<div dir="ltr">On Mon, Apr 5, 2010 at 7:15 PM, Shi Jin <span dir="ltr"><<a href="mailto:jinzishuai@gmail.com">jinzishuai@gmail.com</a>></span> wrote:<br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Thanks Matt.<br>I tried to build petsc-dev-sieve with the IBM compilers by<br>./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 —with-cc=mpxlc —with-cxx=mpxlC —with-fc=mpxlf<br>
<br>It builds petsc-dev seemingly fine. But I got the error building the watson example:<br>"/home/guntaka/src/petsc-dev-xlc/include/sieve/Mesh.hh", line 110.30: 1540-1110 (S) The referenced type "ALE::Bundle" contains a circular reference back to "".<br>
</blockquote><div><br></div><div>I might understand, but it says that there is a circular reference to nothing (""). I look at the code, and</div><div>have no idea what this means. And again, it compilers with many many many other compilers. I use</div>
<div>it every day, the PyLith project does too. On Mac, Linux, PC, BG/P at ANL, etc. I really want to find</div><div>out what is happening there, but I have a hard time seeing what I can do about this. I think these are</div>
<div>bugs to be reported to the compiler maintainers.</div><div><br></div><div> Matt</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
"/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.<br>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.<br>
<br>The mpxlC is of version 9: /opt/ibmcmp/vacpp/bg/9.0/bin/bgxlC<br><br>Thanks.<br>Shi<div><div></div><div class="h5"><br><br><div class="gmail_quote">On Sun, Apr 4, 2010 at 8:32 PM, Matthew Knepley <span dir="ltr"><<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204, 204, 204);padding-left:1ex">So the one thing that I guarantee runs now is unitTests (finally)<div><br></div><div> cd src/dm/mesh/examples/tests</div>
<div> make unitTests</div><div><br></div><div>but watson should link as well. Think looks like a bad compiler bug. The</div>
<div>linker should never SEGV. It should just return unresolved symbols. I am</div><div>not really sure what to do other than report this problem to the sysadmin</div><div>on that machine. I do not have it on the BG/L at BU. We can try and</div>
<div>track it down by adding things to unitTests (if that builds).</div><div><br></div><div> Thanks,</div><div><br></div><div> Matt</div><div><div></div><div><div><br><div class="gmail_quote">On Sun, Apr 4, 2010 at 5:12 PM, Shi Jin <span dir="ltr"><<a href="mailto:jinzishuai@gmail.com" target="_blank">jinzishuai@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204, 204, 204);padding-left:1ex">I tried the wastson example. It has the same error as my code:<br>guntaka@fr0103en:~/src/petsc-dev/src/dm/mesh/examples/tutorials> make watson<br>
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<br>
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 <br>
<div>
collect2: ld terminated with signal 11 [Segmentation fault]<br></div>make: [watson] Error 1 (ignored)<br>/bin/rm -f -f watson.o<br><br>Does this mean anything to you?<br>Thanks.<br>Shi<div><div></div><div><br>
<br><div class="gmail_quote">On Sun, Apr 4, 2010 at 3:54 PM, Shi Jin <span dir="ltr"><<a href="mailto:jinzishuai@gmail.com" target="_blank">jinzishuai@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204, 204, 204);padding-left:1ex">Thanks a lot Matt.<br>After switching to petsc-dev, I've successfully build petsc-dev-sieve with the same configuration options on the BlueGene/L.<br>
However, when I tried to build my code, I got the error at the final linking stage (all objects are compiled sucessfully):<br>
guntaka@fr0103en:~/src/fcpu> make<br>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 <br>
collect2: ld terminated with signal 11 [Segmentation fault]<br>make: *** [fcpu] Error 1<br><br>The error message is not terribly helpful identifying the problem.<br>Do you know what could be wrong here?<br><br>Is there a known sieve test code I can try to build?<br>
I tried to build something inside petsc-dev/src/dm/mesh/examples/tutorials but haven't got anything to work yet.<br><br>Thanks a lot.<br>Shi<div><div></div><div><br><br><div class="gmail_quote">On Sun, Apr 4, 2010 at 12:58 PM, Matthew Knepley <span dir="ltr"><<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204, 204, 204);padding-left:1ex">Yes, this is a bug in the IBM compiler version I have had other places. In the latest<div>petsc-dev, I just commented out the #include of ALE_args.hh in ALE.hh. This fixes</div>
<div>it. Everyone hates compiler bugs.</div><div>
<br></div><div> Thanks,</div><div><br></div><div> Matt</div><div><div><div></div><div><br><div class="gmail_quote">On Sun, Apr 4, 2010 at 1:52 PM, Shi Jin <span dir="ltr"><<a href="mailto:jinzishuai@gmail.com" target="_blank">jinzishuai@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204, 204, 204);padding-left:1ex">Hi, <br><br>I was recently asked to port my code developed a year ago using petsc-dev-sieve.<br>
I just checked, the code works without problem on a Linux cluster with gcc-4.3.2 built against petsc-3.1.0.<br>
<br>However, I got the following error built on the BlueGene. I used the following steps:<br>
<ul><li>./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</li><li>cqsub -q debug -n 2 -t 00:10:00 conftest. Make sure the job is
finished by "cqstat".</li><li>./reconfigure.py</li></ul>It works fine. The output is<br><pre><code>Compilers:<br> C Compiler: mpicc -Wall -Wwrite-strings -Wno-strict-aliasing -O <br> C++ Compiler: mpicxx -Wall -Wwrite-strings -Wno-strict-aliasing -O <br>
Fortran Compiler: mpif77 -Wall -Wno-unused-variable -O <br>Linkers:<br> Static linker: /usr/bin/ar cr<br>MPI:<br> Includes: -I/bgl/BlueLight/V1R3M4_300_2008-080728/ppc/bglsys/include<br>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<br>
Chaco:<br> 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<br>Sieve:<br> Includes: -I/home/guntaka/src/petsc-3.1-p0/include/sieve<br>
Boost:<br> Includes: -I/home/guntaka/src/petsc-3.1-p0/externalpackages/Boost/ -I/bgl/BlueLight/V1R3M4_300_2008-080728/ppc/bglsys/include<br>PETSc:<br> PETSC_ARCH: linux-gnu-cxx-opt<br> PETSC_DIR: /home/guntaka/src/petsc-3.1-p0<br>
Clanguage: Cxx<br> Scalar type: real<br> Precision: double<br> shared libraries: disabled<br> dynamic libraries: disabled<br> Memory alignment: 16<br>xxx=========================================================================xxx<br>
Configure stage complete. Now build PETSc libraries with:<br> make PETSC_DIR=/home/guntaka/src/petsc-3.1-p0 PETSC_ARCH=linux-gnu-cxx-opt all<br><br><br>xxx=========================================================================xxx</code><br>
</pre><br>Then I moved ahead to build it<br><pre><code>make PETSC_DIR=/home/guntaka/src/petsc-3.1-p0 PETSC_ARCH=linux-gnu-cxx-opt all<br>But I got the following error in compiling sieve:<br></code><code>/home/guntaka/src/petsc-3.1-p0/include/sieve/ALE_args.hh: In member function `ALE::ArgValue ALE::ArgDB::operator[](const string&) const':<br>
/home/guntaka/src/petsc-3.1-p0/include/sieve/ALE_args.hh:132: error: call of overloaded `ArgValue(ALE::ArgValue)' is ambiguous<br>/home/guntaka/src/petsc-3.1-p0/include/sieve/ALE_args.hh:64: note: candidates are: ALE::ArgValue::ArgValue(const ALE::ArgValue&)<br>
/home/guntaka/src/petsc-3.1-p0/include/sieve/ALE_args.hh:67: note: ALE::ArgValue::ArgValue(const boost::program_options::variable_value&)<br><br>I am using the mpicxx which is using g++ 3.4.3:<br><br>
</code><code>guntaka@fr0103en:~/src/petsc-3.1-p0> mpicxx -show<br>
/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<br>
<br>guntaka@fr0103en:~/src/petsc-3.1-p0> /bgl/BlueLight/V1R3M4_300_2008-080728/ppc/blrts-gnu/bin/powerpc-bgl-blrts-gnu-g++ --version<br><br>I remember there was some issues with older versions of GCC. Not sure this is the same problem.<br>
Has anyone have any experience on this?<br><br>Thank you very much.<br><br>Shi<br>powerpc-bgl-blrts-gnu-g++ (GCC) 3.4.3<br></code><br><code>/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&)'</code><br>
<br></pre><br><br><br clear="all"><br>-- <br>Shi Jin, Ph.D.<br><br>
</blockquote></div><br><br clear="all"><br></div></div>-- <br>What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>
-- Norbert Wiener<br>
</div>
</blockquote></div><br><br clear="all"><br></div></div><font color="#888888">-- <br>Shi Jin, Ph.D.<br><br>
</font></blockquote></div><br><br clear="all"><br></div></div><font color="#888888">-- <br>Shi Jin, Ph.D.<br><br>
</font></blockquote></div><br><br clear="all"><br>-- <br>What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>-- Norbert Wiener<br>
</div>
</div></div></blockquote></div><br><br clear="all"><br></div></div><font color="#888888">-- <br>Shi Jin, Ph.D.<br><br>
</font></blockquote></div><br><br clear="all"><br>-- <br>What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>-- Norbert Wiener<br>
</div>