IPython module import error: /usr/bin/ld: cannot find -lpython2.7. collect2: ld returned 1 exit status

问题:

I'm using the Python module Theano on a server. It is not pre-installed on there so I installed it in my home folder along with some other modules that weren't on the server. I get the following error when I "import theano" in IPython.

Problem occurred during compilation with the command line below: g++ -shared -g -march=core2 -mcx16 -msahf -maes -mpclmul -mpopcnt -msse4.2 --param l1-cache-size=32 --param l1-cache-line-size=64 --param l2-cache-size=12288 -mtune=generic -D NPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -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/apps/libs/python/2.7.3/lib/python2.7/site-packages/numpy/core/include -I/home/ext_sxc/include/python2.7 -o /home/ext_sxc/.theano/compiledir_Linux-2.6.32-431.1.2.0.1.el6.x86_64-x86_64-with-centos-6.5-Final-x86_64-2.7.3-64/lazylinker_ext/lazylinker_ext.so /home/ext_sxc/.theano/compiledir_Linux-2.6.32-431.1.2.0.1.el6.x86_64-x86_64-with-centos-6.5-Final-x86_64-2.7.3-64/lazylinker_ext/mod.cpp -L/home/ext_sxc/lib -lpython2.7 /usr/bin/ld: cannot find -lpython2.7 collect2: ld returned 1 exit status  --------------------------------------------------------------------------- Exception                                 Traceback (most recent call last) <ipython-input-1-3397704bd624> in <module>() ----> 1 import theano  /home/ext_sxc/lib/python2.7/site-packages/Theano-0.6.0-py2.7.egg/theano/__init__.pyc in <module>()      53     object2, utils      54 ---> 55 from theano.compile import \      56     SymbolicInput, In, \      57     SymbolicOutput, Out, \  /home/ext_sxc/lib/python2.7/site-packages/Theano-0.6.0-py2.7.egg/theano/compile/__init__.py in <module>()       4         ViewOp, view_op, register_view_op_c_code)       5 ----> 6 from theano.compile.function_module import *       7       8 from theano.compile.mode import *  /home/ext_sxc/lib/python2.7/site-packages/Theano-0.6.0-py2.7.egg/theano/compile/function_module.py in <module>()      16 from theano import gof      17 from theano.gof.python25 import partial ---> 18 import theano.compile.mode      19 from theano.compile.io import In, SymbolicInput, SymbolicInputKit, SymbolicOutput      20 from theano.compile.ops import deep_copy_op, view_op  /home/ext_sxc/lib/python2.7/site-packages/Theano-0.6.0-py2.7.egg/theano/compile/mode.py in <module>()       9 import  theano      10 from theano import gof ---> 11 import theano.gof.vm      12 from theano.configparser import config, AddConfigVar, StrParam      13 from theano.compile.ops import register_view_op_c_code, _output_guard  /home/ext_sxc/lib/python2.7/site-packages/Theano-0.6.0-py2.7.egg/theano/gof/vm.py in <module>()     514     515 try: --> 516     import lazylinker_c     517     518     class CVM(lazylinker_c.CLazyLinker, VM):  /home/ext_sxc/lib/python2.7/site-packages/Theano-0.6.0-py2.7.egg/theano/gof/lazylinker_c.py in <module>()      84             args = cmodule.GCC_compiler.compile_args()      85             cmodule.GCC_compiler.compile_str(dirname, code, location=loc, ---> 86                                              preargs=args)      87             # Save version into the __init__.py file.      88             init_py = os.path.join(loc, '__init__.py')  /home/ext_sxc/lib/python2.7/site-packages/Theano-0.6.0-py2.7.egg/theano/gof/cmodule.pyc in compile_str(module_name, src_code, location, include_dirs, lib_dirs, libs, preargs, py_module)    1969             # difficult to read.    1970             raise Exception('Compilation failed (return status=%s): %s' % -> 1971                             (status, compile_stderr.replace('\n', '. ')))    1972         elif config.cmodule.compilation_warning and compile_stderr:    1973             # Print errors just below the command line.  Exception: Compilation failed (return status=1): /usr/bin/ld: cannot find -lpython2.7. collect2: ld returned 1 exit status. 

How can I fix the above error?

Another thing is that whenever I run a Python job on the server, I first do

$ module load libs/python/2.7.3 

before executing my Python script and the server has libpython2.6.so in its /usr/lib64 folder. I think this is related to the problem.

回答1:

Your python installation is incomplete. When you do:

module load libs/python/2.7.3 

information is added to your environment variables to make you use python 2.7.3. But this version doesn't include the development header of python (Theano needs this). Or it doesn't put the right path in your environment.

To debug this, run this before and after running "module load libs/python/2.7.3" to compare what module load does:

env &> BEFORE.txt module load libs/python/2.7.3 env &> AFTER.txt diff BEFORE.txt AFTER.txt 

Then check the paths added to your env variables and look in those directories. It should have modified the LD_LIBRARY_PATH variable, but it should have done the same modification to LIBRARY_PATH. If it doesn't, do that modification yourself and tell your system admin about this.

This will solve your problem.

Otherwise, use the python 2.6 from the OS, maybe in include the development version.

Otherwise, check if other python versions are available via module.

Lastly, contact your system admin to add the development and shared version of python or install it yourself:

wget -c http://www.python.org/ftp/python/2.7.6/Python-2.7.6.tgz tar -jxf Python-2.7.6.tar.bz2  cd Python-2.7.6 ./configure --prefix=~/python2.7.6 --enable-shared make make install 

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