Re: [FEniCS-support] Dolfin crashes with Undefined reference to SCOTCH_randomReset

Sun, 18 May 2014 22:40:16 -0700 

On 2014-05-17 16:51, Imran Ali wrote:

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.
I was mistaken, the build hasn't crashed. It is stuck however. I looked at my jobs, and the build is still running, even though no progress is occuring :
imranal 9148 0.0 0.0 106424 1676 ? SN 11:10 0:00 bash ./dorsal.sh FEniCS/platforms/supported/rhel6.platform root 15856 0.0 0.1 113248 4100 ? Ss 16:45 0:00 sshd: imranal [priv] imranal 15878 0.0 0.0 113248 2152 ? S 16:45 0:00 sshd: imranal@pts/0 
imranal  15879  0.0  0.0 123560  2144 pts/0    Ss   16:45   0:00 -bash
imranal  17773  0.0  0.0 125356  1344 pts/0    R+   16:53   0:00 ps aux
imranal 17774 0.0 0.0 103248 864 pts/0 S+ 16:53 0:00 grep imranal imranal 19467 0.0 0.0 106244 1464 ? SN 13:04 0:00 bash ./dorsal_configure imranal 19468 0.0 0.0 100924 680 ? SN 13:04 0:00 tee dorsal_configure.log imranal 19471 0.0 0.2 28028 8900 ? SN 13:04 0:01 cmake -DCMAKE_SKIP_RPATH:BOOL=ON -DCGAL_DISABLE_ROUNDING_MATH_CHECK:BOOL=ON -D SWIG_EXECUTABLE:FILEPATH=/mn/anatu/studenter-u1/imranal/Work/FEniCS/bin/swig -D PYTHON_EXECUTABLE:FILEPATH=/mn/anatu/studenter-u1/imranal/Work/FEniCS/bin/python -D PYTHON_INCLUDE_DIR:PATH=/mn/anatu/studenter-u1/imranal/Work/FEniCS/include/python2.7 -D PYTHON_LIBRARY:PATH=/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/libpython2.7.so -D Boost_USE_MULTITHREADED:BOOL=OFF -D HDF5_INCLUDE_DIRS=/mn/anatu/studenter-u1/imranal/Work/FEniCS/include -D CMAKE_INSTALL_PREFIX:PATH=/mn/anatu/studenter-u1/imranal/Work/FEniCS ../ imranal 19851 0.0 0.2 229424 7948 ? SNl 13:04 0:00 /mn/anatu/studenter-u1/imranal/Work/FEniCS/src/dolfin-1.3.0/dorsal_build_dir/CMakeFiles/CMakeTmp/cmTryCompileExec2541691751 






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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