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rskolasinski

h5py problem

rskolasinski
May 15th, 2015
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  1. arymanus:~> source environments/standard/bin/activate
  2. (standard)arymanus:~> pip freeze
  3. backports.ssl-match-hostname==3.4.0.2
  4. certifi==2015.4.28
  5. Cython==0.22
  6. hashdist==0.3
  7. instant==1.5.0
  8. ipython==3.1.0
  9. ipywidgets==0.0.1
  10. Jinja2==2.7.3
  11. jsonschema==2.4.0
  12. kwant==1.0.3
  13. MarkupSafe==0.23
  14. matplotlib==1.4.3
  15. mistune==0.5.1
  16. mock==1.0.1
  17. nose==1.3.6
  18. numpy==1.9.2
  19. ptyprocess==0.4
  20. Pygments==2.0.2
  21. pyparsing==2.0.3
  22. python-dateutil==2.4.2
  23. pytz==2015.2
  24. pyzmq==14.6.0
  25. scipy==0.15.1
  26. six==1.9.0
  27. sympy==0.7.6
  28. terminado==0.5
  29. tinyarray==1.0.5
  30. tornado==4.1
  31. (standard)arymanus:~> pip install h5py
  32. Collecting h5py
  33.   Using cached h5py-2.5.0.tar.gz
  34. Requirement already satisfied (use --upgrade to upgrade): numpy>=1.6.1 in ./environments/standard/lib/python2.7/site-packages (from h5py)
  35. Requirement already satisfied (use --upgrade to upgrade): Cython>=0.17 in ./environments/standard/lib/python2.7/site-packages (from h5py)
  36. Requirement already satisfied (use --upgrade to upgrade): six in ./environments/standard/lib/python2.7/site-packages (from h5py)
  37. Installing collected packages: h5py
  38.   Running setup.py install for h5py
  39.     Complete output from command /home/arymanus/environments/standard/bin/python -c "import setuptools, tokenize;__file__='/tmp/pip-build-JWPLe0/h5py/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-9VuFAr-record/install-record.txt --single-version-externally-managed --compile --install-headers /home/arymanus/environments/standard/include/site/python2.7/h5py:
  40.     running install
  41.     running build
  42.     running build_py
  43.     creating build
  44.     creating build/lib.linux-x86_64-2.7
  45.     creating build/lib.linux-x86_64-2.7/h5py
  46.     copying h5py/__init__.py -> build/lib.linux-x86_64-2.7/h5py
  47.     copying h5py/ipy_completer.py -> build/lib.linux-x86_64-2.7/h5py
  48.     copying h5py/version.py -> build/lib.linux-x86_64-2.7/h5py
  49.     copying h5py/highlevel.py -> build/lib.linux-x86_64-2.7/h5py
  50.     creating build/lib.linux-x86_64-2.7/h5py/_hl
  51.     copying h5py/_hl/__init__.py -> build/lib.linux-x86_64-2.7/h5py/_hl
  52.     copying h5py/_hl/dataset.py -> build/lib.linux-x86_64-2.7/h5py/_hl
  53.     copying h5py/_hl/selections.py -> build/lib.linux-x86_64-2.7/h5py/_hl
  54.     copying h5py/_hl/filters.py -> build/lib.linux-x86_64-2.7/h5py/_hl
  55.     copying h5py/_hl/datatype.py -> build/lib.linux-x86_64-2.7/h5py/_hl
  56.     copying h5py/_hl/dims.py -> build/lib.linux-x86_64-2.7/h5py/_hl
  57.     copying h5py/_hl/group.py -> build/lib.linux-x86_64-2.7/h5py/_hl
  58.     copying h5py/_hl/selections2.py -> build/lib.linux-x86_64-2.7/h5py/_hl
  59.     copying h5py/_hl/attrs.py -> build/lib.linux-x86_64-2.7/h5py/_hl
  60.     copying h5py/_hl/base.py -> build/lib.linux-x86_64-2.7/h5py/_hl
  61.     copying h5py/_hl/files.py -> build/lib.linux-x86_64-2.7/h5py/_hl
  62.     creating build/lib.linux-x86_64-2.7/h5py/tests
  63.     copying h5py/tests/__init__.py -> build/lib.linux-x86_64-2.7/h5py/tests
  64.     copying h5py/tests/common.py -> build/lib.linux-x86_64-2.7/h5py/tests
  65.     creating build/lib.linux-x86_64-2.7/h5py/tests/old
  66.     copying h5py/tests/old/__init__.py -> build/lib.linux-x86_64-2.7/h5py/tests/old
  67.     copying h5py/tests/old/test_slicing.py -> build/lib.linux-x86_64-2.7/h5py/tests/old
  68.     copying h5py/tests/old/test_attrs_data.py -> build/lib.linux-x86_64-2.7/h5py/tests/old
  69.     copying h5py/tests/old/test_objects.py -> build/lib.linux-x86_64-2.7/h5py/tests/old
  70.     copying h5py/tests/old/test_base.py -> build/lib.linux-x86_64-2.7/h5py/tests/old
  71.     copying h5py/tests/old/test_dimension_scales.py -> build/lib.linux-x86_64-2.7/h5py/tests/old
  72.     copying h5py/tests/old/test_file.py -> build/lib.linux-x86_64-2.7/h5py/tests/old
  73.     copying h5py/tests/old/test_datatype.py -> build/lib.linux-x86_64-2.7/h5py/tests/old
  74.     copying h5py/tests/old/test_h5.py -> build/lib.linux-x86_64-2.7/h5py/tests/old
  75.     copying h5py/tests/old/test_selections.py -> build/lib.linux-x86_64-2.7/h5py/tests/old
  76.     copying h5py/tests/old/test_h5t.py -> build/lib.linux-x86_64-2.7/h5py/tests/old
  77.     copying h5py/tests/old/test_dataset.py -> build/lib.linux-x86_64-2.7/h5py/tests/old
  78.     copying h5py/tests/old/test_h5f.py -> build/lib.linux-x86_64-2.7/h5py/tests/old
  79.     copying h5py/tests/old/test_group.py -> build/lib.linux-x86_64-2.7/h5py/tests/old
  80.     copying h5py/tests/old/test_attrs.py -> build/lib.linux-x86_64-2.7/h5py/tests/old
  81.     copying h5py/tests/old/common.py -> build/lib.linux-x86_64-2.7/h5py/tests/old
  82.     copying h5py/tests/old/test_h5p.py -> build/lib.linux-x86_64-2.7/h5py/tests/old
  83.     creating build/lib.linux-x86_64-2.7/h5py/tests/hl
  84.     copying h5py/tests/hl/__init__.py -> build/lib.linux-x86_64-2.7/h5py/tests/hl
  85.     copying h5py/tests/hl/test_file.py -> build/lib.linux-x86_64-2.7/h5py/tests/hl
  86.     copying h5py/tests/hl/test_dataset_swmr.py -> build/lib.linux-x86_64-2.7/h5py/tests/hl
  87.     copying h5py/tests/hl/test_dataset_getitem.py -> build/lib.linux-x86_64-2.7/h5py/tests/hl
  88.     copying h5py/tests/hl/test_attribute_create.py -> build/lib.linux-x86_64-2.7/h5py/tests/hl
  89.     copying h5py/tests/hl/test_dims_dimensionproxy.py -> build/lib.linux-x86_64-2.7/h5py/tests/hl
  90.     running build_ext
  91.     Autodetection skipped [libhdf5.so: cannot open shared object file: No such file or directory]
  92.     ********************************************************************************
  93.                            Summary of the h5py configuration
  94.    
  95.         Path to HDF5: None
  96.         HDF5 Version: '1.8.4'
  97.          MPI Enabled: False
  98.     Rebuild Required: False
  99.    
  100.     ********************************************************************************
  101.     Executing api_gen rebuild of defs
  102.     Executing cythonize()
  103.     Compiling /tmp/pip-build-JWPLe0/h5py/h5py/defs.pyx because it changed.
  104.     Compiling /tmp/pip-build-JWPLe0/h5py/h5py/_errors.pyx because it changed.
  105.     Compiling /tmp/pip-build-JWPLe0/h5py/h5py/_objects.pyx because it changed.
  106.     Compiling /tmp/pip-build-JWPLe0/h5py/h5py/_proxy.pyx because it changed.
  107.     Compiling /tmp/pip-build-JWPLe0/h5py/h5py/h5fd.pyx because it changed.
  108.     Compiling /tmp/pip-build-JWPLe0/h5py/h5py/h5z.pyx because it changed.
  109.     Compiling /tmp/pip-build-JWPLe0/h5py/h5py/h5.pyx because it changed.
  110.     Compiling /tmp/pip-build-JWPLe0/h5py/h5py/h5i.pyx because it changed.
  111.     Compiling /tmp/pip-build-JWPLe0/h5py/h5py/h5r.pyx because it changed.
  112.     Compiling /tmp/pip-build-JWPLe0/h5py/h5py/utils.pyx because it changed.
  113.     Compiling /tmp/pip-build-JWPLe0/h5py/h5py/_conv.pyx because it changed.
  114.     Compiling /tmp/pip-build-JWPLe0/h5py/h5py/h5t.pyx because it changed.
  115.     Compiling /tmp/pip-build-JWPLe0/h5py/h5py/h5s.pyx because it changed.
  116.     Compiling /tmp/pip-build-JWPLe0/h5py/h5py/h5p.pyx because it changed.
  117.     Compiling /tmp/pip-build-JWPLe0/h5py/h5py/h5d.pyx because it changed.
  118.     Compiling /tmp/pip-build-JWPLe0/h5py/h5py/h5a.pyx because it changed.
  119.     Compiling /tmp/pip-build-JWPLe0/h5py/h5py/h5f.pyx because it changed.
  120.     Compiling /tmp/pip-build-JWPLe0/h5py/h5py/h5g.pyx because it changed.
  121.     Compiling /tmp/pip-build-JWPLe0/h5py/h5py/h5l.pyx because it changed.
  122.     Compiling /tmp/pip-build-JWPLe0/h5py/h5py/h5o.pyx because it changed.
  123.     Compiling /tmp/pip-build-JWPLe0/h5py/h5py/h5ds.pyx because it changed.
  124.     Compiling /tmp/pip-build-JWPLe0/h5py/h5py/h5ac.pyx because it changed.
  125.     Cythonizing /tmp/pip-build-JWPLe0/h5py/h5py/_conv.pyx
  126.     Cythonizing /tmp/pip-build-JWPLe0/h5py/h5py/_errors.pyx
  127.     Cythonizing /tmp/pip-build-JWPLe0/h5py/h5py/_objects.pyx
  128.     Cythonizing /tmp/pip-build-JWPLe0/h5py/h5py/_proxy.pyx
  129.     Cythonizing /tmp/pip-build-JWPLe0/h5py/h5py/defs.pyx
  130.     Cythonizing /tmp/pip-build-JWPLe0/h5py/h5py/h5.pyx
  131.     Cythonizing /tmp/pip-build-JWPLe0/h5py/h5py/h5a.pyx
  132.     Cythonizing /tmp/pip-build-JWPLe0/h5py/h5py/h5ac.pyx
  133.     Cythonizing /tmp/pip-build-JWPLe0/h5py/h5py/h5d.pyx
  134.     Cythonizing /tmp/pip-build-JWPLe0/h5py/h5py/h5ds.pyx
  135.     Cythonizing /tmp/pip-build-JWPLe0/h5py/h5py/h5f.pyx
  136.     Cythonizing /tmp/pip-build-JWPLe0/h5py/h5py/h5fd.pyx
  137.     Cythonizing /tmp/pip-build-JWPLe0/h5py/h5py/h5g.pyx
  138.     Cythonizing /tmp/pip-build-JWPLe0/h5py/h5py/h5i.pyx
  139.     Cythonizing /tmp/pip-build-JWPLe0/h5py/h5py/h5l.pyx
  140.     Cythonizing /tmp/pip-build-JWPLe0/h5py/h5py/h5o.pyx
  141.     Cythonizing /tmp/pip-build-JWPLe0/h5py/h5py/h5p.pyx
  142.     Cythonizing /tmp/pip-build-JWPLe0/h5py/h5py/h5r.pyx
  143.     Cythonizing /tmp/pip-build-JWPLe0/h5py/h5py/h5s.pyx
  144.     Cythonizing /tmp/pip-build-JWPLe0/h5py/h5py/h5t.pyx
  145.     Cythonizing /tmp/pip-build-JWPLe0/h5py/h5py/h5z.pyx
  146.     Cythonizing /tmp/pip-build-JWPLe0/h5py/h5py/utils.pyx
  147.     building 'h5py.defs' extension
  148.     creating build/temp.linux-x86_64-2.7
  149.     creating build/temp.linux-x86_64-2.7/tmp
  150.     creating build/temp.linux-x86_64-2.7/tmp/pip-build-JWPLe0
  151.     creating build/temp.linux-x86_64-2.7/tmp/pip-build-JWPLe0/h5py
  152.     creating build/temp.linux-x86_64-2.7/tmp/pip-build-JWPLe0/h5py/h5py
  153.     x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -DH5_USE_16_API -I/tmp/pip-build-JWPLe0/h5py/lzf -I/opt/local/include -I/usr/local/include -I/home/arymanus/environments/standard/local/lib/python2.7/site-packages/numpy/core/include -I/usr/include/python2.7 -c /tmp/pip-build-JWPLe0/h5py/h5py/defs.c -o build/temp.linux-x86_64-2.7/tmp/pip-build-JWPLe0/h5py/h5py/defs.o
  154.     In file included from /home/arymanus/environments/standard/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1804:0,
  155.                      from /home/arymanus/environments/standard/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,
  156.                      from /home/arymanus/environments/standard/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
  157.                      from /tmp/pip-build-JWPLe0/h5py/h5py/api_compat.h:26,
  158.                      from /tmp/pip-build-JWPLe0/h5py/h5py/defs.c:287:
  159.     /home/arymanus/environments/standard/local/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
  160.      #warning "Using deprecated NumPy API, disable it by " \
  161.       ^
  162.     In file included from /tmp/pip-build-JWPLe0/h5py/h5py/defs.c:287:0:
  163.     /tmp/pip-build-JWPLe0/h5py/h5py/api_compat.h:27:18: fatal error: hdf5.h: No such file or directory
  164.      #include "hdf5.h"
  165.                       ^
  166.     compilation terminated.
  167.     error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
  168.    
  169.     ----------------------------------------
  170.     Command "/home/arymanus/environments/standard/bin/python -c "import setuptools, tokenize;__file__='/tmp/pip-build-JWPLe0/h5py/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-9VuFAr-record/install-record.txt --single-version-externally-managed --compile --install-headers /home/arymanus/environments/standard/include/site/python2.7/h5py" failed with error code 1 in /tmp/pip-build-JWPLe0/h5py
  171. (standard)arymanus:~>
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