Sorry, I meant this: python -sc "from dolfin import *" 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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