It still does not work "python -sc "from dolfin import *"
--------------------------------------------------- DOLFIN runtime dependency is not met. Install the following python module: 'ffc' and make sure its location is listed in PYTHONPATH. --------------------------------------------------- " Best, Teng 2015-03-31 10:38 GMT-04:00 Juan Luis Cano <[email protected]>: > 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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