On Mar 31, 2015 4:38 PM, "Juan Luis Cano" <[email protected]> wrote: > > Sorry, I meant this: > > python -sc "from dolfin import *"
If this prints nothing, then the demo_cahn-hilliard.py demo should run. Regards, > > On Mar 31, 2015 4:24 PM, "腾张" <[email protected]> wrote: >> >> Dear Juan Luis Cano, >> >> I removed the file under ~/.local/lib/python2.7 and re-do the installation, but still had the error information: >> >> $ python -s "from dolfin import *" >> python: can't open file 'from dolfin import *': [Errno 2] No such file or directory >> >> Now, by typing the command ~/envs/fenics27/bin/python -c "import sys; from pprint import pprint as p; p(sys.path)" >> >> I can only see the conda environment. >> >> Thanks a lot. >> >> Best, >> Teng >> >> 2015-03-31 9:57 GMT-04:00 Juan Luis Cano <[email protected]>: >>> >>> Hello Teng, >>> >>> On second thought, you might be facing this precise issue: >>> >>> https://github.com/conda/conda/issues/448 >>> >>> Back when I reported it, conda didn't play well with python installations in .local, and in your 'conda info -a' output I can see this line: >>> >>> user site dirs: ~/.local/lib/python2.7 >>> >>> This means that probably there is some kind of clash between the conda packages and the local ones. To verify, please type this: >>> >>> ~/envs/fenics27/bin/python -c "import sys; from pprint import pprint as p; p(sys.path)" >>> >>> And you will see a line reading >>> >>> '/home/teng/.local/lib/python2.7/site-packages' >>> >>> right before the one corresponding to the conda environment. If I am right, this *should* work: >>> >>> source activate fenics27 >>> python -s "from dolfin import *" >>> >>> If this is the case, there are three solutions: >>> >>> a) Remove everything under ~/.local/lib/python*. This is what I ended up doing in my local system, and now I manage everything with conda. >>> b) Always call python with the '-s' option: "don't add user site directory to sys.path". >>> c) Set the environment variable PYTHONNOUSERSITE. >>> >>> Fingers crossed! >>> >>> Regards, >>> >>> Juan Luis >>> >>> >>> On 2015-03-31 15:34, 腾张 wrote: >>>> >>>> Dear Juan Luis Cano, >>>> >>>> Thank you very much for your kind help. >>>> >>>> This is the information I got: >>>> >>>> $ echo $PYTHONPATH >>>> >>>> $ cd ~/envs/fenics27/share/dolfin/demo/documented/cahn-hilliard/python/ >>>> $ python demo_cahn-hilliard.py >>>> >>>> --------------------------------------------------- >>>> DOLFIN runtime dependency is not met. >>>> Install the following python module: 'ffc' >>>> and make sure its location is listed in PYTHONPATH. >>>> --------------------------------------------------- >>>> >>>> >>>> $ cd ~ >>>> $ python -c "from dolfin import *" >>>> >>>> --------------------------------------------------- >>>> DOLFIN runtime dependency is not met. >>>> Install the following python module: 'ffc' >>>> and make sure its location is listed in PYTHONPATH. >>>> >>>> I think something is wrong with the PYTHONPATH? >>>> >>>> Best, >>>> Teng >>>> >>>> >>>> 2015-03-31 2:11 GMT-04:00 Juan Luis Cano <[email protected]>: >>>>> >>>>> Hello Teng, >>>>> >>>>> The procedure seems totally correct, yet I don't understand why the import is failing. By the way, if you want to paste a long output I encourage you to try https://gist.github.com/. More things you can try: >>>>> >>>>> * Is 'demo_cahn-hilliard.py' really under ~/envs/fenics27 or you put it there on purpose? I suggest you to move it to a less conflictive location and try again, for example to /tmp or ~/Development. >>>>> * Or try running it from its default location: >>>>> >>>>> source activate fenics27 >>>>> cd ~/envs/fenics27/share/dolfin/demo/documented/cahn-hilliard/python/ >>>>> python demo_cahn-hilliard.py >>>>> >>>>> * Please print the contents of PYTHONPATH, just in case: >>>>> >>>>> source activate fenics27 >>>>> echo $PYTHONPATH >>>>> >>>>> * What happens if you try a plain import from Python? >>>>> >>>>> source activate fenics27 >>>>> cd ~ >>>>> python -c "from dolfin import *" >>>>> >>>>> I hope we can finally nail down this nasty problem! >>>>> >>>>> Regards, >>>>> >>>>> Juan Luis >>>>> >>>>> On 2015-03-30 22:59, 腾张 wrote: >>>>>> >>>>>> Dear Juan Luis Cano, >>>>>> >>>>>> It still does not work. Attached is the whole output during the installation. >>>>>> >>>>>> " conda create --name fenics27 python=2.7 >>>>>> Fetching package metadata: .. >>>>>> Solving package specifications: . >>>>>> Package plan for installation in environment /home/zhangt/envs/fenics27: >>>>>> >>>>>> The following packages will be downloaded: >>>>>> >>>>>> package | build >>>>>> ---------------------------|----------------- >>>>>> openssl-1.0.1k | 1 2.6 MB >>>>>> python-2.7.9 | 2 13.4 MB >>>>>> sqlite-3.8.4.1 | 1 2.5 MB >>>>>> system-5.8 | 2 170 KB >>>>>> tk-8.5.18 | 0 1.9 MB >>>>>> zlib-1.2.8 | 0 100 KB >>>>>> ------------------------------------------------------------ >>>>>> Total: 20.6 MB >>>>>> >>>>>> The following NEW packages will be INSTALLED: >>>>>> >>>>>> openssl: 1.0.1k-1 >>>>>> python: 2.7.9-2 >>>>>> readline: 6.2-2 (soft-link) >>>>>> sqlite: 3.8.4.1-1 >>>>>> system: 5.8-2 >>>>>> tk: 8.5.18-0 >>>>>> zlib: 1.2.8-0 >>>>>> >>>>>> Proceed ([y]/n)? y >>>>>> >>>>>> Fetching packages ... >>>>>> openssl-1.0.1k 100% |########################################################### >>>>>> python-2.7.9-2 100% |########################################################### >>>>>> sqlite-3.8.4.1 100% |########################################################### >>>>>> system-5.8-2.t 100% |########################################################### >>>>>> tk-8.5.18-0.ta 100% |########################################################### >>>>>> zlib-1.2.8-0.t 100% |########################################################### >>>>>> Extracting packages ... >>>>>> [ COMPLETE ] |######################################################## >>>>>> Linking packages ... >>>>>> [ COMPLETE ] |######################################################## >>>>>> # >>>>>> # To activate this environment, use: >>>>>> # $ source activate fenics27 >>>>>> # >>>>>> # To deactivate this environment, use: >>>>>> # $ source deactivate >>>>>> # >>>>>> [zhangt@eofe4 ~]$ source activate fenics27 >>>>>> discarding /cm/shared/engaging/anaconda/2.1.0/bin from PATH >>>>>> prepending /home/zhangt/envs/fenics27/bin to PATH >>>>>> (fenics27)[zhangt@eofe4 ~]$ conda install dolfin boost=1.55 eigen3 petsc petsc4p y instant ufl fiat ffc --channel juanlu001 >>>>>> Fetching package metadata: ... >>>>>> Solving package specifications: . >>>>>> Package plan for installation in environment /home/zhangt/envs/fenics27: >>>>>> >>>>>> The following packages will be downloaded: >>>>>> >>>>>> package | build >>>>>> ---------------------------|----------------- >>>>>> boost-1.55.0 | 1 6.2 MB >>>>>> cmake-3.0.1 | 0 10.3 MB >>>>>> dolfin-1.5.0 | np19py27_1 42.3 MB >>>>>> eigen3-3.2.1 | 0 524 KB >>>>>> fastcache-1.0.2 | py27_0 40 KB >>>>>> ffc-1.5.0 | np19py27_1 592 KB >>>>>> fiat-1.5.0 | np19py27_1 63 KB >>>>>> fontconfig-2.11.1 | 2 402 KB >>>>>> freetype-2.5.2 | 0 2.5 MB >>>>>> instant-1.5.0 | np19py27_1 45 KB >>>>>> mkl-11.1 | np19py27_p3 4 KB >>>>>> mkl-rt-11.1 | p0 100.1 MB >>>>>> mkl-service-1.0.0 | py27_p1 23 KB >>>>>> nose-1.3.4 | py27_1 189 KB >>>>>> numpy-1.9.2 | py27_0 7.8 MB >>>>>> pcre-8.31 | 0 534 KB >>>>>> petsc-3.5.2 | py27_1 16.8 MB >>>>>> petsc4py-3.5.1 | py27_1 3.1 MB >>>>>> qt-4.8.6 | 0 35.2 MB >>>>>> scipy-0.15.1 | np19py27_0 37.0 MB >>>>>> six-1.9.0 | py27_0 17 KB >>>>>> swig-3.0.2 | 0 1.9 MB >>>>>> sympy-0.7.6 | py27_0 6.2 MB >>>>>> ufl-1.5.0 | py27_1 290 KB >>>>>> vtk-5.10.1 | py27_1 92.2 MB >>>>>> ------------------------------------------------------------ >>>>>> Total: 364.1 MB >>>>>> >>>>>> The following NEW packages will be INSTALLED: >>>>>> >>>>>> boost: 1.55.0-1 >>>>>> cmake: 3.0.1-0 >>>>>> dolfin: 1.5.0-np19py27_1 >>>>>> eigen3: 3.2.1-0 >>>>>> fastcache: 1.0.2-py27_0 >>>>>> ffc: 1.5.0-np19py27_1 >>>>>> fiat: 1.5.0-np19py27_1 >>>>>> fontconfig: 2.11.1-2 >>>>>> freetype: 2.5.2-0 >>>>>> instant: 1.5.0-np19py27_1 >>>>>> libpng: 1.5.13-1 (soft-link) >>>>>> libxml2: 2.9.0-0 (soft-link) >>>>>> mkl: 11.1-np19py27_p3 >>>>>> mkl-rt: 11.1-p0 >>>>>> mkl-service: 1.0.0-py27_p1 >>>>>> mpi4py: 1.3-py27_0 (soft-link) >>>>>> mpich2: 1.4.1p1-0 (soft-link) >>>>>> nose: 1.3.4-py27_1 >>>>>> numexpr: 2.3.1-np19py27_0 (soft-link) >>>>>> numpy: 1.9.2-py27_0 >>>>>> pcre: 8.31-0 >>>>>> petsc: 3.5.2-py27_1 >>>>>> petsc4py: 3.5.1-py27_1 >>>>>> ply: 3.4-py27_0 (soft-link) >>>>>> qt: 4.8.6-0 >>>>>> scikit-learn: 0.15.2-np19py27_0 (soft-link) >>>>>> scipy: 0.15.1-np19py27_0 >>>>>> six: 1.9.0-py27_0 >>>>>> swig: 3.0.2-0 >>>>>> sympy: 0.7.6-py27_0 >>>>>> ufl: 1.5.0-py27_1 >>>>>> vtk: 5.10.1-py27_1 >>>>>> >>>>>> Proceed ([y]/n)? y >>>>>> >>>>>> Fetching packages ... >>>>>> boost-1.55.0-1 100% |################################| Time: 0:00:00 12.70 MB/s >>>>>> cmake-3.0.1-0. 100% |################################| Time: 0:00:01 10.48 MB/s >>>>>> dolfin-1.5.0-n 100% |################################| Time: 0:00:01 23.17 MB/s >>>>>> eigen3-3.2.1-0 100% |################################| Time: 0:00:00 3.17 MB/s >>>>>> fastcache-1.0. 100% |################################| Time: 0:00:00 1.33 MB/s >>>>>> ffc-1.5.0-np19 100% |################################| Time: 0:00:00 1.40 MB/s >>>>>> fiat-1.5.0-np1 100% |################################| Time: 0:00:00 1.07 MB/s >>>>>> fontconfig-2.1 100% |################################| Time: 0:00:00 2.09 MB/s >>>>>> freetype-2.5.2 100% |################################| Time: 0:00:00 5.15 MB/s >>>>>> instant-1.5.0- 100% |################################| Time: 0:00:00 1.03 MB/s >>>>>> mkl-11.1-np19p 100% |################################| Time: 0:00:00 2.72 MB/s >>>>>> mkl-rt-11.1-p0 100% |################################| Time: 0:00:03 34.82 MB/s >>>>>> mkl-service-1. 100% |################################| Time: 0:00:00 1.53 MB/s >>>>>> nose-1.3.4-py2 100% |################################| Time: 0:00:00 1.80 MB/s >>>>>> numpy-1.9.2-py 100% |################################| Time: 0:00:00 9.44 MB/s >>>>>> pcre-8.31-0.ta 100% |################################| Time: 0:00:00 2.76 MB/s >>>>>> petsc-3.5.2-py 100% |################################| Time: 0:00:00 20.50 MB/s >>>>>> petsc4py-3.5.1 100% |################################| Time: 0:00:00 7.92 MB/s >>>>>> qt-4.8.6-0.tar 100% |################################| Time: 0:00:01 18.91 MB/s >>>>>> scipy-0.15.1-n 100% |################################| Time: 0:00:01 21.09 MB/s >>>>>> six-1.9.0-py27 100% |################################| Time: 0:00:00 1.10 MB/s >>>>>> swig-3.0.2-0.t 100% |################################| Time: 0:00:00 4.59 MB/s >>>>>> sympy-0.7.6-py 100% |################################| Time: 0:00:00 8.70 MB/s >>>>>> ufl-1.5.0-py27 100% |################################| Time: 0:00:00 2.39 MB/s >>>>>> vtk-5.10.1-py2 100% |################################| Time: 0:00:03 31.01 MB/s >>>>>> Extracting packages ... >>>>>> [ COMPLETE ] |##########################################################################################################################################| 100% >>>>>> Linking packages ... >>>>>> [ COMPLETE ] |##########################################################################################################################################| 100% >>>>>> (fenics27)[zhangt@eofe4 ~]$ cd envs/fenics27/ >>>>>> (fenics27)[zhangt@eofe4 fenics27]$ python demo_cahn-hilliard.py >>>>>> >>>>>> --------------------------------------------------- >>>>>> DOLFIN runtime dependency is not met. >>>>>> Install the following python module: 'ffc' >>>>>> and make sure its location is listed in PYTHONPATH. >>>>>> ---------------------------------------------------" >>>>>> >>>>>> Thanks a lot for your kind help. >>>>>> >>>>>> Best, >>>>>> Teng >>>>> >>>>> >>>> >>> >>
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