From: <pco...@ue...> - 2007-04-13 15:00:51
Attachments:
make_echo
config.log
|
Hi, I'm still having problems with >make run_examples The result is make[1]: Entering directory `/home/paulo/libmesh/examples' make[2]: Entering directory `/home/paulo/libmesh/examples/ex0' Compiling C++ (in optimized mode) ex0.C... Linking ex0-opt... /home/paulo/libmesh/contrib/tecplot/lib/i686-pc-linux-gnu/tecio.a(tecxxx.o)(.text+0x1a7): In function `tecini': : warning: the use of `mktemp' is dangerous, better use `mkstemp' *************************************************************** * Running Example ./ex0-opt *************************************************************** ./ex0-opt: error while loading shared libraries: libgzstream.so: cannot open shared object file: No such file or directory make[2]: *** [run] Error 127 make[2]: Leaving directory `/home/paulo/libmesh/examples/ex0' make[1]: *** [run] Error 2 make[1]: Leaving directory `/home/paulo/libmesh/examples' make: *** [run_examples] Error 2 I got the cvs version, I installed petsc following the wiki instalation but still... I join the 'make echo' output and the config.log. I greatly appreciate any help. Thanks. Paulo Correia |
From: John P. <pet...@cf...> - 2007-04-13 15:39:05
|
I'm a bit suspicious about your libs, in particular, there is a weird gap before "-llapack -lblas" which makes me wonder if you do not have these things correctly installed. In particular, do you really have a liblapack and a libblas in /home/paulo/libmesh/contrib/petsc-2.3.2-p10/lib/linux ? Also, I can't think of any obvious problems with having petsc installed in your contrib directory, but I've never tried it myself, and I'm not sure anyone else has either... -J LIBS: /home/paulo/libmesh/lib/i686-pc-linux-gnu_opt/libmesh.so /home/paulo/libmesh/contrib/lib/i686-pc-linux-gnu_opt/liblaspack.so /home/paulo/libmesh/contrib/lib/i686-pc-linux-gnu_opt/libparmetis.so /home/paulo/libmesh/contrib/lib/i686-pc-linux-gnu_opt/lib metis.so /home/paulo/libmesh/contrib/lib/i686-pc-linux-gnu_opt/libsfcurves.so /home/paulo/libmesh/contrib/lib/i686-pc-linux-gn u_opt/libgzstream.so -lz /home/paulo/libmesh/contrib/tecplot/lib/i686-pc-linux-gnu/tecio.a /home/paulo/libmesh/contrib/lib/i68 6-pc-linux-gnu_opt/libtetgen.so /home/paulo/libmesh/contrib/lib/i686-pc-linux-gnu_opt/libtriangle.so -L/home/paulo/libmesh/con trib/petsc-2.3.2-p10/lib/linux -lpetscsnes -lpetscksp -lpetscdm -lpetscmat -lpetscvec -lpetscsnes -lpetsc -llapack -lbl as -L/usr/X11R6/lib -lX11 -L/usr/lib/gcc-lib/i486-linux/3.3.5 -L/usr/lib/gcc-lib/i486-linux/3.3.5/../../.. -lfrtbegin -lg2c - lm -lgcc_s -Wl,-rpath,/usr/lib/mpich/lib -L/usr/lib/mpich/lib -lmpi -lmpi++ -lnsl -lrt pco...@ue... writes: > Hi, > > I'm still having problems with > > >make run_examples > > The result is > > make[1]: Entering directory `/home/paulo/libmesh/examples' > make[2]: Entering directory `/home/paulo/libmesh/examples/ex0' > Compiling C++ (in optimized mode) ex0.C... > Linking ex0-opt... > /home/paulo/libmesh/contrib/tecplot/lib/i686-pc-linux-gnu/tecio.a(tecxxx.o)(.text+0x1a7): > In function `tecini': > : warning: the use of `mktemp' is dangerous, better use `mkstemp' > *************************************************************** > * Running Example ./ex0-opt > *************************************************************** > > ./ex0-opt: error while loading shared libraries: libgzstream.so: cannot > open shared object file: No such file or directory > make[2]: *** [run] Error 127 > make[2]: Leaving directory `/home/paulo/libmesh/examples/ex0' > make[1]: *** [run] Error 2 > make[1]: Leaving directory `/home/paulo/libmesh/examples' > make: *** [run_examples] Error 2 > > I got the cvs version, I installed petsc following the wiki instalation > but still... > > I join the 'make echo' output and the config.log. > I greatly appreciate any help. Thanks. > Paulo Correia > > > > [Deleted make_echo (untyped binary data;application/octet-stream)] > ------------------------------------------------------------------------- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share your > opinions on IT & business topics through brief surveys-and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV_______________________________________________ > Libmesh-devel mailing list > Lib...@li... > https://lists.sourceforge.net/lists/listinfo/libmesh-devel |
From: <pco...@ue...> - 2007-04-13 16:04:33
|
> I'm a bit suspicious about your libs, in particular, there is a weird gap > before "-llapack -lblas" which > makes me wonder if you do not have these things correctly installed. In > particular, do you really have > a liblapack and a libblas in > > /home/paulo/libmesh/contrib/petsc-2.3.2-p10/lib/linux > > ? Nope. The contents of /home/paulo/libmesh/contrib/petsc-2.3.2-p10/lib/linux is: libpetsc.a libpetscdm.a libpetscksp.so libpetscsnes.a libpetscts.a libpetscvec.so libpetsccontrib.a libpetscdm.so libpetscmat.a libpetscsnes.so libpetscts.so libpetsccontrib.so libpetscksp.a libpetscmat.so libpetsc.so libpetscvec.a What shall I do? Thanks. Paulo |
From: John P. <pet...@cf...> - 2007-04-13 16:22:00
|
pco...@ue... writes: > > I'm a bit suspicious about your libs, in particular, there is a weird gap > > before "-llapack -lblas" which > > makes me wonder if you do not have these things correctly installed. In > > particular, do you really have > > a liblapack and a libblas in > > > > /home/paulo/libmesh/contrib/petsc-2.3.2-p10/lib/linux > > > > ? > > Nope. > > The contents of /home/paulo/libmesh/contrib/petsc-2.3.2-p10/lib/linux is: > > libpetsc.a libpetscdm.a libpetscksp.so libpetscsnes.a > libpetscts.a libpetscvec.so > libpetsccontrib.a libpetscdm.so libpetscmat.a libpetscsnes.so > libpetscts.so > libpetsccontrib.so libpetscksp.a libpetscmat.so libpetsc.so > libpetscvec.a > > What shall I do? This means that that you probably followed the Wiki instructions a little too closely, and where you were supposed to insert your own BLAS/Lapack diretory in PETScs configuration --with-blas-lapack-dir=/software/ia32/intel/mkl-7.2.1 you did something wrong. This would also maybe be related to the DGEMV error you were reporting about earlier. There's probably a BLAS rpm available for your linux distro (or .deb, or whatever) that you need to download and rebuild petsc against. -John > Thanks. > Paulo > |
From: <pco...@ue...> - 2007-04-13 17:38:23
|
I found /usr/lib/liblapack.so.2.0 /usr/lib/libblas.so.2.0 so I inserted it in PETScs configuration --with-blas-lapack-dir=/usr/lib Then I recompiled petsc and libmesh but the problem maintains... So instead of running make run_examples I did it by parts: > make examples worked ok, but with > make link_examples make[1]: Entering directory `/home/paulo/libmesh/examples' make[2]: Entering directory `/home/paulo/libmesh/examples/ex0' g++ -DNDEBUG -O2 -felide-constructors -fPIC -funroll-loops -fstrict-aliasing -Wdisabled-optimization -DPETSC_USE_DYNAMIC_LIBRARIES ex0.C -o ex0 ex0.C:33:18: mesh.h: No such file or directory ex0.C:34:29: mesh_generation.h: No such file or directory ex0.C:35:24: edge_edge3.h: No such file or directory ex0.C:36:24: gnuplot_io.h: No such file or directory (...) ??? > pco...@ue... writes: > > > I'm a bit suspicious about your libs, in particular, there is a weird > gap > > > before "-llapack -lblas" which > > > makes me wonder if you do not have these things correctly installed. > In > > > particular, do you really have > > > a liblapack and a libblas in > > > > > > /home/paulo/libmesh/contrib/petsc-2.3.2-p10/lib/linux > > > > > > ? > > > > Nope. > > > > The contents of /home/paulo/libmesh/contrib/petsc-2.3.2-p10/lib/linux > is: > > > > libpetsc.a libpetscdm.a libpetscksp.so libpetscsnes.a > > libpetscts.a libpetscvec.so > > libpetsccontrib.a libpetscdm.so libpetscmat.a libpetscsnes.so > > libpetscts.so > > libpetsccontrib.so libpetscksp.a libpetscmat.so libpetsc.so > > libpetscvec.a > > > > What shall I do? > > This means that that you probably followed the Wiki instructions a little > too closely, and where you were supposed to insert your own BLAS/Lapack > diretory > in PETScs configuration > > --with-blas-lapack-dir=/software/ia32/intel/mkl-7.2.1 > > you did something wrong. This would also maybe be related to the DGEMV > error > you were reporting about earlier. There's probably a BLAS rpm available > for > your linux distro (or .deb, or whatever) that you need to download and > rebuild > petsc against. > > -John > > > Thanks. > > Paulo > > > > ------------------------------------------------------------------------- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share > your > opinions on IT & business topics through brief surveys-and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > _______________________________________________ > Libmesh-devel mailing list > Lib...@li... > https://lists.sourceforge.net/lists/listinfo/libmesh-devel > |
From: Roy S. <roy...@ic...> - 2007-04-13 17:41:46
|
On Fri, 13 Apr 2007, pco...@ue... wrote: > Then I recompiled petsc and libmesh but the problem maintains... Actually, now the problem is different. :-P >> make link_examples > > make[1]: Entering directory `/home/paulo/libmesh/examples' > make[2]: Entering directory `/home/paulo/libmesh/examples/ex0' > g++ -DNDEBUG -O2 -felide-constructors -fPIC -funroll-loops > -fstrict-aliasing -Wdisabled-optimization -DPETSC_USE_DYNAMIC_LIBRARIES > ex0.C -o ex0 > ex0.C:33:18: mesh.h: No such file or directory > ex0.C:34:29: mesh_generation.h: No such file or directory > ex0.C:35:24: edge_edge3.h: No such file or directory > ex0.C:36:24: gnuplot_io.h: No such file or directory > (...) Somehow in correcting your library paths you've managed to unset your include paths. The thing to do now is to see what they've been set to and figure out where the Makefiles or your configure options aren't setting them correctly. --- Roy |
From: John P. <pet...@cf...> - 2007-04-13 17:48:25
|
Actually, make link_examples no longer works. I think Roy recently changed all the example Makefiles... Try just typing make in your ex0 directory. -John Roy Stogner writes: > On Fri, 13 Apr 2007, pco...@ue... wrote: > > > Then I recompiled petsc and libmesh but the problem maintains... > > Actually, now the problem is different. :-P > > >> make link_examples > > > > make[1]: Entering directory `/home/paulo/libmesh/examples' > > make[2]: Entering directory `/home/paulo/libmesh/examples/ex0' > > g++ -DNDEBUG -O2 -felide-constructors -fPIC -funroll-loops > > -fstrict-aliasing -Wdisabled-optimization -DPETSC_USE_DYNAMIC_LIBRARIES > > ex0.C -o ex0 > > ex0.C:33:18: mesh.h: No such file or directory > > ex0.C:34:29: mesh_generation.h: No such file or directory > > ex0.C:35:24: edge_edge3.h: No such file or directory > > ex0.C:36:24: gnuplot_io.h: No such file or directory > > (...) > > Somehow in correcting your library paths you've managed to unset your > include paths. The thing to do now is to see what they've been set to > and figure out where the Makefiles or your configure options aren't > setting them correctly. > --- > Roy |
From: Roy S. <roy...@ic...> - 2007-04-13 17:54:44
|
On Fri, 13 Apr 2007, John Peterson wrote: > Actually, make link_examples no longer works. I think Roy recently changed > all the example Makefiles... Whoops! I must have forgotten to change the top level Makefile to match. But anyway he never cleaned the example directories before running make, so what's probably happening is that make is deciding the ex0-opt (or whatever extension) is up to date but ex0 isn't. It's still a compile failure because of messed up INCLUDE arguments, I believe. I'll commit a fixed examples/Makefile shortly. --- Roy |
From: <pco...@ue...> - 2007-04-13 18:43:21
|
> Actually, make link_examples no longer works. I think Roy recently > changed > all the example Makefiles... Try just typing make in your ex0 directory. This is what I did in the ex0 directory: >make clean >make >./ex0-opt and this was the result: -------------------------------------------------------------------------- Petsc Version 2.2.0, Patch 2, Released May 10, 2004 The PETSc Team pet...@mc... http://www.mcs.anl.gov/petsc/ See docs/changes/index.html for recent updates. See docs/troubleshooting.html for hints about trouble shooting. See docs/index.html for manual pages. ----------------------------------------------------------------------- ./ex0-opt on a linux named alinex-2PUb8L by paulo Fri Apr 13 19:12:55 2007 Libraries linked from /home/hazelsct/packages/petsc-2.2.0/lib/libO/linux ----------------------------------------------------------------------- [0]PETSC ERROR: VecSet() line 810 in src/vec/interface/vector.c [0]PETSC ERROR: Null argument, when expecting valid pointer! [0]PETSC ERROR: Null Object: Parameter # 2! [0]PETSC ERROR: User provided function() line 605 in unknowndirectory//home/paulo/libmesh/include/numerics/petsc_vector.h [0] MPI Abort by user Aborting program ! [0] Aborting program! p0_4617: p4_error: : 85 --------------------------------------------------- | Time: Fri Apr 13 19:12:55 2007 | | OS: Linux | | HostName: alinex-2PUb8L | | OS Release: 2.6.12-1-586tsc | | OS Version: #1 Sat Oct 29 08:01:24 EDT 2005 | | Machine: i686 | | Username: paulo | --------------------------------------------------- ------------------------------------------------------------------------------ | libMesh Performance: Alive time=0.027759, Active time=0.000683 | ------------------------------------------------------------------------------ | Event nCalls Total Avg Percent of | | Time Time Active Time | |------------------------------------------------------------------------------| | | | | | DofMap | | create_dof_constraints() 1 0.0000 0.000008 1.17 | | distribute_dofs() 1 0.0003 0.000330 48.32 | | dof_indices() 12 0.0001 0.000006 11.13 | | reinit() 1 0.0001 0.000084 12.30 | | | | Mesh | | find_neighbors() 1 0.0001 0.000128 18.74 | | renumber_nodes_and_elem() 1 0.0000 0.000007 1.02 | | | | MeshTools::Generation | | build_cube() 1 0.0000 0.000050 7.32 | ------------------------------------------------------------------------------ | Totals: 18 0.0007 100.00 | ------------------------------------------------------------------------------ In fact I have version 2.2.0 in /usr/lib/petsc but why finds this version and not the one in libmesh/contrib ?? > -John > > > Roy Stogner writes: > > On Fri, 13 Apr 2007, pco...@ue... wrote: > > > > > Then I recompiled petsc and libmesh but the problem maintains... > > > > Actually, now the problem is different. :-P > > > > >> make link_examples > > > > > > make[1]: Entering directory `/home/paulo/libmesh/examples' > > > make[2]: Entering directory `/home/paulo/libmesh/examples/ex0' > > > g++ -DNDEBUG -O2 -felide-constructors -fPIC -funroll-loops > > > -fstrict-aliasing -Wdisabled-optimization > -DPETSC_USE_DYNAMIC_LIBRARIES > > > ex0.C -o ex0 > > > ex0.C:33:18: mesh.h: No such file or directory > > > ex0.C:34:29: mesh_generation.h: No such file or directory > > > ex0.C:35:24: edge_edge3.h: No such file or directory > > > ex0.C:36:24: gnuplot_io.h: No such file or directory > > > (...) > > > > Somehow in correcting your library paths you've managed to unset your > > include paths. The thing to do now is to see what they've been set to > > and figure out where the Makefiles or your configure options aren't > > setting them correctly. > > --- > > Roy > |
From: John P. <pet...@cf...> - 2007-04-13 18:57:01
|
pco...@ue... writes: > > Actually, make link_examples no longer works. I think Roy recently > > changed > > all the example Makefiles... Try just typing make in your ex0 directory. > > This is what I did in the ex0 directory: > > >make clean > >make > >./ex0-opt > > and this was the result: > > -------------------------------------------------------------------------- > Petsc Version 2.2.0, Patch 2, Released May 10, 2004 > The PETSc Team > pet...@mc... > http://www.mcs.anl.gov/petsc/ > > See docs/changes/index.html for recent updates. > See docs/troubleshooting.html for hints about trouble shooting. > See docs/index.html for manual pages. > ----------------------------------------------------------------------- > ./ex0-opt on a linux named alinex-2PUb8L by paulo Fri Apr 13 19:12:55 2007 > Libraries linked from /home/hazelsct/packages/petsc-2.2.0/lib/libO/linux > ----------------------------------------------------------------------- > [0]PETSC ERROR: VecSet() line 810 in src/vec/interface/vector.c > [0]PETSC ERROR: Null argument, when expecting valid pointer! > [0]PETSC ERROR: Null Object: Parameter # 2! > [0]PETSC ERROR: User provided function() line 605 in > unknowndirectory//home/paulo/libmesh/include/numerics/petsc_vector.h > [0] MPI Abort by user Aborting program ! > [0] Aborting program! > p0_4617: p4_error: : 85 > > In fact I have version 2.2.0 in /usr/lib/petsc but why finds this version > and not the one in libmesh/contrib ?? It will link against whichever one configure found. Configure uses your PETSC_DIR and PETSC_ARCH variables to determine which PETSc to use. Perhaps when you recompiled libmesh, you forgot to set one of these correctly again. Try doing ldd ex0-opt That will tell you exactly which one it ended up linking against. -John |
From: <pco...@ue...> - 2007-04-13 19:17:51
|
> pco...@ue... writes: > > > Actually, make link_examples no longer works. I think Roy recently > > > changed > > > all the example Makefiles... Try just typing make in your ex0 > directory. > > > > This is what I did in the ex0 directory: > > > > >make clean > > >make > > >./ex0-opt > > > > and this was the result: > > > > -------------------------------------------------------------------------- > > Petsc Version 2.2.0, Patch 2, Released May 10, 2004 > > The PETSc Team > > pet...@mc... > > http://www.mcs.anl.gov/petsc/ > > > > See docs/changes/index.html for recent updates. > > See docs/troubleshooting.html for hints about trouble shooting. > > See docs/index.html for manual pages. > > ----------------------------------------------------------------------- > > ./ex0-opt on a linux named alinex-2PUb8L by paulo Fri Apr 13 19:12:55 > 2007 > > Libraries linked from > /home/hazelsct/packages/petsc-2.2.0/lib/libO/linux > > ----------------------------------------------------------------------- > > [0]PETSC ERROR: VecSet() line 810 in src/vec/interface/vector.c > > [0]PETSC ERROR: Null argument, when expecting valid pointer! > > [0]PETSC ERROR: Null Object: Parameter # 2! > > [0]PETSC ERROR: User provided function() line 605 in > > unknowndirectory//home/paulo/libmesh/include/numerics/petsc_vector.h > > [0] MPI Abort by user Aborting program ! > > [0] Aborting program! > > p0_4617: p4_error: : 85 > > > > In fact I have version 2.2.0 in /usr/lib/petsc but why finds this > version > > and not the one in libmesh/contrib ?? > > It will link against whichever one configure found. Configure uses > your PETSC_DIR and PETSC_ARCH variables to determine which PETSc to > use. Perhaps when you recompiled libmesh, you forgot to set one of > these correctly again. > > Try doing > > ldd ex0-opt Ok. /home/paulo/libmesh/lib/i686-pc-linux-gnu_opt/libmesh.so => /home/paulo/libmesh/lib/i686-pc-linux-gnu_opt/libmesh.so (0xb7aff000) /home/paulo/libmesh/contrib/lib/i686-pc-linux-gnu_opt/liblaspack.so => /home/paulo/libmesh/contrib/lib/i686-pc-linux-gnu_opt/liblaspack.so (0xb7ae8000) /home/paulo/libmesh/contrib/lib/i686-pc-linux-gnu_opt/libparmetis.so => /home/paulo/libmesh/contrib/lib/i686-pc-linux-gnu_opt/libparmetis.so (0xb7a90000) /home/paulo/libmesh/contrib/lib/i686-pc-linux-gnu_opt/libmetis.so => /home/paulo/libmesh/contrib/lib/i686-pc-linux-gnu_opt/libmetis.so (0xb7a30000) /home/paulo/libmesh/contrib/lib/i686-pc-linux-gnu_opt/libsfcurves.so => /home/paulo/libmesh/contrib/lib/i686-pc-linux-gnu_opt/libsfcurves.so (0xb7a2d000) /home/paulo/libmesh/contrib/lib/i686-pc-linux-gnu_opt/libgzstream.so => /home/paulo/libmesh/contrib/lib/i686-pc-linux-gnu_opt/libgzstream.so (0xb7a28000) libz.so.1 => /usr/lib/libz.so.1 (0xb7a16000) /home/paulo/libmesh/contrib/lib/i686-pc-linux-gnu_opt/libtetgen.so => /home/paulo/libmesh/contrib/lib/i686-pc-linux-gnu_opt/libtetgen.so (0xb7973000) /home/paulo/libmesh/contrib/lib/i686-pc-linux-gnu_opt/libtriangle.so => /home/paulo/libmesh/contrib/lib/i686-pc-linux-gnu_opt/libtriangle.so (0xb7950000) libpetscsnes.so => /usr/lib/libpetscsnes.so (0xb7924000) libpetscksp.so => /usr/lib/libpetscksp.so (0xb7894000) libpetscdm.so => /usr/lib/libpetscdm.so (0xb782c000) libpetscmat.so => /usr/lib/libpetscmat.so (0xb75a2000) libpetscvec.so => /usr/lib/libpetscvec.so (0xb7526000) libpetsc.so => /usr/lib/libpetsc.so (0xb7492000) liblapack.so.3 => /usr/lib/liblapack.so.3 (0xb6e73000) libblas.so.3 => /usr/lib/libblas.so.3 (0xb6def000) libX11.so.6 => /usr/X11R6/lib/libX11.so.6 (0xb6d1d000) libg2c.so.0 => /usr/lib/libg2c.so.0 (0xb6cff000) libgcc_s.so.1 => /lib/libgcc_s.so.1 (0xb6cf6000) libmpich.so.1.0 => /usr/lib/libmpich.so.1.0 (0xb6c3b000) libpmpich.so.1.0 => /usr/lib/libpmpich.so.1.0 (0xb6b80000) libnsl.so.1 => /lib/tls/libnsl.so.1 (0xb6b6b000) librt.so.1 => /lib/tls/librt.so.1 (0xb6b65000) libstdc++.so.5 => /usr/lib/libstdc++.so.5 (0xb6aab000) libm.so.6 => /lib/tls/libm.so.6 (0xb6a89000) libc.so.6 => /lib/tls/libc.so.6 (0xb6954000) libmpe.so.1.0 => /usr/lib/libmpe.so.1.0 (0xb692c000) libslog.so.1.0 => /usr/lib/libslog.so.1.0 (0xb68fb000) libdl.so.2 => /lib/tls/libdl.so.2 (0xb68f8000) libpthread.so.0 => /lib/tls/libpthread.so.0 (0xb68e9000) /lib/ld-linux.so.2 => /lib/ld-linux.so.2 (0xb7f6d000) Yep, he goes to /usr/lib instead of libmesh/contrib/petsc-2.3.2-p10/ but I still don't understand why... > > That will tell you exactly which one it ended up linking against. > > -John > > > ------------------------------------------------------------------------- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share > your > opinions on IT & business topics through brief surveys-and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > _______________________________________________ > Libmesh-devel mailing list > Lib...@li... > https://lists.sourceforge.net/lists/listinfo/libmesh-devel > |