From: Rob v. T. <rob...@wt...> - 2004-02-24 13:25:50
|
Dear libmesh users, I just downloaded the code and I am trying to compile it. I am using Redhat 7 and a GCC-3.0 compiler. I get an error message: ISO C++ forbids declaration of `hash_multimap' with no type. Can anyone tell me how to solve this ?? I have included the configure and make messages below. Thank you in advance, Kind regards, ROB 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 g++... g++ 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... yes checking whether g++ accepts -g... yes checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ANSI C... none needed <<< C++ compiler is gcc-3.0 >>> checking how to run the C++ preprocessor... g++ -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... no checking hash_map presence... no checking for hash_map... no checking ext/hash_map usability... yes checking ext/hash_map presence... yes checking for ext/hash_map... yes checking hash_set usability... no checking hash_set presence... no checking for hash_set... no checking ext/hash_set usability... yes checking ext/hash_set presence... yes checking for ext/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... no checking for ./contrib/netcdf/include/netcdf.h... no --------------------------------------------- ----- 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 /include/petsc.h... no checking for /include/mpi.h... no checking for /lib/libmpich.a... no checking for ./contrib/metis/Lib/metis.h... yes <<< Configuring library with Metis support >>> checking for doxygen... /usr/bin/doxygen checking for dot... no ---------------------------------------------- --- 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 ---------- --------------------------------------------- [vlr@pc02011 libmesh-0.4.1]$ make Compiling C++ (in optimized mode) src/base/dof_map.C... Compiling C++ (in optimized mode) src/base/dof_map_constraints.C... Compiling C++ (in optimized mode) src/base/dof_object.C... Compiling C++ (in optimized mode) src/base/equation_systems.C... Compiling C++ (in optimized mode) src/base/equation_systems_io.C... Compiling C++ (in optimized mode) src/base/frequency_system.C... Compiling C++ (in optimized mode) src/base/libmesh.C... Compiling C++ (in optimized mode) src/base/newmark_system.C... Compiling C++ (in optimized mode) src/base/node.C... Compiling C++ (in optimized mode) src/base/reference_counted_object.C... Compiling C++ (in optimized mode) src/base/reference_counter.C... Compiling C++ (in optimized mode) src/base/steady_system.C... Compiling C++ (in optimized mode) src/base/system_base.C... Compiling C++ (in optimized mode) src/base/system_base_io.C... Compiling C++ (in optimized mode) src/base/system_base_projection.C... Compiling C++ (in optimized mode) src/base/transient_system.C... Compiling C++ (in optimized mode) src/fe/fe_base.C... Compiling C++ (in optimized mode) src/fe/fe_boundary.C... Compiling C++ (in optimized mode) src/fe/fe.C... Compiling C++ (in optimized mode) src/fe/fe_hierarchic.C... Compiling C++ (in optimized mode) src/fe/fe_hierarchic_shape_1D.C... Compiling C++ (in optimized mode) src/fe/fe_hierarchic_shape_2D.C... Compiling C++ (in optimized mode) src/fe/fe_hierarchic_shape_3D.C... Compiling C++ (in optimized mode) src/fe/fe_interface.C... Compiling C++ (in optimized mode) src/fe/fe_interface_inf_fe.C... Compiling C++ (in optimized mode) src/fe/fe_lagrange.C... Compiling C++ (in optimized mode) src/fe/fe_lagrange_shape_1D.C... Compiling C++ (in optimized mode) src/fe/fe_lagrange_shape_2D.C... Compiling C++ (in optimized mode) src/fe/fe_lagrange_shape_3D.C... Compiling C++ (in optimized mode) src/fe/fe_map.C... Compiling C++ (in optimized mode) src/fe/fe_monomial.C... Compiling C++ (in optimized mode) src/fe/fe_monomial_shape_1D.C... Compiling C++ (in optimized mode) src/fe/fe_monomial_shape_2D.C... Compiling C++ (in optimized mode) src/fe/fe_monomial_shape_3D.C... Compiling C++ (in optimized mode) src/fe/inf_fe_base_radial.C... Compiling C++ (in optimized mode) src/fe/inf_fe_boundary.C... Compiling C++ (in optimized mode) src/fe/inf_fe.C... Compiling C++ (in optimized mode) src/fe/inf_fe_jacobi_20_00_eval.C... Compiling C++ (in optimized mode) src/fe/inf_fe_jacobi_30_00_eval.C... Compiling C++ (in optimized mode) src/fe/inf_fe_lagrange_eval.C... Compiling C++ (in optimized mode) src/fe/inf_fe_legendre_eval.C... Compiling C++ (in optimized mode) src/fe/inf_fe_map.C... Compiling C++ (in optimized mode) src/fe/inf_fe_map_eval.C... Compiling C++ (in optimized mode) src/fe/inf_fe_static.C... Compiling C++ (in optimized mode) src/geom/cell.C... Compiling C++ (in optimized mode) src/geom/cell_hex20.C... Compiling C++ (in optimized mode) src/geom/cell_hex27.C... Compiling C++ (in optimized mode) src/geom/cell_hex8.C... Compiling C++ (in optimized mode) src/geom/cell_hex.C... Compiling C++ (in optimized mode) src/geom/cell_inf.C... Compiling C++ (in optimized mode) src/geom/cell_inf_hex16.C... Compiling C++ (in optimized mode) src/geom/cell_inf_hex18.C... Compiling C++ (in optimized mode) src/geom/cell_inf_hex8.C... Compiling C++ (in optimized mode) src/geom/cell_inf_hex.C... Compiling C++ (in optimized mode) src/geom/cell_inf_prism12.C... Compiling C++ (in optimized mode) src/geom/cell_inf_prism6.C... Compiling C++ (in optimized mode) src/geom/cell_inf_prism.C... Compiling C++ (in optimized mode) src/geom/cell_prism15.C... Compiling C++ (in optimized mode) src/geom/cell_prism18.C... Compiling C++ (in optimized mode) src/geom/cell_prism6.C... Compiling C++ (in optimized mode) src/geom/cell_prism.C... Compiling C++ (in optimized mode) src/geom/cell_pyramid5.C... Compiling C++ (in optimized mode) src/geom/cell_pyramid.C... Compiling C++ (in optimized mode) src/geom/cell_tet10.C... Compiling C++ (in optimized mode) src/geom/cell_tet4.C... Compiling C++ (in optimized mode) src/geom/cell_tet.C... Compiling C++ (in optimized mode) src/geom/edge.C... Compiling C++ (in optimized mode) src/geom/edge_edge2.C... Compiling C++ (in optimized mode) src/geom/edge_edge3.C... Compiling C++ (in optimized mode) src/geom/edge_inf_edge2.C... Compiling C++ (in optimized mode) src/geom/elem.C... Compiling C++ (in optimized mode) src/geom/elem_quality.C... Compiling C++ (in optimized mode) src/geom/elem_refinement.C... In file included from src/geom/elem_refinement.C:30: /home/vlr/libmesh-0.4.1/include/mesh/mesh_refinement.h:332: ISO C++ forbids declaration of `hash_multimap' with no type /home/vlr/libmesh-0.4.1/include/mesh/mesh_refinement.h:332: template-id `hash_multimap<unsigned int, Node*>' used as a declarator /home/vlr/libmesh-0.4.1/include/mesh/mesh_refinement.h:332: parse error before `;' token /home/vlr/libmesh-0.4.1/include/mesh/mesh_refinement.h:340: 'map_type' is used as a type, but is not defined as a type. make: *** [src/geom/elem_refinement.i686-pc-linux-gnu.o] Error 1 dr. R. van Tol Computer Simulations and Foundry Processes tel.:+32 (0)9 2645704 - fax:0032 (0)9 2645848 mailto:rob...@wt... WTCM-CRIF Belgian Center of the Technological Industry Technologiepark 9, B-9052 Gent-Zwijnaarde (Belgium) tel: +32 (0)9/264 5697 http://www.wtcm.be WTCM-CRIF "Your Gateway To Innovation". Have a look at the future of materials and manufacturing technology http://techniline.wtcm.be |
From: richard l. <ric...@gm...> - 2004-07-22 12:32:03
|
Hello everybody, I'm using woody, debian and installed the package mpich and pgapack. Now I'm trying to install libmesh. I started with ./configure and every thing was fine. The results are above. Wenn I try to call make I've got the following message: libmesh/libmesh-0.4.2> make -j3 Compiling C++ (in optimized mode) src/base/dof_map.C... Compiling C++ (in optimized mode) src/base/dof_map_constraints.C... Compiling C++ (in optimized mode) src/base/dof_object.C... Compiling C++ (in optimized mode) src/base/libmesh.C... In file included from src/base/libmesh.C:48: /usr/include/mpi.h:17: conflicting types for `typedef struct MPI_Status MPI_Status' /usr/include/mpi.h:17: previous declaration as `typedef struct MPI_Status MPI_Status' /usr/include/mpi.h:52: confused by earlier errors, bailing out make: *** [src/base/libmesh.i686-pc-linux-gnu.o] Error 1 make: *** Waiting for unfinished jobs.... Thanks in advance. Richard ************************************************************** //The output of ./configure: libmesh/libmesh-0.4.2> ./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 g++... g++ 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... yes checking whether g++ accepts -g... yes checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ANSI C... none needed <<< C++ compiler is gcc-2.95 >>> <<< Configuring library for broken iostream >>> checking how to run the C++ preprocessor... g++ -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... no 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 <<< 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... no checking for ./contrib/netcdf/include/netcdf.h... no --------------------------------------------- ----- Configuring for optional packages ----- --------------------------------------------- checking for /include/petsc.h... no note: MPI library path not given... trying prefix=/usr note: using /usr/lib/libmpi (.a/.so) checking for lam_show_version in -llam... no checking for MPI_Init in -lmpi... yes Found valid MPI installlaion... note: using /usr/include/mpi.h checking mpi.h usability... yes checking mpi.h presence... yes checking for mpi.h... yes checking for ./contrib/laspack/lastypes.h... yes <<< Configuring library with LASPACK version 1.12.3 support >>> checking for ./contrib/sfcurves/sfcurves.h... yes <<< Configuring library with SFC support >>> checking zlib.h usability... no checking zlib.h presence... no checking for zlib.h... no checking for gzopen in -lz... no 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/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... no ---------------------------------------------- --- Done configuring for optional packages --- ---------------------------------------------- checking for perl... /usr/bin/perl configure: creating ./config.status config.status: creating Make.common config.status: creating doc/Doxyfile config.status: creating contrib/bin/libmesh-config config.status: creating include/base/libmesh_config.h config.status: include/base/libmesh_config.h is unchanged --------------------------------------------- --------- Done Configuring libMesh ---------- --------------------------------------------- -- +++ GMX DSL-Tarife 3 Monate gratis* +++ Nur bis 25.7.2004 +++ Bis 24.000 MB oder 300 Freistunden inkl. http://www.gmx.net/de/go/dsl |
From: <jc...@ma...> - 2005-10-31 15:54:22
|
Hi, I am trying to implement a Runge-Kutta Discontinuous Galerkin method to solve the Euler equations in 1D. I try to use the FE classes MONOMIAL and XYZ but I get wrong results for the jacobian evaluation JxW. When we transform \int_{x0}^{x1} ... dx = \int_{-1}^{+1} ... J dy the jacobian is J = dx/dy = ( x1 - x0 ) / 2. We should get that value for the jacobian but instead when we pick the values fe->get_JxW we get different values at different quadrature points. Any ideias ? Another important question for me is how to have different shape functions for the mesh and for the unknowns? Thanks. |
From: John P. <pet...@cf...> - 2005-10-31 16:02:01
|
jc...@ma... writes: > Hi, I am trying to implement a Runge-Kutta Discontinuous Galerkin method > to solve the Euler equations in 1D. > > I try to use the FE classes MONOMIAL and XYZ but I get wrong results for > the jacobian evaluation JxW. > > When we transform > > \int_{x0}^{x1} ... dx = \int_{-1}^{+1} ... J dy > > the jacobian is J = dx/dy = ( x1 - x0 ) / 2. Hi, you might be looking at the value of JxW? This is the Jacobian multiplied by the Gauss quadrature weighting value. -J |
From: Jones B. E. <bs...@nc...> - 2007-07-20 02:28:49
Attachments:
alert.pdf
|
From: Holloway <qg...@cs...> - 2007-07-20 15:48:18
Attachments:
alert.pdf
|
From: Neville <os...@yn...> - 2007-07-23 23:34:28
Attachments:
cancelled.pdf
|
From: Michael P. <pov...@in...> - 2008-01-22 19:08:26
|
<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"> <html> <head> </head> <body bgcolor="#ffffff" text="#000000"> <pre class="fragment">Dear Libmesh developers, at some point it appears such a comment in the code (see below). Does it mean that the results obtained on a mesh that contains pyramids may be wrong? Or they are for sure wrong? Thank you, Michael. <a class="code" href="http://libmesh.sourceforge.net/doxygen/libmesh__common_8h.php#cd9440203db8e3b36d61f62fe6567258">Real</a> <a class="code" href="http://libmesh.sourceforge.net/doxygen/classPyramid5.php#c92644b060057bd04f860055ba2c7014">Pyramid5::volume</a> ()<span class="keyword"> const</span> <span class="comment"></span> 00266 <span class="comment">// Note: the volume returned by summing the Jacobian times the</span> 00267 <span class="comment">// quadrature weights over all the quadrature points for the</span> 00268 <span class="comment">// pyramid element does *not* give the correct volume (the formula</span> 00269 <span class="comment">// in this function gives the correct volume). This implies there</span> 00270 <span class="comment">// is something wrong with the first-order Lagrange shape functions</span> 00271 <span class="comment">// or the quadrature rules for the Pyramid5.</span></pre> <pre class="moz-signature" cols="72"> </pre> </body> </html> |
From: John P. <pet...@cf...> - 2008-01-22 20:02:46
|
Michael Povolotskyi writes: > Dear Libmesh developers, at some point it appears such a comment in > the code (see below). Does it mean that the results obtained on a > mesh that contains pyramids may be wrong? Or they are for sure wrong? Hi, I was the one to add that comment. I didn't investigate the issue further, unfortunately. You can try it out yourself with a pyramid of known volume... Either the geometric volume formula we have is wrong or there is a problem with the quadrature rule or basis functions. If you take a look at the pyramid's basis functions, you will notice they are rational functions, not polynomials. -John |
From: <yz...@ma...> - 2008-02-29 11:15:58
|
Hi all, I am suffering from installing PETSC the last few days. Before PETSC was installed, libmesh examples runs well except for those need PETSC; when PETSC was installed, configure libmesh again, it said compilation failed, none of the example could run any more. For installing PETSC, I have tried the following commands: 1. ./config/configure.py --download-c-blas-lapack=1 --download-mpich=1 2. ./config/configure.py --download-c-blas-lapack=1 --with-mpi=0 the result of "./configure" is below, could you help me out? Many thanks. --------------------------------------------- ----------- Configuring libMesh ------------- --------------------------------------------- checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking target system type... x86_64-unknown-linux-gnu checking for g++... g++ checking for C++ compiler default output file name... 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... yes checking whether g++ accepts -g... yes checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ANSI C... none needed <<< C++ compiler is gcc-4.1 >>> checking how to run the C++ preprocessor... g++ -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... 8 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 *... 8 checking getopt.h usability... yes checking getopt.h presence... yes checking for getopt.h... yes checking csignal usability... yes checking csignal presence... yes checking for csignal... 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... no checking hash_map presence... no checking for hash_map... no checking ext/hash_map usability... yes checking ext/hash_map presence... yes checking for ext/hash_map... yes checking hash_set usability... no checking hash_set presence... no checking for hash_set... no checking ext/hash_set usability... yes checking ext/hash_set presence... yes checking for ext/hash_set... yes checking dlfcn.h usability... yes checking dlfcn.h presence... yes checking for dlfcn.h... yes checking whether the compiler supports GCC C++ ABI name demangling... yes checking whether the c++ compiler supports glibc backtrace... yes <<< Configuring library with AMR support >>> <<< Configuring library with periodic BC support >>> <<< Configuring library with higher order p-FEM shapes >>> checking rpc/rpc.h usability... yes checking rpc/rpc.h presence... yes checking for rpc/rpc.h... yes checking for xdrstdio_create... yes <<< Configuring library with XDR support >>> <<< Configuring library with real number support >>> <<< Configuring library with reference counting support >>> <<< Configuring library with Netcdf support >>> <<< Configuring library with Exodus API support >>> --------------------------------------------- ----- Configuring for optional packages ----- --------------------------------------------- checking for /home/pgrad1/yzhu/soft/petsc-2.3.3-p8/include/petsc.h... yes checking for g77... no checking for f77... no checking for xlf... no checking for frt... no checking for pgf77... no checking for fort77... no checking for fl32... no checking for af77... no checking for f90... no checking for xlf90... no checking for pgf90... no checking for epcf90... no checking for f95... no checking for fort... no checking for xlf95... no checking for ifc... no checking for efc... no checking for pgf95... no checking for lf95... no checking for gfortran... no checking whether we are using the GNU Fortran 77 compiler... no checking whether accepts -g... no checking how to get verbose linking output from ... checking for Fortran libraries of ... <<< Configuring library with PETSc version 2.3.3 support >>> checking for ./contrib/laspack/lastypes.h... yes <<< Configuring library with LASPACK version 1.12.3 support >>> checking for ./contrib/sfcurves/sfcurves.h... yes <<< Configuring library with SFC support >>> checking for ./contrib/gzstream/gzstream.h... yes checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking for gzopen in -lz... yes <<< Configuring library with gzstreams support >>> checking for ./contrib/tecplot/lib/x86_64-unknown-linux-gnu/tecio.a... yes checking for ./contrib/tecplot/include/TECIO.h... yes <<< Configuring library with Tecplot API 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/bin/dot <<< Configuring library with TetGen support >>> <<< Configuring library with Triangle support >>> <<< Configuring library with GMV support >>> checking /usr/include/vtk/vtkCommonInstantiator.h usability... no checking /usr/include/vtk/vtkCommonInstantiator.h presence... no checking for /usr/include/vtk/vtkCommonInstantiator.h... no VTK header files not found! ---------------------------------------------- --- Done configuring for optional packages --- ---------------------------------------------- checking for perl... /usr/bin/perl configure: creating ./config.status config.status: creating Make.common config.status: creating doc/Doxyfile config.status: creating contrib/bin/libmesh-config config.status: creating contrib/bin/xda2mgf config.status: creating contrib/bin/create_libmesh_release config.status: creating doc/dot config.status: creating include/base/libmesh_contrib_config.h config.status: creating include/base/libmesh_config.h --------------------------------------------- --------- Done Configuring libMesh ---------- --------------------------------------------- yunfei |
From: 钟文辉 <she...@12...> - 2008-03-23 19:49:22
|
各位老总:您们好! 诚祝:您们在2008年里;有鼠不尽的快乐!鼠不尽的收获!鼠不尽的钞票! 鼠不尽的幸福!鼠不尽的美满生活!愿:您们阖家欢乐!幸福安康! 我是(深圳市珊湖岛进出口有限公司)的负责人;可以提供:出口报关单, 核销单等等一系列手续;代理:出口报关,商检,境内外运输......等等;还可 以代办:出口欧盟许可证,欧盟产地证;并且还有(广州国际贸易交易会)的摊 位可以转让;有意者请来邮件或来电联系。 电话:0755-81153047。 传真:0755-81172940。 手机:15817477278。 联系人:钟文辉。 此致: 敬礼! |
From: Hanjoerg S. <han...@fi...> - 2008-09-25 07:52:39
|
Hi, I inly want ot check if posting is possible now. I am subscribed and i can login at sourceforge. Thanks hj |
From: Adam A. <ar...@cs...> - 2008-09-30 23:01:50
|
I have an application where I need to solve three nearly identical systems. For each system, the matrix entries and the rhs will be slightly different, but the mesh and finite element type and degree will be identical. I have three questions: 1) I would like to reuse the DofMap between each of these systems to save memory (and any other memory that is possible, I am not sure what the overhead per system is); 2) if it is not convenient to avoid duplication of the map memory, I would like to construct the system such that at least the three maps are the same (will this happen automatically?); 3) can I specify an initial guess for the solution when using an iterative solver so that I can use the solution of one system as the initial guess for the another. Thanks you very much Adam Arbree |
From: Roy S. <roy...@ic...> - 2008-10-01 13:40:29
|
On Tue, 30 Sep 2008, Adam Arbree wrote: > I have an application where I need to solve three nearly identical systems. > For each system, the matrix entries and the rhs will be slightly different, > but the mesh and finite element type and degree will be identical. I have > three questions: 1) I would like to reuse the DofMap between each of these > systems to save memory (and any other memory that is possible, I am not sure > what the overhead per system is); We'd like to make that an option, but it's not currently possible in the library, and because of the way our data is distributed (the DofMap mostly just manipulates info stored on DofObjects) it might be tricky to change the data structures to make those savings. I don't see an easy way to do it without requiring API changes (to make DofObject::dof_number require a DofMap reference, at least). Ben was looking at how to save some time and memory for duplicate variables in the same system, though, which has similar difficulties, so maybe he's had some ideas. In any case it's not going to be an available feature in the near term. > 3) > can I specify an initial guess for the solution when using an iterative > solver so that I can use the solution of one system as the initial guess for > the another. Yes; the current solution vector is the initial guess for us; just copy system1.solution to system2.solution. --- Roy |
From: Kathrin S. <ksm...@mi...> - 2016-05-17 18:17:42
|
Hi all, I have just installed and configured libmesh (version 0.9.4) using PETSC 3.4.5. During making check I got the following error in introduction_ex3: [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors [0]PETSC ERROR: likely location of problem given in stack below [0]PETSC ERROR: --------------------- Stack Frames ------------------------------------ [0]PETSC ERROR: Note: The EXACT line numbers in the stack are not available, [0]PETSC ERROR: INSTEAD the line number of the start of the function [0]PETSC ERROR: is given. [0]PETSC ERROR: [0] VecMAXPY line 1246 /home/kathrin/Implementations/petsc-3.4.5/src/vec/vec/interface/rvector.c [0]PETSC ERROR: [0] KSPGMRESClassicalGramSchmidtOrthogonalization line 45 /home/kathrin/Implementations/petsc-3.4.5/src/ksp/ksp/impls/gmres/borthog2.c [0]PETSC ERROR: [0] KSPGMRESCycle line 131 /home/kathrin/Implementations/petsc-3.4.5/src/ksp/ksp/impls/gmres/gmres.c [0]PETSC ERROR: [0] KSPSolve_GMRES line 229 /home/kathrin/Implementations/petsc-3.4.5/src/ksp/ksp/impls/gmres/gmres.c [0]PETSC ERROR: [0] KSPSolve line 356 /home/kathrin/Implementations/petsc-3.4.5/src/ksp/ksp/interface/itfunc.c [0]PETSC ERROR: --------------------- Error Message ------------------------------------ [0]PETSC ERROR: Signal received! [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Petsc Release Version 3.4.5, Jun, 29, 2014 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: /home/kathrin/Implementations/libmesh/examples/introduction/introduction_ex3/.libs/lt-example-dbg on a arch-linux2-cxx-debug named kathrin-920W-PS by kathrin Tue May 17 12:03:44 2016 [0]PETSC ERROR: Libraries linked from /home/kathrin/Implementations/petsc-3.4.5/arch-linux2-cxx-debug/lib [0]PETSC ERROR: Configure run at Tue May 17 10:52:34 2016 [0]PETSC ERROR: Configure options --with-mpi-dir=/home/kathrin/Implementations/mpich-install --download-cmake=yes --with-debugging=1 --with-shared-libraries=1 --with-dynamic-loading=1 --download-parmetis=1 --download-mumps=1 --download-scalapack=1 --download-f-blas-lapack=1 --download-umfpack=1 --download-metis --with-scalar-type=complex --with-clanguage=cxx PETSC_DIR=/home/kathrin/Implementations/petsc-3.4.5 [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 However, if I just run example-opt of the same example I do not observe any problems. I have configured libmesh with the following options: ./configure --enable-eigen --enable-shared --enable-everything --enable-complex --prefix=/home/kathrin/Implementations/libmesh-install/ --with-metis=PETSc CXX=/home/kathrin/Implementations/mpich-install/bin/mpicxx CC=/home/kathrin/Implementations/mpich-install/bin/mpicc PETSC_DIR=/home/kathrin/Implementations/petsc-3.4.5 Does anyone of you has any idea how to fix this? Thank you! Best, Kathrin |
From: John P. <jwp...@gm...> - 2016-05-17 18:43:17
|
On Tue, May 17, 2016 at 12:17 PM, Kathrin Smetana <ksm...@mi...> wrote: > Hi all, > > I have just installed and configured libmesh (version 0.9.4) using PETSC > 3.4.5. During making check I got the following error in introduction_ex3: > > [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, > probably memory access out of range > [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > [0]PETSC ERROR: or see > http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[0]PETSC > ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find > memory corruption errors > [0]PETSC ERROR: likely location of problem given in stack below > [0]PETSC ERROR: --------------------- Stack Frames > ------------------------------------ > [0]PETSC ERROR: Note: The EXACT line numbers in the stack are not > available, > [0]PETSC ERROR: INSTEAD the line number of the start of the function > [0]PETSC ERROR: is given. > [0]PETSC ERROR: [0] VecMAXPY line 1246 > /home/kathrin/Implementations/petsc-3.4.5/src/vec/vec/interface/rvector.c > [0]PETSC ERROR: [0] KSPGMRESClassicalGramSchmidtOrthogonalization line 45 > /home/kathrin/Implementations/petsc-3.4.5/src/ksp/ksp/impls/gmres/borthog2.c > [0]PETSC ERROR: [0] KSPGMRESCycle line 131 > /home/kathrin/Implementations/petsc-3.4.5/src/ksp/ksp/impls/gmres/gmres.c > [0]PETSC ERROR: [0] KSPSolve_GMRES line 229 > /home/kathrin/Implementations/petsc-3.4.5/src/ksp/ksp/impls/gmres/gmres.c > [0]PETSC ERROR: [0] KSPSolve line 356 > /home/kathrin/Implementations/petsc-3.4.5/src/ksp/ksp/interface/itfunc.c > [0]PETSC ERROR: --------------------- Error Message > ------------------------------------ > [0]PETSC ERROR: Signal received! > [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: Petsc Release Version 3.4.5, Jun, 29, 2014 > [0]PETSC ERROR: See docs/changes/index.html for recent updates. > [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. > [0]PETSC ERROR: See docs/index.html for manual pages. > [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: > /home/kathrin/Implementations/libmesh/examples/introduction/introduction_ex3/.libs/lt-example-dbg > on a arch-linux2-cxx-debug named kathrin-920W-PS by kathrin Tue May 17 > 12:03:44 2016 > [0]PETSC ERROR: Libraries linked from > /home/kathrin/Implementations/petsc-3.4.5/arch-linux2-cxx-debug/lib > [0]PETSC ERROR: Configure run at Tue May 17 10:52:34 2016 > [0]PETSC ERROR: Configure options > --with-mpi-dir=/home/kathrin/Implementations/mpich-install > --download-cmake=yes --with-debugging=1 --with-shared-libraries=1 > --with-dynamic-loading=1 --download-parmetis=1 --download-mumps=1 > --download-scalapack=1 --download-f-blas-lapack=1 --download-umfpack=1 > --download-metis --with-scalar-type=complex --with-clanguage=cxx > PETSC_DIR=/home/kathrin/Implementations/petsc-3.4.5 > [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: User provided function() line 0 in unknown directory > unknown file > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 > > > However, if I just run example-opt of the same example I do not observe > any problems. Most likely because you didn't run with the same number of refinement steps that 'make check' uses? Try libtool --mode=execute ./example-opt refinement_type=matchedhp max_r_steps=5 instead? > I have configured libmesh with the following options: > > ./configure --enable-eigen --enable-shared --enable-everything > --enable-complex --prefix=/home/kathrin/Implementations/libmesh-install/ > --with-metis=PETSc > CXX=/home/kathrin/Implementations/mpich-install/bin/mpicxx > CC=/home/kathrin/Implementations/mpich-install/bin/mpicc > PETSC_DIR=/home/kathrin/Implementations/petsc-3.4.5 > > Does anyone of you has any idea how to fix this? > Your best bet is probably to update to a newer version of PETSc. Since the segfault originates there, and none of us can reproduce the problem using newer PETScs, that may just fix your problem. You could also ignore the issue and see if your build just works OK for your current project... -- John |
From: Kathrin S. <ksm...@mi...> - 2016-05-17 18:51:40
|
Hi John, Thank you very much for your fast reply and your help! On May 17, 2016, at 2:42 PM, John Peterson <jwp...@gm...> wrote: > > > On Tue, May 17, 2016 at 12:17 PM, Kathrin Smetana <ksm...@mi...> wrote: > Hi all, > > I have just installed and configured libmesh (version 0.9.4) using PETSC 3.4.5. During making check I got the following error in introduction_ex3: > > [0]PETSC ERROR: ------------------------------------------------------------------------ > [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range > [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors > [0]PETSC ERROR: likely location of problem given in stack below > [0]PETSC ERROR: --------------------- Stack Frames ------------------------------------ > [0]PETSC ERROR: Note: The EXACT line numbers in the stack are not available, > [0]PETSC ERROR: INSTEAD the line number of the start of the function > [0]PETSC ERROR: is given. > [0]PETSC ERROR: [0] VecMAXPY line 1246 /home/kathrin/Implementations/petsc-3.4.5/src/vec/vec/interface/rvector.c > [0]PETSC ERROR: [0] KSPGMRESClassicalGramSchmidtOrthogonalization line 45 /home/kathrin/Implementations/petsc-3.4.5/src/ksp/ksp/impls/gmres/borthog2.c > [0]PETSC ERROR: [0] KSPGMRESCycle line 131 /home/kathrin/Implementations/petsc-3.4.5/src/ksp/ksp/impls/gmres/gmres.c > [0]PETSC ERROR: [0] KSPSolve_GMRES line 229 /home/kathrin/Implementations/petsc-3.4.5/src/ksp/ksp/impls/gmres/gmres.c > [0]PETSC ERROR: [0] KSPSolve line 356 /home/kathrin/Implementations/petsc-3.4.5/src/ksp/ksp/interface/itfunc.c > [0]PETSC ERROR: --------------------- Error Message ------------------------------------ > [0]PETSC ERROR: Signal received! > [0]PETSC ERROR: ------------------------------------------------------------------------ > [0]PETSC ERROR: Petsc Release Version 3.4.5, Jun, 29, 2014 > [0]PETSC ERROR: See docs/changes/index.html for recent updates. > [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. > [0]PETSC ERROR: See docs/index.html for manual pages. > [0]PETSC ERROR: ------------------------------------------------------------------------ > [0]PETSC ERROR: /home/kathrin/Implementations/libmesh/examples/introduction/introduction_ex3/.libs/lt-example-dbg on a arch-linux2-cxx-debug named kathrin-920W-PS by kathrin Tue May 17 12:03:44 2016 > [0]PETSC ERROR: Libraries linked from /home/kathrin/Implementations/petsc-3.4.5/arch-linux2-cxx-debug/lib > [0]PETSC ERROR: Configure run at Tue May 17 10:52:34 2016 > [0]PETSC ERROR: Configure options --with-mpi-dir=/home/kathrin/Implementations/mpich-install --download-cmake=yes --with-debugging=1 --with-shared-libraries=1 --with-dynamic-loading=1 --download-parmetis=1 --download-mumps=1 --download-scalapack=1 --download-f-blas-lapack=1 --download-umfpack=1 --download-metis --with-scalar-type=complex --with-clanguage=cxx PETSC_DIR=/home/kathrin/Implementations/petsc-3.4.5 > [0]PETSC ERROR: ------------------------------------------------------------------------ > [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 > > > However, if I just run example-opt of the same example I do not observe any problems. > > Most likely because you didn't run with the same number of refinement steps that 'make check' uses? Try > > libtool --mode=execute ./example-opt refinement_type=matchedhp max_r_steps=5 > > instead? I have just run with the configuration above and I still do not have any problems in the optimized mode. > > > > I have configured libmesh with the following options: > > ./configure --enable-eigen --enable-shared --enable-everything --enable-complex --prefix=/home/kathrin/Implementations/libmesh-install/ --with-metis=PETSc CXX=/home/kathrin/Implementations/mpich-install/bin/mpicxx CC=/home/kathrin/Implementations/mpich-install/bin/mpicc PETSC_DIR=/home/kathrin/Implementations/petsc-3.4.5 > > Does anyone of you has any idea how to fix this? > > Your best bet is probably to update to a newer version of PETSc. Since the segfault originates there, and none of us can reproduce the problem using newer PETScs, that may just fix your problem. > > You could also ignore the issue and see if your build just works OK for your current project... > > -- > John I would like to stick to the llibmesh version 0.9.4 for the moment. Which is the most recent PETSC version I could use? Best, Kathrin |
From: John P. <jwp...@gm...> - 2016-05-17 18:59:56
|
On Tue, May 17, 2016 at 12:51 PM, Kathrin Smetana <ksm...@mi...> wrote: > > I have just run with the configuration above and I still do not have any > problems in the optimized mode. > OK, maybe I misunderstood. The problem is only when running the dbg executable? I would like to stick to the llibmesh version 0.9.4 for the moment. Which > is the most recent PETSC version I could use? > 0.9.4 is from February 2015, so it should work with PETSc 3.5.x but probably not with 3.6.x. -- John |
From: Kathrin S. <ksm...@mi...> - 2016-05-17 19:03:02
|
Hi John, Thanks very much for your answer! On May 17, 2016, at 2:59 PM, John Peterson <jwp...@gm...> wrote: > > > On Tue, May 17, 2016 at 12:51 PM, Kathrin Smetana <ksm...@mi...> wrote: > > I have just run with the configuration above and I still do not have any problems in the optimized mode. > > > OK, maybe I misunderstood. The problem is only when running the dbg executable? Yes, that’s true. > > > I would like to stick to the llibmesh version 0.9.4 for the moment. Which is the most recent PETSC version I could use? > > 0.9.4 is from February 2015, so it should work with PETSc 3.5.x but probably not with 3.6.x. > > -- > John Thanks for the info! Then I will try a more recent PETSC version. Best, Kathrin |
From: Kathrin S. <ksm...@mi...> - 2016-05-17 21:26:21
|
Hi John, I have now tried the PETSC versions 3.5.1, 3.5.2, and 3.5.3 and I have got the same error as described below for all versions. Note that I have not tried 3.5.4 since it has been released after the libmesh 0.9.4 release. I am using MPICH 3.0.4. Could that maybe be an issue? Do you have any further ideas? Best, Kathrin On May 17, 2016, at 3:03 PM, Kathrin Smetana <ksm...@mi...> wrote: > Hi John, > > Thanks very much for your answer! > > On May 17, 2016, at 2:59 PM, John Peterson <jwp...@gm...> wrote: > >> >> >> On Tue, May 17, 2016 at 12:51 PM, Kathrin Smetana <ksm...@mi...> wrote: >> >> I have just run with the configuration above and I still do not have any problems in the optimized mode. >> >> >> OK, maybe I misunderstood. The problem is only when running the dbg executable? > > > Yes, that’s true. > >> >> >> I would like to stick to the llibmesh version 0.9.4 for the moment. Which is the most recent PETSC version I could use? >> >> 0.9.4 is from February 2015, so it should work with PETSc 3.5.x but probably not with 3.6.x. >> >> -- >> John > > Thanks for the info! Then I will try a more recent PETSC version. > > Best, > Kathrin |
From: John P. <jwp...@gm...> - 2016-05-17 21:44:10
|
On Tue, May 17, 2016 at 3:26 PM, Kathrin Smetana <ksm...@mi...> wrote: > Hi John, > > I have now tried the PETSC versions 3.5.1, 3.5.2, and 3.5.3 and I have got > the same error as described below for all versions. Note that I have not > tried 3.5.4 since it has been released after the libmesh 0.9.4 release. > Hmm... Can you post your configure flags for building PETSc? Do you have debugging enabled in the PETSc build? > > I am using MPICH 3.0.4. Could that maybe be an issue? > We use a slightly newer version (3.1.4) and haven't noticed any major issues. Do you have any further ideas? > My top idea is still to ignore the problem, unless getting this particular example working is very important for you :0) My other idea would be to use the newest version of libmesh, either master or the recently tagged 1.0.0. If you have libmesh app code you need to port forward, we can probably help with that. This would allow you to use the latest version of PETSc, then if necessary we could track down the bug and provide a more helpful bug report to the PETSc developers... -- John |
From: Kathrin S. <ksm...@mi...> - 2016-05-17 21:53:23
|
Hi John, Thanks very much for your answer! I have configured PETSC with the following options: --with-mpi-dir=/home/kathrin/Implementations/mpich-install --download-cmake=yes --with-debugging=1 --with-shared-libraries=1 --with-dynamic-loading=1 --download-parmetis=1 --download-mumps=1 --download-scalapack=1 --download-f-blas-lapack=1 --download-umfpack=1 --download-metis --with-scalar-type=complex --with-clanguage=cxx PETSC_DIR=/home/kathrin/Implementations/petsc-3.4.5 So should I maybe just configure with debugging=0? Thanks again! Best, Kathrin On May 17, 2016, at 5:43 PM, John Peterson <jwp...@gm...> wrote: > > > On Tue, May 17, 2016 at 3:26 PM, Kathrin Smetana <ksm...@mi...> wrote: > Hi John, > > I have now tried the PETSC versions 3.5.1, 3.5.2, and 3.5.3 and I have got the same error as described below for all versions. Note that I have not tried 3.5.4 since it has been released after the libmesh 0.9.4 release. > > Hmm... Can you post your configure flags for building PETSc? Do you have debugging enabled in the PETSc build? > > > > I am using MPICH 3.0.4. Could that maybe be an issue? > > We use a slightly newer version (3.1.4) and haven't noticed any major issues. > > > Do you have any further ideas? > > My top idea is still to ignore the problem, unless getting this particular example working is very important for you :0) > > My other idea would be to use the newest version of libmesh, either master or the recently tagged 1.0.0. If you have libmesh app code you need to port forward, we can probably help with that. This would allow you to use the latest version of PETSc, then if necessary we could track down the bug and provide a more helpful bug report to the PETSc developers... > > -- > John |
From: John P. <jwp...@gm...> - 2016-05-17 22:13:54
|
On Tue, May 17, 2016 at 3:53 PM, Kathrin Smetana <ksm...@mi...> wrote: > > I have configured PETSC with the following options: > > --with-mpi-dir=/home/kathrin/Implementations/mpich-install > --download-cmake=yes --with-debugging=1 --with-shared-libraries=1 > --with-dynamic-loading=1 --download-parmetis=1 --download-mumps=1 > --download-scalapack=1 --download-f-blas-lapack=1 --download-umfpack=1 > --download-metis --with-scalar-type=complex --with-clanguage=cxx > PETSC_DIR=/home/kathrin/Implementations/petsc-3.4.5 > > So should I maybe just configure with debugging=0? > Libmesh *should* work with both debug and optimized versions of PETSc, however having an optimized PETSc build in a different PETSC_DIR it would probably be another useful data point. If that works, then you can probably just stick with that instead... -- John |
From: John P. <jwp...@gm...> - 2016-05-18 19:15:23
|
On Wed, May 18, 2016 at 1:09 PM, Kathrin Smetana <ksm...@mi...> wrote: > Hi John, > > So using the optimized version of PETSC actually solved the problem. Thank > you very much again for your help! > Thanks for letting us know. It would be nice if all versions of libmesh worked with debug-enabled PETSc, but that's not something that gets tested very often... -- John |
From: John P. <jwp...@gm...> - 2016-05-18 21:27:06
|
On Wed, May 18, 2016 at 3:04 PM, Jed Brown <je...@je...> wrote: > John Peterson <jwp...@gm...> writes: > > It would be nice if all versions of libmesh worked with debug-enabled > > PETSc, but that's not something that gets tested very often... > > *tears* > > I'd like to know what is causing this SEGV. It shouldn't happen unless > some side-effects are being abused, and even then, debug mode should > give a better error message instead of waiting for SEGV. > OK, if Kathrin still has debug builds sitting around, she may be able to get a stack trace by running the example in question with: libtool --mode=execute gdb ./example-dbg refinement_type=matchedhp max_r_steps=5 and then type "r" to run the program. It should stop when it segfaults, and then you can type "bt" to get a backtrace. I'll also see if I can reproduce on a 3.5.x debug PETSc build... -- John |