sieve-dev error compiling PETSc-3.1 with Sieve on Blue Gene/L
Shi Jin
jinzishuai at gmail.com
Sun Apr 4 16:54:09 CDT 2010
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.
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