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manoharan-lab / holopy

Hologram processing and light scattering in python
GNU General Public License v3.0
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Fortran compiling problem #262

Closed blwh closed 5 years ago

blwh commented 5 years ago

Hi, I am trying to run some scattering simulations using holopy but there seem to be some problems with Fortran compilation during installation. When I run the first example from the Users Guide the code throws a NameError:

NameError: name 'mieangfuncs' is not defined

when holopy/scattering/theory/scatteringtheory.py tries to import use the calc_scat_field from the module. I cannot use Conda since I have to compile and run this code from source on a supercomputer. Using a fresh virtualenv with Python 3.7.2, I install reqs by pip install -r requirements.txt and install by python setup.py install. Sorry for the long files below, but this is the output from stdout and stderr when running python setup.py install.

Stdout:

Appending holopy configuration to 
Ignoring attempt to set 'name' (from '' to 'holopy')
Appending holopy.inference configuration to 
Ignoring attempt to set 'name' (from '' to 'holopy.inference')
Appending holopy.scattering configuration to 
Ignoring attempt to set 'name' (from '' to 'holopy.scattering')
Appending holopy.propagation configuration to 
Ignoring attempt to set 'name' (from '' to 'holopy.propagation')
Appending holopy.core configuration to 
Ignoring attempt to set 'name' (from '' to 'holopy.core')
Appending holopy.inference.third_party configuration to 
Ignoring attempt to set 'name' (from '' to 'holopy.inference.third_party')
Appending holopy.scattering.scatterer configuration to 
Ignoring attempt to set 'name' (from '' to 'holopy.scattering.scatterer')
Appending holopy.scattering.tests configuration to 
Ignoring attempt to set 'name' (from '' to 'holopy.scattering.tests')
Appending holopy.scattering.third_party configuration to 
Ignoring attempt to set 'name' (from '' to 'holopy.scattering.third_party')
Appending holopy.scattering.theory configuration to 
Ignoring attempt to set 'name' (from '' to 'holopy.scattering.theory')
Appending holopy.scattering.theory.mie_f configuration to 
Ignoring attempt to set 'name' (from '' to 'holopy.scattering.theory.mie_f')
Appending holopy.propagation.tests configuration to 
Ignoring attempt to set 'name' (from '' to 'holopy.propagation.tests')
Appending holopy.core.process configuration to 
Ignoring attempt to set 'name' (from '' to 'holopy.core.process')
Appending holopy.core.tests configuration to 
Ignoring attempt to set 'name' (from '' to 'holopy.core.tests')
Appending holopy.core.io configuration to 
Ignoring attempt to set 'name' (from '' to 'holopy.core.io')
non-existing path in '/home/lucas/Downloads/holopy-3.3': '/home/lucas/Downloads/holopy-3.3/holopy/scattering/theory/tmatrix_f/S'
running install
running bdist_egg
running egg_info
running build_src
build_src
creating HoloPy.egg-info
writing HoloPy.egg-info/PKG-INFO
writing dependency_links to HoloPy.egg-info/dependency_links.txt
writing requirements to HoloPy.egg-info/requires.txt
writing top-level names to HoloPy.egg-info/top_level.txt
writing manifest file 'HoloPy.egg-info/SOURCES.txt'
reading manifest file 'HoloPy.egg-info/SOURCES.txt'
writing manifest file 'HoloPy.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build
creating build/lib
creating build/lib/holopy
copying /home/lucas/Downloads/holopy-3.3/holopy/fitting.py -> build/lib/holopy
copying /home/lucas/Downloads/holopy-3.3/holopy/__init__.py -> build/lib/holopy
creating build/lib/holopy/inference
copying /home/lucas/Downloads/holopy-3.3/holopy/inference/model.py -> build/lib/holopy/inference
copying /home/lucas/Downloads/holopy-3.3/holopy/inference/__init__.py -> build/lib/holopy/inference
copying /home/lucas/Downloads/holopy-3.3/holopy/inference/emcee.py -> build/lib/holopy/inference
copying /home/lucas/Downloads/holopy-3.3/holopy/inference/scipyfit.py -> build/lib/holopy/inference
copying /home/lucas/Downloads/holopy-3.3/holopy/inference/result.py -> build/lib/holopy/inference
copying /home/lucas/Downloads/holopy-3.3/holopy/inference/prior.py -> build/lib/holopy/inference
copying /home/lucas/Downloads/holopy-3.3/holopy/inference/nmpfit.py -> build/lib/holopy/inference
copying /home/lucas/Downloads/holopy-3.3/holopy/inference/cmaes.py -> build/lib/holopy/inference
creating build/lib/holopy/scattering
copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/__init__.py -> build/lib/holopy/scattering
copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/errors.py -> build/lib/holopy/scattering
copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/calculations.py -> build/lib/holopy/scattering
creating build/lib/holopy/propagation
copying /home/lucas/Downloads/holopy-3.3/holopy/propagation/convolution_propagation.py -> build/lib/holopy/propagation
copying /home/lucas/Downloads/holopy-3.3/holopy/propagation/__init__.py -> build/lib/holopy/propagation
copying /home/lucas/Downloads/holopy-3.3/holopy/propagation/point_source_propagate.py -> build/lib/holopy/propagation
creating build/lib/holopy/core
copying /home/lucas/Downloads/holopy-3.3/holopy/core/__init__.py -> build/lib/holopy/core
copying /home/lucas/Downloads/holopy-3.3/holopy/core/errors.py -> build/lib/holopy/core
copying /home/lucas/Downloads/holopy-3.3/holopy/core/math.py -> build/lib/holopy/core
copying /home/lucas/Downloads/holopy-3.3/holopy/core/metadata.py -> build/lib/holopy/core
copying /home/lucas/Downloads/holopy-3.3/holopy/core/holopy_object.py -> build/lib/holopy/core
copying /home/lucas/Downloads/holopy-3.3/holopy/core/utils.py -> build/lib/holopy/core
creating build/lib/holopy/inference/third_party
copying /home/lucas/Downloads/holopy-3.3/holopy/inference/third_party/__init__.py -> build/lib/holopy/inference/third_party
copying /home/lucas/Downloads/holopy-3.3/holopy/inference/third_party/nmpfit.py -> build/lib/holopy/inference/third_party
creating build/lib/holopy/scattering/scatterer
copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/scatterer/composite.py -> build/lib/holopy/scattering/scatterer
copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/scatterer/ellipsoid.py -> build/lib/holopy/scattering/scatterer
copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/scatterer/scatterer.py -> build/lib/holopy/scattering/scatterer
copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/scatterer/__init__.py -> build/lib/holopy/scattering/scatterer
copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/scatterer/spherecluster.py -> build/lib/holopy/scattering/scatterer
copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/scatterer/spheroid.py -> build/lib/holopy/scattering/scatterer
copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/scatterer/csg.py -> build/lib/holopy/scattering/scatterer
copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/scatterer/cylinder.py -> build/lib/holopy/scattering/scatterer
copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/scatterer/bisphere.py -> build/lib/holopy/scattering/scatterer
copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/scatterer/capsule.py -> build/lib/holopy/scattering/scatterer
copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/scatterer/sphere.py -> build/lib/holopy/scattering/scatterer
copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/scatterer/janus.py -> build/lib/holopy/scattering/scatterer
creating build/lib/holopy/scattering/tests
copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/tests/test_dda.py -> build/lib/holopy/scattering/tests
copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/tests/test_pickle.py -> build/lib/holopy/scattering/tests
copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/tests/__init__.py -> build/lib/holopy/scattering/tests
copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/tests/test_calculations.py -> build/lib/holopy/scattering/tests
copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/tests/test_lowlevel.py -> build/lib/holopy/scattering/tests
copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/tests/test_mielens.py -> build/lib/holopy/scattering/tests
copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/tests/test_spherecluster.py -> build/lib/holopy/scattering/tests
copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/tests/test_layeredmie.py -> build/lib/holopy/scattering/tests
copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/tests/test_multisphere.py -> build/lib/holopy/scattering/tests
copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/tests/common.py -> build/lib/holopy/scattering/tests
copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/tests/test_mielensfunctions.py -> build/lib/holopy/scattering/tests
copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/tests/test_basics.py -> build/lib/holopy/scattering/tests
copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/tests/test_io.py -> build/lib/holopy/scattering/tests
copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/tests/test_mie.py -> build/lib/holopy/scattering/tests
copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/tests/test_scatterer.py -> build/lib/holopy/scattering/tests
copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/tests/test_2_color.py -> build/lib/holopy/scattering/tests
copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/tests/test_tmatrix.py -> build/lib/holopy/scattering/tests
creating build/lib/holopy/scattering/third_party
copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/third_party/__init__.py -> build/lib/holopy/scattering/third_party
creating build/lib/holopy/scattering/theory
copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/theory/mielens.py -> build/lib/holopy/scattering/theory
copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/theory/__init__.py -> build/lib/holopy/scattering/theory
copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/theory/mie.py -> build/lib/holopy/scattering/theory
copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/theory/dda.py -> build/lib/holopy/scattering/theory
copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/theory/multisphere.py -> build/lib/holopy/scattering/theory
copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/theory/tmatrix.py -> build/lib/holopy/scattering/theory
copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/theory/mielensfunctions.py -> build/lib/holopy/scattering/theory
copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/theory/scatteringtheory.py -> build/lib/holopy/scattering/theory
creating build/lib/holopy/scattering/theory/mie_f
copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/theory/mie_f/miescatlib.py -> build/lib/holopy/scattering/theory/mie_f
copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/theory/mie_f/__init__.py -> build/lib/holopy/scattering/theory/mie_f
copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/theory/mie_f/mie_specfuncs.py -> build/lib/holopy/scattering/theory/mie_f
copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/theory/mie_f/multilayer_sphere_lib.py -> build/lib/holopy/scattering/theory/mie_f
copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/theory/mie_f/setup.py -> build/lib/holopy/scattering/theory/mie_f
creating build/lib/holopy/propagation/tests
copying /home/lucas/Downloads/holopy-3.3/holopy/propagation/tests/test_propagation.py -> build/lib/holopy/propagation/tests
copying /home/lucas/Downloads/holopy-3.3/holopy/propagation/tests/__init__.py -> build/lib/holopy/propagation/tests
copying /home/lucas/Downloads/holopy-3.3/holopy/propagation/tests/test_ps_propagate.py -> build/lib/holopy/propagation/tests
creating build/lib/holopy/core/process
copying /home/lucas/Downloads/holopy-3.3/holopy/core/process/__init__.py -> build/lib/holopy/core/process
copying /home/lucas/Downloads/holopy-3.3/holopy/core/process/centerfinder.py -> build/lib/holopy/core/process
copying /home/lucas/Downloads/holopy-3.3/holopy/core/process/img_proc.py -> build/lib/holopy/core/process
copying /home/lucas/Downloads/holopy-3.3/holopy/core/process/fourier.py -> build/lib/holopy/core/process
creating build/lib/holopy/core/tests
copying /home/lucas/Downloads/holopy-3.3/holopy/core/tests/test_process.py -> build/lib/holopy/core/tests
copying /home/lucas/Downloads/holopy-3.3/holopy/core/tests/test_pickle.py -> build/lib/holopy/core/tests
copying /home/lucas/Downloads/holopy-3.3/holopy/core/tests/__init__.py -> build/lib/holopy/core/tests
copying /home/lucas/Downloads/holopy-3.3/holopy/core/tests/test_utils_math.py -> build/lib/holopy/core/tests
copying /home/lucas/Downloads/holopy-3.3/holopy/core/tests/common.py -> build/lib/holopy/core/tests
copying /home/lucas/Downloads/holopy-3.3/holopy/core/tests/test_io.py -> build/lib/holopy/core/tests
copying /home/lucas/Downloads/holopy-3.3/holopy/core/tests/test_vis.py -> build/lib/holopy/core/tests
creating build/lib/holopy/core/io
copying /home/lucas/Downloads/holopy-3.3/holopy/core/io/__init__.py -> build/lib/holopy/core/io
copying /home/lucas/Downloads/holopy-3.3/holopy/core/io/serialize.py -> build/lib/holopy/core/io
copying /home/lucas/Downloads/holopy-3.3/holopy/core/io/vis.py -> build/lib/holopy/core/io
copying /home/lucas/Downloads/holopy-3.3/holopy/core/io/io.py -> build/lib/holopy/core/io
creating build/bdist.linux-x86_64
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/holopy
copying build/lib/holopy/fitting.py -> build/bdist.linux-x86_64/egg/holopy
creating build/bdist.linux-x86_64/egg/holopy/inference
copying build/lib/holopy/inference/model.py -> build/bdist.linux-x86_64/egg/holopy/inference
copying build/lib/holopy/inference/__init__.py -> build/bdist.linux-x86_64/egg/holopy/inference
copying build/lib/holopy/inference/emcee.py -> build/bdist.linux-x86_64/egg/holopy/inference
copying build/lib/holopy/inference/scipyfit.py -> build/bdist.linux-x86_64/egg/holopy/inference
copying build/lib/holopy/inference/result.py -> build/bdist.linux-x86_64/egg/holopy/inference
creating build/bdist.linux-x86_64/egg/holopy/inference/third_party
copying build/lib/holopy/inference/third_party/__init__.py -> build/bdist.linux-x86_64/egg/holopy/inference/third_party
copying build/lib/holopy/inference/third_party/nmpfit.py -> build/bdist.linux-x86_64/egg/holopy/inference/third_party
copying build/lib/holopy/inference/prior.py -> build/bdist.linux-x86_64/egg/holopy/inference
copying build/lib/holopy/inference/nmpfit.py -> build/bdist.linux-x86_64/egg/holopy/inference
copying build/lib/holopy/inference/cmaes.py -> build/bdist.linux-x86_64/egg/holopy/inference
creating build/bdist.linux-x86_64/egg/holopy/scattering
creating build/bdist.linux-x86_64/egg/holopy/scattering/scatterer
copying build/lib/holopy/scattering/scatterer/composite.py -> build/bdist.linux-x86_64/egg/holopy/scattering/scatterer
copying build/lib/holopy/scattering/scatterer/ellipsoid.py -> build/bdist.linux-x86_64/egg/holopy/scattering/scatterer
copying build/lib/holopy/scattering/scatterer/scatterer.py -> build/bdist.linux-x86_64/egg/holopy/scattering/scatterer
copying build/lib/holopy/scattering/scatterer/__init__.py -> build/bdist.linux-x86_64/egg/holopy/scattering/scatterer
copying build/lib/holopy/scattering/scatterer/spherecluster.py -> build/bdist.linux-x86_64/egg/holopy/scattering/scatterer
copying build/lib/holopy/scattering/scatterer/spheroid.py -> build/bdist.linux-x86_64/egg/holopy/scattering/scatterer
copying build/lib/holopy/scattering/scatterer/csg.py -> build/bdist.linux-x86_64/egg/holopy/scattering/scatterer
copying build/lib/holopy/scattering/scatterer/cylinder.py -> build/bdist.linux-x86_64/egg/holopy/scattering/scatterer
copying build/lib/holopy/scattering/scatterer/bisphere.py -> build/bdist.linux-x86_64/egg/holopy/scattering/scatterer
copying build/lib/holopy/scattering/scatterer/capsule.py -> build/bdist.linux-x86_64/egg/holopy/scattering/scatterer
copying build/lib/holopy/scattering/scatterer/sphere.py -> build/bdist.linux-x86_64/egg/holopy/scattering/scatterer
copying build/lib/holopy/scattering/scatterer/janus.py -> build/bdist.linux-x86_64/egg/holopy/scattering/scatterer
copying build/lib/holopy/scattering/__init__.py -> build/bdist.linux-x86_64/egg/holopy/scattering
copying build/lib/holopy/scattering/errors.py -> build/bdist.linux-x86_64/egg/holopy/scattering
creating build/bdist.linux-x86_64/egg/holopy/scattering/tests
copying build/lib/holopy/scattering/tests/test_dda.py -> build/bdist.linux-x86_64/egg/holopy/scattering/tests
copying build/lib/holopy/scattering/tests/test_pickle.py -> build/bdist.linux-x86_64/egg/holopy/scattering/tests
copying build/lib/holopy/scattering/tests/__init__.py -> build/bdist.linux-x86_64/egg/holopy/scattering/tests
copying build/lib/holopy/scattering/tests/test_calculations.py -> build/bdist.linux-x86_64/egg/holopy/scattering/tests
copying build/lib/holopy/scattering/tests/test_lowlevel.py -> build/bdist.linux-x86_64/egg/holopy/scattering/tests
copying build/lib/holopy/scattering/tests/test_mielens.py -> build/bdist.linux-x86_64/egg/holopy/scattering/tests
copying build/lib/holopy/scattering/tests/test_spherecluster.py -> build/bdist.linux-x86_64/egg/holopy/scattering/tests
copying build/lib/holopy/scattering/tests/test_layeredmie.py -> build/bdist.linux-x86_64/egg/holopy/scattering/tests
copying build/lib/holopy/scattering/tests/test_multisphere.py -> build/bdist.linux-x86_64/egg/holopy/scattering/tests
copying build/lib/holopy/scattering/tests/common.py -> build/bdist.linux-x86_64/egg/holopy/scattering/tests
copying build/lib/holopy/scattering/tests/test_mielensfunctions.py -> build/bdist.linux-x86_64/egg/holopy/scattering/tests
copying build/lib/holopy/scattering/tests/test_basics.py -> build/bdist.linux-x86_64/egg/holopy/scattering/tests
copying build/lib/holopy/scattering/tests/test_io.py -> build/bdist.linux-x86_64/egg/holopy/scattering/tests
copying build/lib/holopy/scattering/tests/test_mie.py -> build/bdist.linux-x86_64/egg/holopy/scattering/tests
copying build/lib/holopy/scattering/tests/test_scatterer.py -> build/bdist.linux-x86_64/egg/holopy/scattering/tests
copying build/lib/holopy/scattering/tests/test_2_color.py -> build/bdist.linux-x86_64/egg/holopy/scattering/tests
copying build/lib/holopy/scattering/tests/test_tmatrix.py -> build/bdist.linux-x86_64/egg/holopy/scattering/tests
copying build/lib/holopy/scattering/calculations.py -> build/bdist.linux-x86_64/egg/holopy/scattering
creating build/bdist.linux-x86_64/egg/holopy/scattering/third_party
copying build/lib/holopy/scattering/third_party/__init__.py -> build/bdist.linux-x86_64/egg/holopy/scattering/third_party
creating build/bdist.linux-x86_64/egg/holopy/scattering/theory
copying build/lib/holopy/scattering/theory/mielens.py -> build/bdist.linux-x86_64/egg/holopy/scattering/theory
copying build/lib/holopy/scattering/theory/__init__.py -> build/bdist.linux-x86_64/egg/holopy/scattering/theory
copying build/lib/holopy/scattering/theory/mie.py -> build/bdist.linux-x86_64/egg/holopy/scattering/theory
copying build/lib/holopy/scattering/theory/dda.py -> build/bdist.linux-x86_64/egg/holopy/scattering/theory
copying build/lib/holopy/scattering/theory/multisphere.py -> build/bdist.linux-x86_64/egg/holopy/scattering/theory
copying build/lib/holopy/scattering/theory/tmatrix.py -> build/bdist.linux-x86_64/egg/holopy/scattering/theory
creating build/bdist.linux-x86_64/egg/holopy/scattering/theory/mie_f
copying build/lib/holopy/scattering/theory/mie_f/miescatlib.py -> build/bdist.linux-x86_64/egg/holopy/scattering/theory/mie_f
copying build/lib/holopy/scattering/theory/mie_f/__init__.py -> build/bdist.linux-x86_64/egg/holopy/scattering/theory/mie_f
copying build/lib/holopy/scattering/theory/mie_f/mie_specfuncs.py -> build/bdist.linux-x86_64/egg/holopy/scattering/theory/mie_f
copying build/lib/holopy/scattering/theory/mie_f/multilayer_sphere_lib.py -> build/bdist.linux-x86_64/egg/holopy/scattering/theory/mie_f
copying build/lib/holopy/scattering/theory/mie_f/setup.py -> build/bdist.linux-x86_64/egg/holopy/scattering/theory/mie_f
copying build/lib/holopy/scattering/theory/mielensfunctions.py -> build/bdist.linux-x86_64/egg/holopy/scattering/theory
copying build/lib/holopy/scattering/theory/scatteringtheory.py -> build/bdist.linux-x86_64/egg/holopy/scattering/theory
copying build/lib/holopy/__init__.py -> build/bdist.linux-x86_64/egg/holopy
creating build/bdist.linux-x86_64/egg/holopy/propagation
copying build/lib/holopy/propagation/convolution_propagation.py -> build/bdist.linux-x86_64/egg/holopy/propagation
copying build/lib/holopy/propagation/__init__.py -> build/bdist.linux-x86_64/egg/holopy/propagation
copying build/lib/holopy/propagation/point_source_propagate.py -> build/bdist.linux-x86_64/egg/holopy/propagation
creating build/bdist.linux-x86_64/egg/holopy/propagation/tests
copying build/lib/holopy/propagation/tests/test_propagation.py -> build/bdist.linux-x86_64/egg/holopy/propagation/tests
copying build/lib/holopy/propagation/tests/__init__.py -> build/bdist.linux-x86_64/egg/holopy/propagation/tests
copying build/lib/holopy/propagation/tests/test_ps_propagate.py -> build/bdist.linux-x86_64/egg/holopy/propagation/tests
creating build/bdist.linux-x86_64/egg/holopy/core
copying build/lib/holopy/core/__init__.py -> build/bdist.linux-x86_64/egg/holopy/core
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creating build/bdist.linux-x86_64/egg/holopy/core/tests
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byte-compiling build/bdist.linux-x86_64/egg/holopy/core/tests/test_process.py to test_process.cpython-37.pyc
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byte-compiling build/bdist.linux-x86_64/egg/holopy/core/tests/common.py to common.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/holopy/core/tests/test_io.py to test_io.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/holopy/core/tests/test_vis.py to test_vis.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/holopy/core/utils.py to utils.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/holopy/core/io/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/holopy/core/io/serialize.py to serialize.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/holopy/core/io/vis.py to vis.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/holopy/core/io/io.py to io.cpython-37.pyc
installing package data to build/bdist.linux-x86_64/egg
running install_data
copying /home/lucas/Downloads/holopy-3.3/AUTHORS -> build/bdist.linux-x86_64/egg/.
copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/tests/gold/gold_dda_voxelated_complex.yaml -> build/bdist.linux-x86_64/egg/
copying /home/lucas/Downloads/holopy-3.3/holopy/propagation/tests/gold/gold_recon_multiple.yaml -> build/bdist.linux-x86_64/egg/
copying /home/lucas/Downloads/holopy-3.3/holopy/propagation/tests/gold/full_data/gold_full_ps_recon.h5 -> build/bdist.linux-x86_64/egg/
copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/tests/gold/gold_2_sphere_allow_overlap.yaml -> build/bdist.linux-x86_64/egg/
copying /home/lucas/Downloads/holopy-3.3/holopy/core/tests/exampledata/bg01.jpg -> build/bdist.linux-x86_64/egg/
copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/tests/gold/gold_janus_dda.yaml -> build/bdist.linux-x86_64/egg/
copying /home/lucas/Downloads/holopy-3.3/holopy/propagation/tests/gold/gold_propagate_e_field.yaml -> build/bdist.linux-x86_64/egg/
copying /home/lucas/Downloads/holopy-3.3/holopy/core/tests/exampledata/image0002.h5 -> build/bdist.linux-x86_64/egg/
copying /home/lucas/Downloads/holopy-3.3/holopy/propagation/tests/gold/gold_recon_multiple_gradient_filter.yaml -> build/bdist.linux-x86_64/egg/
copying /home/lucas/Downloads/holopy-3.3/holopy/propagation/tests/gold/gold_ps_recon.yaml -> build/bdist.linux-x86_64/egg/
copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/tests/gold/full_data/gold_full_shell.h5 -> build/bdist.linux-x86_64/egg/
copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/tests/gold/full_data/gold_full_2_sphere_allow_overlap.h5 -> build/bdist.linux-x86_64/egg/
copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/tests/gold/gold_mie_scat_matrix.yaml -> build/bdist.linux-x86_64/egg/
copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/tests/gold/gold_shell.yaml -> build/bdist.linux-x86_64/egg/
copying /home/lucas/Downloads/holopy-3.3/holopy/core/tests/exampledata/image01.jpg -> build/bdist.linux-x86_64/egg/
copying /home/lucas/Downloads/holopy-3.3/holopy/propagation/tests/gold/gold_recon_multiple_with_0.yaml -> build/bdist.linux-x86_64/egg/
copying /home/lucas/Downloads/holopy-3.3/holopy/core/tests/exampledata/df01.jpg -> build/bdist.linux-x86_64/egg/
copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/tests/gold/full_data/gold_full_dda_csg.h5 -> build/bdist.linux-x86_64/egg/
copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/tests/gold/gold_dda_csg_rotated_div.yaml -> build/bdist.linux-x86_64/egg/
copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/tests/gold/gold_ellipsoid_dda.yaml -> build/bdist.linux-x86_64/egg/
copying /home/lucas/Downloads/holopy-3.3/holopy/core/tests/exampledata/bg03.jpg -> build/bdist.linux-x86_64/egg/
copying /home/lucas/Downloads/holopy-3.3/holopy/core/tests/exampledata/ps_bg01.jpg -> build/bdist.linux-x86_64/egg/
copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/tests/gold/gold_dda_csg.yaml -> build/bdist.linux-x86_64/egg/
copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/tests/gold/gold_mie_radiometric.yaml -> build/bdist.linux-x86_64/egg/
copying /home/lucas/Downloads/holopy-3.3/holopy/core/tests/exampledata/image0001.h5 -> build/bdist.linux-x86_64/egg/
copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/tests/gold/full_data/gold_full_mie_multiple_holo.h5 -> build/bdist.linux-x86_64/egg/
copying /home/lucas/Downloads/holopy-3.3/holopy/propagation/tests/gold/full_data/gold_full_recon_single.h5 -> build/bdist.linux-x86_64/egg/
copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/tests/gold/gold_single_holo.yaml -> build/bdist.linux-x86_64/egg/
copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/tests/gold/gold_tmatrix_cylinder.yaml -> build/bdist.linux-x86_64/egg/
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copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/tests/gold/gold_tmatrix_spheroid.yaml -> build/bdist.linux-x86_64/egg/
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copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/tests/gold/full_data/gold_full_dda_csg_rotated_div.h5 -> build/bdist.linux-x86_64/egg/
copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/tests/gold/gold_farfield_matricies.yaml -> build/bdist.linux-x86_64/egg/
copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/tests/gold/gold_mie_multiple_holo.yaml -> build/bdist.linux-x86_64/egg/
copying /home/lucas/Downloads/holopy-3.3/holopy/propagation/tests/gold/gold_recon_single.yaml -> build/bdist.linux-x86_64/egg/
copying /home/lucas/Downloads/holopy-3.3/holopy/scattering/tests/gold/gold_multilayer.yaml -> build/bdist.linux-x86_64/egg/
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running install_clib
customize UnixCCompiler
creating build/bdist.linux-x86_64/egg/EGG-INFO
copying HoloPy.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying HoloPy.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying HoloPy.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying HoloPy.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying HoloPy.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
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holopy.core.io.__pycache__.io.cpython-37: module references __file__
holopy.core.tests.__pycache__.common.cpython-37: module references __file__
holopy.scattering.tests.__pycache__.test_layeredmie.cpython-37: module references __file__
holopy.scattering.tests.__pycache__.test_lowlevel.cpython-37: module references __file__
holopy.scattering.tests.__pycache__.test_mie.cpython-37: module references __file__
holopy.scattering.theory.__pycache__.tmatrix.cpython-37: module references __file__
creating dist
creating 'dist/HoloPy-3.3.0-py3.7.egg' and adding 'build/bdist.linux-x86_64/egg' to it
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
Processing HoloPy-3.3.0-py3.7.egg
creating /home/lucas/Envs/holopy/lib/python3.7/site-packages/HoloPy-3.3.0-py3.7.egg
Extracting HoloPy-3.3.0-py3.7.egg to /home/lucas/Envs/holopy/lib/python3.7/site-packages
Adding HoloPy 3.3.0 to easy-install.pth file

Installed /home/lucas/Envs/holopy/lib/python3.7/site-packages/HoloPy-3.3.0-py3.7.egg
Processing dependencies for HoloPy==3.3.0
Searching for h5netcdf==0.7.1
Best match: h5netcdf 0.7.1
Adding h5netcdf 0.7.1 to easy-install.pth file

Using /home/lucas/Envs/holopy/lib/python3.7/site-packages
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Using /home/lucas/Envs/holopy/lib/python3.7/site-packages
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Adding matplotlib 3.1.0 to easy-install.pth file

Using /home/lucas/Envs/holopy/lib/python3.7/site-packages
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Adding h5py 2.9.0 to easy-install.pth file

Using /home/lucas/Envs/holopy/lib/python3.7/site-packages
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Adding Pillow 6.0.0 to easy-install.pth file

Using /home/lucas/Envs/holopy/lib/python3.7/site-packages
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Using /home/lucas/Envs/holopy/lib/python3.7/site-packages
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Adding scipy 1.3.0 to easy-install.pth file

Using /home/lucas/Envs/holopy/lib/python3.7/site-packages
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Best match: numpy 1.16.3
Adding numpy 1.16.3 to easy-install.pth file
Installing f2py script to /home/lucas/Envs/holopy/bin
Installing f2py3 script to /home/lucas/Envs/holopy/bin
Installing f2py3.7 script to /home/lucas/Envs/holopy/bin

Using /home/lucas/Envs/holopy/lib/python3.7/site-packages
Searching for pandas==0.24.2
Best match: pandas 0.24.2
Adding pandas 0.24.2 to easy-install.pth file

Using /home/lucas/Envs/holopy/lib/python3.7/site-packages
Searching for python-dateutil==2.8.0
Best match: python-dateutil 2.8.0
Adding python-dateutil 2.8.0 to easy-install.pth file

Using /home/lucas/Envs/holopy/lib/python3.7/site-packages
Searching for cycler==0.10.0
Best match: cycler 0.10.0
Adding cycler 0.10.0 to easy-install.pth file

Using /home/lucas/Envs/holopy/lib/python3.7/site-packages
Searching for kiwisolver==1.1.0
Best match: kiwisolver 1.1.0
Adding kiwisolver 1.1.0 to easy-install.pth file

Using /home/lucas/Envs/holopy/lib/python3.7/site-packages
Searching for pyparsing==2.4.0
Best match: pyparsing 2.4.0
Adding pyparsing 2.4.0 to easy-install.pth file

Using /home/lucas/Envs/holopy/lib/python3.7/site-packages
Searching for six==1.12.0
Best match: six 1.12.0
Adding six 1.12.0 to easy-install.pth file

Using /home/lucas/Envs/holopy/lib/python3.7/site-packages
Searching for pytz==2019.1
Best match: pytz 2019.1
Adding pytz 2019.1 to easy-install.pth file

Using /home/lucas/Envs/holopy/lib/python3.7/site-packages
Searching for setuptools==41.0.1
Best match: setuptools 41.0.1
Adding setuptools 41.0.1 to easy-install.pth file
Installing easy_install script to /home/lucas/Envs/holopy/bin
Installing easy_install-3.6 script to /home/lucas/Envs/holopy/bin

Using /home/lucas/Envs/holopy/lib/python3.7/site-packages
Finished processing dependencies for HoloPy==3.3.0

Stderr:

/usr/lib64/python3.7/distutils/dist.py:274: UserWarning: Unknown distribution option: 'package'
  warnings.warn(msg)
Warning: Assuming default configuration (/home/lucas/Downloads/holopy-3.3/holopy/{setup_holopy,setup}.py was not found)Warning: Assuming default configuration (/home/lucas/Downloads/holopy-3.3/holopy/inference/{setup_holopy.inference,setup}.py was not found)Warning: Assuming default configuration (/home/lucas/Downloads/holopy-3.3/holopy/scattering/{setup_holopy.scattering,setup}.py was not found)Warning: Assuming default configuration (/home/lucas/Downloads/holopy-3.3/holopy/propagation/{setup_holopy.propagation,setup}.py was not found)Warning: Assuming default configuration (/home/lucas/Downloads/holopy-3.3/holopy/core/{setup_holopy.core,setup}.py was not found)Warning: Assuming default configuration (/home/lucas/Downloads/holopy-3.3/holopy/inference/third_party/{setup_holopy.inference.third_party,setup}.py was not found)Warning: Assuming default configuration (/home/lucas/Downloads/holopy-3.3/holopy/scattering/scatterer/{setup_holopy.scattering.scatterer,setup}.py was not found)Warning: Assuming default configuration (/home/lucas/Downloads/holopy-3.3/holopy/scattering/tests/{setup_holopy.scattering.tests,setup}.py was not found)Warning: Assuming default configuration (/home/lucas/Downloads/holopy-3.3/holopy/scattering/third_party/{setup_holopy.scattering.third_party,setup}.py was not found)Warning: Assuming default configuration (/home/lucas/Downloads/holopy-3.3/holopy/scattering/theory/{setup_holopy.scattering.theory,setup}.py was not found)Warning: Assuming default configuration (/home/lucas/Downloads/holopy-3.3/holopy/propagation/tests/{setup_holopy.propagation.tests,setup}.py was not found)Warning: Assuming default configuration (/home/lucas/Downloads/holopy-3.3/holopy/core/process/{setup_holopy.core.process,setup}.py was not found)Warning: Assuming default configuration (/home/lucas/Downloads/holopy-3.3/holopy/core/tests/{setup_holopy.core.tests,setup}.py was not found)Warning: Assuming default configuration (/home/lucas/Downloads/holopy-3.3/holopy/core/io/{setup_holopy.core.io,setup}.py was not found)

My guess is there is some problems compiling with Fortran. Any suggestions?

jeromefung commented 5 years ago

Which Fortran compiler are you trying to use on your supercomputer? Can you successfully compile and execute a minimal "hello world" Fortran program to check that your compiler is working properly?

blwh commented 5 years ago

Which Fortran compiler are you trying to use on your supercomputer? Can you successfully compile and execute a minimal "hello world" Fortran program to check that your compiler is working properly?

I am using gfortran. I have no problems with compiling and executing a "hello world"-program

blwh commented 5 years ago

Update: I only get an error if I install the reqs and Holopy inside a virtual env. Outside of the virtual env the code runs fine.

blwh commented 5 years ago

I fixed the issue. I foolishly enough forgot to create my virtual env with --system-site-packages so compilation with the env did not work.