I put a ticket about instalation of FEniCS on SMC on github: https://github.com/sagemathinc/smc/issues/47
Thank you for all the help. André Timótheo Em sex, 17 de jul de 2015 às 04:37, Johannes Ring <[email protected]> escreveu: > I managed to reproduce the problem. The -Wl,-rpath,... flag does not > include the path to the bzip2 library. I am not sure if this is a bug in > CMake, HashDist or DOLFIN. > > A temporary solution is to add the following line at the bottom of the > CMakeLists.txt file for the demo: > > set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} > -Wl,-rpath,/home/fenics/.hashdist/bld/bzip2/yhn7t7sdxdfd/lib") > > Then run cmake and make again. > > Johannes > > On Thu, Jul 16, 2015 at 7:10 PM nguyen dang <[email protected]> > wrote: > >> Dear Johannes, >> Please find below the output. Thanks! >> Best regards, >> Dang >> ================================================================= >> [fenics@localhost cpp]$ make VERBOSE=1 >> /home/fenics/.hashdist/bld/cmake/adha2ex3su3d/bin/cmake >> -H/home/fenics/Documents/demo/documented/poisson/cpp >> -B/home/fenics/Documents/demo/documented/poisson/cpp >> --check-build-system CMakeFiles/Makefile.cmake 0 >> /home/fenics/.hashdist/bld/cmake/adha2ex3su3d/bin/cmake -E >> cmake_progress_start >> /home/fenics/Documents/demo/documented/poisson/cpp/CMakeFiles >> >> /home/fenics/Documents/demo/documented/poisson/cpp/CMakeFiles/progress.marks >> make -f CMakeFiles/Makefile2 all >> make[1]: Entering directory >> `/home/fenics/Documents/demo/documented/poisson/cpp' >> make -f CMakeFiles/demo_poisson.dir/build.make >> CMakeFiles/demo_poisson.dir/depend >> make[2]: Entering directory >> `/home/fenics/Documents/demo/documented/poisson/cpp' >> cd /home/fenics/Documents/demo/documented/poisson/cpp && >> /home/fenics/.hashdist/bld/cmake/adha2ex3su3d/bin/cmake -E >> cmake_depends "Unix Makefiles" >> /home/fenics/Documents/demo/documented/poisson/cpp >> /home/fenics/Documents/demo/documented/poisson/cpp >> /home/fenics/Documents/demo/documented/poisson/cpp >> /home/fenics/Documents/demo/documented/poisson/cpp >> >> /home/fenics/Documents/demo/documented/poisson/cpp/CMakeFiles/demo_poisson.dir/DependInfo.cmake >> --color= >> make[2]: Leaving directory >> `/home/fenics/Documents/demo/documented/poisson/cpp' >> make -f CMakeFiles/demo_poisson.dir/build.make >> CMakeFiles/demo_poisson.dir/build >> make[2]: Entering directory >> `/home/fenics/Documents/demo/documented/poisson/cpp' >> Linking CXX executable demo_poisson >> /home/fenics/.hashdist/bld/cmake/adha2ex3su3d/bin/cmake -E >> cmake_link_script CMakeFiles/demo_poisson.dir/link.txt --verbose=1 >> /usr/bin/c++ -std=c++11 -Wno-deprecated -fopenmp -O2 -g >> -DNDEBUG CMakeFiles/demo_poisson.dir/main.cpp.o -o demo_poisson >> -rdynamic >> /home/fenics/.hashdist/bld/dolfin/7zdpq5r4sgsm/lib/libdolfin.so.1.5.0 >> /home/fenics/.hashdist/bld/libxml2/mlk7x2dhjiud/lib/libxml2.so >> /home/fenics/.hashdist/bld/boost/q4an4kheuulz/lib/libboost_filesystem.so >> >> /home/fenics/.hashdist/bld/boost/q4an4kheuulz/lib/libboost_program_options.so >> /home/fenics/.hashdist/bld/boost/q4an4kheuulz/lib/libboost_system.so >> /home/fenics/.hashdist/bld/boost/q4an4kheuulz/lib/libboost_thread.so >> /home/fenics/.hashdist/bld/boost/q4an4kheuulz/lib/libboost_iostreams.so >> /home/fenics/.hashdist/bld/hdf5/6ib4tocuqwpu/lib/libhdf5.so >> /home/fenics/.hashdist/bld/zlib/v6anirfvk2op/lib/libz.so -ldl -lm >> /home/fenics/.hashdist/bld/slepc/5fm7zpo5qbhc/lib/libslepc.so >> /home/fenics/.hashdist/bld/petsc/btgfgqacdl7c/lib/libpetsc.so >> /home/fenics/.hashdist/bld/suitesparse/fnd3oyibysp3/lib/libumfpack.a >> /home/fenics/.hashdist/bld/suitesparse/fnd3oyibysp3/lib/libamd.a >> /home/fenics/.hashdist/bld/blas/bq7qrgo73lhs/lib/libopenblas.so >> /home/fenics/.hashdist/bld/suitesparse/fnd3oyibysp3/lib/libcholmod.a >> /home/fenics/.hashdist/bld/suitesparse/fnd3oyibysp3/lib/libcamd.a >> /home/fenics/.hashdist/bld/suitesparse/fnd3oyibysp3/lib/libcolamd.a >> /home/fenics/.hashdist/bld/suitesparse/fnd3oyibysp3/lib/libccolamd.a >> >> /home/fenics/.hashdist/bld/suitesparse/fnd3oyibysp3/lib/libsuitesparseconfig.a >> -lrt /home/fenics/.hashdist/bld/parmetis/hbifmb4gf2ps/lib/libparmetis.so >> /home/fenics/.hashdist/bld/parmetis/hbifmb4gf2ps/lib/libmetis.so >> -lgfortran >> /home/fenics/.hashdist/bld/scotch/qaholoekwukv/lib/libptscotch.a >> /home/fenics/.hashdist/bld/scotch/qaholoekwukv/lib/libscotch.a >> /home/fenics/.hashdist/bld/scotch/qaholoekwukv/lib/libptscotcherr.a >> /home/fenics/.hashdist/bld/zlib/v6anirfvk2op/lib/libz.so -ldl -lm >> /home/fenics/.hashdist/bld/slepc/5fm7zpo5qbhc/lib/libslepc.so >> /home/fenics/.hashdist/bld/petsc/btgfgqacdl7c/lib/libpetsc.so >> /home/fenics/.hashdist/bld/suitesparse/fnd3oyibysp3/lib/libumfpack.a >> /home/fenics/.hashdist/bld/suitesparse/fnd3oyibysp3/lib/libamd.a >> /home/fenics/.hashdist/bld/blas/bq7qrgo73lhs/lib/libopenblas.so >> /home/fenics/.hashdist/bld/suitesparse/fnd3oyibysp3/lib/libcholmod.a >> /home/fenics/.hashdist/bld/suitesparse/fnd3oyibysp3/lib/libcamd.a >> /home/fenics/.hashdist/bld/suitesparse/fnd3oyibysp3/lib/libcolamd.a >> /home/fenics/.hashdist/bld/suitesparse/fnd3oyibysp3/lib/libccolamd.a >> >> /home/fenics/.hashdist/bld/suitesparse/fnd3oyibysp3/lib/libsuitesparseconfig.a >> -lrt /home/fenics/.hashdist/bld/parmetis/hbifmb4gf2ps/lib/libparmetis.so >> /home/fenics/.hashdist/bld/parmetis/hbifmb4gf2ps/lib/libmetis.so >> -lgfortran >> /home/fenics/.hashdist/bld/scotch/qaholoekwukv/lib/libptscotch.a >> /home/fenics/.hashdist/bld/scotch/qaholoekwukv/lib/libscotch.a >> /home/fenics/.hashdist/bld/scotch/qaholoekwukv/lib/libptscotcherr.a >> /home/fenics/.hashdist/bld/mpi/gmkx3ftk3tz2/lib/libmpichcxx.so >> /home/fenics/.hashdist/bld/mpi/gmkx3ftk3tz2/lib/libmpich.so >> /home/fenics/.hashdist/bld/mpi/gmkx3ftk3tz2/lib/libopa.so >> /home/fenics/.hashdist/bld/mpi/gmkx3ftk3tz2/lib/libmpl.so -lrt >> -lpthread >> /home/fenics/.hashdist/bld/profile/reh75l7mlrkg/lib/vtk-5.10/libvtkGenericFiltering.so.5.10.1 >> >> /home/fenics/.hashdist/bld/profile/reh75l7mlrkg/lib/vtk-5.10/libvtkGeovis.so.5.10.1 >> >> /home/fenics/.hashdist/bld/profile/reh75l7mlrkg/lib/vtk-5.10/libvtkCharts.so.5.10.1 >> >> /home/fenics/.hashdist/bld/profile/reh75l7mlrkg/lib/vtk-5.10/libvtkViews.so.5.10.1 >> >> /home/fenics/.hashdist/bld/profile/reh75l7mlrkg/lib/vtk-5.10/libvtkInfovis.so.5.10.1 >> >> /home/fenics/.hashdist/bld/profile/reh75l7mlrkg/lib/vtk-5.10/libvtkWidgets.so.5.10.1 >> >> /home/fenics/.hashdist/bld/profile/reh75l7mlrkg/lib/vtk-5.10/libvtkVolumeRendering.so.5.10.1 >> >> /home/fenics/.hashdist/bld/profile/reh75l7mlrkg/lib/vtk-5.10/libvtkHybrid.so.5.10.1 >> >> /home/fenics/.hashdist/bld/profile/reh75l7mlrkg/lib/vtk-5.10/libvtkRendering.so.5.10.1 >> >> /home/fenics/.hashdist/bld/profile/reh75l7mlrkg/lib/vtk-5.10/libvtkImaging.so.5.10.1 >> >> /home/fenics/.hashdist/bld/profile/reh75l7mlrkg/lib/vtk-5.10/libvtkGraphics.so.5.10.1 >> >> /home/fenics/.hashdist/bld/profile/reh75l7mlrkg/lib/vtk-5.10/libvtkIO.so.5.10.1 >> >> /home/fenics/.hashdist/bld/profile/reh75l7mlrkg/lib/vtk-5.10/libvtkFiltering.so.5.10.1 >> >> /home/fenics/.hashdist/bld/profile/reh75l7mlrkg/lib/vtk-5.10/libvtkCommon.so.5.10.1 >> >> /home/fenics/.hashdist/bld/profile/reh75l7mlrkg/lib/vtk-5.10/libvtksys.so.5.10.1 >> -lm -ldl >> -Wl,-rpath,/home/fenics/.hashdist/bld/dolfin/7zdpq5r4sgsm/lib:/home/fenics/.hashdist/bld/libxml2/mlk7x2dhjiud/lib:/home/fenics/.hashdist/bld/boost/q4an4kheuulz/lib:/home/fenics/.hashdist/bld/hdf5/6ib4tocuqwpu/lib:/home/fenics/.hashdist/bld/zlib/v6anirfvk2op/lib:/home/fenics/.hashdist/bld/slepc/5fm7zpo5qbhc/lib:/home/fenics/.hashdist/bld/petsc/btgfgqacdl7c/lib:/home/fenics/.hashdist/bld/blas/bq7qrgo73lhs/lib:/home/fenics/.hashdist/bld/parmetis/hbifmb4gf2ps/lib:/home/fenics/.hashdist/bld/mpi/gmkx3ftk3tz2/lib:/home/fenics/.hashdist/bld/profile/reh75l7mlrkg/lib/vtk-5.10 >> >> -Wl,-rpath-link,/home/fenics/.hashdist/bld/profile/reh75l7mlrkg/lib/vtk-5.10 >> /usr/bin/ld: warning: libbz2.so.1.0, needed by >> /home/fenics/.hashdist/bld/boost/q4an4kheuulz/lib/libboost_iostreams.so, >> not found (try using -rpath or -rpath-link) >> /home/fenics/.hashdist/bld/boost/q4an4kheuulz/lib/libboost_iostreams.so: >> undefined reference to `BZ2_bzDecompress' >> /home/fenics/.hashdist/bld/boost/q4an4kheuulz/lib/libboost_iostreams.so: >> undefined reference to `BZ2_bzCompressInit' >> /home/fenics/.hashdist/bld/boost/q4an4kheuulz/lib/libboost_iostreams.so: >> undefined reference to `BZ2_bzDecompressInit' >> /home/fenics/.hashdist/bld/boost/q4an4kheuulz/lib/libboost_iostreams.so: >> undefined reference to `BZ2_bzDecompressEnd' >> /home/fenics/.hashdist/bld/boost/q4an4kheuulz/lib/libboost_iostreams.so: >> undefined reference to `BZ2_bzCompressEnd' >> /home/fenics/.hashdist/bld/boost/q4an4kheuulz/lib/libboost_iostreams.so: >> undefined reference to `BZ2_bzCompress' >> collect2: error: ld returned 1 exit status >> make[2]: *** [demo_poisson] Error 1 >> make[2]: Leaving directory >> `/home/fenics/Documents/demo/documented/poisson/cpp' >> make[1]: *** [CMakeFiles/demo_poisson.dir/all] Error 2 >> make[1]: Leaving directory >> `/home/fenics/Documents/demo/documented/poisson/cpp' >> make: *** [all] Error 2 >> >> ================================================================= >> >> >> On 7/16/15, Johannes Ring <[email protected]> wrote: >> > This looks fine. Can you do >> > >> > make VERBOSE=1 >> > >> > and send us the output? >> > >> > Johannes >> > >> > On Thu, Jul 16, 2015, 18:44 nguyen dang <[email protected]> wrote: >> > >> >> Dear Johannes, >> >> I send you the ouputs. Thanks for your help! >> >> Best regards, >> >> Dang >> >> >> ========================================================================= >> >> [fenics@localhost src]$ ldd >> >> /home/fenics/.hashdist/bld/boost/q4an4kheuulz/lib/libboost_iostreams.so >> >> linux-vdso.so.1 => (0x00007ffff59fe000) >> >> libz.so.1 => >> >> >> >> >> /home/fenics/.hashdist/bld/boost/q4an4kheuulz/lib/../../../zlib/v6anirfvk2op/lib/libz.so.1 >> >> (0x00007fde3f07b000) >> >> libbz2.so.1.0 => >> >> >> >> >> /home/fenics/.hashdist/bld/boost/q4an4kheuulz/lib/../../../bzip2/yhn7t7sdxdfd/lib/libbz2.so.1.0 >> >> (0x00007fde3ee6a000) >> >> librt.so.1 => /lib64/librt.so.1 (0x00007fde3ec47000) >> >> libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007fde3e940000) >> >> libm.so.6 => /lib64/libm.so.6 (0x00007fde3e63d000) >> >> libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007fde3e427000) >> >> libpthread.so.0 => /lib64/libpthread.so.0 (0x00007fde3e20b000) >> >> libc.so.6 => /lib64/libc.so.6 (0x00007fde3de49000) >> >> /lib64/ld-linux-x86-64.so.2 (0x00007fde3f4b4000) >> >> [fenics@localhost src]$ patchelf --print-rpath >> >> /home/fenics/.hashdist/bld/boost/q4an4kheuulz/lib/libboost_iostreams.so >> >> >> >> >> ${ORIGIN}/../../../bzip2/yhn7t7sdxdfd/lib:${ORIGIN}/../../../zlib/v6anirfvk2op/lib >> >> ======================================================================= >> >> >> >> >> >> >> >> On 7/16/15, Johannes Ring <[email protected]> wrote: >> >> > Can you send the output of the following commands? >> >> > >> >> > ldd >> >> /home/fenics/.hashdist/bld/boost/q4an4kheuulz/lib/libboost_iostreams.so >> >> > patchelf --print-rpath >> >> > >> /home/fenics/.hashdist/bld/boost/q4an4kheuulz/lib/libboost_iostreams.so >> >> > >> >> > Johannes >> >> > >> >> > On Wed, Jul 15, 2015 at 5:31 PM nguyen dang <[email protected]> >> >> wrote: >> >> > >> >> >> Dear Johannes, >> >> >> Thanks! Now, python version works well but there is error with c++ >> >> >> version. >> >> >> cmake . - works well >> >> >> make - error with the attached messages. >> >> >> How to fix the error? Thanks! >> >> >> Dang >> >> >> >> >> >> Linking CXX executable demo_poisson >> >> >> /usr/bin/ld: warning: libbz2.so.1.0, needed by >> >> >> >> /home/fenics/.hashdist/bld/boost/q4an4kheuulz/lib/libboost_iostreams.so, >> >> >> not found (try using -rpath or -rpath-link) >> >> >> >> /home/fenics/.hashdist/bld/boost/q4an4kheuulz/lib/libboost_iostreams.so: >> >> >> undefined reference to `BZ2_bzDecompress' >> >> >> >> /home/fenics/.hashdist/bld/boost/q4an4kheuulz/lib/libboost_iostreams.so: >> >> >> undefined reference to `BZ2_bzCompressInit' >> >> >> >> /home/fenics/.hashdist/bld/boost/q4an4kheuulz/lib/libboost_iostreams.so: >> >> >> undefined reference to `BZ2_bzDecompressInit' >> >> >> >> /home/fenics/.hashdist/bld/boost/q4an4kheuulz/lib/libboost_iostreams.so: >> >> >> undefined reference to `BZ2_bzDecompressEnd' >> >> >> >> /home/fenics/.hashdist/bld/boost/q4an4kheuulz/lib/libboost_iostreams.so: >> >> >> undefined reference to `BZ2_bzCompressEnd' >> >> >> >> /home/fenics/.hashdist/bld/boost/q4an4kheuulz/lib/libboost_iostreams.so: >> >> >> undefined reference to `BZ2_bzCompress' >> >> >> collect2: error: ld returned 1 exit status >> >> >> make[2]: *** [demo_poisson] Error 1 >> >> >> make[1]: *** [CMakeFiles/demo_poisson.dir/all] Error 2 >> >> >> make: *** [all] Error 2 >> >> >> >> >> >> >> >> >> On 7/15/15, Johannes Ring <[email protected]> wrote: >> >> >> > The files in $HOME/.hashdist/bld are write protected, so if you >> copy >> >> >> > from >> >> >> > there you will have to change the permission on them. >> >> >> > >> >> >> > Johannes >> >> >> > >> >> >> > On Wed, Jul 15, 2015, 17:10 nguyen dang <[email protected]> >> >> wrote: >> >> >> > >> >> >> >> Dear Johannes, >> >> >> >> The compilation comes to an end without error. >> >> >> >> I run: source fenics.custom >> >> >> >> then, I can clarify dolfin version 1.5.0 >> >> >> >> I copied the demo from >> >> >> >> .hashdist/bld/dolfin/7zdpq5r4sgsm/share/dolfin/demo to >> /Documents. >> >> >> >> There is an error when the poisson demo in >> >> >> >> /demo/documented/poisson/python is tested >> >> >> >> python demo_poisson.py >> >> >> >> I attach error messages. Can you please show me again how to fix? >> >> >> Thanks! >> >> >> >> Best regards, >> >> >> >> Dang >> >> >> >> >> >> >> >> ================================================== >> >> >> >> Calling FFC just-in-time (JIT) compiler, this may take some time. >> >> >> >> Traceback (most recent call last): >> >> >> >> File "demo_poisson.py", line 41, in <module> >> >> >> >> V = FunctionSpace(mesh, "Lagrange", 1) >> >> >> >> File >> >> >> >> >> >> >> >> >> >> "/home/fenics/.hashdist/bld/profile/reh75l7mlrkg/lib/python2.7/site-packages/dolfin/functions/functionspace.py", >> >> >> >> line 468, in __init__ >> >> >> >> FunctionSpaceBase.__init__(self, mesh, element, >> >> >> >> constrained_domain) >> >> >> >> File >> >> >> >> >> >> >> >> >> >> "/home/fenics/.hashdist/bld/profile/reh75l7mlrkg/lib/python2.7/site-packages/dolfin/functions/functionspace.py", >> >> >> >> line 153, in __init__ >> >> >> >> ufc_element, ufc_dofmap = jit(self._ufl_element, >> >> >> >> mpi_comm=mesh.mpi_comm()) >> >> >> >> File >> >> >> >> >> >> >> >> >> >> "/home/fenics/.hashdist/bld/profile/reh75l7mlrkg/lib/python2.7/site-packages/dolfin/compilemodules/jit.py", >> >> >> >> line 64, in mpi_jit >> >> >> >> return local_jit(*args, **kwargs) >> >> >> >> File >> >> >> >> >> >> >> >> >> >> "/home/fenics/.hashdist/bld/profile/reh75l7mlrkg/lib/python2.7/site-packages/dolfin/compilemodules/jit.py", >> >> >> >> line 128, in jit >> >> >> >> return form_compiler.jit(form, parameters=p) >> >> >> >> File >> >> >> >> >> >> >> >> >> >> "/home/fenics/.hashdist/bld/profile/reh75l7mlrkg/lib/python2.7/site-packages/ffc/jitcompiler.py", >> >> >> >> line 72, in jit >> >> >> >> return jit_element(ufl_object, parameters) >> >> >> >> File >> >> >> >> >> >> >> >> >> >> "/home/fenics/.hashdist/bld/profile/reh75l7mlrkg/lib/python2.7/site-packages/ffc/jitcompiler.py", >> >> >> >> line 177, in jit_element >> >> >> >> compiled_form, module, prefix = jit_form(form, parameters) >> >> >> >> File >> >> >> >> >> >> >> >> >> >> "/home/fenics/.hashdist/bld/profile/reh75l7mlrkg/lib/python2.7/site-packages/ffc/jitcompiler.py", >> >> >> >> line 130, in jit_form >> >> >> >> parameters=parameters) >> >> >> >> File >> >> >> >> >> >> >> >> >> >> "/home/fenics/.hashdist/bld/profile/reh75l7mlrkg/lib/python2.7/site-packages/ffc/compiler.py", >> >> >> >> line 176, in compile_form >> >> >> >> format_code(code, wrapper_code, prefix, parameters) >> >> >> >> File >> >> >> >> >> >> >> >> >> >> "/home/fenics/.hashdist/bld/profile/reh75l7mlrkg/lib/python2.7/site-packages/ffc/formatting.py", >> >> >> >> line 114, in format_code >> >> >> >> _write_file(code_h, prefix, ".h", parameters) >> >> >> >> File >> >> >> >> >> >> >> >> >> >> "/home/fenics/.hashdist/bld/profile/reh75l7mlrkg/lib/python2.7/site-packages/ffc/formatting.py", >> >> >> >> line 137, in _write_file >> >> >> >> hfile = open(filename, "w") >> >> >> >> IOError: [Errno 13] Permission denied: >> >> >> >> './ffc_form_746ebe8521dc9d314e6f65075dbc60d03cfee94b.h' >> >> >> >> ================================================== >> >> >> >> >> >> >> >> >> >> >> >> On 7/15/15, Johannes Ring <[email protected]> wrote: >> >> >> >> > The problem is this: >> >> >> >> > >> >> >> >> > c++: internal compiler error: Killed (program cc1plus) >> >> >> >> > >> >> >> >> > This is usually caused by a bug in the compiler or that you ran >> >> >> >> > out >> >> >> >> > of >> >> >> >> > memory. If it is the latter case, you can try to build with >> only >> >> one >> >> >> >> thread >> >> >> >> > to save some memory: >> >> >> >> > >> >> >> >> > export PROCS=1 >> >> >> >> > >> >> >> >> > Then run fenics-install.sh again. >> >> >> >> > >> >> >> >> > Johannes >> >> >> >> > >> >> >> >> > On Wed, Jul 15, 2015 at 3:45 PM nguyen dang < >> >> [email protected]> >> >> >> >> wrote: >> >> >> >> > >> >> >> >> >> Hello, >> >> >> >> >> I could fix that error by installing libXt-devel >> >> >> >> >> sudo yum install libXt-devel >> >> >> >> >> There is a new error with mshr >> >> >> >> >> [mshr] Building mshr/7olinw2dfk5t, follow log with: >> >> >> >> >> [mshr] tail -f >> >> >> >> >> >> /home/fenics/.hashdist/tmp/mshr-7olinw2dfk5t/_hashdist/build.log >> >> >> >> >> [mshr|ERROR] Command '[u'/bin/bash', '_hashdist/build.sh']' >> >> >> >> >> returned >> >> >> >> >> non-zero exit status 2 >> >> >> >> >> [mshr|ERROR] command failed (code=2); raising >> >> >> >> >> real 3607.89 >> >> >> >> >> user 2537.20 >> >> >> >> >> sys 382.04 >> >> >> >> >> I attach log file. >> >> >> >> >> Thanks again for your help. >> >> >> >> >> Best regards, >> >> >> >> >> Dang >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> On 7/15/15, Johannes Ring <[email protected]> wrote: >> >> >> >> >> > Ok, this is a different error, so I assume that slepc has >> been >> >> >> built >> >> >> >> >> > successfully. The problem with vtk is this: >> >> >> >> >> > >> >> >> >> >> > fatal error: X11/StringDefs.h: No such file or directory >> >> >> >> >> > >> >> >> >> >> > This file can be found in the libxt-dev package on Ubuntu, >> but >> >> >> >> >> > I'm >> >> >> >> >> > not >> >> >> >> >> sure >> >> >> >> >> > what system you are on. You can either install this file or >> >> build >> >> >> >> >> > without >> >> >> >> >> > vtk by removing it from local.yaml. In the latter case, you >> >> >> >> >> > will >> >> >> not >> >> >> >> be >> >> >> >> >> > able to do any plotting with DOLFIN. >> >> >> >> >> > >> >> >> >> >> > Johannes >> >> >> >> >> > >> >> >> >> >> > >> >> >> >> >> > On Wed, Jul 15, 2015 at 11:23 AM nguyen dang >> >> >> >> >> > <[email protected]> >> >> >> >> >> > wrote: >> >> >> >> >> > >> >> >> >> >> >> Dear Johannes, >> >> >> >> >> >> Thanks for your quick response. I followed your >> instructions >> >> but >> >> >> >> >> >> I >> >> >> >> >> >> still get error: >> >> >> >> >> >> [vtk] Building vtk/of7hll3bl2ul, follow log with: >> >> >> >> >> >> [vtk] tail -f >> >> >> >> >> >> >> >> /home/fenics/.hashdist/tmp/vtk-of7hll3bl2ul-3/_hashdist/build.log >> >> >> >> >> >> [vtk|ERROR] Command '[u'/bin/bash', '_hashdist/build.sh']' >> >> >> returned >> >> >> >> >> >> non-zero exit status 2 >> >> >> >> >> >> [vtk|ERROR] command failed (code=2); raising >> >> >> >> >> >> real 1267.00 >> >> >> >> >> >> user 1092.49 >> >> >> >> >> >> sys 147.74 >> >> >> >> >> >> I attach build.log and local.yaml >> >> >> >> >> >> Thanks for your help, >> >> >> >> >> >> Best regards, >> >> >> >> >> >> Dang >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> On 7/15/15, Johannes Ring <[email protected]> wrote: >> >> >> >> >> >> > [Please include fenics-support in Cc] >> >> >> >> >> >> > >> >> >> >> >> >> > The problem is that it links with the system LAPACK and >> >> >> >> >> >> > BLAS >> >> >> >> instead >> >> >> >> >> of >> >> >> >> >> >> > OpenBLAS that HashDist has built. The quick fix will be >> to >> >> >> >> >> >> > build >> >> >> >> >> >> > PETSc >> >> >> >> >> >> > without MUMPS. Try this: >> >> >> >> >> >> > >> >> >> >> >> >> > git clone >> >> >> >> >> >> >> >> https://bitbucket.org/fenics-project/fenics-developer-tools.git >> >> >> >> >> >> > cd fenics-developer-tools >> >> >> >> >> >> > cp install/profiles/fenics.Linux.yaml local.yaml >> >> >> >> >> >> > editor local.yaml >> >> >> >> >> >> > >> >> >> >> >> >> > Now remove the following two lines from local.yaml: >> >> >> >> >> >> > >> >> >> >> >> >> > download: | >> >> >> >> >> >> > mumps, scalapack, blacs, ml >> >> >> >> >> >> > >> >> >> >> >> >> > Finally, run: >> >> >> >> >> >> > >> >> >> >> >> >> > ./install/fenics-install.sh local.yaml >> >> >> >> >> >> > >> >> >> >> >> >> > Johannes >> >> >> >> >> >> > >> >> >> >> >> >> > On Tue, Jul 14, 2015 at 7:13 PM André Timótheo >> >> >> >> >> >> > <[email protected]> >> >> >> >> >> >> > wrote: >> >> >> >> >> >> > >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> Em ter, 14 de jul de 2015 às 09:33, Johannes Ring >> >> >> >> >> >> >> <[email protected] >> >> >> >> >> > >> >> >> >> >> >> >> escreveu: >> >> >> >> >> >> >> >> >> >> >> >> >> >>> The error in the build.log is this: >> >> >> >> >> >> >>> >> >> >> >> >> >> >>> 2015/07/13 23:09:48 - INFO: [package:run_job] ERROR: >> See >> >> >> >> >> >> >>> "arch-linux2-c-opt/conf/configure.log" file for >> >> >> >> >> >> >>> details >> >> >> >> >> >> >>> >> >> >> >> >> >> >>> 2015/07/13 23:09:48 - INFO: [package:run_job] Checking >> >> >> >> >> >> >>> environment... >> >> >> >> >> >> >>> 2015/07/13 23:09:48 - INFO: [package:run_job] Checking >> >> PETSc >> >> >> >> >> >> >>> installation... >> >> >> >> >> >> >>> 2015/07/13 23:09:48 - INFO: [package:run_job] ERROR: >> >> >> >> >> >> >>> Unable >> >> >> >> >> >> >>> to >> >> >> >> >> >> >>> link >> >> >> >> >> >> with >> >> >> >> >> >> >>> PETSc >> >> >> >> >> >> >>> >> >> >> >> >> >> >>> Please send us >> >> >> >> >> >> >>> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> /projects/d800605f-5bec-48c8-8c21-5fa60022fa9a/.hashdist/tmp/slepc-bvy3tmydxkf2-3/arch-linux2-c-opt/conf/configure.log >> >> >> >> >> >> >>> as an attachment. >> >> >> >> >> >> >>> >> >> >> >> >> >> >>> Johannes >> >> >> >> >> >> >>> >> >> >> >> >> >> >>> On Tue, Jul 14, 2015 at 2:26 PM André Timótheo < >> >> >> >> >> [email protected]> >> >> >> >> >> >> >>> wrote: >> >> >> >> >> >> >>> >> >> >> >> >> >> >>>> I am trying to install FEniCS on SageMathCloud via >> curl >> >> >> >> >> >> >>>> -s >> >> >> >> >> >> >>>> http://fenicsproject.org/fenics-install.sh | bash >> >> >> >> >> >> >>>> ( the option [1] stable fenics version ) >> >> >> >> >> >> >>>> >> >> >> >> >> >> >>>> I have some problems with slepc: >> >> >> >> >> >> >>>> [slepc >> >> >> >> >> >> >>>> ] tail -f >> >> >> >> >> >> >>>> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> /projects/d800605f-5bec-48c8-8c21-5fa60022fa9a/.hashdist/tmp/slepc-bvy3tmydx >> >> >> >> >> >> >>>> kf2-3/_hashdist/build.log >> >> >> >> >> >> >>>> [slepc|ERROR >> >> >> >> >> >> >>>> ] Command '[u'/bin/bash', '_hashdist/build.sh']' >> >> >> >> >> >> >>>> returned >> >> >> >> >> >> >>>> non-zero >> >> >> >> >> >> exit >> >> >> >> >> >> >>>> status 1 >> >> >> >> >> >> >>>> [slepc|ERROR] command failed (code=1); raising >> >> >> >> >> >> >>>> >> >> >> >> >> >> >>>> The build.log error file is attached. >> >> >> >> >> >> >>>> >> >> >> >> >> >> >>>> Thank you very much for any kind of *help*. >> >> >> >> >> >> >>>> >> >> >> >> >> >> >>>> André Timótheo >> >> >> >> >> >> >>>> >> >> >> >> >> >> >>> _______________________________________________ >> >> >> >> >> >> >>>> fenics-support mailing list >> >> >> >> >> >> >>>> [email protected] >> >> >> >> >> >> >>>> >> http://fenicsproject.org/mailman/listinfo/fenics-support >> >> >> >> >> >> >>>> >> >> >> >> >> >> >>> >> >> >> >> >> >> > >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> -- >> >> >> >> >> >> Nguyen Van Dang >> >> >> >> >> >> Hand phone: +34 675 16 95 90 >> >> >> >> >> >> Alameda Mazarredo, 14, 48009 Bilbao, Bizkaia >> >> >> >> >> >> Spain >> >> >> >> >> >> >> >> >> >> >> > >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> -- >> >> >> >> >> Nguyen Van Dang >> >> >> >> >> Hand phone: +34 675 16 95 90 >> >> >> >> >> Alameda Mazarredo, 14, 48009 Bilbao, Bizkaia >> >> >> >> >> Spain >> >> >> >> >> >> >> >> >> > >> >> >> >> >> >> >> >> >> >> >> >> -- >> >> >> >> Nguyen Van Dang >> >> >> >> Hand phone: +34 675 16 95 90 >> >> >> >> Alameda Mazarredo, 14, 48009 Bilbao, Bizkaia >> >> >> >> Spain >> >> >> >> >> >> >> > >> >> >> >> >> >> >> >> >> -- >> >> >> Nguyen Van Dang >> >> >> Hand phone: +34 675 16 95 90 >> >> >> Alameda Mazarredo, 14, 48009 Bilbao, Bizkaia >> >> >> Spain >> >> >> >> >> > >> >> >> >> >> >> -- >> >> Nguyen Van Dang >> >> Hand phone: +34 675 16 95 90 >> >> Alameda Mazarredo, 14, 48009 Bilbao, Bizkaia >> >> Spain >> >> >> > >> >> >> -- >> Nguyen Van Dang >> Hand phone: +34 675 16 95 90 >> Alameda Mazarredo, 14, 48009 Bilbao, Bizkaia >> Spain >> >
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