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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