python - Trouble installing scipy in virtualenv on a amazon ec2 linux micro instance

Question

I have successfully installed scipy in the default python compiler on an amazon ec2 micro instance (Ubuntu 13.04). However i am not able to install scipy in a virtualenv.

pip install scipy ends with this error

scipy/sparse/sparsetools/csr_wrap.cxx: In function ‘void init_csr()’:

scipy/sparse/sparsetools/csr_wrap.cxx:73303:21: warning: variable ‘md’ set but not used [-Wunused-but-set-variable]

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

Please submit a full bug report,

with preprocessed source if appropriate.

See <file:///usr/share/doc/gcc-4.7/README.Bugs> for instructions.

----------------------------------------
Cleaning up...
Command /home/ubuntu/pnr/bin/python -c "import setuptools;__file__='/home/ubuntu/pnr/build/scipy/setup.py';exec(compile(open(__file__).read().replace('
', '
'), __file__, 'exec'))" install --record /tmp/pip-t8Drvd-record/install-record.txt --single-version-externally-managed --install-headers /home/ubuntu/pnr/include/site/python2.7 failed with error code -9 in /home/ubuntu/pnr/build/scipy

and

Traceback (most recent call last):
  File "/home/ubuntu/pnr/bin/pip", line 9, in <module>
    load_entry_point('pip==1.4.1', 'console_scripts', 'pip')()
  File "/home/ubuntu/pnr/local/lib/python2.7/site-packages/pip/__init__.py", line 148, in main
    return command.main(args[1:], options)
  File "/home/ubuntu/pnr/local/lib/python2.7/site-packages/pip/basecommand.py", line 169, in main
    text = '
'.join(complete_log)
UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 53: ordinal not in range(128)

Before anyone asks. pip freeze for default compiler returns

Cheetah==2.4.4
Landscape-Client==12.12
M2Crypto==0.21.1
PAM==0.4.2
Pillow==2.0.0
PyYAML==3.10
Twisted-Core==12.3.0
Twisted-Names==12.3.0
Twisted-Web==12.3.0
apt-xapian-index==0.45
argparse==1.2.1
boto==2.3.0
chardet==2.0.1
cloud-init==0.7.2
configobj==4.7.2
distribute==0.6.34
distro-info==0.10
euca2ools==2.1.1
numpy==1.7.1
oauth==1.0.1
paramiko==1.7.7.1
prettytable==0.6.1
pyOpenSSL==0.13
pycrypto==2.6
pycurl==7.19.0
pygobject==3.8.0
pyserial==2.6
python-apt==0.8.8ubuntu6
python-debian==0.1.21-nmu2ubuntu1
requests==1.1.0
scipy==0.11.0
six==1.2.0
ssh-import-id==3.14
urllib3==1.5
virtualenv==1.10.1
wsgiref==0.1.2
zope.interface==4.0.5

pip freeze command for virtualenv returns

Cython==0.19.2
Flask==0.10.1
Flask-Bootstrap==3.0.0.1
Flask-WTF==0.9.3
Jinja2==2.7.1
MarkupSafe==0.18
WTForms==1.0.5
Werkzeug==0.9.4
argparse==1.2.1
beautifulsoup4==4.3.2
itsdangerous==0.23
numpy==1.7.1
pymongo==2.6.2
requests==2.0.0
wsgiref==0.1.2

Answer 1

One solution is to temporarily enable swap on your micro instance. As described at this SO post, enable 1gb swap via:

sudo /bin/dd if=/dev/zero of=/var/swap.1 bs=1M count=1024
sudo /sbin/mkswap /var/swap.1
sudo /sbin/swapon /var/swap.1

Once swap is on, install scipy via pip:

sudo apt-get install -y libatlas-base-dev gfortran python-dev build-essential g++
sudo pip install numpy
sudo pip install scipy

Once scipy successfully installs, you can disable it via:

sudo swapoff /var/swap.1
sudo rm /var/swap.1