There's almost certainly something wrong with your MPI installation. How did you install it? Can you send me the config.log file?
-- John ---------- Forwarded message ---------- From: tschroeder <tschroe...@daad-alumni.de> Date: Wed, Nov 4, 2015 at 1:48 PM Subject: AW: [Libmesh-users] Neumann boundary problem for Laplace equation To: John Peterson <jwpeter...@gmail.com> John, Sorry to bug you again. I installed PETSc and MPI. Then , I configured libMesh as follows: ./configure PETSC_DIR=/home/tobias/PETSc/petsc-3.6.2/lib/petsc PETSC_ARCH=arch-linux2-c-debug --enable-everything --enable-petsc --enable-mpi Then, I ran into an issue when executing "make check." This is the error message that I get (when running example introduction_ex1): ... ================== All 5 tests passed ================== make[3]: Leaving directory `/home/tobias/libMesh/libmesh-0.9.4/contrib/nanoflann' make[2]: Leaving directory `/home/tobias/libMesh/libmesh-0.9.4/contrib/nanoflann' make[2]: Entering directory `/home/tobias/libMesh/libmesh-0.9.4/contrib' make[2]: Nothing to be done for `check-am'. make[2]: Leaving directory `/home/tobias/libMesh/libmesh-0.9.4/contrib' make[1]: Leaving directory `/home/tobias/libMesh/libmesh-0.9.4/contrib' Making check in examples make[1]: Entering directory `/home/tobias/libMesh/libmesh-0.9.4/examples' Making check in introduction/introduction_ex1 make[2]: Entering directory `/home/tobias/libMesh/libmesh-0.9.4/examples/introduction/introduction_ex1' make example-dbg example-devel example-opt run.sh make[3]: Entering directory `/home/tobias/libMesh/libmesh-0.9.4/examples/introduction/introduction_ex1' CXX example_dbg-introduction_ex1.o CXXLD example-dbg /usr/bin/ld: skipping incompatible /lib/libz.so when searching for -lz /usr/bin/ld: skipping incompatible /usr/lib/libz.so when searching for -lz CXX example_devel-introduction_ex1.o CXXLD example-devel /usr/bin/ld: skipping incompatible /lib/libz.so when searching for -lz /usr/bin/ld: skipping incompatible /usr/lib/libz.so when searching for -lz CXX example_opt-introduction_ex1.o CXXLD example-opt /usr/bin/ld: skipping incompatible /lib/libz.so when searching for -lz /usr/bin/ld: skipping incompatible /usr/lib/libz.so when searching for -lz make[3]: Nothing to be done for `run.sh'. make[3]: Leaving directory `/home/tobias/libMesh/libmesh-0.9.4/examples/introduction/introduction_ex1' make check-TESTS make[3]: Entering directory `/home/tobias/libMesh/libmesh-0.9.4/examples/introduction/introduction_ex1' *************************************************************** * Running Example introduction_ex1: * example-dbg -d 3 /home/tobias/libMesh/libmesh-0.9.4/reference_elements/3D/one_hex27.xda *************************************************************** [usbosnavdev-ludwig:09698] *** Process received signal *** [usbosnavdev-ludwig:09698] Signal: Segmentation fault (11) [usbosnavdev-ludwig:09698] Signal code: Address not mapped (1) [usbosnavdev-ludwig:09698] Failing at address: 0x44000098 [usbosnavdev-ludwig:09698] [ 0] /lib64/libpthread.so.0(+0xf130)[0x7f4ee8983130] [usbosnavdev-ludwig:09698] [ 1] /usr/local/lib/libmpi.so.12(MPI_Comm_size+0x46)[0x7f4eeb21a576] [usbosnavdev-ludwig:09698] [ 2] /home/tobias/libMesh/libmesh-0.9.4/.libs/libmesh_dbg.so.0(_ZN7libMesh8Parallel12Communicator6assignERKi+0x44)[0x7f4eecdc28b8] [usbosnavdev-ludwig:09698] [ 3] /home/tobias/libMesh/libmesh-0.9.4/.libs/libmesh_dbg.so.0(_ZN7libMesh8Parallel12CommunicatoraSERKi+0x2f)[0x7f4eecdc286d] [usbosnavdev-ludwig:09698] [ 4] /home/tobias/libMesh/libmesh-0.9.4/.libs/libmesh_dbg.so.0(_ZN7libMesh11LibMeshInitC2EiPKPKci+0x4f4)[0x7f4eecdc05ae] [usbosnavdev-ludwig:09698] [ 5] /home/tobias/libMesh/libmesh-0.9.4/examples/introduction/introduction_ex1/.libs/example-dbg[0x40f447] [usbosnavdev-ludwig:09698] [ 6] /lib64/libc.so.6(__libc_start_main+0xf5)[0x7f4ee85d4af5] [usbosnavdev-ludwig:09698] [ 7] /home/tobias/libMesh/libmesh-0.9.4/examples/introduction/introduction_ex1/.libs/example-dbg[0x40f249] [usbosnavdev-ludwig:09698] *** End of error message *** /home/tobias/libMesh/libmesh-0.9.4/examples/run_common.sh: line 50: 9698 Segmentation fault $LIBMESH_RUN ./$executable $options $LIBMESH_OPTIONS FAIL: run.sh ==================================================== 1 of 1 test failed Please report to libmesh-users@lists.sourceforge.net ==================================================== make[3]: *** [check-TESTS] Error 1 make[3]: Leaving directory `/home/tobias/libMesh/libmesh-0.9.4/examples/introduction/introduction_ex1' make[2]: *** [check-am] Error 2 make[2]: Leaving directory `/home/tobias/libMesh/libmesh-0.9.4/examples/introduction/introduction_ex1' make[1]: *** [check-recursive] Error 1 make[1]: Leaving directory `/home/tobias/libMesh/libmesh-0.9.4/examples' make: *** [check-recursive] Error 1 tobias@usbosnavdev-ludwig ~/libMesh/libmesh-0.9.4 $ This is how I configure libMesh: ./configure PETSC_ARCH=arch-linux2-c-debug PETSC_DIR=/home/tobias/PETSc/petsc-3.6.2 --enable-everything --enable-petsc --enable-mpi ------------------------------ *Von:* tschroeder *Gesendet:* Dienstag, 3. November 2015 16:59 *An:* John Peterson *Betreff:* Re: [Libmesh-users] Neumann boundary problem for Laplace equation Perfect, Thank you Am 03.11.2015 um 16:41 schrieb John Peterson <jwpeter...@gmail.com>: On Tue, Nov 3, 2015 at 2:23 PM, tschroeder <tschroe...@daad-alumni.de> wrote: > This is what happens: > > > CXX src/geom/libmesh_dbg_la-face_quad9.lo > CXX src/geom/libmesh_dbg_la-face_tri.lo > src/geom/elem_cutter.C: In constructor 'libMesh::ElemCutter::ElemCutter()': > src/geom/elem_cutter.C:43:49: error: 'MPI_COMM_SELF' was not declared in > this scope > _comm_self.reset (new Parallel::Communicator (MPI_COMM_SELF)); > ^ > make[1]: *** [src/geom/libmesh_dbg_la-elem_cutter.lo] Error 1 > make[1]: *** Waiting for unfinished jobs.... > make[1]: Leaving directory `/home/tobias/libMesh/libmesh-0.9.4' > make: *** [all-recursive] Error 1 > Ah, looks like an issue with the --disable-mpi code path, which as you can imagine doesn't get tested very often. Installing MPI/PETSc will "fix" the problem, but I'll open an issue to make sure the library builds in this configuration before the next release. -- John ------------------------------------------------------------------------------ _______________________________________________ Libmesh-users mailing list Libmesh-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/libmesh-users
