Dear Dr. Bangerth, I successfully compiled dealii trunk with umfpack/petsc/metis/trilinos by ./configure --with-umfpack-include=/usr/include/suitesparse --with-umfpack-libs=/usr/lib --with-petsc=/usr/lib/petscdir/3.1 --with-petsc-arch=linux-gnu-c-opt --enable-mpi --disable-threads --with-metis-include=/usr/include/metis --with-metis-libs=/usr/lib --with-trilinos-include=/usr/include/trilinos --with-trilinos-libs=/usr/lib --with-blas --with-lapack
And by adding LIBS += -lpetsc -lscotch -lpython2.7 to Makefile under step-17, I am able to build step-17 executable. However I still have the segmentation error. When I built without trilinos only with umfpack/petsc/metis, step-17 worked fine... although metis partition actually slows down the calculation compared to serial run.... It would be great if we can build dealii with debian system umfpack/petsc/metis/trilinos all together. Here is gdb backtrace info when dealii was built with trilinos: jyin1@sid-laptop:~/svn/deal.II/examples/step-17$ ./step-17 Segmentation fault jyin1@sid-laptop:~/svn/deal.II/examples/step-17$ gdb step-17 GNU gdb (GDB) 7.3-debian Copyright (C) 2011 Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html > This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. Type "show copying" and "show warranty" for details. This GDB was configured as "x86_64-linux-gnu". For bug reporting instructions, please see: <http://www.gnu.org/software/gdb/bugs/>... Reading symbols from /home/jyin1/svn/deal.II/examples/step-17/step-17...done. (gdb) r Starting program: /home/jyin1/svn/deal.II/examples/step-17/step-17 [Thread debugging using libthread_db enabled] [New Thread 0x7fffd6396700 (LWP 21687)] Program received signal SIGSEGV, Segmentation fault. 0x0000000000000000 in ?? () (gdb) bt #0 0x0000000000000000 in ?? () #1 0x00007fffe10387c9 in PyEval_GetGlobals () from /usr/lib/libpython2.7.so.1.0 #2 0x00007fffe1059815 in PyImport_Import () from /usr/lib/libpython2.7.so.1.0 #3 0x00007fffe10598bc in PyImport_ImportModule () from /usr/lib/libpython2.7.so.1.0 #4 0x00007ffff1999ed0 in ?? () from /usr/lib/libtrilinos_pytrilinos.so.10.4 #5 0x00007ffff199a1b3 in NumPyImporter::NumPyImporter() () from /usr/lib/libtrilinos_pytrilinos.so.10.4 #6 0x00007ffff199a161 in ?? () from /usr/lib/libtrilinos_pytrilinos.so.10.4 #7 0x00007ffff199a196 in ?? () from /usr/lib/libtrilinos_pytrilinos.so.10.4 #8 0x00007ffff19edf36 in ?? () from /usr/lib/libtrilinos_pytrilinos.so.10.4 #9 0x00007fffdfaf9670 in ?? () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6 #10 0x0000000000000001 in ?? () #11 0x00007fffffffc5f8 in ?? () #12 0x00007ffff1993633 in _init () from /usr/lib/libtrilinos_pytrilinos.so.10.4 #13 0x00007fffe3f07030 in ?? () from /usr/lib/libnetcdf_c++.so.5 #14 0x00007ffff7deac89 in ?? () from /lib64/ld-linux-x86-64.so.2 #15 0x00007ffff7deadc7 in ?? () from /lib64/ld-linux-x86-64.so.2 #16 0x00007ffff7dddb2a in ?? () from /lib64/ld-linux-x86-64.so.2 #17 0x0000000000000001 in ?? () #18 0x00007fffffffca12 in ?? () #19 0x0000000000000000 in ?? () Sincerely, Jichao *Jichao Yin* Email: [email protected] LinkedIn: http://www.linkedin.com/in/jichao On Tue, Oct 18, 2011 at 11:07 PM, Jichao Yin <[email protected]> wrote: > Thank you Dr. Bangerth, > > I finally figured out the errors were because of *libpython2.7.so* not > linked but the system libtrilinos built with python support. Therefore, > adding to Makefile of step-17 (petsc): > *LIBS += -lpetsc -lpython2.7* > $(target)$(EXEEXT) : $(libraries) > ..... > > For step-33, *LIBS += -lpython2.7* > > As for the $LD_LIBRARY_PATH, since the problem with original Makefile > (step-17) occurred during the linking, I guess still problem happened in > configure (or its settings): > > ============================ Linking step-17 > > /usr/bin/ld: step-17.g.o: undefined reference to symbol 'VecSetValues' > /usr/bin/ld: note: 'VecSetValues' is defined in DSO > /usr/lib/libpetsc.so.3.1 so try adding it to the linker command line > /usr/lib/libpetsc.so.3.1: could not read symbols: Invalid operation > collect2: ld returned 1 exit status > make: *** [step-17] Error 1 > > Nevertheless, at least it is possible to build deal.II with system > installed umfpack/petsc/trilinos :) > Though mpirun of step-17 and step-33 still failed, I am going to struggle > myself a little longer before bothering you :) > > > Sincerely, > Jichao > > *Jichao Yin* > Email: [email protected] > LinkedIn: http://www.linkedin.com/in/jichao > > > On Tue, Oct 18, 2011 at 5:43 AM, Wolfgang Bangerth <[email protected] > > wrote: > >> >> > /usr/bin/ld: step-17.g.o: undefined reference to symbol 'VecSetValues' >> > /usr/bin/ld: note: 'VecSetValues' is defined in DSO >> > /usr/lib/libpetsc.so.3.1 so try adding it to the linker command line >> > /usr/lib/libpetsc.so.3.1: could not read symbols: Invalid operation >> >> What happens if you modify LD_LIBRARY_PATH as described here: >> >> http://dealii.sourceforge.net/index.php/Deal.II_Questions_and_Answers#I_can.27t_seem_to_link.2Frun_with_PETSc >> ? >> >> WB >> >> ------------------------------------------------------------------------- >> Wolfgang Bangerth email: [email protected] >> www: http://www.math.tamu.edu/~bangerth/ >> > >
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