I got the following error
"python -sc "from ffc import *"
Traceback (most recent call last):
File "<string>", line 1, in <module>
File
"/home/zhangt/envs/fenics27/lib/python2.7/site-packages/ffc/__init__.py",
line 21, in <module>
from ffc.jitcompiler import jit
File
"/home/zhangt/envs/fenics27/lib/python2.7/site-packages/ffc/jitcompiler.py",
line 30, in <module>
import ufc
File
"/home/zhangt/envs/fenics27/lib/python2.7/site-packages/ufc/__init__.py",
line 7, in <module>
from .ufc import (cell,
File "/home/zhangt/envs/fenics27/lib/python2.7/site-packages/ufc/ufc.py",
line 32, in <module>
_ufc = swig_import_helper()
File "/home/zhangt/envs/fenics27/lib/python2.7/site-packages/ufc/ufc.py",
line 28, in swig_import_helper
_mod = imp.load_module('_ufc', fp, pathname, description)
ImportError: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by
/home/zhangt/envs/fenics27/lib/python2.7/site-packages/ufc/_ufc.so)"
2015-03-31 10:50 GMT-04:00 Juan Luis Cano <[email protected]>:
> Now this is really weird... I wonder what the problem can be. Could you
> try importing ffc directly?
>
> source activate fenics27
> conda list ffc
> python -sc "from ffc import *"
> On Mar 31, 2015 4:43 PM, "腾张" <[email protected]> wrote:
>
>> 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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