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 _______________________________________________ fenics-support mailing list [email protected] http://fenicsproject.org/mailman/listinfo/fenics-support
