Closed crowoy closed 6 years ago
@crowoy If you look at Line 2 & 3, it says that module was compiled using numpy version 12, but the version you have is 11.
Could you verify that by checking numpy.__version__
If yes, install numpy version 1.12 by pip install numpy==1.12
and let me know if that helps!
I tried launching a new instance to start from scratch. There is nothing else on this instance.
I then ran: sudo apt-get update
and sudo apt-get install build-essential manpages-dev
.
Python in already installed, and I installed pip with the get-pip.py
script provided by PIP. This time, installing the pip requirements through sudo pip install -r requirements.txt
doesn't even work.
Collecting h5py==2.5.0 (from -r requirements.txt (line 1))
Downloading h5py-2.5.0.tar.gz (684kB)
100% |████████████████████████████████| 686kB 37.1MB/s
Requirement already satisfied: Keras==2.0.3 in /usr/local/lib/python2.7/dist-packages (from -r requirements.txt (line 2))
Collecting numpy==1.11.2 (from -r requirements.txt (line 3))
Downloading numpy-1.11.2-cp27-cp27mu-manylinux1_x86_64.whl (15.3MB)
100% |████████████████████████████████| 15.3MB 64.0MB/s
Requirement already satisfied: tensorflow==1.1.0 in /usr/local/lib/python2.7/dist-packages (from -r requirements.txt (line 4))
Requirement already satisfied: pandas==0.16.2 in /usr/local/lib/python2.7/dist-packages (from -r requirements.txt (line 5))
Requirement already satisfied: Pillow in /usr/local/lib/python2.7/dist-packages (from -r requirements.txt (line 6))
Requirement already satisfied: Cython>=0.17 in /usr/local/lib/python2.7/dist-packages (from h5py==2.5.0->-r requirements.txt (line 1))
Requirement already satisfied: six in /usr/lib/python2.7/dist-packages (from h5py==2.5.0->-r requirements.txt (line 1))
Requirement already satisfied: pyyaml in /usr/local/lib/python2.7/dist-packages (from Keras==2.0.3->-r requirements.txt (line 2))
Requirement already satisfied: theano in /usr/local/lib/python2.7/dist-packages (from Keras==2.0.3->-r requirements.txt (line 2))
Requirement already satisfied: mock>=2.0.0 in /usr/local/lib/python2.7/dist-packages (from tensorflow==1.1.0->-r requirements.txt (line 4))
Requirement already satisfied: wheel in /usr/local/lib/python2.7/dist-packages (from tensorflow==1.1.0->-r requirements.txt (line 4))
Requirement already satisfied: protobuf>=3.2.0 in /usr/local/lib/python2.7/dist-packages (from tensorflow==1.1.0->-r requirements.txt (line 4))
Requirement already satisfied: werkzeug>=0.11.10 in /usr/local/lib/python2.7/dist-packages (from tensorflow==1.1.0->-r requirements.txt (line 4))
Requirement already satisfied: pytz>=2011k in /usr/local/lib/python2.7/dist-packages (from pandas==0.16.2->-r requirements.txt (line 5))
Requirement already satisfied: python-dateutil in /usr/local/lib/python2.7/dist-packages (from pandas==0.16.2->-r requirements.txt (line 5))
Requirement already satisfied: olefile in /usr/local/lib/python2.7/dist-packages (from Pillow->-r requirements.txt (line 6))
Requirement already satisfied: scipy>=0.14 in /usr/local/lib/python2.7/dist-packages (from theano->Keras==2.0.3->-r requirements.txt (line 2))
Requirement already satisfied: funcsigs>=1; python_version < "3.3" in /usr/local/lib/python2.7/dist-packages (from mock>=2.0.0->tensorflow==1.1.0->-r requirements.txt (line 4))
Requirement already satisfied: pbr>=0.11 in /usr/local/lib/python2.7/dist-packages (from mock>=2.0.0->tensorflow==1.1.0->-r requirements.txt (line 4))
Requirement already satisfied: setuptools in /usr/local/lib/python2.7/dist-packages (from protobuf>=3.2.0->tensorflow==1.1.0->-r requirements.txt (line 4))
Installing collected packages: numpy, h5py
Found existing installation: numpy 1.12.0
Uninstalling numpy-1.12.0:
Successfully uninstalled numpy-1.12.0
Running setup.py install for h5py ... error
Complete output from command /usr/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-7sCuVK/h5py/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-H96iOU-record/install-record.txt --single-version-externally-managed --compile:
running install
running build
running build_py
creating build
creating build/lib.linux-x86_64-2.7
creating build/lib.linux-x86_64-2.7/h5py
copying h5py/__init__.py -> build/lib.linux-x86_64-2.7/h5py
copying h5py/version.py -> build/lib.linux-x86_64-2.7/h5py
copying h5py/ipy_completer.py -> build/lib.linux-x86_64-2.7/h5py
copying h5py/highlevel.py -> build/lib.linux-x86_64-2.7/h5py
creating build/lib.linux-x86_64-2.7/h5py/_hl
copying h5py/_hl/__init__.py -> build/lib.linux-x86_64-2.7/h5py/_hl
copying h5py/_hl/datatype.py -> build/lib.linux-x86_64-2.7/h5py/_hl
copying h5py/_hl/dataset.py -> build/lib.linux-x86_64-2.7/h5py/_hl
copying h5py/_hl/selections.py -> build/lib.linux-x86_64-2.7/h5py/_hl
copying h5py/_hl/dims.py -> build/lib.linux-x86_64-2.7/h5py/_hl
copying h5py/_hl/selections2.py -> build/lib.linux-x86_64-2.7/h5py/_hl
copying h5py/_hl/attrs.py -> build/lib.linux-x86_64-2.7/h5py/_hl
copying h5py/_hl/filters.py -> build/lib.linux-x86_64-2.7/h5py/_hl
copying h5py/_hl/group.py -> build/lib.linux-x86_64-2.7/h5py/_hl
copying h5py/_hl/base.py -> build/lib.linux-x86_64-2.7/h5py/_hl
copying h5py/_hl/files.py -> build/lib.linux-x86_64-2.7/h5py/_hl
creating build/lib.linux-x86_64-2.7/h5py/tests
copying h5py/tests/__init__.py -> build/lib.linux-x86_64-2.7/h5py/tests
copying h5py/tests/common.py -> build/lib.linux-x86_64-2.7/h5py/tests
creating build/lib.linux-x86_64-2.7/h5py/tests/old
copying h5py/tests/old/test_attrs_data.py -> build/lib.linux-x86_64-2.7/h5py/tests/old
copying h5py/tests/old/__init__.py -> build/lib.linux-x86_64-2.7/h5py/tests/old
copying h5py/tests/old/test_objects.py -> build/lib.linux-x86_64-2.7/h5py/tests/old
copying h5py/tests/old/test_h5f.py -> build/lib.linux-x86_64-2.7/h5py/tests/old
copying h5py/tests/old/common.py -> build/lib.linux-x86_64-2.7/h5py/tests/old
copying h5py/tests/old/test_slicing.py -> build/lib.linux-x86_64-2.7/h5py/tests/old
copying h5py/tests/old/test_h5t.py -> build/lib.linux-x86_64-2.7/h5py/tests/old
copying h5py/tests/old/test_selections.py -> build/lib.linux-x86_64-2.7/h5py/tests/old
copying h5py/tests/old/test_file.py -> build/lib.linux-x86_64-2.7/h5py/tests/old
copying h5py/tests/old/test_dimension_scales.py -> build/lib.linux-x86_64-2.7/h5py/tests/old
copying h5py/tests/old/test_h5p.py -> build/lib.linux-x86_64-2.7/h5py/tests/old
copying h5py/tests/old/test_attrs.py -> build/lib.linux-x86_64-2.7/h5py/tests/old
copying h5py/tests/old/test_h5.py -> build/lib.linux-x86_64-2.7/h5py/tests/old
copying h5py/tests/old/test_group.py -> build/lib.linux-x86_64-2.7/h5py/tests/old
copying h5py/tests/old/test_dataset.py -> build/lib.linux-x86_64-2.7/h5py/tests/old
copying h5py/tests/old/test_datatype.py -> build/lib.linux-x86_64-2.7/h5py/tests/old
copying h5py/tests/old/test_base.py -> build/lib.linux-x86_64-2.7/h5py/tests/old
creating build/lib.linux-x86_64-2.7/h5py/tests/hl
copying h5py/tests/hl/__init__.py -> build/lib.linux-x86_64-2.7/h5py/tests/hl
copying h5py/tests/hl/test_attribute_create.py -> build/lib.linux-x86_64-2.7/h5py/tests/hl
copying h5py/tests/hl/test_dataset_getitem.py -> build/lib.linux-x86_64-2.7/h5py/tests/hl
copying h5py/tests/hl/test_dataset_swmr.py -> build/lib.linux-x86_64-2.7/h5py/tests/hl
copying h5py/tests/hl/test_file.py -> build/lib.linux-x86_64-2.7/h5py/tests/hl
copying h5py/tests/hl/test_dims_dimensionproxy.py -> build/lib.linux-x86_64-2.7/h5py/tests/hl
running build_ext
Autodetection skipped [libhdf5.so: cannot open shared object file: No such file or directory]
********************************************************************************
Summary of the h5py configuration
Path to HDF5: None
HDF5 Version: '1.8.4'
MPI Enabled: False
Rebuild Required: False
********************************************************************************
Executing api_gen rebuild of defs
Executing cythonize()
./h5py/api_types_ext.pxd: cannot find cimported module 'mpi4py.MPI'
/tmp/pip-build-7sCuVK/h5py/h5py/h5p.pyx: cannot find cimported module 'mpi4py.mpi_c'
Compiling /tmp/pip-build-7sCuVK/h5py/h5py/defs.pyx because it changed.
Compiling /tmp/pip-build-7sCuVK/h5py/h5py/_errors.pyx because it changed.
Compiling /tmp/pip-build-7sCuVK/h5py/h5py/_objects.pyx because it changed.
Compiling /tmp/pip-build-7sCuVK/h5py/h5py/_proxy.pyx because it changed.
Compiling /tmp/pip-build-7sCuVK/h5py/h5py/h5fd.pyx because it changed.
Compiling /tmp/pip-build-7sCuVK/h5py/h5py/h5z.pyx because it changed.
Compiling /tmp/pip-build-7sCuVK/h5py/h5py/h5.pyx because it changed.
Compiling /tmp/pip-build-7sCuVK/h5py/h5py/h5i.pyx because it changed.
Compiling /tmp/pip-build-7sCuVK/h5py/h5py/h5r.pyx because it changed.
Compiling /tmp/pip-build-7sCuVK/h5py/h5py/utils.pyx because it changed.
Compiling /tmp/pip-build-7sCuVK/h5py/h5py/_conv.pyx because it changed.
Compiling /tmp/pip-build-7sCuVK/h5py/h5py/h5t.pyx because it changed.
Compiling /tmp/pip-build-7sCuVK/h5py/h5py/h5s.pyx because it changed.
Compiling /tmp/pip-build-7sCuVK/h5py/h5py/h5p.pyx because it changed.
Compiling /tmp/pip-build-7sCuVK/h5py/h5py/h5d.pyx because it changed.
Compiling /tmp/pip-build-7sCuVK/h5py/h5py/h5a.pyx because it changed.
Compiling /tmp/pip-build-7sCuVK/h5py/h5py/h5f.pyx because it changed.
Compiling /tmp/pip-build-7sCuVK/h5py/h5py/h5g.pyx because it changed.
Compiling /tmp/pip-build-7sCuVK/h5py/h5py/h5l.pyx because it changed.
Compiling /tmp/pip-build-7sCuVK/h5py/h5py/h5o.pyx because it changed.
Compiling /tmp/pip-build-7sCuVK/h5py/h5py/h5ds.pyx because it changed.
Compiling /tmp/pip-build-7sCuVK/h5py/h5py/h5ac.pyx because it changed.
[ 1/22] Cythonizing /tmp/pip-build-7sCuVK/h5py/h5py/_conv.pyx
[ 2/22] Cythonizing /tmp/pip-build-7sCuVK/h5py/h5py/_errors.pyx
[ 3/22] Cythonizing /tmp/pip-build-7sCuVK/h5py/h5py/_objects.pyx
[ 4/22] Cythonizing /tmp/pip-build-7sCuVK/h5py/h5py/_proxy.pyx
[ 5/22] Cythonizing /tmp/pip-build-7sCuVK/h5py/h5py/defs.pyx
[ 6/22] Cythonizing /tmp/pip-build-7sCuVK/h5py/h5py/h5.pyx
[ 7/22] Cythonizing /tmp/pip-build-7sCuVK/h5py/h5py/h5a.pyx
[ 8/22] Cythonizing /tmp/pip-build-7sCuVK/h5py/h5py/h5ac.pyx
[ 9/22] Cythonizing /tmp/pip-build-7sCuVK/h5py/h5py/h5d.pyx
[10/22] Cythonizing /tmp/pip-build-7sCuVK/h5py/h5py/h5ds.pyx
[11/22] Cythonizing /tmp/pip-build-7sCuVK/h5py/h5py/h5f.pyx
[12/22] Cythonizing /tmp/pip-build-7sCuVK/h5py/h5py/h5fd.pyx
[13/22] Cythonizing /tmp/pip-build-7sCuVK/h5py/h5py/h5g.pyx
[14/22] Cythonizing /tmp/pip-build-7sCuVK/h5py/h5py/h5i.pyx
[15/22] Cythonizing /tmp/pip-build-7sCuVK/h5py/h5py/h5l.pyx
[16/22] Cythonizing /tmp/pip-build-7sCuVK/h5py/h5py/h5o.pyx
[17/22] Cythonizing /tmp/pip-build-7sCuVK/h5py/h5py/h5p.pyx
[18/22] Cythonizing /tmp/pip-build-7sCuVK/h5py/h5py/h5r.pyx
[19/22] Cythonizing /tmp/pip-build-7sCuVK/h5py/h5py/h5s.pyx
[20/22] Cythonizing /tmp/pip-build-7sCuVK/h5py/h5py/h5t.pyx
[21/22] Cythonizing /tmp/pip-build-7sCuVK/h5py/h5py/h5z.pyx
[22/22] Cythonizing /tmp/pip-build-7sCuVK/h5py/h5py/utils.pyx
building 'h5py.defs' extension
creating build/temp.linux-x86_64-2.7
creating build/temp.linux-x86_64-2.7/tmp
creating build/temp.linux-x86_64-2.7/tmp/pip-build-7sCuVK
creating build/temp.linux-x86_64-2.7/tmp/pip-build-7sCuVK/h5py
creating build/temp.linux-x86_64-2.7/tmp/pip-build-7sCuVK/h5py/h5py
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-HVkOs2/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -DH5_USE_16_API -I./h5py -I/tmp/pip-build-7sCuVK/h5py/lzf -I/opt/local/include -I/usr/local/include -I/usr/local/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c /tmp/pip-build-7sCuVK/h5py/h5py/defs.c -o build/temp.linux-x86_64-2.7/tmp/pip-build-7sCuVK/h5py/h5py/defs.o
In file included from /usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1777:0,
from /usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18,
from /usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
from /tmp/pip-build-7sCuVK/h5py/h5py/api_compat.h:26,
from /tmp/pip-build-7sCuVK/h5py/h5py/defs.c:569:
/usr/local/lib/python2.7/dist-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]
#warning "Using deprecated NumPy API, disable it by " \
^~~~~~~
In file included from /tmp/pip-build-7sCuVK/h5py/h5py/defs.c:569:0:
/tmp/pip-build-7sCuVK/h5py/h5py/api_compat.h:27:18: fatal error: hdf5.h: No such file or directory
#include "hdf5.h"
^
compilation terminated.
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
----------------------------------------
Command "/usr/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-7sCuVK/h5py/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-H96iOU-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-build-7sCuVK/h5py/
Also install python-dev - sudo apt-get install python-dev
. That should help.
Ref: https://stackoverflow.com/questions/26053982/error-setup-script-exited-with-error-command-x86-64-linux-gnu-gcc-failed-wit
I am attempting to get this up and running on a Google Cloud Engine (GCE) VM - Debian 4.9.51-1 x86_64. I performed a:
sudo pip install -r requirements.txt
, and everything installed correctly.I then attempt to run
python caption_generator/prepare_dataset.py
. This outputs the following error:Any help would be much appreciated.