sieve-dev error compiling PETSc-3.1 with Sieve on Blue Gene/L
Shi Jin
jinzishuai at gmail.com
Mon Apr 5 18:28:24 CDT 2010
Thanks Matt.
I agree it works with many compilers. I've tried GCC, Intel, PG and they all
work.
The only one I have problem is the IBM XL compilers.
Have you had any success with the IBM compilers?
You mentioned BG/P. You didn't have trouble there?
I would imagine BG/P and BG/L are quite similar. Do you have the GCC and XL
versions there?
Anyway, I am asking the system administrators on this and hopefully will get
it fixed.
Thanks.
Shi
>
> I might understand, but it says that there is a circular reference to
> nothing (""). I look at the code, and
> have no idea what this means. And again, it compilers with many many many
> other compilers. I use
> it every day, the PyLith project does too. On Mac, Linux, PC, BG/P at ANL,
> etc. I really want to find
> out what is happening there, but I have a hard time seeing what I can do
> about this. I think these are
> bugs to be reported to the compiler maintainers.
>
> Matt
>
>
>> "/home/guntaka/src/petsc-dev-xlc/include/sieve/Sifter.hh", line 148.50:
>> 1540-1281 (W) "offsetof" cannot be applied to "struct Rec<int>". It is not
>> a POD (plain old data) type.
>> The Warning message shows many times but I think the real problem is in
>> the ALE::Bundle circular reference. I remember asking this kind of problems
>> before but wonder if there has been any progress in making it work now.
>>
>> The mpxlC is of version 9: /opt/ibmcmp/vacpp/bg/9.0/bin/bgxlC
>>
>> Thanks.
>> Shi
>>
>>
>> On Sun, Apr 4, 2010 at 8:32 PM, Matthew Knepley <knepley at gmail.com>wrote:
>>
>>> So the one thing that I guarantee runs now is unitTests (finally)
>>>
>>> cd src/dm/mesh/examples/tests
>>> make unitTests
>>>
>>> but watson should link as well. Think looks like a bad compiler bug. The
>>> linker should never SEGV. It should just return unresolved symbols. I am
>>> not really sure what to do other than report this problem to the sysadmin
>>> on that machine. I do not have it on the BG/L at BU. We can try and
>>> track it down by adding things to unitTests (if that builds).
>>>
>>> Thanks,
>>>
>>> Matt
>>>
>>> On Sun, Apr 4, 2010 at 5:12 PM, Shi Jin <jinzishuai at gmail.com> wrote:
>>>
>>>> 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.
>>>>
>>>>
>>>
>>>
>>> --
>>> 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.
>>
>>
>
>
> --
> 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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