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
2015-03-30 16:35 GMT-04:00 Juan Luis Cano <[email protected]>:
> I see a problem with boost, for some reason it downloaded the version
> coming from Anaconda and not the one I compiled. Try installing the version
> from my channel:
>
> conda install boost=1.55 --channel=juanlu001
>
> If you still get an error, please copy the entire message from top to
> bottom.
>
>
> On 2015-03-30 22:31, 腾张 wrote:
>
> Dear
>
>
> I tried to add the command you mentioned, but it does not work neither
> with the same error information
>
> ---------------------------------------------------
> DOLFIN runtime dependency is not met.
> Install the following python module: 'ffc'
> and make sure its location is listed in PYTHONPATH.
> ---------------------------------------------------
>
> The output of "conda list" follows:
>
> "# packages in environment at /home/zhangt/envs/fenics27:
> #
> boost 1.57.0 0
> 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
> libxml2 2.9.0 0
> mkl 11.1 np19py27_p3
> mkl-rt 11.1 p0
> mkl-service 1.0.0 py27_p1
> mpi4py 1.3 py27_0
> mpich2 1.4.1p1 0
> nose 1.3.4 py27_1
> numexpr 2.3.1 np19py27_0
> numpy 1.9.2 py27_0
> openssl 1.0.1k 1
> pcre 8.31 0
> petsc 3.5.2 py27_1
> petsc4py 3.5.1 py27_1
> ply 3.4 py27_0
> python 2.7.9 2
> qt 4.8.6 0
> readline 6.2 2
> scikit-learn 0.15.2 np19py27_0
> scipy 0.15.1 np19py27_0
> six 1.9.0 py27_0
> sqlite 3.8.4.1 1
> swig 3.0.2 0
> sympy 0.7.6 py27_0
> system 5.8 2
> tk 8.5.18 0
> ufl 1.5.0 py27_1
> vtk 5.10.1 py27_1
> zlib 1.2.8 0
> "
> I think the error information in my first email is because I did not use
> the command "source activate fenics27" first.
>
> Thanks a lot.
>
> Best,
> Teng
> 2015-03-30 14:36 GMT-04:00 Juan Luis Cano <[email protected]>:
>
>> Hello,
>>
>> If I understood correctly the error message changed when you manually
>> installed dolfin. Could you please try and install ffc and the rest of the
>> requirements too? In principle conda should resolve the dependencies itself
>> but perhaps something is not working well.
>>
>> conda install boost eigen3 petsc petsc4py instant ufl fiat ffc --channel
>> juanlu001
>>
>> Please post also the output of 'conda list' with fenics27 activated.
>>
>> Regards,
>>
>> Juan Luis Cano
>>
>>
>> On 2015-03-30 18:12, 腾张 wrote:
>>
>> Dear Juan Luis Cano,
>>
>> Thanks a lot for your kind reply.
>>
>> The following is the result from the command "which python" after 'source
>> activate fenics27'. I tried to install with the command you recommend "conda
>> install dolfin --channel juanlu001", but it still does not work.
>>
>> ~/envs/fenics27/bin/python
>>
>>
>> The following is the result I got with the command "conda info -a"
>>
>> "Current conda install:
>>
>> platform : linux-64
>> conda version : 3.7.0
>> conda-build version : 1.8.2
>> python version : 2.7.8.final.0
>> requests version : 2.4.1
>> root environment : /cm/shared/engaging/anaconda/2.1.0 (read only)
>> default environment : /home/zhangt/envs/fenics27
>> envs directories : /home/zhangt/envs
>> /cm/shared/engaging/anaconda/2.1.0/envs
>> package cache : /home/zhangt/envs/.pkgs
>> /cm/shared/engaging/anaconda/2.1.0/pkgs
>> channel URLs : http://repo.continuum.io/pkgs/free/linux-64/
>> http://repo.continuum.io/pkgs/pro/linux-64/
>> config file : None
>> is foreign system : False
>>
>> # conda environments:
>> #
>> fenics27 * /home/zhangt/envs/fenics27
>> root /cm/shared/engaging/anaconda/2.1.0
>>
>> sys.version: 2.7.8 |Anaconda 2.1.0 (64-bit)| (default...
>> sys.prefix: /cm/shared/engaging/anaconda/2.1.0
>> sys.executable: /cm/shared/engaging/anaconda/2.1.0/bin/python
>> conda location:
>> /cm/shared/engaging/anaconda/2.1.0/lib/python2.7/site-packages/c
>>
>> onda
>> conda-build: /cm/shared/engaging/anaconda/2.1.0/bin/conda-build
>> conda-convert: /cm/shared/engaging/anaconda/2.1.0/bin/conda-convert
>> conda-develop: /cm/shared/engaging/anaconda/2.1.0/bin/conda-develop
>> conda-index: /cm/shared/engaging/anaconda/2.1.0/bin/conda-index
>> conda-metapackage:
>> /cm/shared/engaging/anaconda/2.1.0/bin/conda-metapackage
>> conda-pipbuild: /cm/shared/engaging/anaconda/2.1.0/bin/conda-pipbuild
>> conda-skeleton: /cm/shared/engaging/anaconda/2.1.0/bin/conda-skeleton
>> user site dirs: ~/.local/lib/python2.7
>>
>> CIO_TEST: <not set>
>> CONDA_DEFAULT_ENV: fenics27
>> CONDA_ENVS_PATH: <not set>
>> LD_LIBRARY_PATH:
>> /cm/shared/engaging/anaconda/2.1.0/lib:/cm/shared/engaging/open
>>
>>
>> mpi/1.8.3/lib:/cm/shared/engaging/python/2.7.8/lib:/cm/shared/apps/gcc/4.8.2/lib
>>
>> :/cm/shared/apps/gcc/4.8.2/lib64
>> PATH:
>> /home/zhangt/envs/fenics27/bin:/cm/shared/engaging/openmpi/1.8.3/bin:/cm/s
>>
>>
>>
>> hared/engaging/python/2.7.8/bin:/cm/shared/apps/gcc/4.8.2/bin:/usr/lib64/qt-3.3/
>>
>>
>>
>> bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/opt/ibutils/bi
>>
>> n:/sbin:/usr/sbin:/opt/dell/srvadmin/bin:/home/zhangt/bin
>> PYTHONHOME: <not set>
>> PYTHONPATH: <not set>
>>
>> License directories:
>> /cm/shared/engaging/anaconda/2.1.0/licenses
>> /home/zhangt/.continuum
>> License files (license*.txt):
>> Package/feature end dates:"
>>
>> When running the demo, the error is
>>
>> "DOLFIN runtime dependency is not met.
>> Install the following python module: 'ffc'
>> and make sure its location is listed in PYTHONPATH."
>>
>> I think the reason may probably be the PYTHONPATH.
>>
>> Best,
>> Teng
>>
>> 2015-03-30 3:27 GMT-04:00 Juan Luis Cano <[email protected]>:
>>
>>> Hello,
>>>
>>> Could you post the result of 'which python' after you do 'source
>>> activate fenics27'? Perhaps doing
>>>
>>> conda install dolfin --channel juanlu001
>>>
>>> works instead. In any case, please post the result of 'conda info -a'
>>> too. Did you download the demo from source or do you have it installed in
>>> your path already?
>>>
>>> Juan Luis
>>> On Mar 30, 2015 12:10 AM, "腾张" <[email protected]> wrote:
>>>
>>>> Dear All,
>>>>
>>>> I installed fenics with conda on our university cluster with the
>>>> following command:
>>>>
>>>> "conda create --name fenics27 python=2.7
>>>>
>>>> source activate fenics27
>>>>
>>>> conda install fenics --channel juanlu001"
>>>>
>>>> The process went well and I have a folder name "envs" containing
>>>> "fenics27" in my home folder. When I tried to run some demo, e,g,
>>>> "demo_cahn-hilliard.py", I got the error:
>>>>
>>>> "Traceback (most recent call last):
>>>> File "demo_cahn-hilliard.py", line 27, in <module>
>>>> from dolfin import *
>>>> ImportError: No module named dolfin"
>>>>
>>>> I think I need some command to add the path library of fenics to my
>>>> system, but I did not how to do that. Could anyone help me on this?
>>>>
>>>> I also tried the command "ldd
>>>> <INSTALL_PATH>/anaconda/envs/fenics27/lib/python2.7/site-packages/dolfin/cpp/_common.so"
>>>> but it still does not work.
>>>>
>>>> Thanks a lot.
>>>>
>>>> Best,
>>>> Teng
>>>>
>>>> _______________________________________________
>>>> fenics mailing list
>>>> [email protected]
>>>> http://fenicsproject.org/mailman/listinfo/fenics
>>>>
>>>>
>>
>>
>
>
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