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astrojuanlu / fenics-recipes

This repository contains conda recipes for the FEniCS libraries
The Unlicense
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unable to set up conda environment -- ImportError: libboost_system.so.1.57.0: cannot open shared object file: No such file or directory #58

Open porphyrius opened 8 years ago

porphyrius commented 8 years ago

Dear Juanlu001,

I am sorry to bother you again, but every time I install a new Ubuntu system (now 15.10) I incur in troubles with setting up fenics in existing conda installations. I tried to follow your previous suggestions, but with no avail. I am testing my installation by running a program 'brwalk.py' which makes calls to dolfin, scipy, matplotlib. The feeling is that there is a problem with incompatible versions, but I cannot debug the problem. I am posting here my tentatives in the hope that you can get a hint from them at what is going wrong. 

andrea@brahma:~/Desktop/ArhGAP15/simulazione.2/1000$ conda create -n fenics27 python=2.7  

Fetching package metadata: ......
Solving package specifications: .........

Package plan for installation in environment /home/andrea/anaconda2/envs/fenics27:

The following NEW packages will be INSTALLED:

    openssl:    1.0.2g-0     
    pip:        8.1.1-py27_1 
    python:     2.7.11-0     
    readline:   6.2-2        
    setuptools: 20.7.0-py27_0
    sqlite:     3.9.2-0      
    tk:         8.5.18-0     
    wheel:      0.29.0-py27_0
    zlib:       1.2.8-0      

Proceed ([y]/n)? y

Linking packages ...
[      COMPLETE      ]|###################################################| 100%

andrea@brahma:~/Desktop/ArhGAP15/simulazione.2/1000$ source activate fenics27 

discarding /home/andrea/anaconda2/bin from PATH
prepending /home/andrea/anaconda2/envs/fenics27/bin to PATH
(fenics27)andrea@brahma:~/Desktop/ArhGAP15/simulazione.2/1000$ conda install fenics mkl --channel juanlu001 
Fetching package metadata: ........
Solving package specifications: .........

Package plan for installation in environment /home/andrea/anaconda2/envs/fenics27:

The following NEW packages will be INSTALLED:

    boost:       1.60.0-py27_0   
    cloog:       0.18.0-0        
    cmake:       3.3.1-0         
    dolfin:      1.6.0-py27_2    
    eigen3:      3.2.1-1         
    fenics:      1.6.0-0         
    ffc:         1.6.0-py27_3    
    fiat:        1.6.0-np19py27_1
    fontconfig:  2.11.1-5        
    freetype:    2.5.5-0         
    gcc:         4.8.5-3         
    gmp:         5.1.2-2         
    icu:         54.1-0          
    instant:     1.6.0-py27_3    
    isl:         0.12.2-0        
    libgcc:      4.8.5-1         
    libgfortran: 3.0-0           
    libpng:      1.6.17-0        
    libxml2:     2.9.2-0         
    mkl:         11.3.1-0        
    mpc:         1.0.1-0         
    mpfr:        3.1.2-0         
    mpi4py:      2.0.0-py27_1    
    mpich2:      1.4.1p1-0       
    mpmath:      0.19-py27_0     
    numpy:       1.9.3-py27_2    
    pcre:        8.31-0          
    petsc:       3.5.2-py27_2    
    petsc4py:    3.5.1-py27_1    
    ply:         3.8-py27_0      
    qt:          4.8.7-1         
    six:         1.10.0-py27_0   
    slepc:       3.5.4-py27_2    
    swig:        3.0.7-0         
    sympy:       1.0-py27_0      
    ufl:         1.6.0-py27_1    
    vtk:         6.3.0-py27_1    

Proceed ([y]/n)? y

Linking packages ...
[      COMPLETE      ]|###################################################| 100%

(fenics27)andrea@brahma:~/Desktop/ArhGAP15/simulazione.2/1000$ python brwalk.py

Traceback (most recent call last):
  File "brwalk.py", line 30, in <module>
    from scipy import *
ImportError: No module named scipy

(fenics27)andrea@brahma:~/Desktop/ArhGAP15/simulazione.2/1000$ conda install scipy --channel juanlu001 

Fetching package metadata: ........
Solving package specifications: .........

Package plan for installation in environment /home/andrea/anaconda2/envs/fenics27:

The following NEW packages will be INSTALLED:

    scipy: 0.17.0-np19py27_2

Proceed ([y]/n)? y

Linking packages ...
[      COMPLETE      ]|###################################################| 100%

(fenics27)andrea@brahma:~/Desktop/ArhGAP15/simulazione.2/1000$ python brwalk.py

Traceback (most recent call last):
  File "brwalk.py", line 31, in <module>
    from pylab import *
ImportError: No module named pylab

(fenics27)andrea@brahma:~/Desktop/ArhGAP15/simulazione.2/1000$ conda install matplotlib --channel juanlu001 

Fetching package metadata: ........
Solving package specifications: .........

Package plan for installation in environment /home/andrea/anaconda2/envs/fenics27:

The following NEW packages will be INSTALLED:

    cairo:           1.12.18-6       
    matplotlib:      1.4.3-np19py27_2
    pixman:          0.32.6-0        
    py2cairo:        1.10.0-py27_2   
    pyparsing:       2.0.3-py27_0    
    pyqt:            4.11.4-py27_1   
    python-dateutil: 2.5.2-py27_0    
    pytz:            2016.3-py27_0   
    sip:             4.16.9-py27_0   

Proceed ([y]/n)? y

Linking packages ...
[      COMPLETE      ]|###################################################| 100%

(fenics27)andrea@brahma:~/Desktop/ArhGAP15/simulazione.2/1000$ python brwalk.py

Traceback (most recent call last):
  File "brwalk.py", line 968, in <module>
    chemo1()
  File "brwalk.py", line 205, in chemo1
    from dolfin import Constant,Expression,Function,FunctionSpace,LUSolver,MeshFunction,Point,SubDomain,TestFunction,TrialFunction,VectorFunctionSpace             #  Solution of PDE
  File "/home/andrea/anaconda2/envs/fenics27/lib/python2.7/site-packages/dolfin/__init__.py", line 16, in <module>
    from . import cpp
  File "/home/andrea/anaconda2/envs/fenics27/lib/python2.7/site-packages/dolfin/cpp/__init__.py", line 42, in <module>
    exec("from . import %s" % module_name)
  File "<string>", line 1, in <module>
  File "/home/andrea/anaconda2/envs/fenics27/lib/python2.7/site-packages/dolfin/cpp/common.py", line 32, in <module>
    _common = swig_import_helper()
  File "/home/andrea/anaconda2/envs/fenics27/lib/python2.7/site-packages/dolfin/cpp/common.py", line 28, in swig_import_helper
    _mod = imp.load_module('_common', fp, pathname, description)
ImportError: libboost_system.so.1.57.0: cannot open shared object file: No such file or directory

(fenics27)andrea@brahma:~/Desktop/ArhGAP15/simulazione.2/1000$ conda install boost --channel juanlu001 

Fetching package metadata: ........
Solving package specifications: .........

All requested packages already installed.
packages in environment at /home/andrea/anaconda2/envs/fenics27:

boost                     1.60.0                   py27_0  

(fenics27)andrea@brahma:~/Desktop/ArhGAP15/simulazione.2/1000$ python brwalk.py

Traceback (most recent call last):
  File "brwalk.py", line 968, in <module>
    chemo1()
  File "brwalk.py", line 205, in chemo1
    from dolfin import Constant,Expression,Function,FunctionSpace,LUSolver,MeshFunction,Point,SubDomain,TestFunction,TrialFunction,VectorFunctionSpace             #  Solution of PDE
  File "/home/andrea/anaconda2/envs/fenics27/lib/python2.7/site-packages/dolfin/__init__.py", line 16, in <module>
    from . import cpp
  File "/home/andrea/anaconda2/envs/fenics27/lib/python2.7/site-packages/dolfin/cpp/__init__.py", line 42, in <module>
    exec("from . import %s" % module_name)
  File "<string>", line 1, in <module>
  File "/home/andrea/anaconda2/envs/fenics27/lib/python2.7/site-packages/dolfin/cpp/common.py", line 32, in <module>
    _common = swig_import_helper()
  File "/home/andrea/anaconda2/envs/fenics27/lib/python2.7/site-packages/dolfin/cpp/common.py", line 28, in swig_import_helper
    _mod = imp.load_module('_common', fp, pathname, description)
ImportError: libboost_system.so.1.57.0: cannot open shared object file: No such file or directory

(fenics27)andrea@brahma:~/Desktop/ArhGAP15/simulazione.2/1000$ conda install numpy=1.10.4 --channel juanlu001 

Fetching package metadata: ........
Solving package specifications: ....

The following specifications were found to be in conflict:
  - dolfin (target=dolfin-1.6.0-py27_2.tar.bz2) -> ffc ==1.6.0
  - fenics (target=fenics-1.6.0-0.tar.bz2) -> dolfin ==1.6.0
  - fenics (target=fenics-1.6.0-0.tar.bz2) -> ffc ==1.6.0
  - fenics (target=fenics-1.6.0-0.tar.bz2) -> fiat ==1.6.0
  - ffc (target=ffc-1.6.0-py27_3.tar.bz2)
  - fiat (target=fiat-1.6.0-np19py27_1.tar.bz2)
  - numpy 1.10.4*
Use "conda info <package>" to see the dependencies for each package.

(fenics27)andrea@brahma:~/Desktop/ArhGAP15/simulazione.2/1000$ conda remove dolfin fenics ffc fiat

Fetching package metadata: ......
Solving package specifications: .........

Package plan for package removal in environment /home/andrea/anaconda2/envs/fenics27:

The following packages will be REMOVED:

    dolfin: 1.6.0-py27_2    
    fenics: 1.6.0-0         
    ffc:    1.6.0-py27_3    
    fiat:   1.6.0-np19py27_1

Proceed ([y]/n)? y

Unlinking packages ...
[      COMPLETE      ]|###################################################| 100%

(fenics27)andrea@brahma:~/Desktop/ArhGAP15/simulazione.2/1000$ conda install numpy=1.10.4 --channel juanlu001 

Fetching package metadata: ........
Solving package specifications: .........

Package plan for installation in environment /home/andrea/anaconda2/envs/fenics27:

The following packages will be UPDATED:

    matplotlib: 1.4.3-np19py27_2  --> 1.4.3-np110py27_2 
    numpy:      1.9.3-py27_2      --> 1.10.4-py27_1     
    scipy:      0.17.0-np19py27_2 --> 0.17.0-np110py27_2

Proceed ([y]/n)? y

Unlinking packages ...
[      COMPLETE      ]|###################################################| 100%
Linking packages ...
[      COMPLETE      ]|###################################################| 100%

(fenics27)andrea@brahma:~/Desktop/ArhGAP15/simulazione.2/1000$ conda install fenics mkl --channel juanlu001

Fetching package metadata: ........
Solving package specifications: .........

Package plan for installation in environment /home/andrea/anaconda2/envs/fenics27:

The following NEW packages will be INSTALLED:

    dolfin:     1.6.0-py27_2     
    fenics:     1.6.0-0          
    ffc:        1.6.0-py27_3     
    fiat:       1.6.0-np19py27_1 

The following packages will be UPDATED:

    matplotlib: 1.4.3-np110py27_2  --> 1.4.3-np19py27_2 
    scipy:      0.17.0-np110py27_2 --> 0.17.0-np19py27_2

The following packages will be DOWNGRADED:

    numpy:      1.10.4-py27_1      --> 1.9.3-py27_2     

Proceed ([y]/n)? y

Unlinking packages ...
[      COMPLETE      ]|###################################################| 100%
Linking packages ...
[      COMPLETE      ]|###################################################| 100%

(fenics27)andrea@brahma:~/Desktop/ArhGAP15/simulazione.2/1000$ python brwalk.py

Traceback (most recent call last):
  File "brwalk.py", line 968, in <module>
    chemo1()
  File "brwalk.py", line 205, in chemo1
    from dolfin import Constant,Expression,Function,FunctionSpace,LUSolver,MeshFunction,Point,SubDomain,TestFunction,TrialFunction,VectorFunctionSpace             #  Solution of PDE
  File "/home/andrea/anaconda2/envs/fenics27/lib/python2.7/site-packages/dolfin/__init__.py", line 16, in <module>
    from . import cpp
  File "/home/andrea/anaconda2/envs/fenics27/lib/python2.7/site-packages/dolfin/cpp/__init__.py", line 42, in <module>
    exec("from . import %s" % module_name)
  File "<string>", line 1, in <module>
  File "/home/andrea/anaconda2/envs/fenics27/lib/python2.7/site-packages/dolfin/cpp/common.py", line 32, in <module>
    _common = swig_import_helper()
  File "/home/andrea/anaconda2/envs/fenics27/lib/python2.7/site-packages/dolfin/cpp/common.py", line 28, in swig_import_helper
    _mod = imp.load_module('_common', fp, pathname, description)
ImportError: libboost_system.so.1.57.0: cannot open shared object file: No such file or directory
GaZ3ll3 commented 8 years ago

@porphyrius

you installed boost 1.60

see your first a few lines: boost: 1.60.0-py27_0

lower the version of boost

conda install boost=1.57

and also the version of vtk

conda install vtk=5.10

also, very important, the mkl.

conda install mkl=11.1

I don't why 11.3.1 could not work, but it seems you can only have trial mode for 30 days.........

astrojuanlu commented 8 years ago

Thanks @GaZ3ll3 for this late answer. Please @porphyrius confirm if this can be closed, boost is a mess and I should take the time to pin the version once and for all...

@GaZ3ll3 what do you mean that 11.3.1 won't work? In principle the new recipes should not depend on MKL but I would have to check to be sure.

GaZ3ll3 commented 8 years ago

@Juanlu001 continuum team seems get another way of installation of mkl, they removes mkl-service and mkl-rt, and only use mkl in current version (point out if I am wrong, I cannot find their thread on this problem in their issue, but it is about some numpy+mkl...). If your recipe does not depend on mkl, you probably should add nomkl as dependency, it will remove all mkl features, which means numpy and those stuff using mkl will change to none-mkl version.

astrojuanlu commented 8 years ago

Thanks for the clarifications, I will have to consider it if I have some time to work on this and other pending issues.

porphyrius commented 8 years ago

Hi https://github.com/Juanlu001 and https://github.com/GaZ3ll3, thanks a lot for your help. So I wiped out my fenics27 environment and started everything anew trying to follow your suggestions. But still no luck:

andrea@brahma:~/Desktop/ArhGAP15/simulazione.2/1000$ conda remove --name fenics27 --all
Fetching package metadata: ......

Package plan for package removal in environment /home/andrea/anaconda2/envs/fenics27:

The following packages will be REMOVED:

    backports:         1.0-py27_0       
    boost:             1.57.0-4         
    cmake:             3.3.1-0          
    decorator:         4.0.9-py27_0     
    dolfin:            1.5.0-np19py27_2 
    eigen3:            3.2.1-1          
    fenics:            1.5.0-0          
    ffc:               1.5.0-np19py27_2 
    fiat:              1.5.0-np19py27_1 
    fontconfig:        2.11.1-5         
    freetype:          2.5.5-0          
    get_terminal_size: 1.0.0-py27_0     
    icu:               54.1-0           
    instant:           1.5.0-np19py27_1 
    ipython:           4.2.0-py27_0     
    ipython_genutils:  0.1.0-py27_0     
    libgcc:            5.2.0-0          
    libgfortran:       3.0-0            
    libpng:            1.6.17-0         
    libxml2:           2.9.2-0          
    mkl:               11.3.1-0         
    mkl-rt:            11.1-p0          
    mkl-service:       1.0.0-py27_p2    
    mpi4py:            2.0.0-py27_1     
    mpich2:            1.4.1p1-0        
    mpmath:            0.19-py27_0      
    nose:              1.3.7-py27_0     
    numexpr:           2.3.1-np19py27_0 
    numpy:             1.9.1-py27_0     
    openblas:          0.2.14-4         
    openssl:           1.0.2g-0         
    path.py:           8.2.1-py27_0     
    pcre:              8.31-0           
    petsc:             3.5.2-py27_2     
    petsc4py:          3.5.1-py27_1     
    pexpect:           4.0.1-py27_0     
    pickleshare:       0.5-py27_0       
    pip:               8.1.1-py27_1     
    ply:               3.8-py27_0       
    ptyprocess:        0.5-py27_0       
    python:            2.7.11-0         
    qt:                4.8.7-1          
    readline:          6.2-2            
    scikit-learn:      0.15.2-np19py27_0
    scipy:             0.17.0-np19py27_2
    setuptools:        20.7.0-py27_0    
    simplegeneric:     0.8.1-py27_0     
    six:               1.10.0-py27_0    
    slepc:             3.5.4-py27_2     
    sqlite:            3.9.2-0          
    swig:              3.0.8-1          
    sympy:             1.0-py27_0       
    tk:                8.5.18-0         
    traitlets:         4.2.1-py27_0     
    ufl:               1.5.0-py27_1     
    vtk:               5.10.1-py27_1    
    wheel:             0.29.0-py27_0    
    zlib:              1.2.8-0          

Proceed ([y]/n)? y

Unlinking packages ...
[      COMPLETE      ]|###################################################| 100%
andrea@brahma:~/Desktop/ArhGAP15/simulazione.2/1000$ conda create -n fenics27 python=2.7
Fetching package metadata: ......
Solving package specifications: .........

Package plan for installation in environment /home/andrea/anaconda2/envs/fenics27:

The following NEW packages will be INSTALLED:

    openssl:    1.0.2g-0     
    pip:        8.1.1-py27_1 
    python:     2.7.11-0     
    readline:   6.2-2        
    setuptools: 20.7.0-py27_0
    sqlite:     3.9.2-0      
    tk:         8.5.18-0     
    wheel:      0.29.0-py27_0
    zlib:       1.2.8-0      

Proceed ([y]/n)? y

Linking packages ...
[      COMPLETE      ]|###################################################| 100%
andrea@brahma:~/Desktop/ArhGAP15/simulazione.2/1000$ source activate fenics27
discarding /home/andrea/anaconda2/bin from PATH
prepending /home/andrea/anaconda2/envs/fenics27/bin to PATH
(fenics27)andrea@brahma:~/Desktop/ArhGAP15/simulazione.2/1000$ conda install numpy=1.9.1
Fetching package metadata: ......
Solving package specifications: .........

Package plan for installation in environment /home/andrea/anaconda2/envs/fenics27:

The following NEW packages will be INSTALLED:

    numpy: 1.9.1-py27_0

Proceed ([y]/n)? y

Linking packages ...
[      COMPLETE      ]|###################################################| 100%
(fenics27)andrea@brahma:~/Desktop/ArhGAP15/simulazione.2/1000$ conda install boost=1.57
Fetching package metadata: ......
Solving package specifications: .........

Package plan for installation in environment /home/andrea/anaconda2/envs/fenics27:

The following NEW packages will be INSTALLED:

    boost: 1.57.0-4
    icu:   54.1-0  

Proceed ([y]/n)? y

Linking packages ...
[      COMPLETE      ]|###################################################| 100%
(fenics27)andrea@brahma:~/Desktop/ArhGAP15/simulazione.2/1000$ conda install vtk=5.10
Fetching package metadata: ......
Solving package specifications: .........

Package plan for installation in environment /home/andrea/anaconda2/envs/fenics27:

The following NEW packages will be INSTALLED:

    vtk: 5.10.1-py27_1

Proceed ([y]/n)? y

Linking packages ...
[      COMPLETE      ]|###################################################| 100%
(fenics27)andrea@brahma:~/Desktop/ArhGAP15/simulazione.2/1000$ conda install mkl=11.1
Fetching package metadata: ......
Solving package specifications: .........

Package plan for installation in environment /home/andrea/anaconda2/envs/fenics27:

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    numpy-1.9.1                |          py27_p0         5.7 MB

The following NEW packages will be INSTALLED:

    mkl:          11.1-np19py27_p3  
    mkl-rt:       11.1-p0           
    mkl-service:  1.0.0-py27_p2     
    nose:         1.3.7-py27_0      
    numexpr:      2.3.1-np19py27_p0  [mkl]
    scikit-learn: 0.15.2-np19py27_p0 [mkl]
    scipy:        0.16.1-np19py27_p0 [mkl]

The following packages will be UPDATED:

    numpy:        1.9.1-py27_0 --> 1.9.1-py27_p0      [mkl]

Proceed ([y]/n)? y

Fetching packages ...
numpy-1.9.1-py 100% |################################| Time: 0:00:02   2.04 MB/s
Extracting packages ...
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(fenics27)andrea@brahma:~/Desktop/ArhGAP15/simulazione.2/1000$ conda install fenics=1.5.0 --channel juanlu001
Fetching package metadata: ........
Solving package specifications: .........

Package plan for installation in environment /home/andrea/anaconda2/envs/fenics27:

The following NEW packages will be INSTALLED:

    cmake:        3.3.1-0          
    dolfin:       1.5.0-np19py27_2 
    eigen3:       3.2.1-1          
    fenics:       1.5.0-0          
    ffc:          1.5.0-np19py27_2 
    fiat:         1.5.0-np19py27_1 
    fontconfig:   2.11.1-5         
    freetype:     2.5.5-0          
    instant:      1.5.0-np19py27_1 
    libgcc:       5.2.0-0          
    libgfortran:  3.0-0            
    libpng:       1.6.17-0         
    libxml2:      2.9.2-0          
    mpi4py:       2.0.0-py27_1     
    mpich2:       1.4.1p1-0        
    mpmath:       0.19-py27_0      
    pcre:         8.31-0           
    petsc:        3.5.2-py27_2     
    petsc4py:     3.5.1-py27_1     
    ply:          3.8-py27_0       
    qt:           4.8.7-1          
    six:          1.10.0-py27_0    
    slepc:        3.5.4-py27_2     
    swig:         3.0.8-1          
    sympy:        1.0-py27_0       
    ufl:          1.5.0-py27_1     

The following packages will be UPDATED:

    mkl:          11.1-np19py27_p3   --> 11.3.1-0         
    numexpr:      2.3.1-np19py27_p0  [mkl] --> 2.3.1-np19py27_0 
    numpy:        1.9.1-py27_p0      [mkl] --> 1.9.1-py27_0     
    scikit-learn: 0.15.2-np19py27_p0 [mkl] --> 0.15.2-np19py27_0
    scipy:        0.16.1-np19py27_p0 [mkl] --> 0.17.0-np19py27_2

Proceed ([y]/n)? y

Unlinking packages ...
[      COMPLETE      ]|###################################################| 100%
Linking packages ...
[      COMPLETE      ]|###################################################| 100%
(fenics27)andrea@brahma:~/Desktop/ArhGAP15/simulazione.2/1000$ conda install mkl=11.1
Fetching package metadata: ......
Solving package specifications: .........

Package plan for installation in environment /home/andrea/anaconda2/envs/fenics27:

The following packages will be UPDATED:

    numexpr:      2.3.1-np19py27_0  --> 2.3.1-np19py27_p0  [mkl]
    numpy:        1.9.1-py27_0      --> 1.9.1-py27_p0      [mkl]
    scikit-learn: 0.15.2-np19py27_0 --> 0.15.2-np19py27_p0 [mkl]

The following packages will be DOWNGRADED:

    mkl:          11.3.1-0          --> 11.1-np19py27_p3  
    scipy:        0.17.0-np19py27_2 --> 0.16.1-np19py27_p0 [mkl]

Proceed ([y]/n)? y

Unlinking packages ...
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(fenics27)andrea@brahma:~/Desktop/ArhGAP15/simulazione.2/1000$ conda install ipython
Fetching package metadata: ......
Solving package specifications: .........

Package plan for installation in environment /home/andrea/anaconda2/envs/fenics27:

The following NEW packages will be INSTALLED:

    backports:         1.0-py27_0       
    decorator:         4.0.9-py27_0     
    get_terminal_size: 1.0.0-py27_0     
    ipython:           4.2.0-py27_0     
    ipython_genutils:  0.1.0-py27_0     
    path.py:           8.2.1-py27_0     
    pexpect:           4.0.1-py27_0     
    pickleshare:       0.5-py27_0       
    ptyprocess:        0.5-py27_0       
    simplegeneric:     0.8.1-py27_0     
    traitlets:         4.2.1-py27_0     

The following packages will be UPDATED:

    mkl:               11.1-np19py27_p3   --> 11.3.1-0         
    numexpr:           2.3.1-np19py27_p0  [mkl] --> 2.3.1-np19py27_0 
    numpy:             1.9.1-py27_p0      [mkl] --> 1.9.1-py27_0     
    scikit-learn:      0.15.2-np19py27_p0 [mkl] --> 0.15.2-np19py27_0
    scipy:             0.16.1-np19py27_p0 [mkl] --> 0.17.0-np19py27_2

Proceed ([y]/n)? y

Unlinking packages ...
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Linking packages ...
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(fenics27)andrea@brahma:~/Desktop/ArhGAP15/simulazione.2/1000$ conda install mkl=11.1
Fetching package metadata: ......
Solving package specifications: .........

Package plan for installation in environment /home/andrea/anaconda2/envs/fenics27:

The following packages will be UPDATED:

    numexpr:      2.3.1-np19py27_0  --> 2.3.1-np19py27_p0  [mkl]
    numpy:        1.9.1-py27_0      --> 1.9.1-py27_p0      [mkl]
    scikit-learn: 0.15.2-np19py27_0 --> 0.15.2-np19py27_p0 [mkl]

The following packages will be DOWNGRADED:

    mkl:          11.3.1-0          --> 11.1-np19py27_p3  
    scipy:        0.17.0-np19py27_2 --> 0.16.1-np19py27_p0 [mkl]

Proceed ([y]/n)? y

Unlinking packages ...
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(fenics27)andrea@brahma:~/Desktop/ArhGAP15/simulazione.2/1000$ ipython
Python 2.7.11 |Continuum Analytics, Inc.| (default, Dec  6 2015, 18:08:32) 
Type "copyright", "credits" or "license" for more information.

IPython 4.2.0 -- An enhanced Interactive Python.
?         -> Introduction and overview of IPython's features.
%quickref -> Quick reference.
help      -> Python's own help system.
object?   -> Details about 'object', use 'object??' for extra details.

In [1]: %run -i brwalk.py
---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
/home/andrea/lavoro/ArhGAP15/simulazione.2/1000/brwalk.py in <module>()
     28 from time import sleep
     29 from timeit import timeit
---> 30 from scipy import *
     31 from pylab import *
     32 from scipy.ndimage import label

/home/andrea/anaconda2/envs/fenics27/lib/python2.7/site-packages/scipy/__init__.py in <module>()
     59 __all__ = ['test']
     60 
---> 61 from numpy import show_config as show_numpy_config
     62 if show_numpy_config is None:
     63     raise ImportError("Cannot import scipy when running from numpy source directory.")

/home/andrea/anaconda2/envs/fenics27/lib/python2.7/site-packages/numpy/__init__.pyc in <module>()
    170         return loader(*packages, **options)
    171 
--> 172     from . import add_newdocs
    173     __all__ = ['add_newdocs',
    174                'ModuleDeprecationWarning',

/home/andrea/anaconda2/envs/fenics27/lib/python2.7/site-packages/numpy/add_newdocs.py in <module>()
     11 from __future__ import division, absolute_import, print_function
     12 
---> 13 from numpy.lib import add_newdoc
     14 
     15 ###############################################################################

/home/andrea/anaconda2/envs/fenics27/lib/python2.7/site-packages/numpy/lib/__init__.py in <module>()
     16 
     17 from . import scimath as emath
---> 18 from .polynomial import *
     19 #import convertcode
     20 from .utils import *

/home/andrea/anaconda2/envs/fenics27/lib/python2.7/site-packages/numpy/lib/polynomial.py in <module>()
     17 from numpy.lib.function_base import trim_zeros, sort_complex
     18 from numpy.lib.type_check import iscomplex, real, imag
---> 19 from numpy.linalg import eigvals, lstsq, inv
     20 
     21 class RankWarning(UserWarning):

/home/andrea/anaconda2/envs/fenics27/lib/python2.7/site-packages/numpy/linalg/__init__.py in <module>()
     49 from .info import __doc__
     50 
---> 51 from .linalg import *
     52 
     53 from numpy.testing import Tester

/home/andrea/anaconda2/envs/fenics27/lib/python2.7/site-packages/numpy/linalg/linalg.py in <module>()
     27     )
     28 from numpy.lib import triu, asfarray
---> 29 from numpy.linalg import lapack_lite, _umath_linalg
     30 from numpy.matrixlib.defmatrix import matrix_power
     31 from numpy.compat import asbytes

ImportError: libmkl_intel_lp64.so: cannot open shared object file: No such file or directory

In [2]: 
Do you really want to exit ([y]/n)? y
(fenics27)andrea@brahma:~/Desktop/ArhGAP15/simulazione.2/1000$ conda install scipy
Fetching package metadata: ......
Solving package specifications: .........

Package plan for installation in environment /home/andrea/anaconda2/envs/fenics27:

The following packages will be UPDATED:

    mkl:          11.1-np19py27_p3   --> 11.3.1-0         
    numexpr:      2.3.1-np19py27_p0  [mkl] --> 2.3.1-np19py27_0 
    numpy:        1.9.1-py27_p0      [mkl] --> 1.9.1-py27_0     
    scikit-learn: 0.15.2-np19py27_p0 [mkl] --> 0.15.2-np19py27_0
    scipy:        0.16.1-np19py27_p0 [mkl] --> 0.17.0-np19py27_2

Proceed ([y]/n)? y

Unlinking packages ...
[      COMPLETE      ]|###################################################| 100%
Linking packages ...
[      COMPLETE      ]|###################################################| 100%
(fenics27)andrea@brahma:~/Desktop/ArhGAP15/simulazione.2/1000$ conda install mkl=11.1
Fetching package metadata: ......
Solving package specifications: .........

Package plan for installation in environment /home/andrea/anaconda2/envs/fenics27:

The following packages will be UPDATED:

    numexpr:      2.3.1-np19py27_0  --> 2.3.1-np19py27_p0  [mkl]
    numpy:        1.9.1-py27_0      --> 1.9.1-py27_p0      [mkl]
    scikit-learn: 0.15.2-np19py27_0 --> 0.15.2-np19py27_p0 [mkl]

The following packages will be DOWNGRADED:

    mkl:          11.3.1-0          --> 11.1-np19py27_p3  
    scipy:        0.17.0-np19py27_2 --> 0.16.1-np19py27_p0 [mkl]

Proceed ([y]/n)? y

Unlinking packages ...
[      COMPLETE      ]|###################################################| 100%
Linking packages ...
[      COMPLETE      ]|###################################################| 100%
(fenics27)andrea@brahma:~/Desktop/ArhGAP15/simulazione.2/1000$ ipython
Python 2.7.11 |Continuum Analytics, Inc.| (default, Dec  6 2015, 18:08:32) 
Type "copyright", "credits" or "license" for more information.

IPython 4.2.0 -- An enhanced Interactive Python.
?         -> Introduction and overview of IPython's features.
%quickref -> Quick reference.
help      -> Python's own help system.
object?   -> Details about 'object', use 'object??' for extra details.

In [1]: %run -i brwalk.py
---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
/home/andrea/lavoro/ArhGAP15/simulazione.2/1000/brwalk.py in <module>()
     28 from time import sleep
     29 from timeit import timeit
---> 30 from scipy import *
     31 from pylab import *
     32 from scipy.ndimage import label

/home/andrea/anaconda2/envs/fenics27/lib/python2.7/site-packages/scipy/__init__.py in <module>()
     59 __all__ = ['test']
     60 
---> 61 from numpy import show_config as show_numpy_config
     62 if show_numpy_config is None:
     63     raise ImportError("Cannot import scipy when running from numpy source directory.")

/home/andrea/anaconda2/envs/fenics27/lib/python2.7/site-packages/numpy/__init__.pyc in <module>()
    170         return loader(*packages, **options)
    171 
--> 172     from . import add_newdocs
    173     __all__ = ['add_newdocs',
    174                'ModuleDeprecationWarning',

/home/andrea/anaconda2/envs/fenics27/lib/python2.7/site-packages/numpy/add_newdocs.py in <module>()
     11 from __future__ import division, absolute_import, print_function
     12 
---> 13 from numpy.lib import add_newdoc
     14 
     15 ###############################################################################

/home/andrea/anaconda2/envs/fenics27/lib/python2.7/site-packages/numpy/lib/__init__.py in <module>()
     16 
     17 from . import scimath as emath
---> 18 from .polynomial import *
     19 #import convertcode
     20 from .utils import *

/home/andrea/anaconda2/envs/fenics27/lib/python2.7/site-packages/numpy/lib/polynomial.py in <module>()
     17 from numpy.lib.function_base import trim_zeros, sort_complex
     18 from numpy.lib.type_check import iscomplex, real, imag
---> 19 from numpy.linalg import eigvals, lstsq, inv
     20 
     21 class RankWarning(UserWarning):

/home/andrea/anaconda2/envs/fenics27/lib/python2.7/site-packages/numpy/linalg/__init__.py in <module>()
     49 from .info import __doc__
     50 
---> 51 from .linalg import *
     52 
     53 from numpy.testing import Tester

/home/andrea/anaconda2/envs/fenics27/lib/python2.7/site-packages/numpy/linalg/linalg.py in <module>()
     27     )
     28 from numpy.lib import triu, asfarray
---> 29 from numpy.linalg import lapack_lite, _umath_linalg
     30 from numpy.matrixlib.defmatrix import matrix_power
     31 from numpy.compat import asbytes

ImportError: libmkl_intel_lp64.so: cannot open shared object file: No such file or directory

In [2]:
astrojuanlu commented 8 years ago

Well, as you can see this is a different breed of problem. Now everything's fine with boost, but the issue now is with Intel MKL, as @GaZ3ll3 anticipated. Please specify also the mkl version, as said in a previous comment.

porphyrius commented 8 years ago

I did that:

conda install mkl=11.1

Then it got upgraded automatically when installing some other program, and I downgraded it each time.

astrojuanlu commented 8 years ago

My fault, I didn't see that part. In fact there must be some nasty interaction between MKL and the switch to OpenBLAS:

https://github.com/Juanlu001/fenics-recipes/commit/f929f3a27e8137a6cd46da33bbb17e36f74c899b

I last touched these packages before Continuum made the latest significant changes to MKL distribution. I'm sorry but I won't have time to fix this in the short term, I encourage you to check the many forks of these recipes that are out there:

https://github.com/Juanlu001/fenics-recipes/network

In particular, the most advanced one is the one by @mikaem.

GaZ3ll3 commented 8 years ago

@porphyrius @Juanlu001 checkout https://github.com/mikaem/fenics-recipes/blob/conda-gcc/build_fenics.sh in https://github.com/mikaem/fenics-recipes/tree/conda-gcc branch

I tried this installation from local, directly bash build_fenics.sh. It looks ok, but it is 1.7.

in the comments, he mentioned a problem which I encountered multiple times. It is about the libgfortran. Hope it helps.