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 >
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