From: Patrick O. L. <ma...@ma...> - 2003-11-28 16:47:21
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Dear Ben, thank you very much for your fast help! I think, it is almost working now. Configure now finds PETSc, which is a real progress. Less positive is, that when I run "make run_examples" now, I get the error message: Catastrophic error: could not open source file "/usr/local/encap/mpich124-intel/lib" compilation aborted for /usr/local/encap/mpich124-intel/lib (code 4) Do you have any idea, what I could do about this? Thank you very much again and best wishes! Patrick On Fri, 28 Nov 2003, Benjamin S. Kirk wrote: > It sounds like configure did not find PETSc... Did you put those directories in the Make.common file yourself? If so, then there are #define's in include/base/libmesh_config.h that are missing, so the PETSc code is not getting compiled. It is best if configure finds PETSc, that way everything else should work OK. > > >From your email I see that you want to use the Intel icc compiler. In that case, the general configuration approach I would suggest is this: > > export CXX=icc > export CC=icc > export F77=ifc > export PETSC_DIR=/usr/local/src/petsc-2.1.5 > export PETSC_ARCH=linux_intel > > ./configure > > > The ./configure script should find PETSc. For exampe, here is my setup: > > voyager(4)$ echo $PETSC_DIR > /usr/local/petsc/petsc-2.1.6 > voyager(5)$ echo $PETSC_ARCH > linux > voyager(6)$ CXX=icc CC=icc F77=ifc ./configure > --------------------------------------------- > ----------- Configuring libMesh ------------- > --------------------------------------------- > checking build system type... i686-pc-linux-gnu > checking host system type... i686-pc-linux-gnu > checking target system type... i686-pc-linux-gnu > checking for C++ compiler default output... a.out > checking whether the C++ compiler works... yes > checking whether we are cross compiling... no > checking for suffix of executables... > checking for suffix of object files... o > checking whether we are using the GNU C++ compiler... no > checking whether icc accepts -g... yes > checking for gcc... icc > checking whether we are using the GNU C compiler... no > checking whether icc accepts -g... yes > checking for icc option to accept ANSI C... none needed > <<< C++ compiler is Intel ICC >>> > checking how to run the C++ preprocessor... icc -E > checking for egrep... grep -E > checking for ANSI C header files... yes > checking for sys/types.h... yes > checking for sys/stat.h... yes > checking for stdlib.h... yes > checking for string.h... yes > checking for memory.h... yes > checking for strings.h... yes > checking for inttypes.h... yes > checking for stdint.h... yes > checking for unistd.h... yes > checking for short int... yes > checking size of short int... 2 > checking for int... yes > checking size of int... 4 > checking for long int... yes > checking size of long int... 4 > checking for float... yes > checking size of float... 4 > checking for double... yes > checking size of double... 8 > checking for void *... yes > checking size of void *... 4 > checking getopt.h usability... yes > checking getopt.h presence... yes > checking for getopt.h... yes > checking whether the compiler implements namespaces... yes > checking whether the compiler has locale... yes > checking whether the compiler has stringstream... yes > checking hash_map usability... yes > checking hash_map presence... yes > checking for hash_map... yes > checking hash_set usability... yes > checking hash_set presence... yes > checking for hash_set... yes > checking zlib.h usability... yes > checking zlib.h presence... yes > checking for zlib.h... yes > <<< Configuring library with AMR support >>> > <<< Configuring library with expensive data structures enabled >>> > checking rpc/rpc.h usability... yes > checking rpc/rpc.h presence... yes > checking for rpc/rpc.h... yes > <<< Configuring library with XDR support >>> > <<< Configuring library with real number support >>> > <<< Configuring library with reference counting support >>> > checking for ./contrib/netcdf/lib/i686-pc-linux-gnu/libnetcdf.a... yes > checking for ./contrib/netcdf/include/netcdf.h... yes > <<< Configuring library with netCDF support >>> > checking for ./contrib/exodus/lib/i686-pc-linux-gnu/libexoIIv2c.a... yes > checking for ./contrib/exodus/include/exodusII.h... yes > <<< Configuring library with Exodus API support >>> > --------------------------------------------- > ----- Configuring for optional packages ----- > --------------------------------------------- > checking for ./contrib/sfcurves/sfcurves.h... yes > <<< Configuring library with SFC support >>> > checking for ./contrib/gzstream/gzstream.h... yes > <<< Configuring library with gzstreams support >>> > checking for ./contrib/tecplot/lib/i686-pc-linux-gnu/tecio.a... yes > checking for ./contrib/tecplot/include/TECIO.h... yes > <<< Configuring library with Tecplot API support >>> > checking for ./contrib/laspack/lastypes.h... yes > <<< Configuring library with LASPACK version 1.12.3 support >>> > checking for /usr/local/petsc/petsc-2.1.6/include/petsc.h... yes > checking whether we are using the GNU Fortran 77 compiler... no > checking whether ifc accepts -g... yes > checking how to get verbose linking output from ifc... -v > checking for Fortran 77 libraries... -L/usr/local/intel/compiler70/ia32/lib -L/usr/lib -lintrins -lIEPCF90 -lF90 -limf -lm -lirc -lcxa -lunwind > <<< Configuring library with PETSc version 2.1.6 support >>> > checking for ./contrib/metis/Lib/metis.h... yes > <<< Configuring library with Metis support >>> > checking for ./contrib/parmetis/Lib/parmetis.h... yes > <<< Configuring library with Parmetis support >>> > checking for doxygen... /usr/bin/doxygen > checking for dot... /usr/local/graphviz/bin/dot > ---------------------------------------------- > --- Done configuring for optional packages --- > ---------------------------------------------- > checking for perl... /usr/bin/perl > configure: creating ./config.status > config.status: creating Make.common > config.status: creating include/base/libmesh_config.h > configure: creating ./config.status > config.status: creating Make.common > config.status: creating doc/Doxyfile > config.status: creating include/base/libmesh_config.h > config.status: include/base/libmesh_config.h is unchanged > --------------------------------------------- > --------- Done Configuring libMesh ---------- > --------------------------------------------- > > Notice how PETSc was found in the "optional packages" section. > Please let me know if you still have an issue. > > -Ben > > > > > > Patrick O. Lechner wrote: > > > Hello Steffen, > > > > thank you very much for your email and your help. > > I've done the modifications, that you mentioned, but it still doesn't work so far. > > The output from make echo, that I get, is: > > > > Source Files: > > src/base/dof_map.C src/base/dof_map_constraints.C src/base/dof_object.C src/base/equation_systems.C src/base/equation_systems_io.C src/base/frequency_system.C src/base/libmesh_base.C src/base/libmesh.C src/base/newmark_system.C src/base/node.C src/base/reference_counted_object.C src/base/reference_counter.C src/base/steady_system.C src/base/system_base.C src/base/system_base_io.C src/base/system_base_projection.C src/base/transient_system.C src/fe/fe_base.C src/fe/fe_boundary.C src/fe/fe.C src/fe/fe_hierarchic.C src/fe/fe_hierarchic_shape_1D.C src/fe/fe_hierarchic_shape_2D.C src/fe/fe_hierarchic_shape_3D.C src/fe/fe_interface.C src/fe/fe_interface_inf_fe.C src/fe/fe_lagrange.C src/fe/fe_lagrange_shape_1D.C src/fe/fe_lagrange_shape_2D.C src/fe/fe_lagrange_shape_3D.C src/fe/fe_map.C src/fe/fe_monomial.C src/fe/fe_monomial_shape_1D.C src/fe/fe_monomial_shape_2D.C src/fe/fe_monomial_shape_3D.C src/fe/inf_fe_base_radial.C src/fe/inf_fe_boundary.C src/fe/inf_fe.C src/fe/inf_fe_j! > acobi_20_00_eval.C src/fe/inf_fe_jacobi_30_00_eval.C src/fe/inf_fe_lagrange_eval.C src/fe/inf_fe_legendre_eval.C src/fe/inf_fe_map.C src/fe/inf_fe_map_eval.C src/fe/inf_fe_static.C src/geom/cell.C src/geom/cell_hex20.C src/geom/cell_hex27.C src/geom/cell_hex8.C src/geom/cell_hex.C src/geom/cell_inf.C src/geom/cell_inf_hex16.C src/geom/cell_inf_hex18.C src/geom/cell_inf_hex8.C src/geom/cell_inf_hex.C src/geom/cell_inf_prism12.C src/geom/cell_inf_prism6.C src/geom/cell_inf_prism.C src/geom/cell_prism15.C src/geom/cell_prism18.C src/geom/cell_prism6.C src/geom/cell_prism.C src/geom/cell_pyramid5.C src/geom/cell_pyramid.C src/geom/cell_tet10.C src/geom/cell_tet4.C src/geom/cell_tet.C src/geom/edge.C src/geom/edge_edge2.C src/geom/edge_edge3.C src/geom/edge_inf_edge2.C src/geom/elem.C src/geom/elem_quality.C src/geom/elem_refinement.C src/geom/elem_type.C src/geom/face.C src/geom/face_inf_quad4.C src/geom/face_inf_quad6.C src/geom/face_inf_quad.C src/geom/face_quad4.C src/geom/fa! > ce_quad8.C src/geom/face_quad9.C src/geom/face_quad.C src/geo! > m/face_tri3.C src/geom/face_tri6.C src/geom/face_tri.C src/geom/plane.C src/geom/point.C src/geom/sphere.C src/geom/surface.C src/mesh/boundary_info.C src/mesh/boundary_mesh.C src/mesh/mesh_base.C src/mesh/mesh_base_modification.C src/mesh/mesh.C src/mesh/mesh_communication.C src/mesh/mesh_data.C src/mesh/mesh_data_unv_support.C src/mesh/mesh_data_xdr_support.C src/mesh/mesh_diva_support.C src/mesh/mesh_exodus_support.C src/mesh/mesh_generation.C src/mesh/mesh_gmv_support.C src/mesh/mesh_misc_support.C src/mesh/mesh_modification.C src/mesh/mesh_refinement.C src/mesh/mesh_refinement_flagging.C src/mesh/mesh_refinement_smoothing.C src/mesh/mesh_smoother.C src/mesh/mesh_smoother_laplace.C src/mesh/mesh_tecplot_support.C src/mesh/mesh_ucd_support.C src/mesh/mesh_unv_support.C src/mesh/mesh_xdr_support.C src/numerics/analytic_function.C src/numerics/coupling_matrix.C src/numerics/dense_matrix_base.C src/numerics/dense_matrix.C src/numerics/dense_submatrix.C src/numerics/dense_sub! > vector.C src/numerics/dense_vector_base.C src/numerics/dense_vector.C src/numerics/distributed_vector.C src/numerics/error_estimator.C src/numerics/function_base.C src/numerics/laspack_interface.C src/numerics/laspack_matrix.C src/numerics/laspack_vector.C src/numerics/linear_solver_interface.C src/numerics/mesh_function.C src/numerics/numeric_vector.C src/numerics/petsc_interface.C src/numerics/petsc_matrix.C src/numerics/petsc_vector.C src/numerics/sparse_matrix.C src/numerics/type_vector.C src/partitioning/centroid_partitioner.C src/partitioning/linear_partitioner.C src/partitioning/metis_partitioner.C src/partitioning/parmetis_partitioner.C src/partitioning/partitioner.C src/partitioning/sfc_partitioner.C src/quadrature/quadrature_build.C src/quadrature/quadrature.C src/quadrature/quadrature_gauss_1D.C src/quadrature/quadrature_gauss_2D.C src/quadrature/quadrature_gauss_3D.C src/quadrature/quadrature_gauss.C src/quadrature/quadrature_jacobi_1D.C src/quadrat > -- Patrick Lechner Phone: (+44) 1225 386974 Department of Mathematical Sciences Fax: (+44) 1225 386343 University of Bath Email: ma...@ma... Bath BA2 7AY United Kingdeom Find out more about me on the WWW: http://www.maths.bath.ac.uk/~mappol "I have little patience for scientists who take a board of wood, look for its thinnest part, and drill a great number of holes when the drilling is easy.", Albert Einstein (1949) |