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]
<mailto:[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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