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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