Package: libdeal.ii
Version: 6.2.1
Libdeal.ii library files like /usr/lib/libdeal_II_2d.so are dynamically
linked to non-existing version of Trilinos: libtrilinos_*.so.1 (for example
libtrilinos_stratimikosamesos.so.1). Therefore building any of the example
programs in package deal.ii-examples fails because of mismatch in Trilinos
version. I think libdeal.ii library files should be dynamically linked
against libtrilinos_*.so
If we make symbolic links from libtrilinos_*.so.1 to libtrilinos_*.so.10.0.4
then these example programs builds succeed but running programs results in
Segmentation Fault. Segfault happens at the end of each example program,
after last line of code has been executed.
There are 2 more library versions mismatch: libamd and libumfpack.
Expected behavior would be that example programs build and execute without
errors.
This is 8 processor machine with Intel(R) Xeon(R) CPU E5310 @
1.60GHz
m...@s2:/tmp/deal.ii-examples/step-1$ uname -a
Linux s2 2.6.26-1-amd64 #1 SMP Fri Mar 13 17:46:45 UTC 2009 x86_64 GNU/Linux
m...@s2:/tmp/deal.ii-examples1/step-2$ ls -l /lib/libc.so.6
lrwxrwxrwx 1 root root 11 Jan 29 22:14 /lib/libc.so.6 -> libc-2.7.so
s2:/usr/share/doc> cp -r deal.ii-examples/ /tmp/
s2:/tmp/deal.ii-examples/step-1> make
Makefile:151: Makefile.dep: No such file or directory
============================ Remaking Makefile.dep
==============optimized===== step-1.cc
============================ Linking step-1
/usr/bin/ld: warning: libtrilinos_stratimikosamesos.so.1, needed by
/usr/lib/libdeal_II_2d.so, not found (try using -rpath or -rpath-link)
/usr/bin/ld: warning: libtrilinos_stratimikosaztecoo.so.1, needed by
/usr/lib/libdeal_II_2d.so, not found (try using -rpath or -rpath-link)
/usr/bin/ld: warning: libtrilinos_stratimikosifpack.so.1, needed by
/usr/lib/libdeal_II_2d.so, not found (try using -rpath or -rpath-link)
/usr/bin/ld: warning: libtrilinos_stratimikosml.so.1, needed by
/usr/lib/libdeal_II_2d.so, not found (try using -rpath or -rpath-link)
/usr/bin/ld: warning: libtrilinos_stratimikos.so.1, needed by
/usr/lib/libdeal_II_2d.so, not found (try using -rpath or -rpath-link)
/usr/bin/ld: warning: libtrilinos_ml.so.1, needed by
/usr/lib/libdeal_II_2d.so, not found (try using -rpath or -rpath-link)
/usr/bin/ld: warning: libtrilinos_amesos.so.1, needed by
/usr/lib/libdeal_II_2d.so, not found (try using -rpath or -rpath-link)
/usr/bin/ld: warning: libtrilinos_aztecoo.so.1, needed by
/usr/lib/libdeal_II_2d.so, not found (try using -rpath or -rpath-link)
/usr/bin/ld: warning: libtrilinos_belos.so.1, needed by
/usr/lib/libdeal_II_2d.so, not found (try using -rpath or -rpath-link)
/usr/bin/ld: warning: libtrilinos_ifpack.so.1, needed by
/usr/lib/libdeal_II_2d.so, not found (try using -rpath or -rpath-link)
/usr/bin/ld: warning: libtrilinos_rtop.so.1, needed by
/usr/lib/libdeal_II_2d.so, not found (try using -rpath or -rpath-link)
/usr/bin/ld: warning: libtrilinos_sacado.so.1, needed by
/usr/lib/libdeal_II_2d.so, not found (try using -rpath or -rpath-link)
/usr/bin/ld: warning: libtrilinos_thyra.so.1, needed by
/usr/lib/libdeal_II_2d.so, not found (try using -rpath or -rpath-link)
/usr/bin/ld: warning: libtrilinos_thyraepetra.so.1, needed by
/usr/lib/libdeal_II_2d.so, not found (try using -rpath or -rpath-link)
/usr/bin/ld: warning: libtrilinos_thyraepetraext.so.1, needed by
/usr/lib/libdeal_II_2d.so, not found (try using -rpath or -rpath-link)
/usr/bin/ld: warning: libtrilinos_epetraext.so.1, needed by
/usr/lib/libdeal_II_2d.so, not found (try using -rpath or -rpath-link)
/usr/bin/ld: warning: libtrilinos_epetra.so.1, needed by
/usr/lib/libdeal_II_2d.so, not found (try using -rpath or -rpath-link)
/usr/bin/ld: warning: libtrilinos_teuchos.so.1, needed by
/usr/lib/libdeal_II_2d.so, not found (try using -rpath or -rpath-link)
/usr/bin/ld: warning: libtrilinos_triutils.so.1, needed by
/usr/lib/libdeal_II_2d.so, not found (try using -rpath or -rpath-link)
/usr/bin/ld: warning: libumfpack.so.5.4.0, needed by
/usr/lib/slepc/linux-gnu-c-opt/lib/libslepc.so, may conflict with
libumfpack.so.3.1.0
/usr/bin/ld: warning: libamd.so.2.2.0, needed by
/usr/lib/slepc/linux-gnu-c-opt/lib/libslepc.so, may conflict with
libamd.so.3.1.0
s2:/usr/lib> ls libtrili*
libtrilinos_amesos.so libtrilinos_komplex.so.10.0.4
libtrilinos_rythmos.so.10.0
libtrilinos_amesos.so.10.0 libtrilinos_locaepetra.so
libtrilinos_rythmos.so.10.0.4
libtrilinos_amesos.so.10.0.4 libtrilinos_locaepetra.so.10.0
libtrilinos_sacado.so
libtrilinos_anasaziepetra.so
libtrilinos_locaepetra.so.10.0.4 libtrilinos_sacado.so.10.0
libtrilinos_anasaziepetra.so.10.0 libtrilinos_loca.so
libtrilinos_sacado.so.10.0.4
libtrilinos_anasaziepetra.so.10.0.4 libtrilinos_loca.so.10.0
libtrilinos_shards.so
libtrilinos_anasazi.so libtrilinos_loca.so.10.0.4
libtrilinos_shards.so.10.0
libtrilinos_anasazi.so.10.0 libtrilinos_locathyra.so
libtrilinos_shards.so.10.0.4
libtrilinos_anasazi.so.10.0.4 libtrilinos_locathyra.so.10.0
libtrilinos_stratimikosamesos.so
libtrilinos_aztecoo.so libtrilinos_locathyra.so.10.0.4
libtrilinos_stratimikosamesos.so.10.0
libtrilinos_aztecoo.so.10.0 libtrilinos_meros.so
libtrilinos_stratimikosamesos.so.10.0.4
libtrilinos_aztecoo.so.10.0.4 libtrilinos_meros.so.10.0
libtrilinos_stratimikosaztecoo.so
libtrilinos_belosepetra.so libtrilinos_meros.so.10.0.4
libtrilinos_stratimikosaztecoo.so.10.0
libtrilinos_belosepetra.so.10.0 libtrilinos_ml.so
libtrilinos_stratimikosaztecoo.so.10.0.4
libtrilinos_belosepetra.so.10.0.4 libtrilinos_ml.so.10.0
libtrilinos_stratimikosbelos.so
libtrilinos_belos.so libtrilinos_ml.so.10.0.4
libtrilinos_stratimikosbelos.so.10.0
libtrilinos_belos.so.10.0 libtrilinos_ModeLaplace.so
libtrilinos_stratimikosbelos.so.10.0.4
libtrilinos_belos.so.10.0.4 libtrilinos_ModeLaplace.so.10.0
libtrilinos_stratimikosifpack.so
libtrilinos_dpliris.so
libtrilinos_ModeLaplace.so.10.0.4
libtrilinos_stratimikosifpack.so.10.0
libtrilinos_dpliris.so.10.0 libtrilinos_moertel.so
libtrilinos_stratimikosifpack.so.10.0.4
libtrilinos_dpliris.so.10.0.4 libtrilinos_moertel.so.10.0
libtrilinos_stratimikosml.so
libtrilinos_epetraext.so libtrilinos_moertel.so.10.0.4
libtrilinos_stratimikosml.so.10.0
libtrilinos_epetraext.so.10.0 libtrilinos_moocho.so
libtrilinos_stratimikosml.so.10.0.4
libtrilinos_epetraext.so.10.0.4 libtrilinos_moocho.so.10.0
libtrilinos_stratimikos.so
libtrilinos_epetra.so libtrilinos_moocho.so.10.0.4
libtrilinos_stratimikos.so.10.0
libtrilinos_epetra.so.10.0 libtrilinos_moochothyra.so
libtrilinos_stratimikos.so.10.0.4
libtrilinos_epetra.so.10.0.4 libtrilinos_moochothyra.so.10.0
libtrilinos_sundanceCore.so
libtrilinos_FEApp.so
libtrilinos_moochothyra.so.10.0.4
libtrilinos_sundanceCore.so.10.0
libtrilinos_FEApp.so.10.0 libtrilinos_noxepetra.so
libtrilinos_sundanceCore.so.10.0.4
libtrilinos_FEApp.so.10.0.4 libtrilinos_noxepetra.so.10.0
libtrilinos_sundanceInterop.so
libtrilinos_fei_base.so libtrilinos_noxepetra.so.10.0.4
libtrilinos_sundanceInterop.so.10.0
libtrilinos_fei_base.so.10.0 libtrilinos_nox.so
libtrilinos_sundanceInterop.so.10.0.4
libtrilinos_fei_base.so.10.0.4 libtrilinos_nox.so.10.0
libtrilinos_sundanceStdFwk.so
libtrilinos_fei_test_utils.so libtrilinos_nox.so.10.0.4
libtrilinos_sundanceStdFwk.so.10.0
libtrilinos_fei_test_utils.so.10.0 libtrilinos_noxthyra.so
libtrilinos_sundanceStdFwk.so.10.0.4
libtrilinos_fei_test_utils.so.10.0.4 libtrilinos_noxthyra.so.10.0
libtrilinos_sundanceStdMesh.so
libtrilinos_fei_trilinos.so libtrilinos_noxthyra.so.10.0.4
libtrilinos_sundanceStdMesh.so.10.0
libtrilinos_fei_trilinos.so.10.0 libtrilinos_pamgen_extras.so
libtrilinos_sundanceStdMesh.so.10.0.4
libtrilinos_fei_trilinos.so.10.0.4
libtrilinos_pamgen_extras.so.10.0 libtrilinos_sundanceUtils.so
libtrilinos_fei_utest_cases.so
libtrilinos_pamgen_extras.so.10.0.4
libtrilinos_sundanceUtils.so.10.0
libtrilinos_fei_utest_cases.so.10.0 libtrilinos_pamgen.so
libtrilinos_sundanceUtils.so.10.0.4
libtrilinos_fei_utest_cases.so.10.0.4 libtrilinos_pamgen.so.10.0
libtrilinos_teuchos.so
libtrilinos_galeri.so libtrilinos_pamgen.so.10.0.4
libtrilinos_teuchos.so.10.0
libtrilinos_galeri.so.10.0 libtrilinos_phdelement_mesh.so
libtrilinos_teuchos.so.10.0.4
libtrilinos_galeri.so.10.0.4
libtrilinos_phdelement_mesh.so.10.0 libtrilinos_thyraepetraext.so
libtrilinos_ifpack.so
libtrilinos_phdelement_mesh.so.10.0.4
libtrilinos_thyraepetraext.so.10.0
libtrilinos_ifpack.so.10.0 libtrilinos_phdmesh_meshio.so
libtrilinos_thyraepetraext.so.10.0.4
libtrilinos_ifpack.so.10.0.4
libtrilinos_phdmesh_meshio.so.10.0 libtrilinos_thyraepetra.so
libtrilinos_intrepid.so
libtrilinos_phdmesh_meshio.so.10.0.4 libtrilinos_thyraepetra.so.10.0
libtrilinos_intrepid.so.10.0 libtrilinos_phdmesh_mesh.so
libtrilinos_thyraepetra.so.10.0.4
libtrilinos_intrepid.so.10.0.4
libtrilinos_phdmesh_mesh.so.10.0 libtrilinos_thyra.so
libtrilinos_isorropia.so
libtrilinos_phdmesh_mesh.so.10.0.4 libtrilinos_thyra.so.10.0
libtrilinos_isorropia.so.10.0 libtrilinos_phdmesh_txblas.so
libtrilinos_thyra.so.10.0.4
libtrilinos_isorropia.so.10.0.4
libtrilinos_phdmesh_txblas.so.10.0 libtrilinos_tpetra.so
libtrilinos_kokkoslinalg.so
libtrilinos_phdmesh_txblas.so.10.0.4 libtrilinos_tpetra.so.10.0
libtrilinos_kokkoslinalg.so.10.0 libtrilinos_phdmesh_util.so
libtrilinos_tpetra.so.10.0.4
libtrilinos_kokkoslinalg.so.10.0.4
libtrilinos_phdmesh_util.so.10.0 libtrilinos_triutils.so
libtrilinos_kokkosnodeapi.so
libtrilinos_phdmesh_util.so.10.0.4 libtrilinos_triutils.so.10.0
libtrilinos_kokkosnodeapi.so.10.0 libtrilinos_pytrilinos.so
libtrilinos_triutils.so.10.0.4
libtrilinos_kokkosnodeapi.so.10.0.4 libtrilinos_pytrilinos.so.10.0
libtrilinos_TSFExtended.so
libtrilinos_kokkos.so
libtrilinos_pytrilinos.so.10.0.4 libtrilinos_TSFExtended.so.10.0
libtrilinos_kokkos.so.10.0 libtrilinos_rtop.so
libtrilinos_TSFExtended.so.10.0.4
libtrilinos_kokkos.so.10.0.4 libtrilinos_rtop.so.10.0
libtrilinos_zoltan.so
libtrilinos_komplex.so libtrilinos_rtop.so.10.0.4
libtrilinos_zoltan.so.10.0
libtrilinos_komplex.so.10.0 libtrilinos_rythmos.so
libtrilinos_zoltan.so.10.0.4
After we make symbolic link from libtrilinos_*.so.1 -> libtrilinos_*.so the
following happens:
m...@s2:/tmp/deal.ii-examples1/step-2$ make
Makefile:151: Makefile.dep: No such file or directory
============================ Remaking Makefile.dep
==============optimized===== step-2.cc
============================ Linking step-2
/home/m/mate/bin/ld: warning: libumfpack.so.5.4.0, needed by
/usr/lib/slepc/linu
x-gnu-c-opt/lib/libslepc.so, may conflict with libumfpack.so.3.1.0
/home/m/mate/bin/ld: warning: libamd.so.2.2.0, needed by
/usr/lib/slepc/linux-gn
u-c-opt/lib/libslepc.so, may conflict with libamd.so.3.1.0
m...@s2:/tmp/deal.ii-examples1/step-2$ ./step-2
Segmentacijska greška
