undefined symbol: __intel_sse2_strcpy

Question

I am trying to install phonopy on our super computer's login node following the instruction on under the Building using setup.py section here https://atztogo.github.io/phonopy/install.html.

Basically, just two commands:

tar xvfz phonopy-1.11.2.tar.gz
python setup.py install --user

It installs with no problem; however, when I use it, I get the following errors saying undefined symbol: __intel_sse2_strcpy. Here is the complete error message:

/home/syuan43/.local/bin/bandplot 
Traceback (most recent call last):
  File "/home/syuan43/.local/bin/bandplot", line 4, in <module>
    __import__('pkg_resources').run_script('phonopy==1.11.8.5', 'bandplot')
  File "/software/CentOS-6/tools/python-2.7.9/lib/python2.7/site-packages/pkg_resources/__init__.py", line 726, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/software/CentOS-6/tools/python-2.7.9/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1491, in run_script
    exec(script_code, namespace, namespace)
  File "/home/syuan43/.local/lib/python2.7/site-packages/phonopy-1.11.8.5-py2.7-linux-x86_64.egg/EGG-INFO/scripts/bandplot", line 52, in <module>

  File "build/bdist.linux-x86_64/egg/phonopy/__init__.py", line 37, in <module>
  File "build/bdist.linux-x86_64/egg/phonopy/api_phonopy.py", line 39, in <module>
  File "build/bdist.linux-x86_64/egg/phonopy/structure/symmetry.py", line 37, in <module>
  File "build/bdist.linux-x86_64/egg/phonopy/structure/spglib.py", line 35, in <module>
  File "build/bdist.linux-x86_64/egg/phonopy/_spglib.py", line 7, in <module>
  File "build/bdist.linux-x86_64/egg/phonopy/_spglib.py", line 6, in __bootstrap__
ImportError: /home/syuan43/.python-eggs/phonopy-1.11.8.5-py2.7-linux-x86_64.egg-tmp/phonopy/_spglib.so: undefined symbol: __intel_sse2_strcpy

Not sure if this may help, here is the module that I am using:

$ module list
Currently Loaded Modules:
  1) ifort_icc/15.0   2) intel_mpi/5.0.1   3) python/2.7.9

Any idea how to resolve the problem above? Or any suggestions what might be the cause of it?

Answer 1

(Old issue but I'll add an answer for the next me.)

For me it was a compiler issue. Doing:

export CC=gcc

before doing the pip installs fixed this for me.

See also: https://github.com/jswhit/pyproj/issues/76