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
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