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Error with MED module

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  • Error with MED module

    Posted by Erwann at January 16. 2007
    Hello,

    Thank you Vadim and Erwan.

    I compiled KERNEL, GUI and GEOM modules.
       Notes for GEOM:
           SALOME_GenericObj.hh is missing in /salome3.2.2_SRC/GEOM_BUILD/src/GEOM_I
           SALOME_Component.hh  is missing in /salome3.2.2_SRC/GEOM_BUILD/src/GEOMBase
       Notes for VTK (4.4.2):
           options with cmake -i before doing 'make':
                 BUILD_SHARED_LIBS=ON
                 CMAKE_BACKWARDS_COMPATIBILITY=2.2
                 VTK_USE_HYBRID=ON
                 VTK_WRAP_PYTHON=ON
                 VTK_WRAP_TCL=ON

    But in MED module some problems occurs.
    I use med2-2.3 built from sources.
    Everything is ok after './configure'
    The compilation failed in sub-directory /salome3.2.2_SRC/MED_BUILD/src/MEDMEM
    :
    :
    (cd . && ln -s MEDMEM_TopLevel.lo MEDMEM_TopLevel.o)
    (cd . && ln -s MEDMEM_MEDMEMgaussEcr.lo MEDMEM_MEDMEMgaussEcr.o)
    (cd . && ln -s MEDMEM_MEDMEMprofilEcr.lo MEDMEM_MEDMEMprofilEcr.o)
    (cd . && ln -s MEDMEM_MEDMEMchampLire.lo MEDMEM_MEDMEMchampLire.o)
    /opt/GCC/bin/gcc -shared  MEDMEM_Init.lo MEDMEM_CellModel.lo MEDMEM_Connectivity.lo MEDMEM_Coordinate.lo MEDMEM_DriversDef.lo MEDMEM_DriverFactory.lo MEDMEM_Family.lo MEDMEM_Field.lo MEDMEM_GenDriver.lo MEDMEM_Group.lo MEDMEM_Med.lo MEDMEM_Exception.lo MEDMEM_MedMedDriver.lo MEDMEM_MedMeshDriver.lo MEDMEM_GibiMeshDriver.lo MEDMEM_PorflowMeshDriver.lo MEDMEM_DriverTools.lo MEDMEM_SkyLineArray.lo MEDMEM_Mesh.lo MEDMEM_Meshing.lo MEDMEM_Support.lo MEDMEM_Unit.lo MEDMEM_VtkMedDriver.lo MEDMEM_VtkMeshDriver.lo MEDMEM_Grid.lo MEDMEM_MedVersion.lo MEDMEM_MedMeshDriver21.lo MEDMEM_MedMedDriver21.lo MEDMEM_medimport_src.lo MEDMEM_PolyhedronArray.lo MEDMEM_MedMedDriver22.lo MEDMEM_MedMeshDriver22.lo MEDMEM_TopLevel.lo MEDMEM_MEDMEMgaussEcr.lo MEDMEM_MEDMEMprofilEcr.lo MEDMEM_MEDMEMchampLire.lo  -L../../lib/salome -lstdc++ -L/usr/local/MED/2.2.3/lib -lmed -L/usr/local/Code_Aster/9.0/public/hdf5-1.6.4/lib -lhdf5 -lhdf5 -lmed_V2_1 -L/usr/local/Salome/3.2.2/KERNEL_install/lib/salome -lSALOMELocalTrace -lc  -Wl,-soname -Wl,libmedmem.so.0 -o .libs/libmedmem.so.0.0.0
    `.L17219' referenced in section `.rodata' of MEDMEM_Mesh.lo: defined in discarded section `.gnu.linkonce.t._ZNK6MEDMEM18ASCII_FIELD_DRIVERIdE5writeEv' of MEDMEM_Mesh.lo
    `.L17220' referenced in section `.rodata' of MEDMEM_Mesh.lo: defined in discarded section `.gnu.linkonce.t._ZNK6MEDMEM18ASCII_FIELD_DRIVERIdE5writeEv' of MEDMEM_Mesh.lo
    `.L17217' referenced in section `.rodata' of MEDMEM_Mesh.lo: defined in discarded section `.gnu.linkonce.t._ZNK6MEDMEM18ASCII_FIELD_DRIVERIdE5writeEv' of MEDMEM_Mesh.lo
    `.L17218' referenced in section `.rodata' of MEDMEM_Mesh.lo: defined in discarded section `.gnu.linkonce.t._ZNK6MEDMEM18ASCII_FIELD_DRIVERIdE5writeEv' of MEDMEM_Mesh.lo
    `.L17215' referenced in section `.rodata' of MEDMEM_Mesh.lo: defined in discarded section `.gnu.linkonce.t._ZNK6MEDMEM18ASCII_FIELD_DRIVERIdE5writeEv' of MEDMEM_Mesh.lo
    `.L17216' referenced in section `.rodata' of MEDMEM_Mesh.lo: defined in discarded section `.gnu.linkonce.t._ZNK6MEDMEM18ASCII_FIELD_DRIVERIdE5writeEv' of MEDMEM_Mesh.lo
    `.L17214' referenced in section `.rodata' of MEDMEM_Mesh.lo: defined in discarded section `.gnu.linkonce.t._ZNK6MEDMEM18ASCII_FIELD_DRIVERIdE5writeEv' of MEDMEM_Mesh.lo
    `.L24664' referenced in section `.rodata' of MEDMEM_MedMedDriver21.lo: defined in discarded section `.gnu.linkonce.t._ZNK6MEDMEM18ASCII_FIELD_DRIVERIdE5writeEv' of MEDMEM_MedMedDriver21.lo
    :
    :
    collect2: ld returned 1 exit status
    make[3]: *** [libmedmem.la] Error 1
    make[3]: Leaving directory `/opt/Salome/salome3.2.2_SRC/MED_BUILD/src/MEDMEM'
    make[2]: *** [lib_MEDMEM] Error 2
    make[2]: Leaving directory `/opt/Salome/salome3.2.2_SRC/MED_BUILD/src'
    make[1]: *** [lib_src] Error 2
    make[1]: Leaving directory `/opt/Salome/salome3.2.2_SRC/MED_BUILD'
    make: *** [all] Error 2


    I can't find what's the error cause.
    Thank to anyone who can help me.
    • Re: Error with MED module

      Posted by Erwan ADAM at January 16. 2007
      Erwann wrote:
      Hello,

      Thank you Vadim and Erwan.

      I compiled KERNEL, GUI and GEOM modules.
         Notes for GEOM:
             SALOME_GenericObj.hh is missing in /salome3.2.2_SRC/GEOM_BUILD/src/GEOM_I
             SALOME_Component.hh  is missing in /salome3.2.2_SRC/GEOM_BUILD/src/GEOMBase
         Notes for VTK (4.4.2):
             options with cmake -i before doing 'make':
                   BUILD_SHARED_LIBS=ON
                   CMAKE_BACKWARDS_COMPATIBILITY=2.2
                   VTK_USE_HYBRID=ON
                   VTK_WRAP_PYTHON=ON
                   VTK_WRAP_TCL=ON

      But in MED module some problems occurs.
      I use med2-2.3 built from sources.
      Everything is ok after './configure'
      The compilation failed in sub-directory /salome3.2.2_SRC/MED_BUILD/src/MEDMEM
      :
      :
      (cd . && ln -s MEDMEM_TopLevel.lo MEDMEM_TopLevel.o)
      (cd . && ln -s MEDMEM_MEDMEMgaussEcr.lo MEDMEM_MEDMEMgaussEcr.o)
      (cd . && ln -s MEDMEM_MEDMEMprofilEcr.lo MEDMEM_MEDMEMprofilEcr.o)
      (cd . && ln -s MEDMEM_MEDMEMchampLire.lo MEDMEM_MEDMEMchampLire.o)
      /opt/GCC/bin/gcc -shared  MEDMEM_Init.lo MEDMEM_CellModel.lo MEDMEM_Connectivity.lo MEDMEM_Coordinate.lo MEDMEM_DriversDef.lo MEDMEM_DriverFactory.lo MEDMEM_Family.lo MEDMEM_Field.lo MEDMEM_GenDriver.lo MEDMEM_Group.lo MEDMEM_Med.lo MEDMEM_Exception.lo MEDMEM_MedMedDriver.lo MEDMEM_MedMeshDriver.lo MEDMEM_GibiMeshDriver.lo MEDMEM_PorflowMeshDriver.lo MEDMEM_DriverTools.lo MEDMEM_SkyLineArray.lo MEDMEM_Mesh.lo MEDMEM_Meshing.lo MEDMEM_Support.lo MEDMEM_Unit.lo MEDMEM_VtkMedDriver.lo MEDMEM_VtkMeshDriver.lo MEDMEM_Grid.lo MEDMEM_MedVersion.lo MEDMEM_MedMeshDriver21.lo MEDMEM_MedMedDriver21.lo MEDMEM_medimport_src.lo MEDMEM_PolyhedronArray.lo MEDMEM_MedMedDriver22.lo MEDMEM_MedMeshDriver22.lo MEDMEM_TopLevel.lo MEDMEM_MEDMEMgaussEcr.lo MEDMEM_MEDMEMprofilEcr.lo MEDMEM_MEDMEMchampLire.lo  -L../../lib/salome -lstdc++ -L/usr/local/MED/2.2.3/lib -lmed -L/usr/local/Code_Aster/9.0/public/hdf5-1.6.4/lib -lhdf5 -lhdf5 -lmed_V2_1 -L/usr/local/Salome/3.2.2/KERNEL_install/lib/salome -lSALOMELocalTrace -lc  -Wl,-soname -Wl,libmedmem.so.0 -o .libs/libmedmem.so.0.0.0
      `.L17219' referenced in section `.rodata' of MEDMEM_Mesh.lo: defined in discarded section `.gnu.linkonce.t._ZNK6MEDMEM18ASCII_FIELD_DRIVERIdE5writeEv' of MEDMEM_Mesh.lo
      `.L17220' referenced in section `.rodata' of MEDMEM_Mesh.lo: defined in discarded section `.gnu.linkonce.t._ZNK6MEDMEM18ASCII_FIELD_DRIVERIdE5writeEv' of MEDMEM_Mesh.lo
      `.L17217' referenced in section `.rodata' of MEDMEM_Mesh.lo: defined in discarded section `.gnu.linkonce.t._ZNK6MEDMEM18ASCII_FIELD_DRIVERIdE5writeEv' of MEDMEM_Mesh.lo
      `.L17218' referenced in section `.rodata' of MEDMEM_Mesh.lo: defined in discarded section `.gnu.linkonce.t._ZNK6MEDMEM18ASCII_FIELD_DRIVERIdE5writeEv' of MEDMEM_Mesh.lo
      `.L17215' referenced in section `.rodata' of MEDMEM_Mesh.lo: defined in discarded section `.gnu.linkonce.t._ZNK6MEDMEM18ASCII_FIELD_DRIVERIdE5writeEv' of MEDMEM_Mesh.lo
      `.L17216' referenced in section `.rodata' of MEDMEM_Mesh.lo: defined in discarded section `.gnu.linkonce.t._ZNK6MEDMEM18ASCII_FIELD_DRIVERIdE5writeEv' of MEDMEM_Mesh.lo
      `.L17214' referenced in section `.rodata' of MEDMEM_Mesh.lo: defined in discarded section `.gnu.linkonce.t._ZNK6MEDMEM18ASCII_FIELD_DRIVERIdE5writeEv' of MEDMEM_Mesh.lo
      `.L24664' referenced in section `.rodata' of MEDMEM_MedMedDriver21.lo: defined in discarded section `.gnu.linkonce.t._ZNK6MEDMEM18ASCII_FIELD_DRIVERIdE5writeEv' of MEDMEM_MedMedDriver21.lo
      :
      :
      collect2: ld returned 1 exit status
      make[3]: *** [libmedmem.la] Error 1
      make[3]: Leaving directory `/opt/Salome/salome3.2.2_SRC/MED_BUILD/src/MEDMEM'
      make[2]: *** [lib_MEDMEM] Error 2
      make[2]: Leaving directory `/opt/Salome/salome3.2.2_SRC/MED_BUILD/src'
      make[1]: *** [lib_src] Error 2
      make[1]: Leaving directory `/opt/Salome/salome3.2.2_SRC/MED_BUILD'
      make: *** [all] Error 2


      I can't find what's the error cause.
      Thank to anyone who can help me.


      Strange ... Have you tried a make clean, make in the MEDMEM
      directory ?

      Why don't you use the native gcc4.1 ??

      E.A.

      • Re: Error with MED module

        Posted by Erwann at January 16. 2007
        Hello Erwan,

        I just solved this problem: binutils are incompatibles with gcc-3.4.x / gcc-3.3.x
        I downgraded binutils-1.16.91 to binutils-1.16.1 and it works.
        Now I've compiled MED and SMESH modules (VISU still running)
        I'll soon send my configuration for OpenSuSE-10.1.

        Regards

        Note: I had several problems with gcc-4.1 at the beginning and I immediately switched to an older package.
        But may be it's compatible. I'll try later.
        • Re: Error with MED module

          Posted by Erwan ADAM at January 16. 2007
          Erwann wrote:
          Hello Erwan,

          I just solved this problem: binutils are incompatibles with gcc-3.4.x / gcc-3.3.x
          I downgraded binutils-1.16.91 to binutils-1.16.1 and it works.
          Now I've compiled MED and SMESH modules (VISU still running)
          I'll soon send my configuration for OpenSuSE-10.1.

          Regards

          Note: I had several problems with gcc-4.1 at the beginning and I immediately switched to an older package.
          But may be it's compatible. I'll try later.


          Indeed, there is no more problems with gcc-4.1 now but we have done some
          patches in cascade and salome ... and this version is not available on
          the web site for the moment.

          E.A.
          • Re: Error with MED module

            Posted by Erwann at January 16. 2007
            ADAM Erwan wrote:
            Erwann wrote:
            Hello Erwan,

            I just solved this problem: binutils are incompatibles with gcc-3.4.x / gcc-3.3.x
            I downgraded binutils-1.16.91 to binutils-1.16.1 and it works.
            Now I've compiled MED and SMESH modules (VISU still running)
            I'll soon send my configuration for OpenSuSE-10.1.

            Regards

            Note: I had several problems with gcc-4.1 at the beginning and I immediately switched to an older package.
            But may be it's compatible. I'll try later.


            Indeed, there is no more problems with gcc-4.1 now but we have done some
            patches in cascade and salome ... and this version is not available on
            the web site for the moment.

            E.A.


            Have you an idea about this error message in SUPERV_BUILD module ?

            /usr/include/python2.4/pyconfig.h:838:1: warning: "_POSIX_C_SOURCE" redefined
            In file included from /usr/include/stdlib.h:25,
                             from ../../../SUPERV_SRC_3.2.2/src/GraphExecutor/DataFlowExecutor_InNodeThreads.cxx:31:
            /usr/include/features.h:154:1: warning: this is the location of the previous definition
            ../../../SUPERV_SRC_3.2.2/src/GraphExecutor/DataFlowExecutor_InNodeThreads.cxx: In member function `int GraphExecutor::InNode::executeAction()':
            ../../../SUPERV_SRC_3.2.2/src/GraphExecutor/DataFlowExecutor_InNodeThreads.cxx:624: error: `PTHREAD_THREADS_MAX' was not declared in this scope
            ../../../SUPERV_SRC_3.2.2/src/GraphExecutor/DataFlowExecutor_InNodeThreads.cxx:624: warning: unused variable 'PTHREAD_THREADS_MAX'
            make[3]: *** [DataFlowExecutor_InNodeThreads.lo] Error 1
            make[3]: Leaving directory `/opt/Salome/salome3.2.2_SRC/SUPERV_BUILD/src/GraphExecutor'
            make[2]: *** [lib_GraphExecutor] Error 2
            make[2]: Leaving directory `/opt/Salome/salome3.2.2_SRC/SUPERV_BUILD/src'
            make[1]: *** [lib_src] Error 2
            make[1]: Leaving directory `/opt/Salome/salome3.2.2_SRC/SUPERV_BUILD'
            make: *** [all] Error 2

            • Re: Error with MED module

              Posted by Erwan ADAM at January 16. 2007
              Erwann wrote:
              ADAM Erwan wrote:
              Erwann wrote:
              Hello Erwan,

              I just solved this problem: binutils are incompatibles with gcc-3.4.x / gcc-3.3.x
              I downgraded binutils-1.16.91 to binutils-1.16.1 and it works.
              Now I've compiled MED and SMESH modules (VISU still running)
              I'll soon send my configuration for OpenSuSE-10.1.

              Regards

              Note: I had several problems with gcc-4.1 at the beginning and I immediately switched to an older package.
              But may be it's compatible. I'll try later.


              Indeed, there is no more problems with gcc-4.1 now but we have done some
              patches in cascade and salome ... and this version is not available on
              the web site for the moment.

              E.A.


              Have you an idea about this error message in SUPERV_BUILD module ?

              /usr/include/python2.4/pyconfig.h:838:1: warning: "_POSIX_C_SOURCE" redefined
              In file included from /usr/include/stdlib.h:25,
                               from ../../../SUPERV_SRC_3.2.2/src/GraphExecutor/DataFlowExecutor_InNodeThreads.cxx:31:
              /usr/include/features.h:154:1: warning: this is the location of the previous definition
              ../../../SUPERV_SRC_3.2.2/src/GraphExecutor/DataFlowExecutor_InNodeThreads.cxx: In member function `int GraphExecutor::InNode::executeAction()':
              ../../../SUPERV_SRC_3.2.2/src/GraphExecutor/DataFlowExecutor_InNodeThreads.cxx:624: error: `PTHREAD_THREADS_MAX' was not declared in this scope
              ../../../SUPERV_SRC_3.2.2/src/GraphExecutor/DataFlowExecutor_InNodeThreads.cxx:624: warning: unused variable 'PTHREAD_THREADS_MAX'
              make[3]: *** [DataFlowExecutor_InNodeThreads.lo] Error 1
              make[3]: Leaving directory `/opt/Salome/salome3.2.2_SRC/SUPERV_BUILD/src/GraphExecutor'
              make[2]: *** [lib_GraphExecutor] Error 2
              make[2]: Leaving directory `/opt/Salome/salome3.2.2_SRC/SUPERV_BUILD/src'
              make[1]: *** [lib_src] Error 2
              make[1]: Leaving directory `/opt/Salome/salome3.2.2_SRC/SUPERV_BUILD'
              make: *** [all] Error 2


              You have to comment the lines 623 and 624 of this file.
              An easy patch, uhh ? I assume that PTHREAD_THREADS_MAX is an
              obsolete variable ... Anyway, on cvs repository, those lines
              have been commented !

              E.A.


              • Re: Error with MED module

                Posted by Erwann at January 16. 2007
                ADAM Erwan wrote:
                Erwann wrote:
                ADAM Erwan wrote:
                Erwann wrote:
                Hello Erwan,

                I just solved this problem: binutils are incompatibles with gcc-3.4.x / gcc-3.3.x
                I downgraded binutils-1.16.91 to binutils-1.16.1 and it works.
                Now I've compiled MED and SMESH modules (VISU still running)
                I'll soon send my configuration for OpenSuSE-10.1.

                Regards

                Note: I had several problems with gcc-4.1 at the beginning and I immediately switched to an older package.
                But may be it's compatible. I'll try later.


                Indeed, there is no more problems with gcc-4.1 now but we have done some
                patches in cascade and salome ... and this version is not available on
                the web site for the moment.

                E.A.


                Have you an idea about this error message in SUPERV_BUILD module ?

                /usr/include/python2.4/pyconfig.h:838:1: warning: "_POSIX_C_SOURCE" redefined
                In file included from /usr/include/stdlib.h:25,
                                 from ../../../SUPERV_SRC_3.2.2/src/GraphExecutor/DataFlowExecutor_InNodeThreads.cxx:31:
                /usr/include/features.h:154:1: warning: this is the location of the previous definition
                ../../../SUPERV_SRC_3.2.2/src/GraphExecutor/DataFlowExecutor_InNodeThreads.cxx: In member function `int GraphExecutor::InNode::executeAction()':
                ../../../SUPERV_SRC_3.2.2/src/GraphExecutor/DataFlowExecutor_InNodeThreads.cxx:624: error: `PTHREAD_THREADS_MAX' was not declared in this scope
                ../../../SUPERV_SRC_3.2.2/src/GraphExecutor/DataFlowExecutor_InNodeThreads.cxx:624: warning: unused variable 'PTHREAD_THREADS_MAX'
                make[3]: *** [DataFlowExecutor_InNodeThreads.lo] Error 1
                make[3]: Leaving directory `/opt/Salome/salome3.2.2_SRC/SUPERV_BUILD/src/GraphExecutor'
                make[2]: *** [lib_GraphExecutor] Error 2
                make[2]: Leaving directory `/opt/Salome/salome3.2.2_SRC/SUPERV_BUILD/src'
                make[1]: *** [lib_src] Error 2
                make[1]: Leaving directory `/opt/Salome/salome3.2.2_SRC/SUPERV_BUILD'
                make: *** [all] Error 2


                You have to comment the lines 623 and 624 of this file.
                An easy patch, uhh ? I assume that PTHREAD_THREADS_MAX is an
                obsolete variable ... Anyway, on cvs repository, those lines
                have been commented !

                E.A.


                Thank you ! compilation go on.
                • Re: Error with MED module

                  Posted by Erwann at January 16. 2007
                  Configuration for OpenSuSE-10.1

                  #++++++++++++++++++++++++++++++++++++++++++++++++++
                  gcc              3.4.5        (compiled)
                  binutils         2.16.1       (compiled)

                  tcltk            8.4.12       (native)
                  Python           2.4.2        (native)
                  Qt & msg2qm      3.3.5        (native)
                  Sip              4.2.1        (native)
                  PyQt             3.5.1        (native)
                  Boost            1.33.1       (native)
                  Swig             1.3.27       (native)
                  Open CASCASDE    6.1          (compiled)
                  Qwt              4.2.0        (native)
                  OmniORB          4.0.7        (compiled)
                  Hdf              5-1.6.4      (compiled)
                  Med              2.2.3        (compiled)
                  Vtk              4.4.2        (compiled)
                  Numeric          24.2         (native)
                  Graphviz         2.6          (native)
                  Doxygen          1.4.6        (native)
                  NETGEN           4.5
                  docutils         0.3.7        (compiled)
                  #++++++++++++++++++++++++++++++++++++++++++++++++++

                  add in GUI_SRC_3.2.2/src/SALOME_PYQT/Makefile.i
                         GUI_SRC_3.2.2/src/SALOME_PYQT/SalomePyQt/Makefile.i
                         GUI_SRC_3.2.2/src/SALOME_PYQT/SALOME_PYQT_GUI
                               ifeq ($(QT_VERS),Qt_3_3_5)
                               QT_VERS = Qt_3_3_0
                               endif

                  add in salome3.2.2_SRC/GEOM_BUILD/src/GEOM_I             -> SALOME_GenericObj.hh
                         salome3.2.2_SRC/GEOM_BUILD/src/GEOMBase           -> SALOME_Component.hh

                  add in salome3.2.2_SRC/SMESH_BUILD/src/OBJECT            -> SALOME_Component.hh
                         salome3.2.2_SRC/SMESH_BUILD/src/StdMeshers_I      -> SALOME_Component.hh
                                                                           -> SALOME_GenericObj.hh
                                                                           -> SMESH_Mesh.hh

                  cd /usr/lib ; ln -s libboost_signals.so.1.33.1 libboost_signals-mt.so

                  in /bin add ln -s g77 f77

                  uncomment lines 623 and 624 in salome3.2.2_SRC/SUPERV_SRC_3.2.2/src/GraphExecutor/DataFlowExecutor_InNodeThreads.cxx

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