'mpicc' fail on pip3 install matplotlib==1.3.1, using Install notes for NASA/Pleiades: Intel stack

[louisalexan...@gmail.com]

Hello Dedalus Dev Team and Users,

With the help of Daniel I was able to install Dedalus on a cluster in France (Rheticus) as well as on Pleiades. (I'm a postdoc in France.)

Unfortunately, for both clusters, it seems that mpi does not work properly (most efficient #iter/walltime is always 1 node), which is why I am in the process of re-installing Dedalus.

The original bashable install script for Pleiades was largely taken from the Install notes for Intel Stack with MPI-SGI. Since it did not seem to work so well, I am now trying to do the manual Intel Stack Install (+ install of my own openmpi), following rigorously the notes on the website (everything on the front nodes, except for the install of openmpi which I did on a compute haswell node).

Everything went relatively smoothly until I got to
pip3 install matplotlib==1.3.1 (which I did on ~/)
which returned
error: command 'mpicc' failed with exit status 2

I copied/pasted the output below, along with (at the end), some warnings I got during the install of previous packages.

It'd be great if you can help me out with this install (and with the one on Rheticus--upcoming!) as I'll be using Dedalus quite extensively for the next 2 years !

Thanks,
Louis


OUTPUT**********************************

lcouston@pfe26:~> pip3 install matplotlib==1.3.1
Collecting matplotlib==1.3.1
Downloading matplotlib-1.3.1.tar.gz (42.7MB)
100% |################################| 42.7MB 25kB/s
Requirement already satisfied (use --upgrade to upgrade): numpy>=1.5 in ./build/lib/python3.5/site-packages (from matplotlib==1.3.1)
Collecting python-dateutil (from matplotlib==1.3.1)
Using cached python_dateutil-2.5.3-py2.py3-none-any.whl
Collecting tornado (from matplotlib==1.3.1)
Using cached tornado-4.4.1.tar.gz
Collecting pyparsing!=2.0.0,>=1.5.6 (from matplotlib==1.3.1)
Using cached pyparsing-2.1.9-py2.py3-none-any.whl
Requirement already satisfied (use --upgrade to upgrade): nose in ./build/lib/python3.5/site-packages (from matplotlib==1.3.1)
Collecting six>=1.5 (from python-dateutil->matplotlib==1.3.1)
Using cached six-1.10.0-py2.py3-none-any.whl
Installing collected packages: six, python-dateutil, tornado, pyparsing, matplotlib
Running setup.py install for tornado ... done
Running setup.py install for matplotlib ... error
Complete output from command /u/lcouston/build/bin/python3.5 -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-q997hxsh/matplotlib/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-d4c18bg1-record/install-record.txt --single-version-externally-managed --compile:
============================================================================
Edit setup.cfg to change the build options

BUILDING MATPLOTLIB
matplotlib: yes [1.3.1]
python: yes [3.5.0 (default, Sep 22 2016, 07:50:37) [GCC
Intel(R) C++ gcc 4.3 mode]]
platform: yes [linux]

REQUIRED DEPENDENCIES AND EXTENSIONS
numpy: yes [version 1.10.1]
dateutil: yes [using dateutil version 2.5.3]
tornado: yes [using tornado version 4.4.1]
pyparsing: yes [using pyparsing version 2.1.9]
pycxx: yes [Official versions of PyCXX are not compatible
with Python 3.x. Using local copy]
libagg: yes [pkg-config information for 'libagg' could not
be found. Using local copy.]
freetype: yes [version 9.18.3]
png: yes [version 1.2.31]

OPTIONAL SUBPACKAGES
sample_data: yes [installing]
toolkits: yes [installing]
tests: yes [using nose version 1.3.7]

OPTIONAL BACKEND EXTENSIONS
macosx: no [Mac OS-X only]
qt4agg: no [PyQt4 not found]
gtk3agg: no [gtk3agg backend does not work on Python 3]
gtk3cairo: no [Requires cairo to be installed.]
gtkagg: no [Requires pygtk]
tkagg: yes [installing, version version not identified]
wxagg: no [requires wxPython]
gtk: no [Requires pygtk]
agg: yes [installing]
cairo: no [cairo not found]
windowing: no [Microsoft Windows only]

OPTIONAL LATEX DEPENDENCIES
dvipng: no
ghostscript: yes [version 8.62]
latex: no
pdftops: no

running install
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.5
copying lib/pylab.py -> build/lib.linux-x86_64-3.5
creating build/lib.linux-x86_64-3.5/matplotlib
copying lib/matplotlib/table.py -> build/lib.linux-x86_64-3.5/matplotlib

++++++++++++++++++++++++
copying a BUNCH of FILES
++++++++++++++++++++++++

Fixing build/lib.linux-x86_64-3.5/pylab.py build/lib.linux-x86_64-3.5/matplotlib/table.py build/lib.linux-x86_64-3.5/matplotlib/quiver.py build/lib.linux-x86_64-3.5/matplotlib/text.py build/lib.linux-x86_64-3.5/matplotlib/transforms.py build/lib.linux-x86_64-3.5/matplotlib/hatch.py build/lib.linux-x86_64-3.5/matplotlib/sankey.py build/lib.linux-x86_64-3.5/matplotlib/collections.py build/lib.linux-x86_64-3.5/matplotlib/offsetbox.py build/lib.linux-x86_64-3.5/matplotlib/image.py build/lib.linux-x86_64-3.5/matplotlib/rcsetup.py build/lib.linux-x86_64-3.5/matplotlib/axes.py build/lib.linux-x86_64-3.5/matplotlib/widgets.py build/lib.linux-x86_64-3.5/matplotlib/afm.py build/lib.linux-x86_64-3.5/matplotlib/font_manager.py build/lib.linux-x86_64-3.5/matplotlib/tight_bbox.py build/lib.linux-x86_64-3.5/matplotlib/axis.py build/lib.linux-x86_64-3.5/matplotlib/__init__.py build/lib.linux-x86_64-3.5/matplotlib/patches.py build/lib.linux-x86_64-3.5/matplotlib/lines.py build/lib.linux-x86_64-3.5/matplotlib/colorbar.py build/lib.linux-x86_64-3.5/matplotlib/cbook.py build/lib.linux-x86_64-3.5/matplotlib/colors.py build/lib.linux-x86_64-3.5/matplotlib/fontconfig_pattern.py build/lib.linux-x86_64-3.5/matplotlib/spines.py build/lib.linux-x86_64-3.5/matplotlib/finance.py build/lib.linux-x86_64-3.5/matplotlib/bezier.py build/lib.linux-x86_64-3.5/matplotlib/scale.py build/lib.linux-x86_64-3.5/matplotlib/patheffects.py build/lib.linux-x86_64-3.5/matplotlib/textpath.py build/lib.linux-x86_64-3.5/matplotlib/gridspec.py build/lib.linux-x86_64-3.5/matplotlib/mpl.py build/lib.linux-x86_64-3.5/matplotlib/blocking_input.py build/lib.linux-x86_64-3.5/matplotlib/legend.py build/lib.linux-x86_64-3.5/matplotlib/backend_bases.py build/lib.linux-x86_64-3.5/matplotlib/ticker.py build/lib.linux-x86_64-3.5/matplotlib/streamplot.py build/lib.linux-x86_64-3.5/matplotlib/texmanager.py build/lib.linux-x86_64-3.5/matplotlib/docstring.py build/lib.linux-x86_64-3.5/matplotlib/_cm.py build/lib.linux-x86_64-3.5/matplotlib/cm.py build/lib.linux-x86_64-3.5/matplotlib/_pylab_helpers.py build/lib.linux-x86_64-3.5/matplotlib/legend_handler.py build/lib.linux-x86_64-3.5/matplotlib/_mathtext_data.py build/lib.linux-x86_64-3.5/matplotlib/figure.py build/lib.linux-x86_64-3.5/matplotlib/path.py build/lib.linux-x86_64-3.5/matplotlib/pyplot.py build/lib.linux-x86_64-3.5/matplotlib/pylab.py build/lib.linux-x86_64-3.5/matplotlib/mlab.py build/lib.linux-x86_64-3.5/matplotlib/animation.py build/lib.linux-x86_64-3.5/matplotlib/artist.py build/lib.linux-x86_64-3.5/matplotlib/tight_layout.py build/lib.linux-x86_64-3.5/matplotlib/stackplot.py build/lib.linux-x86_64-3.5/matplotlib/contour.py build/lib.linux-x86_64-3.5/matplotlib/dates.py build/lib.linux-x86_64-3.5/matplotlib/container.py build/lib.linux-x86_64-3.5/matplotlib/type1font.py build/lib.linux-x86_64-3.5/matplotlib/markers.py build/lib.linux-x86_64-3.5/matplotlib/units.py build/lib.linux-x86_64-3.5/matplotlib/dviread.py build/lib.linux-x86_64-3.5/matplotlib/mathtext.py build/lib.linux-x86_64-3.5/matplotlib/backends/backend_qt4.py build/lib.linux-x86_64-3.5/matplotlib/backends/tkagg.py build/lib.linux-x86_64-3.5/matplotlib/backends/qt4_compat.py build/lib.linux-x86_64-3.5/matplotlib/backends/windowing.py build/lib.linux-x86_64-3.5/matplotlib/backends/backend_macosx.py build/lib.linux-x86_64-3.5/matplotlib/backends/backend_mixed.py build/lib.linux-x86_64-3.5/matplotlib/backends/backend_gtk3cairo.py build/lib.linux-x86_64-3.5/matplotlib/backends/backend_pgf.py build/lib.linux-x86_64-3.5/matplotlib/backends/backend_gtk.py build/lib.linux-x86_64-3.5/matplotlib/backends/backend_tkagg.py build/lib.linux-x86_64-3.5/matplotlib/backends/__init__.py build/lib.linux-x86_64-3.5/matplotlib/backends/backend_cairo.py build/lib.linux-x86_64-3.5/matplotlib/backends/backend_gtkcairo.py build/lib.linux-x86_64-3.5/matplotlib/backends/backend_webagg.py build/lib.linux-x86_64-3.5/matplotlib/backends/backend_gtk3agg.py build/lib.linux-x86_64-3.5/matplotlib/backends/backend_pdf.py build/lib.linux-x86_64-3.5/matplotlib/backends/backend_gdk.py build/lib.linux-x86_64-3.5/matplotlib/backends/backend_gtk3.py build/lib.linux-x86_64-3.5/matplotlib/backends/backend_ps.py build/lib.linux-x86_64-3.5/matplotlib/backends/backend_svg.py build/lib.linux-x86_64-3.5/matplotlib/backends/backend_wx.py build/lib.linux-x86_64-3.5/matplotlib/backends/backend_cocoaagg.py build/lib.linux-x86_64-3.5/matplotlib/backends/backend_qt4agg.py build/lib.linux-x86_64-3.5/matplotlib/backends/backend_wxagg.py build/lib.linux-x86_64-3.5/matplotlib/backends/backend_template.py build/lib.linux-x86_64-3.5/matplotlib/backends/backend_agg.py build/lib.linux-x86_64-3.5/matplotlib/backends/backend_gtkagg.py build/lib.linux-x86_64-3.5/matplotlib/backends/qt4_editor/__init__.py build/lib.linux-x86_64-3.5/matplotlib/backends/qt4_editor/formlayout.py build/lib.linux-x86_64-3.5/matplotlib/backends/qt4_editor/figureoptions.py build/lib.linux-x86_64-3.5/matplotlib/compat/__init__.py build/lib.linux-x86_64-3.5/matplotlib/compat/subprocess.py build/lib.linux-x86_64-3.5/matplotlib/projections/__init__.py build/lib.linux-x86_64-3.5/matplotlib/projections/polar.py build/lib.linux-x86_64-3.5/matplotlib/projections/geo.py build/lib.linux-x86_64-3.5/matplotlib/sphinxext/plot_directive.py build/lib.linux-x86_64-3.5/matplotlib/sphinxext/only_directives.py build/lib.linux-x86_64-3.5/matplotlib/sphinxext/ipython_console_highlighting.py build/lib.linux-x86_64-3.5/matplotlib/sphinxext/__init__.py build/lib.linux-x86_64-3.5/matplotlib/sphinxext/mathmpl.py build/lib.linux-x86_64-3.5/matplotlib/sphinxext/ipython_directive.py build/lib.linux-x86_64-3.5/matplotlib/testing/compare.py build/lib.linux-x86_64-3.5/matplotlib/testing/__init__.py build/lib.linux-x86_64-3.5/matplotlib/testing/decorators.py build/lib.linux-x86_64-3.5/matplotlib/testing/image_util.py build/lib.linux-x86_64-3.5/matplotlib/testing/noseclasses.py build/lib.linux-x86_64-3.5/matplotlib/testing/jpl_units/UnitDblFormatter.py build/lib.linux-x86_64-3.5/matplotlib/testing/jpl_units/UnitDblConverter.py build/lib.linux-x86_64-3.5/matplotlib/testing/jpl_units/EpochConverter.py build/lib.linux-x86_64-3.5/matplotlib/testing/jpl_units/StrConverter.py build/lib.linux-x86_64-3.5/matplotlib/testing/jpl_units/__init__.py build/lib.linux-x86_64-3.5/matplotlib/testing/jpl_units/Epoch.py build/lib.linux-x86_64-3.5/matplotlib/testing/jpl_units/Duration.py build/lib.linux-x86_64-3.5/matplotlib/testing/jpl_units/UnitDbl.py build/lib.linux-x86_64-3.5/matplotlib/tri/tricontour.py build/lib.linux-x86_64-3.5/matplotlib/tri/tritools.py build/lib.linux-x86_64-3.5/matplotlib/tri/__init__.py build/lib.linux-x86_64-3.5/matplotlib/tri/triangulation.py build/lib.linux-x86_64-3.5/matplotlib/tri/triinterpolate.py build/lib.linux-x86_64-3.5/matplotlib/tri/trirefine.py build/lib.linux-x86_64-3.5/matplotlib/tri/tripcolor.py build/lib.linux-x86_64-3.5/matplotlib/tri/triplot.py build/lib.linux-x86_64-3.5/matplotlib/tri/trifinder.py build/lib.linux-x86_64-3.5/matplotlib/delaunay/interpolate.py build/lib.linux-x86_64-3.5/matplotlib/delaunay/testfuncs.py build/lib.linux-x86_64-3.5/matplotlib/delaunay/__init__.py build/lib.linux-x86_64-3.5/matplotlib/delaunay/triangulate.py build/lib.linux-x86_64-3.5/mpl_toolkits/exceltools.py build/lib.linux-x86_64-3.5/mpl_toolkits/__init__.py build/lib.linux-x86_64-3.5/mpl_toolkits/gtktools.py build/lib.linux-x86_64-3.5/mpl_toolkits/mplot3d/axes3d.py build/lib.linux-x86_64-3.5/mpl_toolkits/mplot3d/__init__.py build/lib.linux-x86_64-3.5/mpl_toolkits/mplot3d/art3d.py build/lib.linux-x86_64-3.5/mpl_toolkits/mplot3d/proj3d.py build/lib.linux-x86_64-3.5/mpl_toolkits/mplot3d/axis3d.py build/lib.linux-x86_64-3.5/mpl_toolkits/axes_grid/angle_helper.py build/lib.linux-x86_64-3.5/mpl_toolkits/axes_grid/axes_size.py build/lib.linux-x86_64-3.5/mpl_toolkits/axes_grid/axisline_style.py build/lib.linux-x86_64-3.5/mpl_toolkits/axes_grid/anchored_artists.py build/lib.linux-x86_64-3.5/mpl_toolkits/axes_grid/__init__.py build/lib.linux-x86_64-3.5/mpl_toolkits/axes_grid/parasite_axes.py build/lib.linux-x86_64-3.5/mpl_toolkits/axes_grid/colorbar.py build/lib.linux-x86_64-3.5/mpl_toolkits/axes_grid/axes_grid.py build/lib.linux-x86_64-3.5/mpl_toolkits/axes_grid/axes_divider.py build/lib.linux-x86_64-3.5/mpl_toolkits/axes_grid/axislines.py build/lib.linux-x86_64-3.5/mpl_toolkits/axes_grid/axes_rgb.py build/lib.linux-x86_64-3.5/mpl_toolkits/axes_grid/grid_finder.py build/lib.linux-x86_64-3.5/mpl_toolkits/axes_grid/floating_axes.py build/lib.linux-x86_64-3.5/mpl_toolkits/axes_grid/grid_helper_curvelinear.py build/lib.linux-x86_64-3.5/mpl_toolkits/axes_grid/clip_path.py build/lib.linux-x86_64-3.5/mpl_toolkits/axes_grid/inset_locator.py build/lib.linux-x86_64-3.5/mpl_toolkits/axes_grid/axis_artist.py build/lib.linux-x86_64-3.5/mpl_toolkits/axes_grid1/mpl_axes.py build/lib.linux-x86_64-3.5/mpl_toolkits/axes_grid1/axes_size.py build/lib.linux-x86_64-3.5/mpl_toolkits/axes_grid1/anchored_artists.py build/lib.linux-x86_64-3.5/mpl_toolkits/axes_grid1/__init__.py build/lib.linux-x86_64-3.5/mpl_toolkits/axes_grid1/parasite_axes.py build/lib.linux-x86_64-3.5/mpl_toolkits/axes_grid1/colorbar.py build/lib.linux-x86_64-3.5/mpl_toolkits/axes_grid1/axes_grid.py build/lib.linux-x86_64-3.5/mpl_toolkits/axes_grid1/axes_divider.py build/lib.linux-x86_64-3.5/mpl_toolkits/axes_grid1/axes_rgb.py build/lib.linux-x86_64-3.5/mpl_toolkits/axes_grid1/inset_locator.py build/lib.linux-x86_64-3.5/mpl_toolkits/axisartist/angle_helper.py build/lib.linux-x86_64-3.5/mpl_toolkits/axisartist/axisline_style.py build/lib.linux-x86_64-3.5/mpl_toolkits/axisartist/__init__.py build/lib.linux-x86_64-3.5/mpl_toolkits/axisartist/axislines.py build/lib.linux-x86_64-3.5/mpl_toolkits/axisartist/grid_finder.py build/lib.linux-x86_64-3.5/mpl_toolkits/axisartist/floating_axes.py build/lib.linux-x86_64-3.5/mpl_toolkits/axisartist/grid_helper_curvelinear.py
build/lib.linux-x86_64-3.5/mpl_toolkits/axisartist/clip_path.py build/lib.linux-x86_64-3.5/mpl_toolkits/axisartist/axis_artist.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_subplots.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_dates.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_mathtext.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_table.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_rcparams.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_triangulation.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_collections.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_text.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_sankey.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_legend.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_tightlayout.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_ticker.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_cbook.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_figure.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_scale.py build/lib.linux-x86_64-3.5/matplotlib/tests/__init__.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_animation.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_backend_pgf.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_bbox_tight.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_backend_svg.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_ttconv.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_mlab.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_artist.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_colorbar.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_spines.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_png.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_transforms.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_patches.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_colors.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_dviread.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_path.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_agg.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_pickle.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_lines.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_delaunay.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_arrow_patches.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_backend_qt4.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_axes.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_simplification.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_contour.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_image.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_backend_pdf.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_compare_images.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_patheffects.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_basic.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_streamplot.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_coding_standards.py
Skipping optional fixer: buffer
Skipping optional fixer: idioms
Skipping optional fixer: set_literal
Skipping optional fixer: ws_comma
Fixing build/lib.linux-x86_64-3.5/pylab.py build/lib.linux-x86_64-3.5/matplotlib/table.py build/lib.linux-x86_64-3.5/matplotlib/quiver.py build/lib.linux-x86_64-3.5/matplotlib/text.py build/lib.linux-x86_64-3.5/matplotlib/transforms.py build/lib.linux-x86_64-3.5/matplotlib/hatch.py build/lib.linux-x86_64-3.5/matplotlib/sankey.py build/lib.linux-x86_64-3.5/matplotlib/collections.py build/lib.linux-x86_64-3.5/matplotlib/offsetbox.py build/lib.linux-x86_64-3.5/matplotlib/image.py build/lib.linux-x86_64-3.5/matplotlib/rcsetup.py build/lib.linux-x86_64-3.5/matplotlib/axes.py build/lib.linux-x86_64-3.5/matplotlib/widgets.py build/lib.linux-x86_64-3.5/matplotlib/afm.py build/lib.linux-x86_64-3.5/matplotlib/font_manager.py build/lib.linux-x86_64-3.5/matplotlib/tight_bbox.py build/lib.linux-x86_64-3.5/matplotlib/axis.py build/lib.linux-x86_64-3.5/matplotlib/__init__.py build/lib.linux-x86_64-3.5/matplotlib/patches.py build/lib.linux-x86_64-3.5/matplotlib/lines.py build/lib.linux-x86_64-3.5/matplotlib/colorbar.py build/lib.linux-x86_64-3.5/matplotlib/cbook.py build/lib.linux-x86_64-3.5/matplotlib/colors.py build/lib.linux-x86_64-3.5/matplotlib/fontconfig_pattern.py build/lib.linux-x86_64-3.5/matplotlib/spines.py build/lib.linux-x86_64-3.5/matplotlib/finance.py build/lib.linux-x86_64-3.5/matplotlib/bezier.py build/lib.linux-x86_64-3.5/matplotlib/scale.py build/lib.linux-x86_64-3.5/matplotlib/patheffects.py build/lib.linux-x86_64-3.5/matplotlib/textpath.py build/lib.linux-x86_64-3.5/matplotlib/gridspec.py build/lib.linux-x86_64-3.5/matplotlib/mpl.py build/lib.linux-x86_64-3.5/matplotlib/blocking_input.py build/lib.linux-x86_64-3.5/matplotlib/legend.py build/lib.linux-x86_64-3.5/matplotlib/backend_bases.py build/lib.linux-x86_64-3.5/matplotlib/ticker.py build/lib.linux-x86_64-3.5/matplotlib/streamplot.py build/lib.linux-x86_64-3.5/matplotlib/texmanager.py build/lib.linux-x86_64-3.5/matplotlib/docstring.py build/lib.linux-x86_64-3.5/matplotlib/_cm.py build/lib.linux-x86_64-3.5/matplotlib/cm.py build/lib.linux-x86_64-3.5/matplotlib/_pylab_helpers.py build/lib.linux-x86_64-3.5/matplotlib/legend_handler.py build/lib.linux-x86_64-3.5/matplotlib/_mathtext_data.py build/lib.linux-x86_64-3.5/matplotlib/figure.py build/lib.linux-x86_64-3.5/matplotlib/path.py build/lib.linux-x86_64-3.5/matplotlib/pyplot.py build/lib.linux-x86_64-3.5/matplotlib/pylab.py build/lib.linux-x86_64-3.5/matplotlib/mlab.py build/lib.linux-x86_64-3.5/matplotlib/animation.py build/lib.linux-x86_64-3.5/matplotlib/artist.py build/lib.linux-x86_64-3.5/matplotlib/tight_layout.py build/lib.linux-x86_64-3.5/matplotlib/stackplot.py build/lib.linux-x86_64-3.5/matplotlib/contour.py build/lib.linux-x86_64-3.5/matplotlib/dates.py build/lib.linux-x86_64-3.5/matplotlib/container.py build/lib.linux-x86_64-3.5/matplotlib/type1font.py build/lib.linux-x86_64-3.5/matplotlib/markers.py build/lib.linux-x86_64-3.5/matplotlib/units.py build/lib.linux-x86_64-3.5/matplotlib/dviread.py build/lib.linux-x86_64-3.5/matplotlib/mathtext.py build/lib.linux-x86_64-3.5/matplotlib/backends/backend_qt4.py build/lib.linux-x86_64-3.5/matplotlib/backends/tkagg.py build/lib.linux-x86_64-3.5/matplotlib/backends/qt4_compat.py build/lib.linux-x86_64-3.5/matplotlib/backends/windowing.py build/lib.linux-x86_64-3.5/matplotlib/backends/backend_macosx.py build/lib.linux-x86_64-3.5/matplotlib/backends/backend_mixed.py build/lib.linux-x86_64-3.5/matplotlib/backends/backend_gtk3cairo.py build/lib.linux-x86_64-3.5/matplotlib/backends/backend_pgf.py build/lib.linux-x86_64-3.5/matplotlib/backends/backend_gtk.py build/lib.linux-x86_64-3.5/matplotlib/backends/backend_tkagg.py build/lib.linux-x86_64-3.5/matplotlib/backends/__init__.py build/lib.linux-x86_64-3.5/matplotlib/backends/backend_cairo.py build/lib.linux-x86_64-3.5/matplotlib/backends/backend_gtkcairo.py build/lib.linux-x86_64-3.5/matplotlib/backends/backend_webagg.py build/lib.linux-x86_64-3.5/matplotlib/backends/backend_gtk3agg.py build/lib.linux-x86_64-3.5/matplotlib/backends/backend_pdf.py build/lib.linux-x86_64-3.5/matplotlib/backends/backend_gdk.py build/lib.linux-x86_64-3.5/matplotlib/backends/backend_gtk3.py build/lib.linux-x86_64-3.5/matplotlib/backends/backend_ps.py build/lib.linux-x86_64-3.5/matplotlib/backends/backend_svg.py build/lib.linux-x86_64-3.5/matplotlib/backends/backend_wx.py build/lib.linux-x86_64-3.5/matplotlib/backends/backend_cocoaagg.py build/lib.linux-x86_64-3.5/matplotlib/backends/backend_qt4agg.py build/lib.linux-x86_64-3.5/matplotlib/backends/backend_wxagg.py build/lib.linux-x86_64-3.5/matplotlib/backends/backend_template.py build/lib.linux-x86_64-3.5/matplotlib/backends/backend_agg.py build/lib.linux-x86_64-3.5/matplotlib/backends/backend_gtkagg.py build/lib.linux-x86_64-3.5/matplotlib/backends/qt4_editor/__init__.py build/lib.linux-x86_64-3.5/matplotlib/backends/qt4_editor/formlayout.py build/lib.linux-x86_64-3.5/matplotlib/backends/qt4_editor/figureoptions.py build/lib.linux-x86_64-3.5/matplotlib/compat/__init__.py build/lib.linux-x86_64-3.5/matplotlib/compat/subprocess.py build/lib.linux-x86_64-3.5/matplotlib/projections/__init__.py build/lib.linux-x86_64-3.5/matplotlib/projections/polar.py build/lib.linux-x86_64-3.5/matplotlib/projections/geo.py build/lib.linux-x86_64-3.5/matplotlib/sphinxext/plot_directive.py build/lib.linux-x86_64-3.5/matplotlib/sphinxext/only_directives.py build/lib.linux-x86_64-3.5/matplotlib/sphinxext/ipython_console_highlighting.py build/lib.linux-x86_64-3.5/matplotlib/sphinxext/__init__.py build/lib.linux-x86_64-3.5/matplotlib/sphinxext/mathmpl.py build/lib.linux-x86_64-3.5/matplotlib/sphinxext/ipython_directive.py build/lib.linux-x86_64-3.5/matplotlib/testing/compare.py build/lib.linux-x86_64-3.5/matplotlib/testing/__init__.py build/lib.linux-x86_64-3.5/matplotlib/testing/decorators.py build/lib.linux-x86_64-3.5/matplotlib/testing/image_util.py build/lib.linux-x86_64-3.5/matplotlib/testing/noseclasses.py build/lib.linux-x86_64-3.5/matplotlib/testing/jpl_units/UnitDblFormatter.py build/lib.linux-x86_64-3.5/matplotlib/testing/jpl_units/UnitDblConverter.py build/lib.linux-x86_64-3.5/matplotlib/testing/jpl_units/EpochConverter.py build/lib.linux-x86_64-3.5/matplotlib/testing/jpl_units/StrConverter.py build/lib.linux-x86_64-3.5/matplotlib/testing/jpl_units/__init__.py build/lib.linux-x86_64-3.5/matplotlib/testing/jpl_units/Epoch.py build/lib.linux-x86_64-3.5/matplotlib/testing/jpl_units/Duration.py build/lib.linux-x86_64-3.5/matplotlib/testing/jpl_units/UnitDbl.py build/lib.linux-x86_64-3.5/matplotlib/tri/tricontour.py build/lib.linux-x86_64-3.5/matplotlib/tri/tritools.py build/lib.linux-x86_64-3.5/matplotlib/tri/__init__.py build/lib.linux-x86_64-3.5/matplotlib/tri/triangulation.py build/lib.linux-x86_64-3.5/matplotlib/tri/triinterpolate.py build/lib.linux-x86_64-3.5/matplotlib/tri/trirefine.py build/lib.linux-x86_64-3.5/matplotlib/tri/tripcolor.py build/lib.linux-x86_64-3.5/matplotlib/tri/triplot.py build/lib.linux-x86_64-3.5/matplotlib/tri/trifinder.py build/lib.linux-x86_64-3.5/matplotlib/delaunay/interpolate.py build/lib.linux-x86_64-3.5/matplotlib/delaunay/testfuncs.py build/lib.linux-x86_64-3.5/matplotlib/delaunay/__init__.py build/lib.linux-x86_64-3.5/matplotlib/delaunay/triangulate.py build/lib.linux-x86_64-3.5/mpl_toolkits/exceltools.py build/lib.linux-x86_64-3.5/mpl_toolkits/__init__.py build/lib.linux-x86_64-3.5/mpl_toolkits/gtktools.py build/lib.linux-x86_64-3.5/mpl_toolkits/mplot3d/axes3d.py build/lib.linux-x86_64-3.5/mpl_toolkits/mplot3d/__init__.py build/lib.linux-x86_64-3.5/mpl_toolkits/mplot3d/art3d.py build/lib.linux-x86_64-3.5/mpl_toolkits/mplot3d/proj3d.py build/lib.linux-x86_64-3.5/mpl_toolkits/mplot3d/axis3d.py build/lib.linux-x86_64-3.5/mpl_toolkits/axes_grid/angle_helper.py build/lib.linux-x86_64-3.5/mpl_toolkits/axes_grid/axes_size.py build/lib.linux-x86_64-3.5/mpl_toolkits/axes_grid/axisline_style.py build/lib.linux-x86_64-3.5/mpl_toolkits/axes_grid/anchored_artists.py build/lib.linux-x86_64-3.5/mpl_toolkits/axes_grid/__init__.py build/lib.linux-x86_64-3.5/mpl_toolkits/axes_grid/parasite_axes.py build/lib.linux-x86_64-3.5/mpl_toolkits/axes_grid/colorbar.py build/lib.linux-x86_64-3.5/mpl_toolkits/axes_grid/axes_grid.py build/lib.linux-x86_64-3.5/mpl_toolkits/axes_grid/axes_divider.py build/lib.linux-x86_64-3.5/mpl_toolkits/axes_grid/axislines.py build/lib.linux-x86_64-3.5/mpl_toolkits/axes_grid/axes_rgb.py build/lib.linux-x86_64-3.5/mpl_toolkits/axes_grid/grid_finder.py build/lib.linux-x86_64-3.5/mpl_toolkits/axes_grid/floating_axes.py build/lib.linux-x86_64-3.5/mpl_toolkits/axes_grid/grid_helper_curvelinear.py build/lib.linux-x86_64-3.5/mpl_toolkits/axes_grid/clip_path.py build/lib.linux-x86_64-3.5/mpl_toolkits/axes_grid/inset_locator.py build/lib.linux-x86_64-3.5/mpl_toolkits/axes_grid/axis_artist.py build/lib.linux-x86_64-3.5/mpl_toolkits/axes_grid1/mpl_axes.py build/lib.linux-x86_64-3.5/mpl_toolkits/axes_grid1/axes_size.py build/lib.linux-x86_64-3.5/mpl_toolkits/axes_grid1/anchored_artists.py build/lib.linux-x86_64-3.5/mpl_toolkits/axes_grid1/__init__.py build/lib.linux-x86_64-3.5/mpl_toolkits/axes_grid1/parasite_axes.py build/lib.linux-x86_64-3.5/mpl_toolkits/axes_grid1/colorbar.py build/lib.linux-x86_64-3.5/mpl_toolkits/axes_grid1/axes_grid.py build/lib.linux-x86_64-3.5/mpl_toolkits/axes_grid1/axes_divider.py build/lib.linux-x86_64-3.5/mpl_toolkits/axes_grid1/axes_rgb.py build/lib.linux-x86_64-3.5/mpl_toolkits/axes_grid1/inset_locator.py build/lib.linux-x86_64-3.5/mpl_toolkits/axisartist/angle_helper.py build/lib.linux-x86_64-3.5/mpl_toolkits/axisartist/axisline_style.py build/lib.linux-x86_64-3.5/mpl_toolkits/axisartist/__init__.py build/lib.linux-x86_64-3.5/mpl_toolkits/axisartist/axislines.py build/lib.linux-x86_64-3.5/mpl_toolkits/axisartist/grid_finder.py build/lib.linux-x86_64-3.5/mpl_toolkits/axisartist/floating_axes.py build/lib.linux-x86_64-3.5/mpl_toolkits/axisartist/grid_helper_curvelinear.py
build/lib.linux-x86_64-3.5/mpl_toolkits/axisartist/clip_path.py build/lib.linux-x86_64-3.5/mpl_toolkits/axisartist/axis_artist.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_subplots.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_dates.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_mathtext.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_table.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_rcparams.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_triangulation.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_collections.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_text.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_sankey.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_legend.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_tightlayout.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_ticker.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_cbook.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_figure.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_scale.py build/lib.linux-x86_64-3.5/matplotlib/tests/__init__.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_animation.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_backend_pgf.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_bbox_tight.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_backend_svg.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_ttconv.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_mlab.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_artist.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_colorbar.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_spines.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_png.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_transforms.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_patches.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_colors.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_dviread.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_path.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_agg.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_pickle.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_lines.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_delaunay.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_arrow_patches.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_backend_qt4.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_axes.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_simplification.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_contour.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_image.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_backend_pdf.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_compare_images.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_patheffects.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_basic.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_streamplot.py build/lib.linux-x86_64-3.5/matplotlib/tests/test_coding_standards.py
Skipping optional fixer: buffer
Skipping optional fixer: idioms
Skipping optional fixer: set_literal
Skipping optional fixer: ws_comma
running build_ext
building 'matplotlib.ft2font' extension
creating build/temp.linux-x86_64-3.5
creating build/temp.linux-x86_64-3.5/src
creating build/temp.linux-x86_64-3.5/CXX
mpicc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -mkl -O3 -axCORE-AVX2 -xSSE4.2 -fPIC -ipo -w -vec-report0 -opt-report0 -fPIC -DPY_ARRAY_UNIQUE_SYMBOL=MPL_matplotlib_ft2font_ARRAY_API -DPYCXX_ISO_CPP_LIB=1 -DPYCXX_PYTHON_2TO3=1 -I/u/lcouston/build/lib/python3.5/site-packages/numpy/core/include -I/u/lcouston/build/lib/python3.5/site-packages/numpy/core/include -I/usr/local/include -I/usr/include -I. -I/usr/include/freetype2 -I/u/lcouston/build/include/python3.5m -c src/ft2font.cpp -o build/temp.linux-x86_64-3.5/src/ft2font.o
mpicc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -mkl -O3 -axCORE-AVX2 -xSSE4.2 -fPIC -ipo -w -vec-report0 -opt-report0 -fPIC -DPY_ARRAY_UNIQUE_SYMBOL=MPL_matplotlib_ft2font_ARRAY_API -DPYCXX_ISO_CPP_LIB=1 -DPYCXX_PYTHON_2TO3=1 -I/u/lcouston/build/lib/python3.5/site-packages/numpy/core/include -I/u/lcouston/build/lib/python3.5/site-packages/numpy/core/include -I/usr/local/include -I/usr/include -I. -I/usr/include/freetype2 -I/u/lcouston/build/include/python3.5m -c src/mplutils.cpp -o build/temp.linux-x86_64-3.5/src/mplutils.o
mpicc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -mkl -O3 -axCORE-AVX2 -xSSE4.2 -fPIC -ipo -w -vec-report0 -opt-report0 -fPIC -DPY_ARRAY_UNIQUE_SYMBOL=MPL_matplotlib_ft2font_ARRAY_API -DPYCXX_ISO_CPP_LIB=1 -DPYCXX_PYTHON_2TO3=1 -I/u/lcouston/build/lib/python3.5/site-packages/numpy/core/include -I/u/lcouston/build/lib/python3.5/site-packages/numpy/core/include -I/usr/local/include -I/usr/include -I. -I/usr/include/freetype2 -I/u/lcouston/build/include/python3.5m -c CXX/IndirectPythonInterface.cxx -o build/temp.linux-x86_64-3.5/CXX/IndirectPythonInterface.o
mpicc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -mkl -O3 -axCORE-AVX2 -xSSE4.2 -fPIC -ipo -w -vec-report0 -opt-report0 -fPIC -DPY_ARRAY_UNIQUE_SYMBOL=MPL_matplotlib_ft2font_ARRAY_API -DPYCXX_ISO_CPP_LIB=1 -DPYCXX_PYTHON_2TO3=1 -I/u/lcouston/build/lib/python3.5/site-packages/numpy/core/include -I/u/lcouston/build/lib/python3.5/site-packages/numpy/core/include -I/usr/local/include -I/usr/include -I. -I/usr/include/freetype2 -I/u/lcouston/build/include/python3.5m -c CXX/cxxsupport.cxx -o build/temp.linux-x86_64-3.5/CXX/cxxsupport.o
mpicc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -mkl -O3 -axCORE-AVX2 -xSSE4.2 -fPIC -ipo -w -vec-report0 -opt-report0 -fPIC -DPY_ARRAY_UNIQUE_SYMBOL=MPL_matplotlib_ft2font_ARRAY_API -DPYCXX_ISO_CPP_LIB=1 -DPYCXX_PYTHON_2TO3=1 -I/u/lcouston/build/lib/python3.5/site-packages/numpy/core/include -I/u/lcouston/build/lib/python3.5/site-packages/numpy/core/include -I/usr/local/include -I/usr/include -I. -I/usr/include/freetype2 -I/u/lcouston/build/include/python3.5m -c CXX/cxx_extensions.cxx -o build/temp.linux-x86_64-3.5/CXX/cxx_extensions.o
mpicc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -mkl -O3 -axCORE-AVX2 -xSSE4.2 -fPIC -ipo -w -vec-report0 -opt-report0 -fPIC -DPY_ARRAY_UNIQUE_SYMBOL=MPL_matplotlib_ft2font_ARRAY_API -DPYCXX_ISO_CPP_LIB=1 -DPYCXX_PYTHON_2TO3=1 -I/u/lcouston/build/lib/python3.5/site-packages/numpy/core/include -I/u/lcouston/build/lib/python3.5/site-packages/numpy/core/include -I/usr/local/include -I/usr/include -I. -I/usr/include/freetype2 -I/u/lcouston/build/include/python3.5m -c CXX/cxxextensions.c -o build/temp.linux-x86_64-3.5/CXX/cxxextensions.o
mpicxx -shared -lpthread build/temp.linux-x86_64-3.5/src/ft2font.o build/temp.linux-x86_64-3.5/src/mplutils.o build/temp.linux-x86_64-3.5/CXX/IndirectPythonInterface.o build/temp.linux-x86_64-3.5/CXX/cxxsupport.o build/temp.linux-x86_64-3.5/CXX/cxx_extensions.o build/temp.linux-x86_64-3.5/CXX/cxxextensions.o -L/usr/local/lib -L/usr/local/lib64 -L/usr/lib -L/usr/lib64 -L/u/lcouston/build/lib -lfreetype -lz -lstdc++ -lm -lpython3.5m -o build/lib.linux-x86_64-3.5/matplotlib/ft2font.cpython-35m-x86_64-linux-gnu.so
src/ft2font.cpp(347): (col. 1) remark: _ZN8FT2Image13py_as_rgb_strERKN2Py5TupleE has been targeted for automatic cpu dispatch
src/ft2font.cpp(2239): (col. 1) remark: _ZN14ft2font_moduleC1Ev has been targeted for automatic cpu dispatch
CXX/Python3/cxx_extensions.cxx(358): (col. 13) remark: _ZN2Py10PythonTypeC2EmiPKc has been targeted for automatic cpu dispatch
CXX/Python3/cxx_extensions.cxx(364): (col. 1) remark: _ZN2Py10PythonTypeC1EmiPKc has been targeted for automatic cpu dispatch
src/ft2font.cpp(1501): (col. 1) remark: _ZN7FT2Font7get_xysERKN2Py5TupleERKNS0_4DictE has been targeted for automatic cpu dispatch
src/ft2font.cpp(1447): (col. 1) remark: _ZN7FT2Font21draw_glyphs_to_bitmapERKN2Py5TupleERKNS0_4DictE has been targeted for automatic cpu dispatch
/usr/include/c++/4.3/bits/vector.tcc(351): (col. 5) remark: _ZNSt6vectorIP12FT_GlyphRec_SaIS1_EE14_M_fill_insertEN9__gnu_cxx17__normal_iteratorIPS1_S3_EEmRKS1_ has been targeted for automatic cpu dispatch
src/ft2font.cpp(368): (col. 1) remark: _Z33_callVarArgsMethod__py_as_rgb_strP7_objectS0_S0_ has been targeted for automatic cpu dispatch
ld: skipping incompatible /usr/lib/libpthread.so when searching for -lpthread
ld: skipping incompatible /usr/lib/libpthread.a when searching for -lpthread
ld: skipping incompatible /usr/lib/libz.so when searching for -lz
ld: skipping incompatible /usr/lib/libz.a when searching for -lz
ld: skipping incompatible /usr/lib/libm.so when searching for -lm
ld: skipping incompatible /usr/lib/libm.a when searching for -lm
ld: skipping incompatible /usr/lib/libm.so when searching for -lm
ld: skipping incompatible /usr/lib/libm.a when searching for -lm
ld: skipping incompatible /usr/lib/libpthread.so when searching for -lpthread
ld: skipping incompatible /usr/lib/libpthread.a when searching for -lpthread
ld: skipping incompatible /usr/lib/libc.so when searching for -lc
ld: skipping incompatible /usr/lib/libc.a when searching for -lc
ld: skipping incompatible /usr/lib/libdl.so when searching for -ldl
ld: skipping incompatible /usr/lib/libdl.a when searching for -ldl
ld: skipping incompatible /usr/lib/libc.so when searching for -lc
ld: skipping incompatible /usr/lib/libc.a when searching for -lc
building 'matplotlib._png' extension
mpicc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -mkl -O3 -axCORE-AVX2 -xSSE4.2 -fPIC -ipo -w -vec-report0 -opt-report0 -fPIC -DPY_ARRAY_UNIQUE_SYMBOL=MPL_matplotlib__png_ARRAY_API -DPYCXX_ISO_CPP_LIB=1 -DPYCXX_PYTHON_2TO3=1 -I/u/lcouston/build/lib/python3.5/site-packages/numpy/core/include -I/u/lcouston/build/lib/python3.5/site-packages/numpy/core/include -I/usr/local/include -I/usr/include -I. -I/usr/include/libpng12 -I/u/lcouston/build/include/python3.5m -c src/_png.cpp -o build/temp.linux-x86_64-3.5/src/_png.o
src/_png.cpp(147): error: identifier "npy_PyFile_Dup" is undefined
if ((fp = npy_PyFile_Dup(py_file, (char *)"wb")))
^

src/_png.cpp(243): error: identifier "npy_PyFile_DupClose" is undefined
if (npy_PyFile_DupClose(py_file, fp)) {
^

src/_png.cpp(264): error: identifier "npy_PyFile_DupClose" is undefined
if (npy_PyFile_DupClose(py_file, fp)) {
^

src/_png.cpp(329): error: identifier "npy_PyFile_Dup" is undefined
if ((fp = npy_PyFile_Dup(py_file, "rb")))
^

src/_png.cpp(577): error: identifier "npy_PyFile_DupClose" is undefined
if (npy_PyFile_DupClose(py_file, fp)) {
^

error: command 'mpicc' failed with exit status 2

----------------------------------------
Command "/u/lcouston/build/bin/python3.5 -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-q997hxsh/matplotlib/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-d4c18bg1-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-build-q997hxsh/matplotlib/
lcouston@pfe26:~> echo $PATH
/u/lcouston/build/bin:/u/lcouston/build://u/lcouston/dedalus/bin:/u/lcouston/dedalus://u/lcouston/scripts:/nasa/emacs/24.3/bin:/nasa/openssl/1.0.1h/bin:/nasa/sles11/git/2.4.5/bin:/nasa/intel/Compiler/2016.2.181/compilers_and_libraries_2016.2.181/linux/bin/intel64:/nasa/intel/Compiler/2016.2.181/debugger_2016/gdb/intel64_mic/bin:/nasa/sgi/mpt/2.12r26/bin:/usr/local/bin:/usr/bin:/bin:/usr/X11R6/bin:/PBS/bin:/usr/sbin:/sbin:/opt/c3/bin:/opt/sgi/sbin:/opt/sgi/bin
lcouston@pfe26:~>





+++++++++++++++++++++++++++++
SOME PREVIOUS OUTPUTS
+++++++++++++++++++++++++++++

+++++++++++++++++++++++++++++
openmpi install, on the ./configure, I got
***
configure: WARNING: unrecognized options: --without-portals
***
ATTENTION! pax archive volume change required.
Ready for archive volume: 1
Input archive name or "." to quit pax.
Archive name >
*** => I hit '.'

++++++++++++++++++++++++++++++++++
python install, on the make, I got
***
Python build finished successfully!
The necessary bits to build these optional modules were not found:
_lzma                                                         
To find the necessary bits, look in setup.py in detect_modules() for the module's name.

Failed to build these modules:
_curses_panel
***
# Substitution happens here, as the completely-expanded BINDIR
# is not available in configure
sed -e "s,@EXENAME@,/u/lcouston/build/bin/python3.5m," < ./Misc/python-config.in >python-config.py
# Replace makefile compat. variable references with shell script compat. ones;  ->
sed -e 's,\$(\([A-Za-z0-9_]*\)),\$\{\1\},g' < Misc/python-config.sh >python-config
# On Darwin, always use the python version of the script, the shell
# version doesn't use the compiler customizations that are provided
# in python (_osx_support.py).
if test `uname -s` = Darwin; then \
        cp python-config.py python-config; \
    fi
***

++++++++++++++++++++++++++++++
./numpy_test_full
***
slow blas
version: 1.10.1

dot: 0.04580252934247255 sec
lapack_mkl_info:
    include_dirs = ['/nasa/intel/Compiler/2015.3.187/composer_xe_2015.3.187/mkl/include']
    library_dirs = ['/nasa/intel/Compiler/2015.3.187/composer_xe_2015.3.187/mkl/lib/intel64/']
    define_macros = [('SCIPY_MKL_H', None), ('HAVE_CBLAS', None)]
    libraries = ['mkl_rt', 'pthread']
lapack_opt_info:
    include_dirs = ['/nasa/intel/Compiler/2015.3.187/composer_xe_2015.3.187/mkl/include']
    library_dirs = ['/nasa/intel/Compiler/2015.3.187/composer_xe_2015.3.187/mkl/lib/intel64/']
    define_macros = [('SCIPY_MKL_H', None), ('HAVE_CBLAS', None)]
    libraries = ['mkl_rt', 'pthread']
openblas_lapack_info:
  NOT AVAILABLE
mkl_info:
    include_dirs = ['/nasa/intel/Compiler/2015.3.187/composer_xe_2015.3.187/mkl/include']
    library_dirs = ['/nasa/intel/Compiler/2015.3.187/composer_xe_2015.3.187/mkl/lib/intel64/']
    define_macros = [('SCIPY_MKL_H', None), ('HAVE_CBLAS', None)]
    libraries = ['mkl_rt', 'pthread']
blas_mkl_info:
    include_dirs = ['/nasa/intel/Compiler/2015.3.187/composer_xe_2015.3.187/mkl/include']
    library_dirs = ['/nasa/intel/Compiler/2015.3.187/composer_xe_2015.3.187/mkl/lib/intel64/']
    define_macros = [('SCIPY_MKL_H', None), ('HAVE_CBLAS', None)]
    libraries = ['mkl_rt', 'pthread']
blas_opt_info:
    include_dirs = ['/nasa/intel/Compiler/2015.3.187/composer_xe_2015.3.187/mkl/include']
    library_dirs = ['/nasa/intel/Compiler/2015.3.187/composer_xe_2015.3.187/mkl/lib/intel64/']
    define_macros = [('SCIPY_MKL_H', None), ('HAVE_CBLAS', None)]
    libraries = ['mkl_rt', 'pthread']
None
Running unit tests for numpy
NumPy version 1.10.1
NumPy relaxed strides checking option: True
NumPy is installed in /u/lcouston/build/lib/python3.5/site-packages/numpy
Python version 3.5.0 (default, Sep 22 2016, 07:50:37) [GCC Intel(R) C++ gcc 4.3 mode]
nose version 1.3.7
***

[louisalexan...@gmail.com]

and here is the .profile

+++++++
# $Header: /cvsroot/bcfg2/bcfg2/Cfg/etc/skel_NAS/.profile/.profile,v 1.1 2009/12/11 16:05:13 dtalcott Exp $
# These commands are executed on a login or start of a PBS job.

# First, run the NAS standard setup.

if [ -e /usr/local/lib/init/global.profile ]; then
. /usr/local/lib/init/global.profile
fi

# Add your commands here to extend your PATH, etc.

module load comp-intel
module load git
module load openssl
module load emacs

export BUILD_HOME=$HOME/build

export PATH=$BUILD_HOME/bin:$BUILD_HOME:/$PATH # Add private commands to PATH

export LD_LIBRARY_PATH=$BUILD_HOME/lib:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH=/nasa/openssl/1.0.1h/lib/:$LD_LIBRARY_PATH

export CC=mpicc

#pathing for Dedalus
export LOCAL_MPI_VERSION=openmpi-1.10.1
export LOCAL_MPI_SHORT=v1.10

# falling back to 1.8 until we resolve tcp wireup errors
# (probably at runtime with MCA parameters)
export LOCAL_MPI_VERSION=openmpi-1.8.6
export LOCAL_MPI_SHORT=v1.8

export LOCAL_PYTHON_VERSION=3.5.0
export LOCAL_NUMPY_VERSION=1.10.1
export LOCAL_SCIPY_VERSION=0.16.1
export LOCAL_HDF5_VERSION=1.8.15-patch1
export LOCAL_MERCURIAL_VERSION=3.6

export MPI_ROOT=$BUILD_HOME/$LOCAL_MPI_VERSION
export PYTHONPATH=$BUILD_HOME/dedalus:$PYTHONPATH
export MPI_PATH=$MPI_ROOT
export FFTW_PATH=$BUILD_HOME
export HDF5_DIR=$BUILD_HOME

# Openmpi forks:
export OMPI_MCA_mpi_warn_on_fork=0

# don't mess up Pleiades for everyone else
export OMPI_MCA_btl_openib_if_include=mlx4_0:1

[Ben Brown]

Louis,

     I'd prefer to debug the cluster install script at this point; it is the direction we want to take these cluster installs.  Also, the best MPI performance on Pleiades is coming from MPI-SGI at this point.

Could you please remove your prior dedalus directory from cluster_install.sh and try the attached version of the script (8/24/16 version)?  Please carefully read the message to screen as the required modules on Pleiades are slightly different then you have in your .profile.  If this fails, please send me the install log and we can work to get you up and running!

--Ben

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[Daniel Lecoanet]

Hi all,

I just tried this out myself.  I changed dedalus_directory as to not overwrite my normal dedalus installation, cleared my .profile file, and then I ran:

dlecoane@pfe26:~> module load mpi-sgi/mpt
dlecoane@pfe26:~> module load comp-intel
dlecoane@pfe26:~> module load git
dlecoane@pfe26:~> module load openssl
dlecoane@pfe26:~> bash cluster_install.sh

Everything seemed to work fine until the end:

Installing mercurial
ModuleCmd_Switch.c(172):ERROR:152: Module 'intel' is currently not loaded
Currently Loaded Modulefiles:

  1) mpi-sgi/mpt.2.12r26     2) mpi-sgi/mpt             3) comp-intel/2016.2.181   4) git/2.4.5               5) openssl/1.0.1h          6) python/2.7.9

ModuleCmd_Switch.c(172):ERROR:152: Module 'gcc' is currently not loaded
cluster_install.sh: line 697: [: -eq: unary operator expected

However, the installation then seemed to finish normally.  I then ran one of Louis's 1024 Fourier x 256 Chebyshev boussinesq scripts.  The key thing to remember is to run using mpiexec_mpt instead of mpirun.

Here's how the sgi installation compared to my non-sgi installation:

sgi: 

32 cores: 77 seconds

64 cores: 60 seconds

128 cores: 61 seconds

256 cores: 68 seconds

non-sgi:

32 cores: 82 seconds

64 cores: 61 seconds

128 cores: 52 seconds

256 cores: 77 seconds

I don't know how much of this is job-to-job variation, but it looks to me like the non-sgi installation scales out better (by ~15%) than the sgi one.  Might be useful for big 2D runs to switch off sgi.

Daniel

On Thu, Sep 22, 2016 at 6:23 PM, Ben Brown <bpb...@gmail.com> wrote:

Louis,

     I'd prefer to debug the cluster install script at this point; it is the direction we want to take these cluster installs.  Also, the best MPI performance on Pleiades is coming from MPI-SGI at this point.

Could you please remove your prior dedalus directory from cluster_install.sh and try the attached version of the script (8/24/16 version)?  Please carefully read the message to screen as the required modules on Pleiades are slightly different then you have in your .profile.  If this fails, please send me the install log and we can work to get you up and running!

--Ben

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[Daniel Lecoanet]

Looks like I had underestimated the amount of job-to-job variability...  I just ran the non-sgi installation on the same cores as I used for the sgi runs.  Here's the performance:

32 cores: 87 sec

64 cores: 77 sec

128 cores: 87 sec

256 cores: 89 sec

So looks like sgi is faster after all!

Daniel

[Ben Brown]

Daniel,

    Thanks for the SGI/non-SGI tests!  Neat.

--Ben

To view this discussion on the web visit https://groups.google.com/d/msgid/dedalus-users/CAJoYf%3DjKnt1hCXpjkFD2EcUgPum2_pvcUS2vEKx%2BnE0_wRCT0g%40mail.gmail.com.

[louisalexan...@gmail.com]

Hi Ben and Daniel,

Thank you so much for getting back to me this quickly !
I agree that installing with a script would be useful for most users so I'll do that right now. I'll keep you updated. If it works I'll do a speed test and I'll let you know the results.

Best,
Louis

[louisalexan...@gmail.com]

Hi everybody,

I did the install using the new bashable script provided by Ben on Pleiades.
I did it on the front-end nodes.

I changed my .profile as shown below.

The install worked like a charm and I got similar outputs as Daniel (also shown below).

I ran the same script that I gave Daniel, and with sgi I got (I grabbed 260 Ivy cores)

32 cores: 67.55 sec
64 cores: 54.8 sec
128 cores: 47.1 sec
256 cores: 49.5 sec

I'll do some additional tests but this install looks fine to me !
Thank you so much for putting this script together !
Best,
Louis

.profile
===========================================

# $Header: /cvsroot/bcfg2/bcfg2/Cfg/etc/skel_NAS/.profile/.profile,v 1.1 2009/12/11 16:05:13 dtalcott Exp $
# These commands are executed on a login or start of a PBS job.

# First, run the NAS standard setup.

if [ -e /usr/local/lib/init/global.profile ]; then
. /usr/local/lib/init/global.profile
fi

# Add your commands here to extend your PATH, etc.

module load mpi-sgi/mpt

module load comp-intel
module load git
module load openssl

export PATH=$HOME/scripts:$PATH

alias dedalus="source /u/lcouston/dedalus/bin/activate"

# support lots of text output to stdio for analysis
export MPI_UNBUFFERED_STDIO=true

OUTPUTS
====================================
Here are your module files:
Currently Loaded Modulefiles:
1) mpi-sgi/mpt.2.12r26 3) comp-intel/2016.2.181 5) openssl/1.0.1h
2) mpi-sgi/mpt 4) git/2.4.5 6) emacs/24.3
====================================
numpy speed test
dot: 0.013150278199464082 sec
====================================

Installing mercurial
ModuleCmd_Switch.c(172):ERROR:152: Module 'intel' is currently not loaded
Currently Loaded Modulefiles:

1) mpi-sgi/mpt.2.12r26 4) git/2.4.5 7) python/2.7.9
2) mpi-sgi/mpt 5) openssl/1.0.1h
3) comp-intel/2016.2.181 6) emacs/24.3

ModuleCmd_Switch.c(172):ERROR:152: Module 'gcc' is currently not loaded

cluster_install-Ben8-24-16.sh: line 697: [: -eq: unary operator expected
Setting DEDALUS_DIR=/u/lcouston/dedalus/src/dedalus/

[Ben Brown]

Louis,

     That's great news!

--Ben

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[louisalexan...@gmail.com]

Hey,

I'm running in the same problem as with the last install regarding PBS jobs.
Somehow, PBS does not know how to run an mpiexec_mpt -np X python3 command, probably because it does not know it should be doing it in dedalus mode. Note that dedalus is not automatically activated with my install, but in interactive mode I can just activate it (typing the alias dedalus) and then my mpi_exec/mpt work perfectly.

====================================
#PBS -l select=2:ncpus=16:model=ivy
#PBS -l walltime=00:30:00
#PBS -j oe
#PBS -q debug

export PYTHONPATH=$HOME/dedalus
mpiexec_mpt -np 32 python3 e6-main2N.py
====================================

I tried the same PBS script with
dedalus
added just below cd $... in the PBS script, but this returned a
dedalus: command not found

I also tried activating dedalus before doing qsub ...
but it did not work either.

Any idea on how to submit PBS jobs properly ?
My .profile can be found below as well as the output of the failed qsub command.

Thanks
Louis

.profile

# Add your commands here to extend your PATH, etc.

module load mpi-sgi/mpt
module load comp-intel
module load git
module load openssl

export PATH=$HOME/scripts:$PATH

alias dedalus="source /u/lcouston/dedalus/bin/activate"

# support lots of text output to stdio for analysis
export MPI_UNBUFFERED_STDIO=true

OUTPUT

Job 564034.pbspl1.nas.nasa.gov started on Fri Sep 23 07:52:44 PDT 2016
The job requested the following resources:
ncpus=32
place=scatter:excl
walltime=00:30:00

PBS set the following environment variables:
FORT_BUFFERED = 1
TZ = PST8PDT

On r463i5n5:
Current directory is /u/lcouston/workdir/NsNc/r8
MPT: Launch error on r463i5n5
python3: No such file or directory
MPT ERROR: could not run executable
/nasa/sgi/mpt/2.12r26/bin/mpiexec_mpt.real: line 393: 39202 Killed $mpicmdline_prefix -f $paramfile

[Daniel Lecoanet]

Are you reloading the modules when you submit a job?

Daniel

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[louisalexan...@gmail.com]

No, and I just do a
qsub ./30min-32cores.q
in the directory where I have the .q script

I just tried adding

module load mpi-sgi/mpt
module load comp-intel
module load git
module load openssl

to the PBS script but it didn't change anything (and it shouldn't right ? I think .profile is supposed to be re-loaded on a PBS job)

[Ben Brown]

Louis,

     As you were suspecting, you need to specifically activate the dedalus environment within your job script.  Here's one of my job scripts on Pleiades.  You can see me activating the dedalus environment with the "source" line just before the "mpiexec_mpt" line.  And no, I haven't had any luck using my predefined aliases either (e.g., "dedalus") within my job scripts on Pleiades:

bpbrown@pfe24:~/workdir/Dash2> more pleiades_1e8_B3e1_oz
#PBS -S /bin/bash
#PBS -N Ra1e8_B3e1
#PBS -l select=44:ncpus=12:mpiprocs=12:model=has
#PBS -l walltime=24:00:00
#PBS -j oe
#PBS -q long

export dedalus_script=Dash2

cd $PBS_O_WORKDIR

source /u/bpbrown/dedalus/bin/activate

date
mpiexec_mpt -np 512 python3 $dedalus_script.py --nz_cz=1024 --nx=2048 --single --label=B3e1 \
    --Rayleigh=1e8 --MHD --B0_amplitude=3e1 > $dedalus_script.out.$PBS_JOBID
date
bpbrown@pfe24:~/workdir/Dash2>

--Ben

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[louisalexan...@gmail.com]

It worked !
Thanks !

As a side note I did some other speed tests and for the 3d rayleigh_benard.py script...
Grabbing 260 Ivy cores...
It runs on...

16 cores in 1524 seconds (406 process minutes)
32 cores in 951 seconds (507 process minutes)
64 cores in 689 seconds (735 process minutes)
128 cores in 758 seconds (1617 process minutes)

Pretty good I assume !
I'll open another discussion for the installation on Rheticus.
Cheers,
Louis