Habitat: `Not enough room for program headers` error during `do_strip()` phase of build

[bixu]

The error in full looks like (as pip install finishes inside the build):

  Running setup.py install for <module> ... done
Successfully installed <module>-<version>
   api: Writing configuration
   api: Writing service management scripts
   api: Using run hook /src/habitat/hooks/run
   api: Stripping unneeded symbols from binaries and libraries
strip: /hab/pkgs/<origin>/<package>/2.0.0/20161125203757/lib/python2.7/site-packages/.libs_cffi_backend/stkCxH1R: Not enough room for program headers, try linking with -N
strip:/hab/pkgs/<origin>/<package>/2.0.0/20161125203757/lib/python2.7/site-packages/.libs_cffi_backend/stkCxH1R[.note.gnu.build-id]: Bad value

I'm seeing this on macOS El Capitan when building a fairly complex Python app inside the Studio. While I can't share the source code, I _can_ share edited requirements.txt and plan.sh content:

$ cat plan.sh

pkg_name=<pkgname>
pkg_version=2.0.0
pkg_maintainer=""
pkg_license=("All Rights Reserved")
pkg_source=""
pkg_origin="<origin>"
pkg_deps=(
  bixu/hdf5
  core/libffi
  core/postgresql
  core/python2
)
pkg_build_deps=(
  core/cacerts
  core/gcc
  core/git
  core/openssl
)
pkg_bin_dirs=(bin)
pkg_lib_dirs=(lib)
pkg_include_dirs=(include)
pkg_expose=(8080)

do_download(){
  return 0
}

do_verify(){
  return 0
}

do_unpack(){
  return 0
}

do_prepare(){
  export LD_LIBRARY_PATH=$(hab pkg path core/gcc)/lib
  export SSL_CERT_FILE=$(hab pkg path core/cacerts)/ssl/cert.pem
  export HOME=/src

  pip install --upgrade pip virtualenv
  virtualenv "$pkg_prefix"
  source "$pkg_prefix/bin/activate"
}

do_build(){
  return 0
}

do_install(){
  # we have to pre-install some modules in a certain order to get around `pip` dep problems
  pip install $(grep numpy /src/requirements.txt)
  pip install $(grep numexpr /src/requirements.txt)
  pip install $(grep Cython /src/requirements.txt)
  pip install -r /src/requirements.dev.txt
  pip install /src  # here we are installing our internal python module
}

$ cat requirements.txt

astroid==1.4.8
cov-core==1.15.0
coverage==4.2
execnet==1.4.1
ipdb==0.10.1
ipython==5.1.0
logilab-common==1.2.2
mock==2.0.0
nose==1.3.7
pdbpp==0.8.3
py==1.4.30
pytest==3.0.3
pytest-catchlog==1.2.2
pytest-mock==1.3.0
pytest-cov==2.4.0
pytest-cache==1.0
pytest-pep8==1.0.6
pytest-random==0.02
pytest-watch==4.1.0
pytest-pylint==0.6.0
pytest-timeout==1.0.0
pep8==1.7.0
pylint==1.6.4
Sphinx==1.5a2
sqlalchemy-schemadisplay==1.2
WTForms==2.1
Babel==2.2.0
backports.ssl-match-hostname==3.5.0.1
Cython==0.25.1
Flask-Autodoc==0.1.2
Flask-SQLALchemy==2.1
Flask==0.11.1
ftputil==3.3.1
Jinja2==2.7.3
Mako==1.0.1
MarkupSafe==0.23
SQLAlchemy==1.1.4
Werkzeug==0.11.11
alembic==0.8.8
ansible==1.8.2
argparse==1.2.1
bcrypt==2.0.0
blinker==1.4
boto3==1.2.2
boto==2.38.0
bugsnag==2.5.2
celery==3.1.23
click==6.2
greenlet==0.4.7
itsdangerous==0.24
newrelic==2.66.0.49
numexpr==2.6.1
numpy==1.11.1
pandas==0.18.1
pdfkit==0.5.0
perfmetrics==2.0
prettytable==0.7.2
psycopg2==2.6.2
python-dateutil==2.4.0
python-redis-lock==3.1.0
pytz==2016.6.1
requests[security]==2.7.0
redis==2.10.5
scikit-learn==0.15.2
scipy==0.18.0
setuptools==17.1
six==1.10.0
structlog==16.1.0
termcolor==1.1.0
uwsgi==2.0.11.2
wsgiref==0.1.2

I have no custom HAB environment variables set.

[fnichol]

Hi there!

If the default behavior of stripping ELF binaries isn't working for you, do adding a

do_strip() {
  return 0
}

help you out? Not every Plan works with this default, but we hypothesize that the vast majority benefit from this (similar to most other Linux distribution packaging systems).

[bixu]

Yes that does work :)

Sent from my iPhone

On 27 Nov 2016, at 19:05, Fletcher Nichol [e-mail] wrote:

Hi there!

If the default behavior of stripping ELF binaries isn't working for you, do adding a

do_strip() {
return 0
}
help you out? Not every Plan works with this default, but we hypothesize that the vast majority benefit from this (similar to most other Linux distribution packaging systems).

—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub, or mute the thread.

[bdangit]

Ran into this today. I didn't like the answer of not stripping your binaries.

Pythoners like to include pre-built binaries inside their module. You have the option to ignore these pre-built things and always build from source.

pip install --no-binary :all: <package> or pip install --no-binary :all: -r requirements.txt will force pip to build from source. Be prepared to add more dependencies other than just core/python, as you’ll need core/gcc and any other libraries needed.

ref: http://serverfault.com/questions/774546/linux-binary-strip-error-when-using-pip-install-not-enough-room-for-program-hea
ref: https://github.com/numpy/numpy/issues/7570

now i can use the default do_strip() without any stubs.

[smartb-pair]

@eeyun, perhaps @bdangit's advice (I think I remember @georgemarshall saying the same thing) should be part of core/scaffolding-python?

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