On the compute nodes you are running on, there is no X support. You should either run your code on nodes with hardware graphic support (on stampede: development, largemem and vis queues), or link dolfin to a build of vtk that uses off-screen rendering (with OSMESA). Also note, your PETSc should be build without X.
Best, Andrés A. León Baldelli — LSU Center for Computation & Technology 2099 Louisiana Digital Media Center On Jul 1, 2014, at 1:31 PM, Sai Rajeshwar <[email protected]> wrote: > thanks.. at last reached following error.. what could have gone wrong now > at last moment.. > > ---------------------------------------------------------- > > login3$ ./demo_poisson > Solving linear variational problem. > ERROR: In > /home1/03023/rajeswar/VTK-6.1.0/Rendering/OpenGL/vtkXOpenGLRenderWindow.cxx, > line 322 > vtkXOpenGLRenderWindow (0x1024870): bad X server connection. > DISPLAY=[login3.stampede.tacc.utexas.edu:mpi_rank_0][error_sighandler] Caught > error: Aborted (signal 6) > Aborted (core dumped) > ------------------------------ > > with regards.. > > M. Sai Rajeswar > M-tech Computer Technology > IIT Delhi > ----------------------------------Cogito Ergo Sum--------- > > > On Tue, Jul 1, 2014 at 10:27 PM, Sai Rajeshwar <[email protected]> wrote: > suitsparse compiler flags by default has -fPIC flags in SuitsparseConfig.mk > file.. > > so should i rebuild > > with regards.. > > M. Sai Rajeswar > M-tech Computer Technology > IIT Delhi > ----------------------------------Cogito Ergo Sum--------- > > > On Tue, Jul 1, 2014 at 8:49 PM, Johannes Ring <[email protected]> wrote: > You need to rebuild SuiteSparse with the -fPIC flag. > > Johannes > > On Jul 1, 2014 5:06 PM, "Sai Rajeshwar" <[email protected]> wrote: > that really helped.. thanks a lot.. > > now while make install there is a error in using libumfpack.a > > -------------------------------------------------- > > [ 96%] Building CXX object > dolfin/CMakeFiles/dolfin.dir/generation/GeometryToCGALConverter.cpp.o > [ 96%] Building CXX object > dolfin/CMakeFiles/dolfin.dir/generation/CSGPrimitives2D.cpp.o > Linking CXX shared library libdolfin.so > /usr/bin/ld: /home1/03023/rajeswar/lib/libumfpack.a(umf_dl_local_search.o): > relocation R_X86_64_32 against `.rodata.str1.4' can not be used when making a > shared object; recompile with -fPIC > /home1/03023/rajeswar/lib/libumfpack.a: could not read symbols: Bad value > collect2: ld returned 1 exit status > make[2]: *** [dolfin/libdolfin.so.1.4.0] Error 1 > make[1]: *** [dolfin/CMakeFiles/dolfin.dir/all] Error 2 > make: *** [all] Error 2 > -------------------------------------------------- > > is it missing something.. > > with regards.. > > M. Sai Rajeswar > M-tech Computer Technology > IIT Delhi > ----------------------------------Cogito Ergo Sum--------- > > > On Tue, Jul 1, 2014 at 7:23 PM, Johannes Ring <[email protected]> wrote: > Is the library libirc.so (or libirc.a) in > /opt/apps/intel/13/composer_xe_2013_sp1.1.106/mkl/lib/intel64? If not, you > should locate the library and modify the -L path in LDFLAGS. > > Johannes > > > On Tue, Jul 1, 2014 at 3:44 PM, Sai Rajeshwar <[email protected]> wrote: > ok i tried the exporting as you mentioned.. then ran cmake.. > > --------------------------------------------------- > > login3$ cmake -DCMAKE_INSTALL_PREFIX=/home1/03023/rajeswar/ > -DCMAKE_PREFIX_PATH=/home/03023/rajeswar -DDOLFIN_ENABLE_SCOTCH=OFF > -DDOLFIN_ENABLE_UMFPACK=ON > 0-DGMP_LIBRARIES:FILEPATH=/home1/03023/rajeswar/lib/libgmp.so .. > > > > -- 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/gcc > -- Check for working C compiler: /usr/bin/gcc -- broken > CMake Error at > /opt/apps/cmake/2.8.9/share/cmake-2.8/Modules/CMakeTestCCompiler.cmake:52 > (MESSAGE): > The C compiler "/usr/bin/gcc" is not able to compile a simple test program. > > It fails with the following output: > > Change Dir: > /home1/03023/rajeswar/mine/dolfin-1.4.0/build/CMakeFiles/CMakeTmp > > > > Run Build Command:/usr/bin/gmake "cmTryCompileExec665115447/fast" > > /usr/bin/gmake -f CMakeFiles/cmTryCompileExec665115447.dir/build.make > CMakeFiles/cmTryCompileExec665115447.dir/build > > gmake[1]: Entering directory > `/home1/03023/rajeswar/mine/dolfin-1.4.0/build/CMakeFiles/CMakeTmp' > > /opt/apps/cmake/2.8.9/bin/cmake -E cmake_progress_report > /home1/03023/rajeswar/mine/dolfin-1.4.0/build/CMakeFiles/CMakeTmp/CMakeFiles > 1 > > Building C object > CMakeFiles/cmTryCompileExec665115447.dir/testCCompiler.c.o > > /usr/bin/gcc -o CMakeFiles/cmTryCompileExec665115447.dir/testCCompiler.c.o > -c > > /home1/03023/rajeswar/mine/dolfin-1.4.0/build/CMakeFiles/CMakeTmp/testCCompiler.c > > > Linking C executable cmTryCompileExec665115447 > > /opt/apps/cmake/2.8.9/bin/cmake -E cmake_link_script > CMakeFiles/cmTryCompileExec665115447.dir/link.txt --verbose=1 > > /usr/bin/gcc > -L/opt/apps/intel/13/composer_xe_2013_sp1.1.106/mkl/lib/intel64 -lirc > CMakeFiles/cmTryCompileExec665115447.dir/testCCompiler.c.o -o > cmTryCompileExec665115447 -rdynamic > > /usr/bin/ld: cannot find -lirc > > > collect2: ld returned 1 exit status > > gmake[1]: *** [cmTryCompileExec665115447] Error 1 > > gmake[1]: Leaving directory > `/home1/03023/rajeswar/mine/dolfin-1.4.0/build/CMakeFiles/CMakeTmp' > > gmake: *** [cmTryCompileExec665115447/fast] Error 2 > > > > > > CMake will not be able to correctly generate this project. > > Call Stack (most recent call first): > CMakeLists.txt:9 (project) > > > -- Configuring incomplete, errors occurr > > with regards.. > > M. Sai Rajeswar > M-tech Computer Technology > IIT Delhi > ----------------------------------Cogito Ergo Sum--------- > > > On Tue, Jul 1, 2014 at 7:05 PM, Johannes Ring <[email protected]> wrote: > It looks like you are linking to Intel compiled libraries but are missing a > library: > > /opt/apps/cmake/2.8.9/bin/cmake -E cmake_link_script > CMakeFiles/cmTryCompileExec1785079256.dir/link.txt --verbose=1 > /usr/bin/c++ -std=c++0x -DUMFPACK_TEST_RUNS -fopenmp > CMakeFiles/cmTryCompileExec1785079256.dir/src.cxx.o -o > cmTryCompileExec1785079256 -rdynamic > -L/opt/apps/intel/13/composer_xe_2013_sp1.1.106/mkl/lib/intel64 > /home1/03023/rajeswar/lib/libumfpack.a /home1/03023/rajeswar/lib/libamd.a > -lmkl_intel_lp64 -lmkl_gnu_thread -lmkl_core > /home1/03023/rajeswar/lib/libsuitesparseconfig.a > /home1/03023/rajeswar/lib/libsuitesparseconfig.a -lgfortran > -Wl,-rpath,/opt/apps/intel/13/composer_xe_2013_sp1.1.106/mkl/lib/intel64 > /home1/03023/rajeswar/lib/libumfpack.a(umf_di_kernel_init.o): In function > `packsp': > ../Source/umf_kernel_init.c:(.text+0xf8): undefined reference to > `__intel_ssse3_rep_memcpy' > ../Source/umf_kernel_init.c:(.text+0x132): undefined reference to > `__intel_ssse3_rep_memcpy' > ... > > The symbol __intel_ssse3_rep_memcpy is provided by libirc.so. Try adding it > to LDFLAGS: > > export > LDFLAGS="-L/opt/apps/intel/13/composer_xe_2013_sp1.1.106/mkl/lib/intel64 > -lirc" > > Then run cmake again. > > Johannes > > > > On Tue, Jul 1, 2014 at 12:12 PM, Sai Rajeshwar <[email protected]> wrote: > i made findpath(UMFPACK REQUIRED) in CMakeLists.txt to get following log file > CMakeError.log > > > with findpath(UMFPACK QUIET) the following is the log file > > > CMakeError2.log > > > thought i will send you both > > with regards.. > > M. Sai Rajeswar > M-tech Computer Technology > IIT Delhi > ----------------------------------Cogito Ergo Sum--------- > > > On Tue, Jul 1, 2014 at 3:24 PM, Johannes Ring <[email protected]> wrote: > On Tue, Jul 1, 2014 at 11:40 AM, Sai Rajeshwar <[email protected]> wrote: > i installed Suitsparse in /home1/03023/rajeswar/lib and > /home1/03023/rajeswar/include as lib and include directories.. the package > it self is in /home1/03023/rajeswar/Suitsparse from which i built it.. > > now for dolfin i did the following... > ------------------------------------------ > cmake -DCMAKE_INSTALL_PREFIX=/home1/03023/rajeswar/ > -DCMAKE_PREFIX_PATH=/home/03023/rajeswar -DDOLFIN_ENABLE_SCOTCH=OFF > -DGMP_LIBRARIES:FILEPATH=/home1/03023/rajeswar/lib/libgmp.so .. > > > still it gave the same result.. umfpack, cholmod tests failed > > Please attach CMakeFiles/CMakeError.log from the DOLFIN build directory. > > Johannes > > > > > > > > _______________________________________________ > fenics-support mailing list > [email protected] > http://fenicsproject.org/mailman/listinfo/fenics-support
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