On Thu, 5 Feb 2015 14:30:43 +0100 (CET) Birgitte Maria Elisabeth Brydso <[email protected]> wrote:
> I am trying to install fenics on an Ubuntu 12.04 cluster, > without root permissions. > > My home-directory is on afs, and not big enough to install > in. I am instead trying to install in a non-backed up parallel > filesystem called pfs. I am having some problems setting the > directory. I tried downloading fenics-install.sh and making some > changes: > > #export PROFILE_INSTALL_DIR=\$HOME/.hashdist/bld/profile/\$PROFILE > export > PROFILE_INSTALL_DIR=/pfs/nobackup/home/b/bbrydsoe/fenics_install/.hashdist/bld/profile/\$PROFILE > > but that did not seem to help. Regardless I got the same error as I > did when running fenics-install.sh without downloading first. Tail of > build.log: > > 2015/02/04 15:24:21 - INFO: [package:run_job] make[1]: Leaving > directory > `/afs/hpc2n.umu.se/home/b/bbrydsoe/.hashdist/tmp/ncurses-viognkgus4nj/form' > 2015/02/04 15:24:21 - INFO: [package:run_job] cd misc && make > DESTDIR="" install 2015/02/04 15:24:21 - INFO: [package:run_job] > make[1]: Entering directory > `/afs/hpc2n.umu.se/home/b/bbrydsoe/.hashdist/tmp/ncurses-viognkgus4nj/misc' > 2015/02/04 15:24:21 - INFO: [package:run_job] mkdir > -p /afs/hpc2n.umu.se/home/b/bbrydsoe/.hashdist/bld/ncurses/viognkgus4nj/share > 2015/02/04 15:24:21 - INFO: [package:run_job] mkdir > -p > /afs/hpc2n.umu.se/home/b/bbrydsoe/.hashdist/bld/ncurses/viognkgus4nj/share/tabset > 2015/02/04 15:24:21 - INFO: [package:run_job] DESTDIR= \ 2015/02/04 > 15:24:21 - INFO: [package:run_job] > prefix=/afs/hpc2n.umu.se/home/b/bbrydsoe/.hashdist/bld/ncurses/viognkgus4nj > \ 2015/02/04 15:24:21 - INFO: [package:run_job] > exec_prefix=/afs/hpc2n.umu.se/home/b/bbrydsoe/.hashdist/bld/ncurses/viognkgus4nj > > \ > 2015/02/04 15:24:21 - INFO: [package:run_job] > bindir=/afs/hpc2n.umu.se/home/b/bbrydsoe/.hashdist/bld/ncurses/viognkgus4nj/bin > > \ > 2015/02/04 15:24:21 - INFO: [package:run_job] top_srcdir=.. \ > 2015/02/04 15:24:21 - INFO: [package:run_job] srcdir=. \ > 2015/02/04 15:24:21 - INFO: [package:run_job] > datadir=/afs/hpc2n.umu.se/home/b/bbrydsoe/.hashdist/bld/ncurses/viognkgus4nj/share > > \ > 2015/02/04 15:24:21 - INFO: [package:run_job] > ticdir=/afs/hpc2n.umu.se/home/b/bbrydsoe/.hashdist/bld/ncurses/viognkgus4nj/share/terminfo > > \ > 2015/02/04 15:24:21 - INFO: [package:run_job] source=terminfo.tmp \ > 2015/02/04 15:24:21 - INFO: [package:run_job] cross_compiling=no \ > 2015/02/04 15:24:21 - INFO: [package:run_job] /bin/sh ./run_tic.sh > 2015/02/04 15:24:21 - INFO: [package:run_job] ** Building terminfo > database, please wait... > 2015/02/04 15:24:21 - INFO: [package:run_job] Running sh ./shlib tic > to install > /afs/hpc2n.umu.se/home/b/bbrydsoe/.hashdist/bld/ncurses/viognkgus4nj/share/terminfo > > ... > 2015/02/04 15:24:21 - INFO: [package:run_job] > 2015/02/04 15:24:21 - INFO: [package:run_job] You may see messages > regarding extended capabilities, e.g., AX. > 2015/02/04 15:24:21 - INFO: [package:run_job] These are extended > terminal capabilities which are compiled > 2015/02/04 15:24:21 - INFO: [package:run_job] using > 2015/02/04 15:24:21 - INFO: [package:run_job] tic -x > 2015/02/04 15:24:21 - INFO: [package:run_job] If you have ncurses > 4.2 applications, you should read the INSTALL > 2015/02/04 15:24:21 - INFO: [package:run_job] document, and install > the terminfo without the -x option. > 2015/02/04 15:24:21 - INFO: [package:run_job] > 2015/02/04 15:24:22 - INFO: [package:run_job] "terminfo.tmp", line > 306, terminal 'lpr': can't link l/lpr to p/printer > 2015/02/04 15:24:22 - INFO: [package:run_job] ? tic could not build > /afs/hpc2n.umu.se/home/b/bbrydsoe/.hashdist/bld/ncurses/viognkgus4nj/share/terminfo > 2015/02/04 15:24:22 - INFO: [package:run_job] make[1]: *** > [install.data] Error 1 > 2015/02/04 15:24:22 - INFO: [package:run_job] make[1]: Leaving > directory > `/afs/hpc2n.umu.se/home/b/bbrydsoe/.hashdist/tmp/ncurses-viognkgus4nj/misc' > 2015/02/04 15:24:22 - INFO: [package:run_job] make: *** [install] > Error 2 2015/02/04 15:24:22 - ERROR: [package:run_job] Command > '[u'/bin/bash', '_hashdist/build.sh']' returned non-zero exit status > 2 2015/02/04 15:24:22 - ERROR: [package:run_job] command failed > (code=2); raising This seems like priviliges problem which I assume you have solved by tweaking hashdist profile below, right? > > > I then downloaded hashdist and hashstack too, and created my own > profile: > > extends: > - name: hashstack > urls: ['https://github.com/hashdist/hashstack.git'] > key: 'git:1a97d560b12d86d8c36f8e574a1ebb3ea00067b7' > file: debian.yaml > > parameters: > HOST_MPICC: /lap/openmpi/1.6.5/gcc-4.6/bin/mpicc > HOST_MPICXX: /lap/openmpi/1.6.5/gcc-4.6/bin/mpic++ > HOST_MPIF77: /lap/openmpi/1.6.5/gcc-4.6/bin/mpif77 > HOST_MPIF90: /lap/openmpi/1.6.5/gcc-4.6/bin/mpif90 > HOST_MPIEXEC: /lap/openmpi/1.6.5/gcc-4.6/bin/mpiexec > HOST_CMAKE: /lap/cmake/2.8.12.1/bin/cmake > HOST_PYTHON: /usr/bin/python > HOST_SWIG_EXECUTABLE: /usr/bin/swig > HOST_PETSC_DIR: /lap/petsc/3.4.3/gcc/ompi/opt > HOST_PETSC_ARCH: linux-gnu-c-opt > HOST_SLEPC_DIR: /lap/slepc/3.4.3/gcc/ompi/opt > HOST_BLAS_DIR: /lap/openblas/0.2.9/lib/gcc > > packages: > blas: > use: host-blas > # alternative to system blas: > # use: openblas > mpi: > # On debian: apt-get install mpich > use: host-mpi > # alternative to system mpi: > # use: openmpi > zlib: > nose: > launcher: > jinja2: > python: > host: true > use_python_host_packages: true > numpy: > use: host-numpy > cmake: > use: host-cmake > petsc: > use: host-petsc > slepc: > swig: > use: host-swig > boost: > toolset: gcc > address_model: 64 > dolfin: > build_with: | > suitesparse, scotch, parmetis, petsc, slepc, zlib, hdf5, vtk > > > > and did > > hit build > > > I know get errors while building vtk. Last part of the build.log: > > 2015/02/05 12:57:12 - INFO: [package:run_job] CMake Warning (dev) in > Geovis/CMakeLists.txt: > 2015/02/05 12:57:12 - INFO: [package:run_job] Policy CMP0022 is not > set: INTERFACE_LINK_LIBRARIES defines the link > 2015/02/05 12:57:12 - INFO: [package:run_job] interface. Run > "cmake --help-policy CMP0022" for policy details. Use the > 2015/02/05 12:57:12 - INFO: [package:run_job] cmake_policy command > to set the policy and suppress this warning. > 2015/02/05 12:57:12 - INFO: [package:run_job] > 2015/02/05 12:57:12 - INFO: [package:run_job] Target "vtkGeovis" > has an INTERFACE_LINK_LIBRARIES property which differs > 2015/02/05 12:57:12 - INFO: [package:run_job] from its > LINK_INTERFACE_LIBRARIES properties. > 2015/02/05 12:57:12 - INFO: [package:run_job] > 2015/02/05 12:57:12 - INFO: [package:run_job] > INTERFACE_LINK_LIBRARIES: 2015/02/05 12:57:12 - INFO: > [package:run_job] 2015/02/05 12:57:12 - INFO: [package:run_job] > vtkWidgets;vtkViews;vtkproj4;vtkWidgets;vtkViews > 2015/02/05 12:57:12 - INFO: [package:run_job] > 2015/02/05 12:57:12 - INFO: [package:run_job] > LINK_INTERFACE_LIBRARIES: 2015/02/05 12:57:12 - INFO: > [package:run_job] 2015/02/05 12:57:12 - INFO: [package:run_job] > vtkWidgets;vtkViews 2015/02/05 12:57:12 - INFO: [package:run_job] > 2015/02/05 12:57:12 - INFO: [package:run_job] This warning is for > project developers. Use -Wno-dev to suppress it. > 2015/02/05 12:57:12 - INFO: [package:run_job] > 2015/02/05 12:57:12 - INFO: [package:run_job] CMake Warning (dev) in > Charts/CMakeLists.txt: > 2015/02/05 12:57:12 - INFO: [package:run_job] Policy CMP0022 is not > set: INTERFACE_LINK_LIBRARIES defines the link > 2015/02/05 12:57:12 - INFO: [package:run_job] interface. Run > "cmake --help-policy CMP0022" for policy details. Use the > 2015/02/05 12:57:12 - INFO: [package:run_job] cmake_policy command > to set the policy and suppress this warning. > 2015/02/05 12:57:12 - INFO: [package:run_job] > 2015/02/05 12:57:12 - INFO: [package:run_job] Target "vtkCharts" > has an INTERFACE_LINK_LIBRARIES property which differs > 2015/02/05 12:57:12 - INFO: [package:run_job] from its > LINK_INTERFACE_LIBRARIES properties. > 2015/02/05 12:57:12 - INFO: [package:run_job] > 2015/02/05 12:57:12 - INFO: [package:run_job] > INTERFACE_LINK_LIBRARIES: 2015/02/05 12:57:12 - INFO: > [package:run_job] 2015/02/05 12:57:12 - INFO: [package:run_job] > vtkViews;vtkftgl;vtkViews > 2015/02/05 12:57:12 - INFO: [package:run_job] > 2015/02/05 12:57:12 - INFO: [package:run_job] > LINK_INTERFACE_LIBRARIES: 2015/02/05 12:57:12 - INFO: > [package:run_job] 2015/02/05 12:57:12 - INFO: [package:run_job] > vtkViews 2015/02/05 12:57:12 - INFO: [package:run_job] > 2015/02/05 12:57:12 - INFO: [package:run_job] This warning is for > project developers. Use -Wno-dev to suppress it. > 2015/02/05 12:57:12 - INFO: [package:run_job] > 2015/02/05 12:57:12 - INFO: [package:run_job] -- Configuring > incomplete, errors occurred! > 2015/02/05 12:57:12 - INFO: [package:run_job] See also > "/afs/hpc2n.umu.se/home/b/bbrydsoe/.hashdist/tmp/vtk-izqbwqpiwzwf/_build/CMakeFiles/CMakeOutput.log". > 2015/02/05 12:57:12 - INFO: [package:run_job] See also > "/afs/hpc2n.umu.se/home/b/bbrydsoe/.hashdist/tmp/vtk-izqbwqpiwzwf/_build/CMakeFiles/CMakeError.log". > 2015/02/05 12:57:12 - ERROR: [package:run_job] Command > '[u'/bin/bash', '_hashdist/build.sh']' returned non-zero exit status 1 > 2015/02/05 12:57:12 - ERROR: [package:run_job] command failed > (code=1); raising > > > > I have no idea what is going on. Any ideas? Sure, you have to look into CMake logs what's going wrong /afs/hpc2n.umu.se/home/b/bbrydsoe/.hashdist/tmp/vtk-izqbwqpiwzwf/_build/CMakeFiles/CMakeOutput.log /afs/hpc2n.umu.se/home/b/bbrydsoe/.hashdist/tmp/vtk-izqbwqpiwzwf/_build/CMakeFiles/CMakeError.log In case of troubles you can post the files (or just relevant content) here. BTW, do you need visualization facilities in DOLFIN on cluster installation at all? You could just remove VTK from hashdist profile. Jan > > > -Birgitte > _______________________________________________ fenics-support mailing list [email protected] http://fenicsproject.org/mailman/listinfo/fenics-support
