Public bug reported:
TensorFlow 2.5 requires python3 h5py 3.1.0. On Ubuntu Focal arm64, the
following sequence
of commands fails (full log is given at the bottom)
# apt-get install --install-recommends python3-pip
# apt-get build-dep h5py
# pip3 install h5py==3.1.0
The same sequence of commands succeeds on Ubuntu Hirsute arm64,
Debian Buster arm64 and Debian Bullseye arm64.
The main reason of the failure is
aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g
-fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security
-g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security
-Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DH5_USE_18_API -DNPY_NO_DEPRECATED_API=0
-I./h5py -I/usr/include/openmpi -I/usr/include/hdf5/openmpi
-I/tmp/pip-install-f0eh53x0/h5py/lzf -I/tmp/pip-install-f0eh53x0/h5py/lzf/lzf
-I/tmp/pip-build-env-jau4onvg/normal/lib/python3.8/site-packages/numpy/core/include
-I/usr/include/python3.8 -c /tmp/pip-install-f0eh53x0/h5py/h5py/defs.c -o
build/temp.linux-aarch64-3.8/tmp/pip-install-f0eh53x0/h5py/h5py/defs.o
In file included from /usr/include/hdf5/openmpi/hdf5.h:22,
from /tmp/pip-install-f0eh53x0/h5py/h5py/api_compat.h:27,
from /tmp/pip-install-f0eh53x0/h5py/h5py/defs.c:669:
/usr/include/hdf5/openmpi/H5public.h:60:13: fatal error: mpi.h: No such file
or directory
60 | # include <mpi.h>
| ^~~~~~~
compilation terminated.
warning: h5py/h5pl.pyx:65:14: cpdef variables will not be supported in Cython
3; currently they are no different from cdef variables
warning: h5py/h5pl.pyx:66:14: cpdef variables will not be supported in Cython
3; currently they are no different from cdef variables
warning: h5py/h5pl.pyx:81:14: cpdef variables will not be supported in Cython
3; currently they are no different from cdef variables
error: command 'aarch64-linux-gnu-gcc' failed with exit status 1
The full log is given as attachment:
** Affects: arm-ports
Importance: Undecided
Status: New
** Affects: python-pip (Ubuntu)
Importance: Undecided
Status: New
** Tags: arm arm64 focal
** Attachment added: "Full log"
https://bugs.launchpad.net/bugs/1929259/+attachment/5499312/+files/h5py-focal-arm64.txt
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https://bugs.launchpad.net/bugs/1929259
Title:
Focal arm64: pip3 install h5py==3.1.0 fails with
/usr/include/hdf5/openmpi/H5public.h:60:13: fatal error: mpi.h: No
such file or directory
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