Error importing Theano

Question

After installing python, numpy, scipy and theano to ~/.local, I tried to import theano but it threw an error:

>>> import theano
Problem occurred during compilation with the command line below:
g++ -shared -g -march=core2 -mcx16 -msahf --param l1-cache-size=32 --param l1-cache-line-size=64 --param l2-cache-size=4096 -mtune=core2 -D NPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -D NPY_ARRAY_ENSUREARRAY=NPY_ENSUREARRAY -D NPY_ARRAY_ENSURECOPY=NPY_ENSURECOPY -D NPY_ARRAY_ALIGNED=NPY_ALIGNED -D NPY_ARRAY_WRITEABLE=NPY_WRITEABLE -D NPY_ARRAY_UPDATE_ALL=NPY_UPDATE_ALL -D NPY_ARRAY_C_CONTIGUOUS=NPY_C_CONTIGUOUS -D NPY_ARRAY_F_CONTIGUOUS=NPY_F_CONTIGUOUS -m64 -fPIC -I/opt/python/lib/python2.7/site-packages/numpy/core/include -I/home/minh.lengoc/.local/include/python2.7 -o /home/minh.lengoc/.theano/compiledir_Linux-2.6.32-279.14.1.el6.x86_64-x86_64-with-centos-6.3-Final-x86_64-2.7.6-64/lazylinker_ext/lazylinker_ext.so /home/minh.lengoc/.theano/compiledir_Linux-2.6.32-279.14.1.el6.x86_64-x86_64-with-centos-6.3-Final-x86_64-2.7.6-64/lazylinker_ext/mod.cpp -L/home/minh.lengoc/.local/lib -lpython2.7
/usr/bin/ld: /home/minh.lengoc/.local/lib/libpython2.7.a(abstract.o): relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a shared object; recompile with -fPIC
/home/minh.lengoc/.local/lib/libpython2.7.a: could not read symbols: Bad value
collect2: ld returned 1 exit status

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/minh.lengoc/setup/Theano/theano/__init__.py", line 55, in <module>
    from theano.compile import \
  File "/home/minh.lengoc/setup/Theano/theano/compile/__init__.py", line 6, in <module>
    from theano.compile.function_module import *
  File "/home/minh.lengoc/setup/Theano/theano/compile/function_module.py", line 18, in <module>
    import theano.compile.mode
  File "/home/minh.lengoc/setup/Theano/theano/compile/mode.py", line 11, in <module>
    import theano.gof.vm
  File "/home/minh.lengoc/setup/Theano/theano/gof/vm.py", line 516, in <module>
    import lazylinker_c
  File "/home/minh.lengoc/setup/Theano/theano/gof/lazylinker_c.py", line 86, in <module>
    preargs=args)
  File "/home/minh.lengoc/setup/Theano/theano/gof/cmodule.py", line 1975, in compile_str
    (status, compile_stderr.replace('\n', '. ')))
Exception: Compilation failed (return status=1): /usr/bin/ld: /home/minh.lengoc/.local/lib/libpython2.7.a(abstract.o): relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a shared object; recompile with -fPIC. /home/minh.lengoc/.local/lib/libpython2.7.a: could not read symbols: Bad value. collect2: ld returned 1 exit status. 

I'm installing on a Red Hat box:

$ cat /proc/version
Linux version 2.6.32-279.14.1.el6.x86_64 ([email protected]) (gcc version 4.4.6 20120305 (Red Hat 4.4.6-4) (GCC) ) #1 SMP Tue Nov 6 23:43:09 UTC 2012

What should I do...?

Ashtray

Answer 1

You didn't build correctly python. It wasn't compiled with the -fPIC parameter. Look at how to compile python with a shared library.

EDIT: You need to compile python like this:

./configure --enable-shared
make
make install

Unreadable

Thank you! I also needed to run export LD_LIBRARY_PATH=/home/minh.lengoc/.local/lib:$LD_LIBRARY_PATH to make it work. – Ashtray

@ngọcminh.oss: What's in your lib directory, that you needed to add it to the LD_LIBRARY_PATH? – Mexico

Nevermind, found the answer here: #7880954 – Mexico

Answer 2

In case you are using pyenv you can do that with

CONFIGURE_OPTS=--enable-shared pyenv install 3.6.5

Signora

Answer 3

I used a virtualenv on Ubuntu 16.04, and before installing python with pyenv install 3.6.1 I ran the following command to ensure python is built with the fPIC flag:

export CONFIGURE_OPTS="OPT=\"-fPIC\""

Then I was able to install and run theano properly.

Deoxyribose