/V1R3M4_300_2008-080728/ppc/blrts-gnu/powerpc-bgl-blrts-gnu/lib
> -lmpich.rts -lmsglayer.rts -ldevices.rts -lrts.rts -lg2c -lm -lm
> -lcxxmpich.rts -lstdc++ -lmpich.rts -lmsglayer.rts -ldevices.rts -lrts.rts
> -Wl,-rpath,/home/guntaka/src/petsc-dev/linux-gnu-cxx-opt/lib
> -L/home/guntaka/src/petsc-dev/linux-gnu-cxx-opt/lib -lpetsc
> -Wl,-rpath,/home/guntaka/src/petsc-dev/linux-gnu-cxx-opt/lib
> -L/home/guntaka/src/petsc-dev/linux-gnu-cxx-opt/lib -lchaco -lflapack
> -lfblas -lm -L/bgl/BlueLight/V1R3M4_300_2008-080728/ppc/bglsys/lib
> -L/bgl/BlueLight/V1R3M4_300_2008-080728/ppc/blrts-gnu/lib/gcc/powerpc-bgl-blrts-gnu/3.4.3
> -L/bgl/BlueLight/V1R3M4_300_2008-080728/ppc/blrts-gnu/powerpc-bgl-blrts-gnu/lib
> -lmpich.rts -lmsglayer.rts -ldevices.rts -lrts.rts -lg2c -lm -lm
> -lcxxmpich.rts -lstdc++ -lmpich.rts -lmsglayer.rts -ldevices.rts -lrts.rts
> collect2: ld terminated with signal 11 [Segmentation fault]
> make: *** [fcpu] Error 1
>
> The error message is not terribly helpful identifying the problem.
> Do you know what could be wrong here?
>
> Is there a known sieve test code I can try to build?
> I tried to build something inside petsc-dev/src/dm/mesh/examples/tutorials
> but haven't got anything to work yet.
>
> Thanks a lot.
> Shi
>
>
> On Sun, Apr 4, 2010 at 12:58 PM, Matthew Knepley <knepley at gmail.com>wrote:
>
>> Yes, this is a bug in the IBM compiler version I have had other places. In
>> the latest
>> petsc-dev, I just commented out the #include of ALE_args.hh in ALE.hh.
>> This fixes
>> it. Everyone hates compiler bugs.
>>
>>  Thanks,
>>
>>    Matt
>>
>> On Sun, Apr 4, 2010 at 1:52 PM, Shi Jin <jinzishuai at gmail.com> wrote:
>>
>>> Hi,
>>>
>>> I was recently asked to port my code developed a year ago using
>>> petsc-dev-sieve.
>>> I just checked, the code works without problem on a Linux cluster with
>>> gcc-4.3.2 built against petsc-3.1.0.
>>>
>>> However, I got the following error built on the BlueGene. I used the
>>> following steps:
>>>
>>>    - ./configure —with-clanguage=C++ —with-sieve=1 —with-opt-sieve=1
>>>    —download-chaco=1 —download-boost=1 —with-shared=0 —with-debugging=no
>>>    —with-mpi-shared=0 —download-f-blas-lapack=1 —with-batch
>>>    - cqsub -q debug -n 2 -t 00:10:00 conftest. Make sure the job is
>>>    finished by "cqstat".
>>>    - ./reconfigure.py
>>>
>>> It works fine. The output is
>>>
>>> Compilers:
>>>   C Compiler:         mpicc  -Wall -Wwrite-strings -Wno-strict-aliasing -O
>>>   C++ Compiler:       mpicxx  -Wall -Wwrite-strings -Wno-strict-aliasing -O
>>>
>>>
>>>
>>>   Fortran Compiler:   mpif77  -Wall -Wno-unused-variable -O
>>> Linkers:
>>>   Static linker:   /usr/bin/ar cr
>>> MPI:
>>>   Includes: -I/bgl/BlueLight/V1R3M4_300_2008-080728/ppc/bglsys/include
>>> BLAS/LAPACK: -Wl,-rpath,/home/guntaka/src/petsc-3.1-p0/linux-gnu-cxx-opt/lib -L/home/guntaka/src/petsc-3.1-p0/linux-gnu-cxx-opt/lib -lflapack -Wl,-rpath,/home/guntaka/src/petsc-3.1-p0/linux-gnu-cxx-opt/lib -L/home/guntaka/src/petsc-3.1-p0/linux-gnu-cxx-opt/lib -lfblas
>>>
>>>
>>>
>>> Chaco:
>>>   Library:  -Wl,-rpath,/home/guntaka/src/petsc-3.1-p0/linux-gnu-cxx-opt/lib -L/home/guntaka/src/petsc-3.1-p0/linux-gnu-cxx-opt/lib -lchaco
>>> Sieve:
>>>   Includes: -I/home/guntaka/src/petsc-3.1-p0/include/sieve
>>>
>>>
>>>
>>> Boost:
>>>   Includes: -I/home/guntaka/src/petsc-3.1-p0/externalpackages/Boost/ -I/bgl/BlueLight/V1R3M4_300_2008-080728/ppc/bglsys/include
>>> PETSc:
>>>   PETSC_ARCH: linux-gnu-cxx-opt
>>>   PETSC_DIR: /home/guntaka/src/petsc-3.1-p0
>>>
>>>
>>>
>>>   Clanguage: Cxx
>>>   Scalar type: real
>>>   Precision: double
>>>   shared libraries: disabled
>>>   dynamic libraries: disabled
>>>   Memory alignment: 16
>>> xxx=========================================================================xxx
>>>
>>>
>>>
>>>    Configure stage complete. Now build PETSc libraries with:
>>>    make PETSC_DIR=/home/guntaka/src/petsc-3.1-p0 PETSC_ARCH=linux-gnu-cxx-opt all
>>>
>>>
>>> xxx=========================================================================xxx
>>>
>>>
>>>
>>> Then I moved ahead to build it
>>>
>>> make PETSC_DIR=/home/guntaka/src/petsc-3.1-p0 PETSC_ARCH=linux-gnu-cxx-opt all
>>> But I got the following error in compiling sieve:
>>> /home/guntaka/src/petsc-3.1-p0/include/sieve/ALE_args.hh: In member function `ALE::ArgValue ALE::ArgDB::operator[](const string&) const':
>>>
>>>
>>>
>>> /home/guntaka/src/petsc-3.1-p0/include/sieve/ALE_args.hh:132: error: call of overloaded `ArgValue(ALE::ArgValue)' is ambiguous
>>> /home/guntaka/src/petsc-3.1-p0/include/sieve/ALE_args.hh:64: note: candidates are: ALE::ArgValue::ArgValue(const ALE::ArgValue&)
>>>
>>>
>>>
>>> /home/guntaka/src/petsc-3.1-p0/include/sieve/ALE_args.hh:67: note:                 ALE::ArgValue::ArgValue(const boost::program_options::variable_value&)
>>>
>>> I am using the mpicxx which is using g++ 3.4.3:
>>>
>>>
>>> guntaka at fr0103en:~/src/petsc-3.1-p0> mpicxx -show
>>>
>>> /bgl/BlueLight/V1R3M4_300_2008-080728/ppc/blrts-gnu/bin/powerpc-bgl-blrts-gnu-g++ -I/bgl/BlueLight/V1R3M4_300_2008-080728/ppc/bglsys/include -L/bgl/BlueLight/V1R3M4_300_2008-080728/ppc/bglsys/lib -lcxxmpich.rts -lmpich.rts -L/bgl/BlueLight/V1R3M4_300_2008-080728/ppc/bglsys/lib -lmsglayer.rts -ldevices.rts -lrts.rts -ldevices.rts -lrts.rts
>>>
>>>
>>>
>>> guntaka at fr0103en:~/src/petsc-3.1-p0> /bgl/BlueLight/V1R3M4_300_2008-080728/ppc/blrts-gnu/bin/powerpc-bgl-blrts-gnu-g++ --version
>>>
>>> I remember there was some issues with older versions of GCC. Not sure this is the same problem.
>>>
>>>
>>>
>>> Has anyone have any experience on this?
>>>
>>> Thank you very much.
>>>
>>> Shi
>>> powerpc-bgl-blrts-gnu-g++ (GCC) 3.4.3
>>>
>>> /home/guntaka/src/petsc-3.1-p0/include/sieve/ALE_args.hh:132: error:   initializing temporary from result of `ALE::ArgValue::ArgValue(const boost::program_options::variable_value&)'
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> --
>>> Shi Jin, Ph.D.
>>>
>>>
>>
>>
>> --
>> What most experimenters take for granted before they begin their
>> experiments is infinitely more interesting than any results to which their
>> experiments lead.
>> -- Norbert Wiener
>>
>
>
>
> --
> Shi Jin, Ph.D.
>
>


-- 
Shi Jin, Ph.D.
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