On Fri, Feb 20, 2015 at 11:46 AM, Martin <[email protected]> wrote: > On 02/19/2015 09:54 PM, Terje Kvernes wrote > > On RHEL7 hashstack / fenics-install.sh works very well. I use my own profile > to build nearly everything possible to make the installation very > self-contained and it’s very smooth. > > > Hello Terje, > > Thanks for your input. I'm on Centos 6.6 and although the install script > looks like it works really well, unfortunately it seemed like it almost > completed but something is not completely right... > > > ----------------- > $ curl -s http://fenicsproject.org/fenics-install.sh | bash > Created temporary directory /tmp/fenics-install.kET3YL for FEniCS > installation. > > Downloading HashDist... > Initialized empty Git repository in > /tmp/fenics-install.kET3YL/hashdist/.git/ > remote: Counting objects: 4775, done. > remote: Total 4775 (delta 0), reused 0 (delta 0) > Receiving objects: 100% (4775/4775), 2.13 MiB | 446 KiB/s, done. > Resolving deltas: 100% (2889/2889), done. > > Downloading HashStack... > Initialized empty Git repository in > /tmp/fenics-install.kET3YL/hashstack/.git/ > remote: Counting objects: 6211, done. > remote: Compressing objects: 100% (23/23), done. > remote: Total 6211 (delta 11), reused 0 (delta 0) > Receiving objects: 100% (6211/6211), 1.18 MiB | 493 KiB/s, done. > Resolving deltas: 100% (3699/3699), done. > > Downloading FEniCS Install... > Initialized empty Git repository in > /tmp/fenics-install.kET3YL/fenics-developer-tools/.git/ > remote: Counting objects: 242, done. > remote: Compressing objects: 100% (237/237), done. > remote: Total 242 (delta 146), reused 0 (delta 0) > Receiving objects: 100% (242/242), 103.61 KiB, done. > Resolving deltas: 100% (146/146), done. > > patching file pkgs/petsc/petsc.py > Hunk #1 succeeded at 88 (offset 8 lines). > patching file pkgs/petsc/petsc.yaml > patching file pkgs/dolfin/dolfin-cmake-find_path.patch > patching file pkgs/dolfin/dolfin.yaml > patching file pkgs/hypre.yaml > patching file pkgs/petsc/petsc.py > Hunk #3 succeeded at 91 with fuzz 2 (offset 8 lines). > Hunk #4 succeeded at 116 (offset 8 lines). > Hunk #5 succeeded at 140 (offset 8 lines). > patching file pkgs/hypre.yaml > patching file pkgs/petsc/petsc.py > Hunk #1 succeeded at 118 (offset 8 lines). > patching file pkgs/hypre.yaml > patching file pkgs/hypre.yaml > patching file pkgs/hypre.yaml > patching file pkgs/hypre.yaml > Ready to build FEniCS. This may take about 2 hours. > > The following build types are supported: > > [0] development version of FEniCS [default] > [1] latest stable version of FEniCS, currently 1.5 > [2] only dependencies, including e.g. MPI, PETSc, Swig, Boost > > Please select build type [0, 1, 2]: > 1 > Using HashDist profile > /tmp/fenics-install.kET3YL/fenics-developer-tools/install/profiles/fenics.Linux.yaml. > > Stable build requested. > > Starting build... > > /tmp/fenics-install.kET3YL/hashdist/hashdist/formats/marked_yaml.py:72: > DeprecationWarning: object.__init__() takes no parameters > cls.__init__(self, x) > Downloading > http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/parmetis-4.0.3.tar.gz... > [=========================] 100.0% (5.3MB of 5.3MB) 0.327MB/s ETA 0s 15s > [parmetis] Building parmetis/3gybo4badomn, follow log with: > [parmetis] tail -f > /home/laptop/.hashdist/tmp/parmetis-3gybo4badomn/build.log > Downloading > http://www.cise.ufl.edu/research/sparse/SuiteSparse/SuiteSparse-4.0.2.tar.gz... > [=========================] 100.0% (21.4MB of 21.4MB) 0.207MB/s ETA 0s 0s > [suitesparse] Building suitesparse/msvbuax5rd2z, follow log with: > [suitesparse] tail -f > /home/laptop/.hashdist/tmp/suitesparse-msvbuax5rd2z/build.log > Downloading http://mirrors.kernel.org/gnu/gmp/gmp-5.1.3.tar.bz2... > > [ERROR] Unhandled Exception in Download: zero length field name in format > Downloading http://mirrors.kernel.org/gnu/gmp/gmp-5.1.3.tar.bz2... > > [ERROR] Unhandled Exception in Download: zero length field name in format > Downloading http://mirrors.kernel.org/gnu/gmp/gmp-5.1.3.tar.bz2... > [=========================] 100.0% (2.1MB of 2.1MB) 0.323MB/s ETA 0s > [gmp] Building gmp/vadkrj43wtyr, follow log with: > [gmp] tail -f /home/laptop/.hashdist/tmp/gmp-vadkrj43wtyr/build.log > [launcher] Building launcher/wvmh5uvayzv3, follow log with: > [launcher] tail -f > /home/laptop/.hashdist/tmp/launcher-wvmh5uvayzv3/build.log > Downloading > http://downloads.sourceforge.net/project/libpng/zlib/1.2.7/zlib-1.2.7.tar.bz2... > [=========================] 100.0% (0.5MB of 0.5MB) 0.352MB/s ETA 0s > [zlib] Building zlib/3el5ccejre7b, follow log with: > [zlib] tail -f /home/laptop/.hashdist/tmp/zlib-3el5ccejre7b/build.log > Downloading http://xmlsoft.org/sources/libxml2-2.9.1.tar.gz... > [=========================] 100.0% (4.9MB of 4.9MB) 1.766MB/s ETA 0s > [libxml2] Building libxml2/rnluwaluut6h, follow log with: > [libxml2] tail -f > /home/laptop/.hashdist/tmp/libxml2-rnluwaluut6h/build.log > Downloading http://download.osgeo.org/libtiff/tiff-4.0.3.tar.gz... > [=========================] 100.0% (2.0MB of 2.0MB) 0.206MB/s ETA 0s > [libtiff] Building libtiff/pignbw7m5fpk, follow log with: > [libtiff] tail -f > /home/laptop/.hashdist/tmp/libtiff-pignbw7m5fpk/build.log > Downloading > http://download.savannah.gnu.org/releases/freetype/freetype-2.4.11.tar.gz... > [=========================] 100.0% (2.0MB of 2.0MB) 2.325MB/s ETA 0s > [freetype] Building freetype/3j5vs5xri633, follow log with: > [freetype] tail -f > /home/laptop/.hashdist/tmp/freetype-3j5vs5xri633/build.log > Downloading > http://sourceforge.net/projects/libpng/files/libpng16/older-releases/1.6.6/libpng-1.6.6.tar.gz... > [=========================] 100.0% (1.2MB of 1.2MB) 0.449MB/s ETA 0s > [png] Building png/q24b4y6ojqdw, follow log with: > [png] tail -f /home/laptop/.hashdist/tmp/png-q24b4y6ojqdw/build.log > Downloading > http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8.13/src/hdf5-1.8.13.tar.bz2... > [=========================] 100.0% (9.1MB of 9.1MB) 0.206MB/s ETA 0s 10s > [hdf5] Building hdf5/526csz6keqgw, follow log with: > [hdf5] tail -f /home/laptop/.hashdist/tmp/hdf5-526csz6keqgw/build.log > Downloading http://ftp.gnu.org/gnu/bison/bison-3.0.tar.gz... > [=========================] 100.0% (3.1MB of 3.1MB) 0.119MB/s ETA 0s 11s > [bison] Building bison/jri2642x26uh, follow log with: > [bison] tail -f /home/laptop/.hashdist/tmp/bison-jri2642x26uh/build.log > Downloading http://www.mpfr.org/mpfr-3.1.2/mpfr-3.1.2.tar.bz2... > [ERROR] urllib failed to download (reason: [Errno -2] Name or service not > known): http://www.mpfr.org/mpfr-3.1.2/mpfr-3.1.2.tar.bz2 > Downloading http://www.mpfr.org/mpfr-3.1.2/mpfr-3.1.2.tar.bz2... > [=========================] 100.0% (1.2MB of 1.2MB) 0.245MB/s ETA 0s 14s > [mpfr] Building mpfr/vxwmnxjsshse, follow log with: > [mpfr] tail -f /home/laptop/.hashdist/tmp/mpfr-vxwmnxjsshse/build.log > Downloading > http://fenicsproject.org/pub/software/contrib/scotch_6.0.0_esmumps.tar.gz... > [=========================] 100.0% (4.3MB of 4.3MB) 2.793MB/s ETA 0s > [scotch] Building scotch/2xawkbuuknog, follow log with: > [scotch] tail -f /home/laptop/.hashdist/tmp/scotch-2xawkbuuknog/build.log > Downloading > http://rabbit.dereferenced.org/~nenolod/distfiles/pkgconf-0.9.6.tar.bz2... > [=========================] 100.0% (0.1MB of 0.1MB) 0.452MB/s ETA 0s > [pkg-config] Building pkg-config/pjksilnbb4iy, follow log with: > [pkg-config] tail -f > /home/laptop/.hashdist/tmp/pkg-config-pjksilnbb4iy/build.log > Downloading https://www.openssl.org/source/openssl-1.0.1g.tar.gz... > [=========================] 100.0% (4.3MB of 4.3MB) 2.995MB/s ETA 0s > [openssl] Building openssl/rllrkhgb6wbe, follow log with: > [openssl] tail -f > /home/laptop/.hashdist/tmp/openssl-rllrkhgb6wbe/build.log > Downloading http://python.org/ftp/python/2.7.8/Python-2.7.8.tgz... > [=========================] 100.0% (14.2MB of 14.2MB) 0.821MB/s ETA 0s > [python] Building python/orrcxy7cg2hd, follow log with: > [python] tail -f /home/laptop/.hashdist/tmp/python-orrcxy7cg2hd/build.log > Downloading > https://bitbucket.org/fenics-project/uflacs/downloads/uflacs-1.5.0.tar.gz... > [=========================] 100.0% (1.3MB of 1.3MB) 0.098MB/s ETA 0s > [uflacs] Building uflacs/vl2bjn5qbriw, follow log with: > [uflacs] tail -f /home/laptop/.hashdist/tmp/uflacs-vl2bjn5qbriw/build.log > Downloading > https://pypi.python.org/packages/source/i/ipython/ipython-2.3.0.tar.gz... > [=========================] 100.0% (11.4MB of 11.4MB) 0.154MB/s ETA 0s 0s > [ipython] Building ipython/c2e64kwdtan4, follow log with: > [ipython] tail -f > /home/laptop/.hashdist/tmp/ipython-c2e64kwdtan4/build.log > Downloading > https://pypi.python.org/packages/source/P/Pygments/Pygments-1.6.tar.gz... > [=========================] 100.0% (1.4MB of 1.4MB) 0.593MB/s ETA 0s > [pygments] Building pygments/z3ryl4uu4fjk, follow log with: > [pygments] tail -f > /home/laptop/.hashdist/tmp/pygments-z3ryl4uu4fjk/build.log > Downloading > https://pypi.python.org/packages/source/t/tornado/tornado-3.1.1.tar.gz... > [=========================] 100.0% (0.4MB of 0.4MB) 2.480MB/s ETA 0s > [tornado] Building tornado/zedf2ypeioia, follow log with: > [tornado] tail -f > /home/laptop/.hashdist/tmp/tornado-zedf2ypeioia/build.log > Downloading http://cython.org/release/Cython-0.19.2.tar.gz... > [=========================] 100.0% (1.3MB of 1.3MB) 0.163MB/s ETA 0s > [cython] Building cython/syizlj7mkisb, follow log with: > [cython] tail -f /home/laptop/.hashdist/tmp/cython-syizlj7mkisb/build.log > Downloading > https://pypi.python.org/packages/source/d/docutils/docutils-0.10.tar.gz... > [=========================] 100.0% (1.5MB of 1.5MB) 1.412MB/s ETA 0s > [docutils] Building docutils/plqp77g72ls7, follow log with: > [docutils] tail -f > /home/laptop/.hashdist/tmp/docutils-plqp77g72ls7/build.log > Downloading > https://github.com/sympy/sympy/releases/download/sympy-0.7.5/sympy-0.7.5.tar.gz... > [=========================] 100.0% (5.7MB of 5.7MB) 0.460MB/s ETA 0s > [sympy] Building sympy/fdwp2btihc4m, follow log with: > [sympy] tail -f /home/laptop/.hashdist/tmp/sympy-fdwp2btihc4m/build.log > Downloading http://downloads.sourceforge.net/numpy/numpy-1.8.2.tar.gz... > [=========================] 100.0% (3.6MB of 3.6MB) 1.098MB/s ETA 0s > [numpy] Building numpy/7ce6ttlbgjgv, follow log with: > [numpy] tail -f /home/laptop/.hashdist/tmp/numpy-7ce6ttlbgjgv/build.log > [mpi4py] Building mpi4py/2dpcoy6ojdp2, follow log with: > [mpi4py] tail -f /home/laptop/.hashdist/tmp/mpi4py-2dpcoy6ojdp2/build.log > Downloading > https://pypi.python.org/packages/source/p/pyzmq/pyzmq-14.3.1.tar.gz... > [=========================] 100.0% (0.9MB of 0.9MB) 0.258MB/s ETA 0s > [pyzmq] Building pyzmq/6cthje3usch7, follow log with: > [pyzmq] tail -f /home/laptop/.hashdist/tmp/pyzmq-6cthje3usch7/build.log > Downloading > https://bitbucket.org/fenics-project/ufl/downloads/ufl-1.5.0.tar.gz... > [=========================] 100.0% (0.3MB of 0.3MB) 0.336MB/s ETA 0s > [ufl] Building ufl/3wxuowubijc6, follow log with: > [ufl] tail -f /home/laptop/.hashdist/tmp/ufl-3wxuowubijc6/build.log > Downloading http://downloads.sourceforge.net/swig/swig-3.0.2.tar.gz... > [=========================] 100.0% (5.4MB of 5.4MB) 0.683MB/s ETA 0s > [swig] Building swig/mrfq3x4qfa36, follow log with: > [swig] tail -f /home/laptop/.hashdist/tmp/swig-mrfq3x4qfa36/build.log > Downloading > https://bitbucket.org/fenics-project/ffc/downloads/ffc-1.5.0.tar.gz... > [=========================] 100.0% (0.4MB of 0.4MB) 0.171MB/s ETA 0s > [ffc] Building ffc/5inibm75la4y, follow log with: > [ffc] tail -f /home/laptop/.hashdist/tmp/ffc-5inibm75la4y/build.log > Downloading > https://bitbucket.org/fenics-project/fiat/downloads/fiat-1.5.0.tar.gz... > [=========================] 100.0% (0.1MB of 0.1MB) 0.094MB/s ETA 0s > [fiat] Building fiat/et37hxlwxn6k, follow log with: > [fiat] tail -f /home/laptop/.hashdist/tmp/fiat-et37hxlwxn6k/build.log > Downloading > https://bitbucket.org/fenics-project/instant/downloads/instant-1.5.0.tar.gz... > [=========================] 100.0% (0.1MB of 0.1MB) 0.097MB/s ETA 0s > [instant] Building instant/ubfb4oksry62, follow log with: > [instant] tail -f > /home/laptop/.hashdist/tmp/instant-ubfb4oksry62/build.log > Downloading http://downloads.sourceforge.net/boost/boost_1_55_0.tar.bz2... > [=========================] 100.0% (55.5MB of 55.5MB) 0.651MB/s ETA 0s 0s > [boost] Building boost/xmgetfsbrztb, follow log with: > [boost] tail -f /home/laptop/.hashdist/tmp/boost-xmgetfsbrztb/build.log > Downloading > http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-lite-3.5.2.tar.gz... > [=========================] 100.0% (7.2MB of 7.2MB) 0.208MB/s ETA 0s 12s > [petsc] Building petsc/ehpcasna2fya, follow log with: > [petsc] tail -f /home/laptop/.hashdist/tmp/petsc-ehpcasna2fya/build.log > [petsc4py] Building petsc4py/b3nw63jqeadz, follow log with: > [petsc4py] tail -f > /home/laptop/.hashdist/tmp/petsc4py-b3nw63jqeadz/build.log > Downloading > http://www.grycap.upv.es/slepc/download/download.php?filename=slepc-3.5.2.tar.gz... > [=========================] 100.0% (3.0MB of 3.0MB) 0.669MB/s ETA 0s > [slepc] Building slepc/pbbvorls3nl6, follow log with: > [slepc] tail -f /home/laptop/.hashdist/tmp/slepc-pbbvorls3nl6/build.log > Downloading > https://bitbucket.org/slepc/slepc4py/downloads/slepc4py-3.5.1.tar.gz... > [=========================] 100.0% (0.7MB of 0.7MB) 0.404MB/s ETA 0s > [slepc4py] Building slepc4py/jqs7mmx7bu4e, follow log with: > [slepc4py] tail -f > /home/laptop/.hashdist/tmp/slepc4py-jqs7mmx7bu4e/build.log > Downloading > https://pypi.python.org/packages/source/s/setuptools/setuptools-3.4.3.tar.gz... > [=========================] 100.0% (0.8MB of 0.8MB) 1.018MB/s ETA 0s > [setuptools] Building setuptools/pmldlh6jt5iy, follow log with: > [setuptools] tail -f > /home/laptop/.hashdist/tmp/setuptools-pmldlh6jt5iy/build.log > Downloading > https://pypi.python.org/packages/source/p/pyparsing/pyparsing-2.0.1.zip... > [=========================] 100.0% (1.2MB of 1.2MB) 1.427MB/s ETA 0s > [pyparsing] Building pyparsing/5qpv4m6kaq4c, follow log with: > [pyparsing] tail -f > /home/laptop/.hashdist/tmp/pyparsing-5qpv4m6kaq4c/build.log > Downloading http://www.vtk.org/files/release/5.10/vtk-5.10.1.tar.gz... > [=========================] 100.0% (23.7MB of 23.7MB) 0.335MB/s ETA 0s 0s > [vtk] Building vtk/zh4ul3mzm3c5, follow log with: > [vtk] tail -f /home/laptop/.hashdist/tmp/vtk-zh4ul3mzm3c5/build.log > [vtk|ERROR] Command '[u'/bin/bash', '_hashdist/build.sh']' returned non-zero > exit status 1 > [vtk|ERROR] command failed (code=1); raising > ----------------- > > > I've looked into the > /home/laptop/.hashdist/tmp/vtk-zh4ul3mzm3c5/_build/CMakeFiles/CMakeError.log > file: > > At least one problem seems to be this: > ----- > /laptop/.hashdist/bld/python/orrcxy7cg2hd/lib > -L/home/laptop/.hashdist/bld/setuptools/pmldlh6jt5iy/lib > -Wl,-rpath=/home/laptop/.hashdist/bld/setuptools/pmldlh6jt5iy/lib > CMakeFiles/cmTryCompileExec972611203.dir/CheckFunctionExists.c.o -o > cmTryCompileExec972611203 -rdynamic -lpthread -lm > CMakeFiles/cmTryCompileExec972611203.dir/CheckFunctionExists.c.o: In > function `main': > CheckFunctionExists.c:(.text+0x15): undefined reference to > `glXGetProcAddressARB' > collect2: ld returned 1 exit status > gmake[1]: Leaving directory > `/home/laptop/.hashdist/tmp/vtk-zh4ul3mzm3c5/_build/CMakeFiles/CMakeTmp' > gmake[1]: *** [cmTryCompileExec972611203] Error 1 > gmake: *** [cmTryCompileExec972611203/fast] Error 2 > ----- > > hmm..... That's the problem with these big builts... I typically find that > somewhere things are not working which destroys everything... > > Does any of you have any suggestions for how to fix this? I would be > grateful for a few hints/advice, thank you.
Please upload /home/laptop/.hashdist/tmp/vtk-zh4ul3mzm3c5/build.log somewhere such that we can read it or send it to us as an attachment. Johannes _______________________________________________ fenics-support mailing list [email protected] http://fenicsproject.org/mailman/listinfo/fenics-support
