Thank you in advance for your help. Good night. Jing
2015/07/16 22:23:42 - INFO: [package:run_job] [ 36%] Building CXX object dolfin/CMakeFiles/dolfin.dir/graph/ZoltanPartition.cpp.o 2015/07/16 22:23:45 - INFO: [package:run_job] [ 37%] Building CXX object dolfin/CMakeFiles/dolfin.dir/io/base64.cpp.o 2015/07/16 22:23:46 - INFO: [package:run_job] [ 37%] Building CXX object dolfin/CMakeFiles/dolfin.dir/io/File.cpp.o 2015/07/16 22:23:49 - INFO: [package:run_job] [ 37%] Building CXX object dolfin/CMakeFiles/dolfin.dir/io/GenericFile.cpp.o 2015/07/16 22:23:50 - INFO: [package:run_job] [ 39%] Building CXX object dolfin/CMakeFiles/dolfin.dir/io/HDF5Attribute.cpp.o 2015/07/16 22:23:51 - INFO: [package:run_job] [ 39%] Building CXX object dolfin/CMakeFiles/dolfin.dir/io/HDF5File.cpp.o 2015/07/16 22:23:51 - INFO: [package:run_job] [ 39%] Building CXX object dolfin/CMakeFiles/dolfin.dir/io/HDF5Interface.cpp.o 2015/07/16 22:23:51 - INFO: [package:run_job] [ 40%] Building CXX object dolfin/CMakeFiles/dolfin.dir/io/HDF5Utility.cpp.o 2015/07/16 22:23:51 - INFO: [package:run_job] [ 40%] Building CXX object dolfin/CMakeFiles/dolfin.dir/io/pugixml.cpp.o 2015/07/16 22:23:53 - INFO: [package:run_job] [ 40%] Building CXX object dolfin/CMakeFiles/dolfin.dir/io/RAWFile.cpp.o 2015/07/16 22:23:54 - INFO: [package:run_job] [ 41%] Building CXX object dolfin/CMakeFiles/dolfin.dir/io/SVGFile.cpp.o 2015/07/16 22:23:56 - INFO: [package:run_job] [ 41%] Building CXX object dolfin/CMakeFiles/dolfin.dir/io/VTKFile.cpp.o 2015/07/16 22:24:02 - INFO: [package:run_job] [ 41%] Building CXX object dolfin/CMakeFiles/dolfin.dir/io/VTKWriter.cpp.o 2015/07/16 22:24:02 - INFO: [package:run_job] [ 43%] Building CXX object dolfin/CMakeFiles/dolfin.dir/io/X3DFile.cpp.o 2015/07/16 22:24:04 - INFO: [package:run_job] [ 43%] Building CXX object dolfin/CMakeFiles/dolfin.dir/io/XDMFFile.cpp.o 2015/07/16 22:24:04 - INFO: [package:run_job] [ 43%] Building CXX object dolfin/CMakeFiles/dolfin.dir/io/XDMFxml.cpp.o 2015/07/16 22:24:04 - INFO: [package:run_job] [ 44%] Building CXX object dolfin/CMakeFiles/dolfin.dir/io/XMLFile.cpp.o 2015/07/16 22:24:08 - INFO: [package:run_job] [ 44%] Building CXX object dolfin/CMakeFiles/dolfin.dir/io/XMLFunctionData.cpp.o 2015/07/16 22:24:12 - INFO: [package:run_job] In file included from /home/Jing/.hashdist/tmp/dolfin-4qvw2mljxwgt-1/dolfin/io/XMLMeshFunction.h:37:0, 2015/07/16 22:24:12 - INFO: [package:run_job] from /home/Jing/.hashdist/tmp/dolfin-4qvw2mljxwgt-1/dolfin/io/XMLFile.cpp:48: 2015/07/16 22:24:12 - INFO: [package:run_job] /home/Jing/.hashdist/tmp/dolfin-4qvw2mljxwgt-1/dolfin/io/XMLMeshValueCollection.h: In static member function 'static void dolfin::XMLMeshValueCollection::write(const dolfin::MeshValueCollection<T>&, std::string, pugi::xml_node)': 2015/07/16 22:24:12 - INFO: [package:run_job] /home/Jing/.hashdist/tmp/dolfin-4qvw2mljxwgt-1/dolfin/io/XMLMeshValueCollection.h:173:11: error: 'to_string' is not a member of 'std' 2015/07/16 22:24:12 - INFO: [package:run_job] = std::to_string(it->second).c_str();2015/07/16 22:24:12 - INFO: [package:run_job] ^2015/07/16 22:24:14 - INFO: [package:run_job] [ 44%] Building CXX object dolfin/CMakeFiles/dolfin.dir/io/XMLMesh.cpp.o 2015/07/16 22:24:15 - INFO: [package:run_job] [ 45%] Building CXX object dolfin/CMakeFiles/dolfin.dir/io/XMLParameters.cpp.o 2015/07/16 22:24:16 - INFO: [package:run_job] dolfin/CMakeFiles/dolfin.dir/build.make:2446: recipe for target 'dolfin/CMakeFiles/dolfin.dir/io/XMLFile.cpp.o' failed 2015/07/16 22:24:16 - INFO: [package:run_job] make[2]: *** [dolfin/CMakeFiles/dolfin.dir/io/XMLFile.cpp.o] Error 1 2015/07/16 22:24:16 - INFO: [package:run_job] make[2]: *** Waiting for unfinished jobs.... 2015/07/16 22:24:19 - INFO: [package:run_job] In file included from /home/Jing/.hashdist/tmp/dolfin-4qvw2mljxwgt-1/dolfin/io/XMLMeshFunction.h:37:0, 2015/07/16 22:24:19 - INFO: [package:run_job] from /home/Jing/.hashdist/tmp/dolfin-4qvw2mljxwgt-1/dolfin/io/XMLMesh.cpp:45: 2015/07/16 22:24:19 - INFO: [package:run_job] /home/Jing/.hashdist/tmp/dolfin-4qvw2mljxwgt-1/dolfin/io/XMLMeshValueCollection.h: In static member function 'static void dolfin::XMLMeshValueCollection::write(const dolfin::MeshValueCollection<T>&, std::string, pugi::xml_node)': 2015/07/16 22:24:19 - INFO: [package:run_job] /home/Jing/.hashdist/tmp/dolfin-4qvw2mljxwgt-1/dolfin/io/XMLMeshValueCollection.h:173:11: error: 'to_string' is not a member of 'std' 2015/07/16 22:24:19 - INFO: [package:run_job] = std::to_string(it->second).c_str();2015/07/16 22:24:19 - INFO: [package:run_job] ^2015/07/16 22:24:19 - INFO: [package:run_job] /home/Jing/.hashdist/tmp/dolfin-4qvw2mljxwgt-1/dolfin/io/XMLMesh.cpp: In static member function 'static void dolfin::XMLMesh::read_mesh(dolfin::Mesh&, pugi::xml_node)': 2015/07/16 22:24:19 - INFO: [package:run_job] /home/Jing/.hashdist/tmp/dolfin-4qvw2mljxwgt-1/dolfin/io/XMLMesh.cpp:134:22: error: 'to_string' is not a member of 'std' 2015/07/16 22:24:19 - INFO: [package:run_job] v_str[i] = "v" + std::to_string(i);2015/07/16 22:24:19 - INFO: [package:run_job] ^2015/07/16 22:24:20 - INFO: [package:run_job] dolfin/CMakeFiles/dolfin.dir/build.make:2492: recipe for target 'dolfin/CMakeFiles/dolfin.dir/io/XMLMesh.cpp.o' failed 2015/07/16 22:24:20 - INFO: [package:run_job] make[2]: *** [dolfin/CMakeFiles/dolfin.dir/io/XMLMesh.cpp.o] Error 1 2015/07/16 22:24:20 - INFO: [package:run_job] CMakeFiles/Makefile2:170: recipe for target 'dolfin/CMakeFiles/dolfin.dir/all' failed 2015/07/16 22:24:20 - INFO: [package:run_job] make[1]: *** [dolfin/CMakeFiles/dolfin.dir/all] Error 2 2015/07/16 22:24:20 - INFO: [package:run_job] Makefile:117: recipe for target 'all' failed2015/07/16 22:24:20 - INFO: [package:run_job] make: *** [all] Error 22015/07/16 22:24:20 - ERROR: [package:run_job] Command '[u'/bin/bash', '_hashdist/build.sh']' returned non-zero exit status 2 2015/07/16 22:24:20 - ERROR: [package:run_job] command failed (code=2); raising
On 7/16/2015 2:27 PM, Johannes Ring wrote:
[Cc fenics-support]On Thu, Jul 16, 2015 at 2:26 PM Johannes Ring <[email protected] <mailto:[email protected]>> wrote:On Thu, Jul 16, 2015 at 11:11 AM Jing-Rebecca Li <[email protected] <mailto:[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.customAnd$ 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-infoThis is only needed if you want to install the fenics-developer-tools. And I checked$ dolfin-version 1.5.0Then 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] <mailto:[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/bxiszvx5g3psquw42azpe3q3odi4gkl7freetype/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 LiResearch Scientist INRIA Saclay-Equipe DEFI CMAP, Ecole Polytechnique Route de Saclay, 91128, Palaiseau Cedex, France +33-(0)6-42-07-12-49 [email protected] <mailto:[email protected]>http://www.cmap.polytechnique.fr/~jingrebeccali/ <http://www.cmap.polytechnique.fr/%7Ejingrebeccali/>_______________________________________________ fenics-support mailing list [email protected] <mailto:[email protected]> http://fenicsproject.org/mailman/listinfo/fenics-support-- Jing-Rebecca LiResearch Scientist INRIA Saclay-Equipe DEFI CMAP, Ecole Polytechnique Route de Saclay, 91128, Palaiseau Cedex, France +33-(0)6-42-07-12-49 [email protected] <mailto:[email protected]>http://www.cmap.polytechnique.fr/~jingrebeccali/ <http://www.cmap.polytechnique.fr/%7Ejingrebeccali/>
-- Jing-Rebecca Li Research Scientist INRIA Saclay-Equipe DEFI CMAP, Ecole Polytechnique Route de Saclay, 91128, Palaiseau Cedex, France +33-(0)6-42-07-12-49 [email protected] http://www.cmap.polytechnique.fr/~jingrebeccali/
_______________________________________________ fenics-support mailing list [email protected] http://fenicsproject.org/mailman/listinfo/fenics-support
