Hi Andrew,
I had a go at building this 2.4.0 beta1 in mpi mode, but ran into a problem at
compile-time: missing h5py/defs.c (see attached trace of the configuration and
build).
I use the following dependencies:
* hdf5 1.8.11 (parallel, shared)
* Cython 0.19.1
* Numpy 1.7.1
* mpi5py 1.3.1
* python 2.7.3
The relevant binaries are all in the path and python modules in the pythonpath.
I have built and used h5py several times before, but not come across this kind
of issue before... Am I just forgetting some configuration?
Cheers,
Ulrik
________________________________________
From: Andrew Collette [[email protected]]
Sent: 03 November 2014 18:32
To: [email protected]; HDF Users Discussion List
Subject: [Hdf-forum] ANN: HDF5 for Python 2.4.0 BETA
Announcing HDF5 for Python (h5py) 2.4.0 BETA
============================================
The h5py team is happy to announce the availability of h5py 2.4.0 (beta).
This beta version will be available for approximately two weeks. Because
of the substantial number of changes to the code base, we welcome feedback,
particularly from MPI users.
Documentation for the beta is at:
http://docs.h5py.org/en/latest/
Download at PyPI:
https://pypi.python.org/pypi/h5py/2.4.0b1
Changes
-------
This release incorporates a total re-write of the identifier management
system in h5py. As part of this refactoring, the entire API is also now
protected by threading locks. User-visible changes include:
* Files are now automatically closed when all objects within them
are unreachable. Previously, if File.close() was not explicitly called,
files would remain open and "leaks" were possible if the File object
was lost.
* The entire API is now believed to be thread-safe (feedback welcome!).
* External links now work if the target file is already open. Previously
this was not possible because of a mismatch in the file close strengths.
* The options to setup.py have changed; a new top-level "configure"
command handles options like --hdf5=/path/to/hdf5 and --mpi. Setup.py
now works correctly under Python 3 when these options are used.
* Cython (0.17+) is now required when building from source.
* The minimum NumPy version is now 1.6.1.
* Various other enhancements and bug fixes
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[up45@pc0009 h5py-2.4.0b1]$ export PYTHONPATH=/dls_sw/prod/tools/RHEL6-x86_64/numpy/1-7-0/prefix/lib/python2.7/site-packages/numpy-1.7.0-py2.7-linux-x86_64.egg:/dls_sw/prod/tools/RHEL6-x86_64/Cython/0-19-1/prefix/lib/python2.7/site-packages:/dls_sw/prod/tools/RHEL6-x86_64/mpi4py/1-3-1/prefix/lib/python2.7/site-packages
[up45@pc0009 h5py-2.4.0b1]$
[up45@pc0009 h5py-2.4.0b1]$ export PATH=/dls_sw/prod/tools/RHEL6-x86_64/phdf5/1-8-11/prefix/bin:/dls_sw/prod/tools/RHEL6-x86_64/openmpi/1-6-5/prefix/bin:/dls_sw/prod/tools/RHEL6-x86_64/Cython/0-19-1/prefix/bin:$PATH
[up45@pc0009 h5py-2.4.0b1]$ export CC=/dls_sw/prod/tools/RHEL6-x86_64/phdf5/1-8-11/prefix/bin/ph5pcc
[up45@pc0009 h5py-2.4.0b1]$ dls-python setup.py configure --hdf5=/dls_sw/prod/tools/RHEL6-x86_64/phdf5/1-8-11/prefix --mpi
running configure
Autodetected HDF5 1.8.11
********************************************************************************
Summary of the h5py configuration
Path to HDF5: '/dls_sw/prod/tools/RHEL6-x86_64/phdf5/1-8-11/prefix'
HDF5 Version: '1.8.11'
MPI Enabled: True
Rebuild Required: True
********************************************************************************
[up45@pc0009 h5py-2.4.0b1]$
[up45@pc0009 h5py-2.4.0b1]$
[up45@pc0009 h5py-2.4.0b1]$
[up45@pc0009 h5py-2.4.0b1]$ dls-python setup.py build
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/ipy_completer.py -> build/lib.linux-x86_64-2.7/h5py
copying h5py/highlevel.py -> build/lib.linux-x86_64-2.7/h5py
copying h5py/version.py -> build/lib.linux-x86_64-2.7/h5py
copying h5py/__init__.py -> build/lib.linux-x86_64-2.7/h5py
creating 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/selections2.py -> build/lib.linux-x86_64-2.7/h5py/_hl
copying h5py/_hl/files.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/selections.py -> 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/dims.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/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
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_group.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_h5t.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_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_selections.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
copying h5py/tests/old/test_dimension_scales.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_attrs.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_h5p.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_h5f.py -> 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/common.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/test_file.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/__init__.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
Autodetected HDF5 1.8.11
********************************************************************************
Summary of the h5py configuration
Path to HDF5: '/dls_sw/prod/tools/RHEL6-x86_64/phdf5/1-8-11/prefix'
HDF5 Version: '1.8.11'
MPI Enabled: True
Rebuild Required: True
********************************************************************************
Executing api_gen rebuild of defs
building 'h5py.defs' extension
creating build/temp.linux-x86_64-2.7
creating build/temp.linux-x86_64-2.7/dls_sw
creating build/temp.linux-x86_64-2.7/dls_sw/work
creating build/temp.linux-x86_64-2.7/dls_sw/work/tools
creating build/temp.linux-x86_64-2.7/dls_sw/work/tools/RHEL6-x86_64
creating build/temp.linux-x86_64-2.7/dls_sw/work/tools/RHEL6-x86_64/h5py
creating build/temp.linux-x86_64-2.7/dls_sw/work/tools/RHEL6-x86_64/h5py/src
creating build/temp.linux-x86_64-2.7/dls_sw/work/tools/RHEL6-x86_64/h5py/src/h5py-2.4.0b1
creating build/temp.linux-x86_64-2.7/dls_sw/work/tools/RHEL6-x86_64/h5py/src/h5py-2.4.0b1/h5py
gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -DH5_USE_16_API -I/dls_sw/prod/tools/RHEL6-x86_64/phdf5/1-8-11/prefix/include -I/dls_sw/work/tools/RHEL6-x86_64/h5py/src/h5py-2.4.0b1/lzf -I/opt/local/include -I/usr/local/include -I/dls_sw/prod/tools/RHEL6-x86_64/numpy/1-7-0/prefix/lib/python2.7/site-packages/numpy-1.7.0-py2.7-linux-x86_64.egg/numpy/core/include -I/dls_sw/prod/tools/RHEL6-x86_64/mpi4py/1-3-1/prefix/lib/python2.7/site-packages/mpi4py/include -I/dls_sw/prod/tools/RHEL6-x86_64/Python/2-7-3/prefix/include/python2.7 -c /dls_sw/work/tools/RHEL6-x86_64/h5py/src/h5py-2.4.0b1/h5py/defs.c -o build/temp.linux-x86_64-2.7/dls_sw/work/tools/RHEL6-x86_64/h5py/src/h5py-2.4.0b1/h5py/defs.o
gcc: /dls_sw/work/tools/RHEL6-x86_64/h5py/src/h5py-2.4.0b1/h5py/defs.c: No such file or directory
gcc: no input files
error: command 'gcc' failed with exit status 1
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