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.
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