Hi Matt and Brad<br><br>First of all, thanks for the rapid replys. The short story is that I followed your suggestions and I still have the same question. More complete answers to your questions/suggestions are below.<br>
<br>Matt:<br>I built PETSc in the following manner. <br>1) I used "hg pull" then "hg update" in my petsc-dev folder<br>2) I cd'ed into my config/BuildSystem folder and did "hg pull" and "hg update"<br>
3) I configured PETSc using the following script:<br><br> ARCH_FLAGS="--PETSC_ARCH=linux_${TOOLS_FORMAT}_opt --with-debugging=0"<br> LANG_FLAGS="--with-clanguage=cxx"<br> BUILD_FLAGS="--with-mpi-compilers=0 --with-gnu-compilers=1 --with-shared-libraries=1 --with-dynamic-loading=1 --with-64-bit-points=1 --with-large-file-io=1 --cc=gcc --cxx=g++ --fc=gfortran"<br>
MPI_FLAGS="--with-mpi-dir=${TOOLS_DIR}/mpich-1.2.1/gcc-4.1.1_64 --with-mpi-shared=0"<br> OPTIONS="--with-lgrind=0 --with-c2html=0 "<br> PART_FLAGS="--with-chaco=1 --download-chaco=1 --with-parmetis=1 --with-parmetis-dir=~/tools/ParMetis-3.1.1/${TOOLS_FORMAT} --with-f-blas-lapack=1 --download-f-blas-lapack=1"<br>
SIEVE_FLAGS="--with-sieve=1 --download-sieve=1 --with-boost=1 --download-boost=1"<br> config/configure.py ${ARCH_FLAGS} ${LANG_FLAGS} ${BUILD_FLAGS} ${MPI_FLAGS} ${OPTIONS} ${PART_FLAGS} ${SIEVE_FLAGS} ${EXTRA_FLAGS}<br>
<br>4) Following the advice of Barry Smith, I cd'ed into src/dm/impls/da/ftn-custom and ran "make" in this folder<br>5) I ran "make fortranstubs" in my petsc-dev folder<br>6) I ran "make" and then "make test" in my petsc-dev folder<br>
<br>Make test is successful. As you can see, I do have my clanguage set to cxx.<br><br>Brad:<br>I've reconfigured and rebuilt PETSc and Pylith, and I have run into the same error. My configuration script for Pylith is:<br>
<br>./configure > configure.log --enable-swig --enable-testing --enable-cubit --prefix=${CIG_DIR} CPPFLAGS="-I${PROJ4_INCDIR} -I${CPPUNIT_INCDIR} -I${CIG_INCDIR} -I${PYTHIA_INCDIR} -I${NETCDF_INCDIR}" LDFLAGS="-L${PROJ4_LIBDIR} -L${CPPUNIT_LIBDIR} -L${CIG_LIBDIR} -L${NETCDF_LIBDIR}" LIBS="" CC=gcc CXX=g++ FC=gfortran F77=gfortran<br>
<br>Is there anything that I'm missing from this configuration that may be causing my problem?<br><br>Thanks again,<br>Jeff Thompson<br>Seismolab<br>California Institute of Technology<br><br><div class="gmail_quote">On Wed, Oct 20, 2010 at 2:42 PM, Brad Aagaard <span dir="ltr"><<a href="mailto:baagaard@usgs.gov">baagaard@usgs.gov</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;">Jeff,<br>
<br>
Try reconfiguring and rebuilding Petsc and then pylith. There have been recent changes to the petsc build system that required changes to the pylith configure to keep them in sync.<br>
<br>
Brad<br>
<div><div></div><div class="h5"><br>
<br>
<br>
On Oct 20, 2010, at 2:12 PM, Jeffrey Thompson <<a href="mailto:jeffremt@gmail.com">jeffremt@gmail.com</a>> wrote:<br>
<br>
> Hello CIG-Short,<br>
><br>
> I'm trying to make and install the stable version of Pylith, and I ran into the error below after issuing the "make" command. It seems to me that the main error is that Pylith cannot find the petscmesh.hh file. I updated PETSc and spatialdata before Pylith, so I should have the most recent versions of these programs. I also tried installing the version Pylith from the trunk directory, and the same error occured. I've attached my config.log file from the 'stable' pylith install.<br>
><br>
> Thanks in advance,<br>
> Jeff Thompson<br>
> Seismolab<br>
> California Institute of Technology<br>
><br>
> make[3]: Entering directory `/home/jeffremt/tools/cig/v1.5-stable/libsrc'<br>
> if /bin/sh ../libtool --mode=compile --tag=CXX g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -I/home/jeffremt/tools/cig/gcc-4.1.1_64/lib/python2.5/site-packages/pythia-0.8.1.11-py2.5.egg -I/usr/include/python2.5 -DENABLE_CUBIT -I/home/jeffremt/tools/proj-4.7.0/gcc-4.1.1_64/include -I/home/jeffremt/tools/cppunit-1.12.1/gcc-4.1.1_64/include -I/home/jeffremt/tools/cig/gcc-4.1.1_64/include -I/home/jeffremt/tools/cig/gcc-4.1.1_64/include/pythia-0.8.1.10 -I/home/jeffremt/tools/netcdf-4.0.1/gcc-4.1.1_64/include -g -O2 -MT BoundaryCondition.lo -MD -MP -MF ".deps/BoundaryCondition.Tpo" -c -o BoundaryCondition.lo `test -f 'bc/BoundaryCondition.cc' || echo './'`bc/BoundaryCondition.cc; \<br>
> then mv -f ".deps/BoundaryCondition.Tpo" ".deps/BoundaryCondition.Plo"; else rm -f ".deps/BoundaryCondition.Tpo"; exit 1; fi<br>
> mkdir .libs<br>
> g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -I/home/jeffremt/tools/cig/gcc-4.1.1_64/lib/python2.5/site-packages/pythia-0.8.1.11-py2.5.egg -I/usr/include/python2.5 -DENABLE_CUBIT -I/home/jeffremt/tools/proj-4.7.0/gcc-4.1.1_64/include -I/home/jeffremt/tools/cppunit-1.12.1/gcc-4.1.1_64/include -I/home/jeffremt/tools/cig/gcc-4.1.1_64/include -I/home/jeffremt/tools/cig/gcc-4.1.1_64/include/pythia-0.8.1.10 -I/home/jeffremt/tools/netcdf-4.0.1/gcc-4.1.1_64/include -g -O2 -MT BoundaryCondition.lo -MD -MP -MF .deps/BoundaryCondition.Tpo -c bc/BoundaryCondition.cc -fPIC -DPIC -o .libs/BoundaryCondition.o<br>
> In file included from bc/BoundaryCondition.cc:23:<br>
> ../include/pylith/topology/Mesh.hh:33:43: petscmesh.hh: No such file or directory<br>
> In file included from bc/BoundaryCondition.cc:23:<br>
> ../include/pylith/topology/Mesh.hh:59: error: `ALE' has not been declared<br>
> ../include/pylith/topology/Mesh.hh:59: error: ISO C++ forbids declaration of `IMesh' with no type<br>
> ../include/pylith/topology/Mesh.hh:59: error: expected `;' before '<' token<br>
> ../include/pylith/topology/Mesh.hh:60: error: `SieveMesh' has not been declared<br>
> ../include/pylith/topology/Mesh.hh:60: error: ISO C++ forbids declaration of `real_section_type' with no type<br>
> ../include/pylith/topology/Mesh.hh:60: error: expected `;' before "RealSection"<br>
> ../include/pylith/topology/Mesh.hh:61: error: `SieveMesh' has not been declared<br>
> ../include/pylith/topology/Mesh.hh:61: error: ISO C++ forbids declaration of `int_section_type' with no type<br>
> ../include/pylith/topology/Mesh.hh:61: error: expected `;' before "IntSection"<br>
> ../include/pylith/topology/Mesh.hh:62: error: `ALE' has not been declared<br>
> ../include/pylith/topology/Mesh.hh:62: error: ISO C++ forbids declaration of `IMesh' with no type<br>
> ../include/pylith/topology/Mesh.hh:62: error: expected `;' before '<' token<br>
> ../include/pylith/topology/Mesh.hh:63: error: `ALE' has not been declared<br>
> ../include/pylith/topology/Mesh.hh:63: error: ISO C++ forbids declaration of `RestrictVisitor' with no type<br>
> ../include/pylith/topology/Mesh.hh:63: error: expected `;' before '<' token<br>
> ../include/pylith/topology/Mesh.hh:64: error: `ALE' has not been declared<br>
> ../include/pylith/topology/Mesh.hh:64: error: ISO C++ forbids declaration of `UpdateAddVisitor' with no type<br>
> ../include/pylith/topology/Mesh.hh:64: error: expected `;' before '<' token<br>
> ../include/pylith/topology/Mesh.hh:65: error: `ALE' has not been declared<br>
> ../include/pylith/topology/Mesh.hh:65: error: ISO C++ forbids declaration of `UpdateAllVisitor' with no type<br>
> ../include/pylith/topology/Mesh.hh:65: error: expected `;' before '<' token<br>
> ../include/pylith/topology/Mesh.hh:66: error: `ALE' has not been declared<br>
> ../include/pylith/topology/Mesh.hh:66: error: ISO C++ forbids declaration of `IndicesVisitor' with no type<br>
> ../include/pylith/topology/Mesh.hh:66: error: expected `;' before '<' token<br>
> ../include/pylith/topology/Mesh.hh:82: error: expected `,' or `...' before '&' token<br>
> ../include/pylith/topology/Mesh.hh:82: error: ISO C++ forbids declaration of `MPI_Comm' with no type<br>
> ../include/pylith/topology/Mesh.hh:100: error: `ALE' has not been declared<br>
> ../include/pylith/topology/Mesh.hh:100: error: ISO C++ forbids declaration of `Obj' with no type<br>
> ../include/pylith/topology/Mesh.hh:100: error: expected `;' before '<' token<br>
> ../include/pylith/topology/Mesh.hh:106: error: `ALE' has not been declared<br>
> ../include/pylith/topology/Mesh.hh:106: error: ISO C++ forbids declaration of `Obj' with no type<br>
> ../include/pylith/topology/Mesh.hh:106: error: expected `;' before '<' token<br>
> ../include/pylith/topology/Mesh.hh:160: error: expected `,' or `...' before "value"<br>
> ../include/pylith/topology/Mesh.hh:160: error: ISO C++ forbids declaration of `MPI_Comm' with no type<br>
> ../include/pylith/topology/Mesh.hh:166: error: `MPI_Comm' does not name a type<br>
> ../include/pylith/topology/Mesh.hh:195: error: `ALE' has not been declared<br>
> ../include/pylith/topology/Mesh.hh:195: error: ISO C++ forbids declaration of `Obj' with no type<br>
> ../include/pylith/topology/Mesh.hh:195: error: expected `;' before '<' token<br>
> ../include/pylith/topology/Mesh.hh:197: error: `MPI_Comm' does not name a type<br>
> In file included from ../include/pylith/topology/Mesh.hh:208,<br>
> from bc/BoundaryCondition.cc:23:<br>
> ../include/pylith/topology/Mesh.icc:25: error: `ALE' has not been declared<br>
> ../include/pylith/topology/Mesh.icc:25: error: expected initializer before '<' token<br>
> ../include/pylith/topology/Mesh.icc:32: error: `ALE' has not been declared<br>
> ../include/pylith/topology/Mesh.icc:32: error: expected initializer before '<' token<br>
> ../include/pylith/topology/Mesh.icc: In member function `void pylith::topology::Mesh::debug(bool)':<br>
> ../include/pylith/topology/Mesh.icc:49: error: `_mesh' was not declared in this scope<br>
> ../include/pylith/topology/Mesh.icc: In member function `int pylith::topology::Mesh::dimension() const':<br>
> ../include/pylith/topology/Mesh.icc:64: error: `_mesh' was not declared in this scope<br>
> ../include/pylith/topology/Mesh.icc: In member function `int pylith::topology::Mesh::coneSize() const':<br>
> ../include/pylith/topology/Mesh.icc:71: error: `_mesh' was not declared in this scope<br>
> ../include/pylith/topology/Mesh.icc: In member function `int pylith::topology::Mesh::numVertices() const':<br>
> ../include/pylith/topology/Mesh.icc:78: error: `_mesh' was not declared in this scope<br>
> ../include/pylith/topology/Mesh.icc: In member function `int pylith::topology::Mesh::numCells() const':<br>
> ../include/pylith/topology/Mesh.icc:85: error: `_mesh' was not declared in this scope<br>
> ../include/pylith/topology/Mesh.icc: At global scope:<br>
> ../include/pylith/topology/Mesh.icc:91: error: expected `,' or `...' before "value"<br>
> ../include/pylith/topology/Mesh.icc:91: error: ISO C++ forbids declaration of `MPI_Comm' with no type<br>
> ../include/pylith/topology/Mesh.icc: In member function `void pylith::topology::Mesh::comm(int)':<br>
> ../include/pylith/topology/Mesh.icc:92: error: `_comm' was not declared in this scope<br>
> ../include/pylith/topology/Mesh.icc:92: error: `value' was not declared in this scope<br>
> ../include/pylith/topology/Mesh.icc: At global scope:<br>
> ../include/pylith/topology/Mesh.icc:97: error: `MPI_Comm' does not name a type<br>
> ../include/pylith/topology/Mesh.icc: In member function `void pylith::topology::Mesh::view(const char*) const':<br>
> ../include/pylith/topology/Mesh.icc:106: error: `_mesh' was not declared in this scope<br>
> bc/BoundaryCondition.cc: In member function `virtual void pylith::bc::BoundaryCondition::verifyConfiguration(const pylith::topology::Mesh&) const':<br>
> bc/BoundaryCondition.cc:53: error: `ALE' has not been declared<br>
> bc/BoundaryCondition.cc:53: error: expected initializer before '<' token<br>
> bc/BoundaryCondition.cc:54: error: `sieveMesh' was not declared in this scope<br>
> bc/BoundaryCondition.cc:57: error: aggregate `std::ostringstream msg' has incomplete type and cannot be defined<br>
> make[3]: *** [BoundaryCondition.lo] Error 1<br>
> make[3]: Leaving directory `/home/jeffremt/tools/cig/v1.5-stable/libsrc'<br>
> make[2]: *** [all-recursive] Error 1<br>
> make[2]: Leaving directory `/home/jeffremt/tools/cig/v1.5-stable/libsrc'<br>
> make[1]: *** [all-recursive] Error 1<br>
> make[1]: Leaving directory `/home/jeffremt/tools/cig/v1.5-stable'<br>
> make: *** [all] Error 2<br>
><br>
</div></div>> <config.log><br>
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</div></div></blockquote></div><br>