On 2014-05-16 09:27, Johannes Ring wrote:
On Wed, May 14, 2014 at 12:05 PM, Imran Ali
<[email protected]> wrote:
14. mai 2014 kl. 08:03 skrev Johannes Ring <[email protected]>:
On Tue, May 13, 2014 at 4:36 PM, Imran Ali
<[email protected]> wrote:
I have tried to run both the cpp and python documented poisson
demo, but I get the same error.
Work/FEniCS/lib/libdolfin.so: Undefined reference to
’SCOTCH_randomReset’
This should be defined in libscotch.a:
$ nm Work/FEniCS/lib/libscotch.a | grep SCOTCH_randomReset
0000000000000000 T SCOTCH_randomReset
U SCOTCH_randomReset
I get a slightly different output then you :
0000000000000010 T SCOTCH_randomReset
U SCOTCH_randomReset
Notice the 1 and the second last digit.
Does it link to libscotch.a when you build the C++ demo? Try "make
VERBOSE=1" to see which libraries it links to.
I ran make with VERBOSE = 1 and got the following output :
$ make VERBOSE=1
/mn/anatu/studenter-u1/imranal/Work/FEniCS/bin/cmake
-H/mn/anatu/studenter-u1/imranal/Work/FEniCS/src/dolfin-1.3.0/demo/documented/poisson/cpp
-B/mn/anatu/studenter-u1/imranal/Work/FEniCS/src/dolfin-1.3.0/demo/documented/poisson/cpp
--check-build-system CMakeFiles/Makefile.cmake 0
/mn/anatu/studenter-u1/imranal/Work/FEniCS/bin/cmake -E
cmake_progress_start
/mn/anatu/studenter-u1/imranal/Work/FEniCS/src/dolfin-1.3.0/demo/documented/poisson/cpp/CMakeFiles
/mn/anatu/studenter-u1/imranal/Work/FEniCS/src/dolfin-1.3.0/demo/documented/poisson/cpp/CMakeFiles/progress.marks
make -f CMakeFiles/Makefile2 all
make[1]: Entering directory
`/mn/anatu/studenter-u1/imranal/Work/FEniCS/src/dolfin-1.3.0/demo/documented/poisson/cpp'
make -f CMakeFiles/demo_poisson.dir/build.make
CMakeFiles/demo_poisson.dir/depend
make[2]: Entering directory
`/mn/anatu/studenter-u1/imranal/Work/FEniCS/src/dolfin-1.3.0/demo/documented/poisson/cpp'
cd
/mn/anatu/studenter-u1/imranal/Work/FEniCS/src/dolfin-1.3.0/demo/documented/poisson/cpp
&& /mn/anatu/studenter-u1/imranal/Work/FEniCS/bin/cmake -E
cmake_depends "Unix Makefiles"
/mn/anatu/studenter-u1/imranal/Work/FEniCS/src/dolfin-1.3.0/demo/documented/poisson/cpp
/mn/anatu/studenter-u1/imranal/Work/FEniCS/src/dolfin-1.3.0/demo/documented/poisson/cpp
/mn/anatu/studenter-u1/imranal/Work/FEniCS/src/dolfin-1.3.0/demo/documented/poisson/cpp
/mn/anatu/studenter-u1/imranal/Work/FEniCS/src/dolfin-1.3.0/demo/documented/poisson/cpp
/mn/anatu/studenter-u1/imranal/Work/FEniCS/src/dolfin-1.3.0/demo/documented/poisson/cpp/CMakeFiles/demo_poisson.dir/DependInfo.cmake
--color=
make[2]: Leaving directory
`/mn/anatu/studenter-u1/imranal/Work/FEniCS/src/dolfin-1.3.0/demo/documented/poisson/cpp'
make -f CMakeFiles/demo_poisson.dir/build.make
CMakeFiles/demo_poisson.dir/build
make[2]: Entering directory
`/mn/anatu/studenter-u1/imranal/Work/FEniCS/src/dolfin-1.3.0/demo/documented/poisson/cpp'
Linking CXX executable demo_poisson
/mn/anatu/studenter-u1/imranal/Work/FEniCS/bin/cmake -E
cmake_link_script CMakeFiles/demo_poisson.dir/link.txt --verbose=1
/usr/bin/c++ -O2 -g -DNDEBUG
CMakeFiles/demo_poisson.dir/main.cpp.o -o demo_poisson -rdynamic
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/libdolfin.so -lxml2
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/libboost_filesystem.so
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/libboost_program_options.so
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/libboost_system.so
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/libboost_thread.so
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/libboost_iostreams.so
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/libboost_mpi.so
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/libboost_serialization.so
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/libboost_timer.so
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/libboost_chrono.so
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/libhdf5.so -lz -lm
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/libslepc.so
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/libpetsc.so
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/libumfpack.a
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/libamd.a
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/libblas.a -lgfortran
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/libptscotch.a
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/libptesmumps.a
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/libptscotcherr.a
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/libparmetis.so
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/libmetis.so
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/libCGAL.so
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/libboost_thread.so
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/libboost_system.so
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/libgmp.so
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/libmpfr.so -lz
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/libmpi_cxx.so
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/libmpi.so -lQtGui
-lQtCore
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/vtk-5.8/libvtkCommon.so
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/vtk-5.8/libvtkFiltering.so
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/vtk-5.8/libvtkImaging.so
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/vtk-5.8/libvtkGraphics.so
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/vtk-5.8/libvtkGenericFiltering.so
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/vtk-5.8/libvtkIO.so
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/vtk-5.8/libvtkRendering.so
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/vtk-5.8/libvtkVolumeRendering.so
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/vtk-5.8/libvtkHybrid.so
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/vtk-5.8/libvtkWidgets.so
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/vtk-5.8/libvtkInfovis.so
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/vtk-5.8/libvtkGeovis.so
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/vtk-5.8/libvtkViews.so
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/vtk-5.8/libvtkCharts.so
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/libboost_system.so
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/libboost_thread.so
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/libboost_iostreams.so
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/libboost_mpi.so
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/libboost_serialization.so
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/libboost_timer.so
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/libboost_chrono.so
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/libhdf5.so -lm
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/libslepc.so
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/libpetsc.so
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/libumfpack.a
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/libamd.a
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/libblas.a -lgfortran
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/libptscotch.a
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/libptesmumps.a
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/libptscotcherr.a
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/libparmetis.so
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/libmetis.so
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/libCGAL.so
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/libgmp.so
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/libmpfr.so
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/libmpi_cxx.so
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/libmpi.so -lQtGui
-lQtCore
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/vtk-5.8/libvtkCommon.so
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/vtk-5.8/libvtkFiltering.so
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/vtk-5.8/libvtkImaging.so
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/vtk-5.8/libvtkGraphics.so
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/vtk-5.8/libvtkGenericFiltering.so
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/vtk-5.8/libvtkIO.so
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/vtk-5.8/libvtkRendering.so
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/vtk-5.8/libvtkVolumeRendering.so
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/vtk-5.8/libvtkHybrid.so
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/vtk-5.8/libvtkWidgets.so
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/vtk-5.8/libvtkInfovis.so
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/vtk-5.8/libvtkGeovis.so
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/vtk-5.8/libvtkViews.so
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/vtk-5.8/libvtkCharts.so
-Wl,-rpath,/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib:/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/vtk-5.8
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/libdolfin.so:
undefined reference to `SCOTCH_randomReset'
collect2: ld returned 1 exit status
make[2]: *** [demo_poisson] Error 1
make[2]: Leaving directory
`/mn/anatu/studenter-u1/imranal/Work/FEniCS/src/dolfin-1.3.0/demo/documented/poisson/cpp'
make[1]: *** [CMakeFiles/demo_poisson.dir/all] Error 2
make[1]: Leaving directory
`/mn/anatu/studenter-u1/imranal/Work/FEniCS/src/dolfin-1.3.0/demo/documented/poisson/cpp'
make: *** [all] Error 2
The problem is that libdolfin.so is not linked to libscotch.a. Turning
off DOLFIN_SKIP_BUILD_TESTS will fix this problem.
I turned off DOLFIN_SKIP_BUILD_TESTS, however I got the following error
then during the build :
-- Found petscconf.h
gmake: Warning: File
`/mn/anatu/studenter-u1/imranal/Work/FEniCS/src/dolfin-1.3.0/dorsal_build_dir/Makefile.petsc'
ha
s modification time 0.0025 s in the future
gmake: warning: Clock skew detected. Your build may be incomplete.
Here is the whole build message :
patching file demo/undocumented/plot-qt/cpp/CMakeLists.txt
patching file dolfin/CMakeLists.txt
-- The C compiler identification is GNU 4.4.7
-- The CXX compiler identification is GNU 4.4.7
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
fatal: Not a git repository (or any parent up to mount point
/mn/anatu/studenter-u1)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not
set).
-- Performing Test HAVE_PIPE
-- Performing Test HAVE_PIPE - Success
-- Performing Test HAVE_PEDANTIC
-- Performing Test HAVE_PEDANTIC - Success
-- Performing Test HAVE_STD
-- Performing Test HAVE_STD - Success
-- Performing Test HAVE_DEBUG
-- Performing Test HAVE_DEBUG - Success
-- Performing Test HAVE_O2_OPTIMISATION
-- Performing Test HAVE_O2_OPTIMISATION - Success
-- The Fortran compiler identification is GNU
-- Check for working Fortran compiler: /usr/bin/gfortran
-- Check for working Fortran compiler: /usr/bin/gfortran -- works
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Checking whether /usr/bin/gfortran supports Fortran 90
-- Checking whether /usr/bin/gfortran supports Fortran 90 -- yes
-- Found MPI_C:
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/libmpi.so
-- Found MPI_CXX:
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/libmpi_cxx.so;/mn/anatu/studenter-u1/imranal/Work/FE
niCS/lib/libmpi.so
-- Found MPI_Fortran:
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/libmpi_usempi.so;/mn/anatu/studenter-u1/imranal/
Work/FEniCS/lib/libmpi_mpifh.so;/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/libmpi.so
-- Try OpenMP C flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Try OpenMP CXX flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Found OpenMP: -fopenmp
-- Performing Test OPENMP_UINT_TEST_RUNS
-- Performing Test OPENMP_UINT_TEST_RUNS - Success
-- Boost version: 1.55.0
-- Found the following Boost libraries:
-- filesystem
-- program_options
-- system
-- thread
-- iostreams
-- mpi
-- serialization
-- timer
-- chrono
-- UFC version: 2.3.0
-- Found Eigen3:
/mn/anatu/studenter-u1/imranal/Work/FEniCS/include/eigen3 (Required is
at least version "3.0.0")
-- Found LibXml2: /usr/lib64/libxml2.so (found version "2.7.6")
-- Found PythonInterp:
/mn/anatu/studenter-u1/imranal/Work/FEniCS/bin/python (found suitable
version "2.7.6", minimum
required is "2")
-- NumPy header version 1.8.1 found
-- Found SWIG: /mn/anatu/studenter-u1/imranal/Work/FEniCS/bin/swig
(found version "2.0.8")
-- Checking for package 'PETSc'
-- PETSC_DIR is /mn/anatu/studenter-u1/imranal/Work/FEniCS
-- PETSC_ARCH is empty
-- Found petscconf.h
gmake: Warning: File
`/mn/anatu/studenter-u1/imranal/Work/FEniCS/src/dolfin-1.3.0/dorsal_build_dir/Makefile.petsc'
ha
s modification time 0.0025 s in the future
gmake: warning: Clock skew detected. Your build may be incomplete.
Johannes
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