Your message dated Fri, 15 Jul 2016 03:55:43 -0500 with message-id <[email protected]> and subject line probable mismatch in dynamically linked Trilinos library has caused the Debian Bug report #575010, regarding probable mismatch in dynamically linked Trilinos library to be marked as done.
This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact [email protected] immediately.) -- 575010: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=575010 Debian Bug Tracking System Contact [email protected] with problems
--- Begin Message ---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 mate@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 mate@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: mate@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 mate@s2:/tmp/deal.ii-examples1/step-2$ ./step-2 Segmentacijska greška
--- End Message ---
--- Begin Message ---Version: 8.1.0-1 This problem was resolved a long time ago. The current versions currently do not link against trilinos.
--- End Message ---
