[Cc fenics-support]
On Thu, Jul 16, 2015 at 2:26 PM Johannes Ring <[email protected]> wrote: > On Thu, Jul 16, 2015 at 11:11 AM Jing-Rebecca Li <[email protected]> > wrote: > >> Dear Johannes, thank you very much for your reply. >> This is my first time installing fenics on any platform so I have a lot >> of questions unfortunately. >> (My former PhD student worked with fenics on Ubuntu but not on cygwin.) >> I haven't found a manual on installation so I am coming back to ask you >> for more directions. >> >> After I did >> ./install/fenics-install.sh local.yaml >> I didn't get any errors so I assume it's correctly installed... >> > > Great! Did you remove more than matplotlib from local.yaml? > > >> Then I did >> >> $ source fenics.custom >> >> And >> >> $ python setup.py install >> running install >> running build >> running build_scripts >> running install_scripts >> changing mode of >> /home/Jing/.hashdist/bld/profile/cvu7wnv5cjao/bin/fenics-install-all.sh to >> 755 >> changing mode of >> /home/Jing/.hashdist/bld/profile/cvu7wnv5cjao/bin/fenics-install-component.sh >> to 755 >> changing mode of >> /home/Jing/.hashdist/bld/profile/cvu7wnv5cjao/bin/fenics-install.sh to 755 >> changing mode of >> /home/Jing/.hashdist/bld/profile/cvu7wnv5cjao/bin/fenics-release.sh to 755 >> running install_egg_info >> Removing >> /home/Jing/.hashdist/bld/profile/cvu7wnv5cjao/lib/python2.7/site-packages/fenics_developer_tools-1.5-py2.7.egg-info >> Writing >> /home/Jing/.hashdist/bld/profile/cvu7wnv5cjao/lib/python2.7/site-packages/fenics_developer_tools-1.5-py2.7.egg-info >> >> > This is only needed if you want to install the fenics-developer-tools. > > >> And I checked >> >> $ dolfin-version >> 1.5.0 >> >> Then I copied >> >> $ cp >> /home/Jing/.hashdist/bld/dolfin/ycxvnuxrkzth/share/dolfin/demo/documented/poisson/python/demo_poisson.py >> . >> >> And I tried the demo >> >> $ python demo_poisson.py >> Traceback (most recent call last): >> File "demo_poisson.py", line 37, in <module> >> from dolfin import * >> File >> "/home/Jing/.hashdist/bld/profile/cvu7wnv5cjao/lib/python2.7/site-packages/dolfin/__init__.py", >> line 16, in <module> >> from . import cpp >> File >> "/home/Jing/.hashdist/bld/profile/cvu7wnv5cjao/lib/python2.7/site-packages/dolfin/cpp/__init__.py", >> line 42, in <module> >> exec("from . import %s" % module_name) >> File "<string>", line 1, in <module> >> File >> "/home/Jing/.hashdist/bld/profile/cvu7wnv5cjao/lib/python2.7/site-packages/dolfin/cpp/common.py", >> line 132, in <module> >> __pythonversion__ = "%d.%d.%d"%(tuple(map(int, [tmp[2], tmp[4], >> tmp[6]]))) >> ValueError: invalid literal for int() with base 10: 'a' >> >> >> So it's not getting the version number for python? >> Could you guide me through this? I haven't been able to find detailed >> installation instructions on the fenics website... >> > > This is a bug in DOLFIN 1.5.0 when using Python 2.7.10 that has been fixed > in the development version of DOLFIN. To use the development version, > replace this part of local.yaml: > > ffc: > fiat: > instant: > ufl: > dolfin: > > with this: > > ffc: > sources: > - key: git:9fa258309ebb94f441c993e949a42621f113ef34 > url: https://bitbucket.org/fenics-project/ffc.git > fiat: > sources: > - key: git:a1430d4ad9df22b58da2cbeb3de75063fe519cd6 > url: https://bitbucket.org/fenics-project/fiat.git > instant: > sources: > - key: git:6618f89725a0abef469aabc3e56ac7cbd407cb85 > url: https://bitbucket.org/fenics-project/instant.git > ufl: > sources: > - key: git:34f8129210c2c080b67c0ec5e16913e1218b3948 > url: https://bitbucket.org/fenics-project/ufl.git > dolfin: > sources: > - key: git:5ec6384529c117e06d2a65900e78759ada9761ab > url: https://bitbucket.org/fenics-project/dolfin.git > > > By the way, for running the C++ demos, I went into >> >> $ cd >> /home/Jing/.hashdist/bld/dolfin/ycxvnuxrkzth/share/dolfin/demo/documented/poisson/cpp/ >> >> and typed cmake . and make and ./demo_poisson.exe >> and I get >> >> $ ./demo_poisson.exe >> Solving linear variational problem. >> [Jing-PC:06712] *** Process received signal *** >> [Jing-PC:06712] Signal: Segmentation fault (11) >> [Jing-PC:06712] Signal code: (23) >> [Jing-PC:06712] Failing at address: 0x234000 >> Unable to print stack trace! >> [Jing-PC:06712] *** End of error message *** >> Segmentation fault (core dumped) >> >> > I am not sure. I think I will have to look into it myself, but that will > not be before mid august. > > Johannes > > > >> Thank you so much for any help you can give me! >> >> Sincerely, Jing-Rebecca Li >> >> >> On 7/15/2015 1:45 PM, Johannes Ring wrote: >> >> Hi, >> >> I had FEniCS working on Cygwin earlier this year using HashDist. I >> didn't use the fenics-install.sh script, but it is basically the same. >> >> The problem you have with matplotlib looks like a patch that cannot be >> applied to the version of matplotlib currently in hashstack. This is a bug >> and I will report it. >> >> To build without matplotlib, you can do the following: >> >> git clone >> https://bitbucket.org/fenics-project/fenics-developer-tools.git >> cd fenics-developer-tools >> cp install/profiles/fenics.Cygwin.yaml local.yaml >> >> Open local.yaml in your favorite editor and remove matplotlib and >> anything else you don't need. Finally, run: >> >> ./install/fenics-install.sh local.yaml >> >> Note that the profile (fenics.Cygwin.yaml) assumes that you have at >> least cmake, blas, lapack, swig, pkg-config, opengl headers and gcc already >> installed with Cygwin (I don't have the complete list unfortunately). >> >> Johannes >> >> On Mon, Jul 13, 2015 at 12:21 PM Jing-Rebecca Li < >> [email protected]> wrote: >> >> Hello, I am trying to install fenics on cygwin 64bit running on Window 7. >>> I just downloaded cygwin last week so I think all the packages are up to >>> date (gcc, etc). >>> >>> I tried out the script >>> >>> wget -O - http://fenicsproject.org/fenics-install.sh | bash >>> >>> and it was successful in installing a lot of components of fenics, ffc >>> (I needed to add swig to cygwin), vkt (I needed to add opengl, etc), but I >>> am stuck on matplotlib. Below is the build.log. By the way, is it >>> possible to provide only the core components of fenics in a build, without >>> all the visualization? I just would like to solve the PDE and save the >>> solution so I'd like to avoid installing anything extra. >>> >>> Thank you in advance for your help. I've already gotten much further >>> with installing fenics on cygwin with this new script than all my previous >>> attempts of the past years! Sincerely, Jing-Rebecca Li >>> >>> 2015/07/12 08:26:59 - INFO: [package:run_job] running [u'/bin/bash', >>> '_hashdist/build.sh'] >>> 2015/07/12 08:26:59 - INFO: [package:run_job] environment: >>> 2015/07/12 08:26:59 - INFO: [package:run_job] {'ARTIFACT': u' >>> */home/Jing/*.hashdist/bld/matplotlib/ayvuahxambp7', >>> 2015/07/12 08:26:59 - INFO: [package:run_job] 'BASH': u'/bin/bash', >>> 2015/07/12 08:26:59 - INFO: [package:run_job] 'BUILD': u' >>> */home/Jing/*.hashdist/tmp/matplotlib-ayvuahxambp7-4', >>> 2015/07/12 08:26:59 - INFO: [package:run_job] u'BZIP2_DIR': u' >>> */home/Jing/*.hashdist/bld/bzip2/bxiszvx5g3ps', >>> 2015/07/12 08:26:59 - INFO: [package:run_job] u'BZIP2_ID': >>> u'bzip2/bxiszvx5g3psquw42azpe3q3odi4gkl7', >>> 2015/07/12 08:26:59 - INFO: [package:run_job] u'FREETYPE_DIR': u' >>> */home/Jing/*.hashdist/bld/freetype/dg2tfjnamcnz', >>> 2015/07/12 08:26:59 - INFO: [package:run_job] u'FREETYPE_ID': >>> u'freetype/dg2tfjnamcnzfcy2jkkzlmuyjoeyh4j3', >>> 2015/07/12 08:26:59 - INFO: [package:run_job] 'HASHDIST_CPU_COUNT': '4', >>> 2015/07/12 08:26:59 - INFO: [package:run_job] 'HDIST_CONFIG': >>> '{"gc_roots":"*/home/Jing/*.hashdist/gcroots","build_stores":[{"dir":" >>> */home/Jing/*.hashdist/bld"}],"source_caches":[{"dir":"*/home/Jing/* >>> .hashdist/src"}],"cache":"*/home/Jing/*.hashdist/cache","build_temp":" >>> */home/Jing/*.hashdist/tmp"}', >>> 2015/07/12 08:26:59 - INFO: [package:run_job] 'HDIST_IMPORT': >>> u'bzip2/bxiszvx5g3psquw42azpe3q3odi4gkl7 >>> freetype/dg2tfjnamcnzfcy2jkkzlmuyjoeyh4j3 >>> numpy/nzwmnt25foajpcv665tqebacyoxem6vw >>> pkg-config/satmw7zew7c2iuseoajzctg57hgubgjb >>> png/nhgc5kurctteaj6b3z7ajjrzlgtueo4l >>> python/qlvjlzdbishmango7jzlj5b2nnx7qr7q >>> setuptools/v3ljecso2k6ln5omin6zxb5326v3cug5 >>> zlib/5oalmcorn2mrgjvqsdqij2g2t3eo4hro', >>> 2015/07/12 08:26:59 - INFO: [package:run_job] 'HDIST_IMPORT_PATHS': u' >>> */home/Jing/*.hashdist/bld/bzip2/bxiszvx5g3ps:*/home/Jing/* >>> .hashdist/bld/freetype/dg2tfjnamcnz:*/home/Jing/* >>> .hashdist/bld/numpy/nzwmnt25foaj:*/home/Jing/* >>> .hashdist/bld/pkg-config/satmw7zew7c2:*/home/Jing/* >>> .hashdist/bld/png/nhgc5kurctte:*/home/Jing/* >>> .hashdist/bld/python/qlvjlzdbishm:*/home/Jing/* >>> .hashdist/bld/setuptools/v3ljecso2k6l:*/home/Jing/*.hashdist/bld/zlib/5oalmcorn2mr', >>> >>> 2015/07/12 08:26:59 - INFO: [package:run_job] 'HDIST_VIRTUALS': '', >>> 2015/07/12 08:26:59 - INFO: [package:run_job] u'NUMPY_DIR': u' >>> */home/Jing/*.hashdist/bld/numpy/nzwmnt25foaj', >>> 2015/07/12 08:26:59 - INFO: [package:run_job] u'NUMPY_ID': >>> u'numpy/nzwmnt25foajpcv665tqebacyoxem6vw', >>> 2015/07/12 08:26:59 - INFO: [package:run_job] 'PATH': >>> u'*/home/Jing/*.hashdist/bld/freetype/dg2tfjnamcnz/bin:/usr/bin:/bin', >>> >>> 2015/07/12 08:26:59 - INFO: [package:run_job] u'PKG_CONFIG_DIR': u' >>> */home/Jing/*.hashdist/bld/pkg-config/satmw7zew7c2', >>> 2015/07/12 08:26:59 - INFO: [package:run_job] 'PKG_CONFIG_EXECUTABLE': >>> u'/usr/bin/pkgconfig', >>> 2015/07/12 08:26:59 - INFO: [package:run_job] u'PKG_CONFIG_ID': >>> u'pkg-config/satmw7zew7c2iuseoajzctg57hgubgjb', >>> 2015/07/12 08:26:59 - INFO: [package:run_job] 'PKG_CONFIG_PATH': u' >>> */home/Jing/*.hashdist/bld/png/nhgc5kurctte/lib/pkgconfig:*/home/Jing/*.hashdist/bld/freetype/dg2tfjnamcnz/lib/pkgconfig', >>> >>> 2015/07/12 08:26:59 - INFO: [package:run_job] u'PNG_DIR': u' >>> */home/Jing/*.hashdist/bld/png/nhgc5kurctte', >>> 2015/07/12 08:26:59 - INFO: [package:run_job] u'PNG_ID': >>> u'png/nhgc5kurctteaj6b3z7ajjrzlgtueo4l', >>> 2015/07/12 08:26:59 - INFO: [package:run_job] 'PWD': >>> u'*/home/Jing/*.hashdist/tmp/matplotlib-ayvuahxambp7-4', >>> >>> 2015/07/12 08:26:59 - INFO: [package:run_job] 'PYTHON': u' >>> */home/Jing/*.hashdist/bld/python/qlvjlzdbishm/bin/python', >>> 2015/07/12 08:26:59 - INFO: [package:run_job] 'PYTHONPATH': u' >>> */home/Jing/* >>> .hashdist/bld/setuptools/v3ljecso2k6l/lib/python2.7/site-packages: >>> */home/Jing/*.hashdist/bld/numpy/nzwmnt25foaj/lib/python2.7/site-packages', >>> >>> 2015/07/12 08:26:59 - INFO: [package:run_job] u'PYTHON_DIR': u' >>> */home/Jing/*.hashdist/bld/python/qlvjlzdbishm', >>> 2015/07/12 08:26:59 - INFO: [package:run_job] u'PYTHON_ID': >>> u'python/qlvjlzdbishmango7jzlj5b2nnx7qr7q', >>> 2015/07/12 08:26:59 - INFO: [package:run_job] u'SETUPTOOLS_DIR': u' >>> */home/Jing/*.hashdist/bld/setuptools/v3ljecso2k6l', >>> 2015/07/12 08:26:59 - INFO: [package:run_job] u'SETUPTOOLS_ID': >>> u'setuptools/v3ljecso2k6ln5omin6zxb5326v3cug5', >>> 2015/07/12 08:26:59 - INFO: [package:run_job] u'ZLIB_DIR': u' >>> */home/Jing/*.hashdist/bld/zlib/5oalmcorn2mr', >>> 2015/07/12 08:26:59 - INFO: [package:run_job] u'ZLIB_ID': >>> u'zlib/5oalmcorn2mrgjvqsdqij2g2t3eo4hro'} >>> 2015/07/12 08:26:59 - INFO: [package:run_job] patching file >>> lib/matplotlib/tri/_tri.cpp >>> 2015/07/12 08:26:59 - INFO: [package:run_job] Reversed (or previously >>> applied) patch detected! Assume -R? [n] >>> 2015/07/12 08:26:59 - INFO: [package:run_job] Apply anyway? [n] >>> 2015/07/12 08:26:59 - INFO: [package:run_job] Skipping patch. >>> 2015/07/12 08:26:59 - INFO: [package:run_job] 1 out of 1 hunk ignored -- >>> saving rejects to file lib/matplotlib/tri/_tri.cpp.rej >>> 2015/07/12 08:26:59 - INFO: [package:run_job] patching file >>> lib/matplotlib/tri/_tri.h >>> 2015/07/12 08:26:59 - INFO: [package:run_job] Reversed (or previously >>> applied) patch detected! Assume -R? [n] >>> 2015/07/12 08:26:59 - INFO: [package:run_job] Apply anyway? [n] >>> 2015/07/12 08:26:59 - INFO: [package:run_job] Skipping patch. >>> 2015/07/12 08:26:59 - INFO: [package:run_job] 1 out of 1 hunk ignored -- >>> saving rejects to file lib/matplotlib/tri/_tri.h.rej >>> 2015/07/12 08:26:59 - ERROR: [package:run_job] Command '[u'/bin/bash', >>> '_hashdist/build.sh']' returned non-zero exit status 1 >>> 2015/07/12 08:26:59 - ERROR: [package:run_job] command failed (code=1); >>> raising >>> >> -- >>> Jing-Rebecca Li >>> Research Scientist >>> INRIA Saclay-Equipe DEFI >>> CMAP, Ecole Polytechnique >>> Route de Saclay, 91128, Palaiseau Cedex, France >>> +33-(0)[email protected] >>> >>> http://www.cmap.polytechnique.fr/~jingrebeccali/ >>> >>> _______________________________________________ >>> fenics-support mailing list >>> [email protected] >>> http://fenicsproject.org/mailman/listinfo/fenics-support >>> >> >> -- >> Jing-Rebecca Li >> Research Scientist >> INRIA Saclay-Equipe DEFI >> CMAP, Ecole Polytechnique >> Route de Saclay, 91128, Palaiseau Cedex, France >> +33-(0)[email protected]http://www.cmap.polytechnique.fr/~jingrebeccali/ >> >>
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