scipy install with pip and virtualenv ends with error and g++ exit status 4

Question

I am using an micro instance on AWS (Amazon Web Services) and installing inside a python 3.3.2 virtual environment. I have tried:

pip install scipy

pip install -e git+https://github.com/scipy/scipy.git#egg=scipy

and they end with:

  Please submit a full bug report,

with preprocessed source if appropriate.

See <file:///usr/share/doc/gcc-4.6/README.Bugs> for instructions.

In file included from /home/ubuntu/rose/lib/python3.3/site-packages/numpy/core/include/numpy/ndarraytypes.h:1760:0,

                 from /home/ubuntu/rose/lib/python3.3/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,

                 from scipy/sparse/sparsetools/sparsetools.h:5,

                 from scipy/sparse/sparsetools/bsr.cxx:4:

/home/ubuntu/rose/lib/python3.3/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]

g++: internal compiler error: Killed (program cc1plus)

Please submit a full bug report,

with preprocessed source if appropriate.

See <file:///usr/share/doc/gcc-4.6/README.Bugs> for instructions.

Running from scipy source directory.

"object of type 'type' has no len()" in evaluating 'len(list)' (available names: [])

"object of type 'type' has no len()" in evaluating 'len(list)' (available names: [])

"object of type 'type' has no len()" in evaluating 'len(list)' (available names: [])

"object of type 'type' has no len()" in evaluating 'len(list)' (available names: [])

"object of type 'type' has no len()" in evaluating 'len(list)' (available names: [])

"object of type 'type' has no len()" in evaluating 'len(list)' (available names: [])

error: Command "g++ -pthread -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -D__STDC_FORMAT_MACROS=1 -Iscipy/sparse/sparsetools -I/home/ubuntu/rose/lib/python3.3/site-packages/numpy/core/include -I/usr/local/include/python3.3m -c scipy/sparse/sparsetools/bsr.cxx -o build/temp.linux-x86_64-3.3/scipy/sparse/sparsetools/bsr.o" failed with exit status 4

----------------------------------------
Cleaning up...
  Removing temporary dir /home/ubuntu/rose/build...
Command /home/ubuntu/rose/bin/python3.3 -c "import setuptools, tokenize; __file__='/home/ubuntu/rose/src/scipy/setup.py'; exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" develop --no-deps failed with error code 1 in /home/ubuntu/rose/src/scipy
Exception information:
Traceback (most recent call last):
  File "/home/ubuntu/rose/lib/python3.3/site-packages/pip/basecommand.py", line 122, in main
    status = self.run(options, args)
  File "/home/ubuntu/rose/lib/python3.3/site-packages/pip/commands/install.py", line 283, in run
    requirement_set.install(install_options, global_options, root=options.root_path)
  File "/home/ubuntu/rose/lib/python3.3/site-packages/pip/req.py", line 1435, in install
    requirement.install(install_options, global_options, *args, **kwargs)
  File "/home/ubuntu/rose/lib/python3.3/site-packages/pip/req.py", line 665, in install
    self.install_editable(install_options, global_options)
  File "/home/ubuntu/rose/lib/python3.3/site-packages/pip/req.py", line 775, in install_editable
    show_stdout=False)
  File "/home/ubuntu/rose/lib/python3.3/site-packages/pip/util.py", line 697, in call_subprocess
    % (command_desc, proc.returncode, cwd))
pip.exceptions.InstallationError: Command /home/ubuntu/rose/bin/python3.3 -c "import setuptools, tokenize; __file__='/home/ubuntu/rose/src/scipy/setup.py'; exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" develop --no-deps failed with error code 1 in /home/ubuntu/rose/src/scipy

Then, I tried doing something to the swap, following this post: Trouble installing scipy in virtualenv on a amazon ec2 linux micro instance but it just hangs for ages.

Can someone help with this?

Answer 1

I just ran into a similar error, and think I fixed it by increasing the memory on my VM from 368MB to 1024MB. I had previously built successfully on the VM with 368MB, but I guess other programs may have been using more memory.

AWS micro instances don't have lots of memory available to them, so I guess that may have been the cause here too.