Command errored out with exit status -4: while installing h5py

I try to install h5py 2.10.0 in the Jetson Nano, always get the error that Command errored out with exit status -4. I search a long time for a solution, I install cython (pip3 install Cython), I also pre-install the package dependencies.(sudo apt-get ). However, None of the solutions work for me either git clone the repository directly and install. Can anyone please help? The error logs for reference:

    ERROR: Command errored out with exit status -4:
     command: /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-req-build-jja5oowt/setup.py'"'"'; __file__='"'"'/tmp/pip-req-build-jja5oowt/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-record-zufa6fjz/install-record.txt --single-version-externally-managed --user --prefix= --compile --install-headers /home/jetson/.local/include/python3.6m/h5py
         cwd: /tmp/pip-req-build-jja5oowt/
    Complete output (62 lines):
    running install
    running build
    running build_py
    creating build
    creating build/lib.linux-aarch64-3.6
    creating build/lib.linux-aarch64-3.6/h5py
    copying h5py/__init__.py -> build/lib.linux-aarch64-3.6/h5py
    copying h5py/ipy_completer.py -> build/lib.linux-aarch64-3.6/h5py
    copying h5py/h5py_warnings.py -> build/lib.linux-aarch64-3.6/h5py
    copying h5py/version.py -> build/lib.linux-aarch64-3.6/h5py
    copying h5py/highlevel.py -> build/lib.linux-aarch64-3.6/h5py
    creating build/lib.linux-aarch64-3.6/h5py/_hl
    copying h5py/_hl/__init__.py -> build/lib.linux-aarch64-3.6/h5py/_hl
    copying h5py/_hl/group.py -> build/lib.linux-aarch64-3.6/h5py/_hl
    copying h5py/_hl/vds.py -> build/lib.linux-aarch64-3.6/h5py/_hl
    copying h5py/_hl/dataset.py -> build/lib.linux-aarch64-3.6/h5py/_hl
    copying h5py/_hl/selections2.py -> build/lib.linux-aarch64-3.6/h5py/_hl
    copying h5py/_hl/datatype.py -> build/lib.linux-aarch64-3.6/h5py/_hl
    copying h5py/_hl/selections.py -> build/lib.linux-aarch64-3.6/h5py/_hl
    copying h5py/_hl/filters.py -> build/lib.linux-aarch64-3.6/h5py/_hl
    copying h5py/_hl/files.py -> build/lib.linux-aarch64-3.6/h5py/_hl
    copying h5py/_hl/dims.py -> build/lib.linux-aarch64-3.6/h5py/_hl
    copying h5py/_hl/attrs.py -> build/lib.linux-aarch64-3.6/h5py/_hl
    copying h5py/_hl/compat.py -> build/lib.linux-aarch64-3.6/h5py/_hl
    copying h5py/_hl/base.py -> build/lib.linux-aarch64-3.6/h5py/_hl
    creating build/lib.linux-aarch64-3.6/h5py/tests
    copying h5py/tests/test_dataset_getitem.py -> build/lib.linux-aarch64-3.6/h5py/tests
    copying h5py/tests/__init__.py -> build/lib.linux-aarch64-3.6/h5py/tests
    copying h5py/tests/test_filters.py -> build/lib.linux-aarch64-3.6/h5py/tests
    copying h5py/tests/test_deprecation.py -> build/lib.linux-aarch64-3.6/h5py/tests
    copying h5py/tests/test_attribute_create.py -> build/lib.linux-aarch64-3.6/h5py/tests
    copying h5py/tests/test_dataset_swmr.py -> build/lib.linux-aarch64-3.6/h5py/tests
    copying h5py/tests/test_dimension_scales.py -> build/lib.linux-aarch64-3.6/h5py/tests
    copying h5py/tests/test_objects.py -> build/lib.linux-aarch64-3.6/h5py/tests
    copying h5py/tests/test_slicing.py -> build/lib.linux-aarch64-3.6/h5py/tests
    copying h5py/tests/test_dtype.py -> build/lib.linux-aarch64-3.6/h5py/tests
    copying h5py/tests/test_file2.py -> build/lib.linux-aarch64-3.6/h5py/tests
    copying h5py/tests/test_selections.py -> build/lib.linux-aarch64-3.6/h5py/tests
    copying h5py/tests/test_datatype.py -> build/lib.linux-aarch64-3.6/h5py/tests
    copying h5py/tests/common.py -> build/lib.linux-aarch64-3.6/h5py/tests
    copying h5py/tests/test_file.py -> build/lib.linux-aarch64-3.6/h5py/tests
    copying h5py/tests/test_h5.py -> build/lib.linux-aarch64-3.6/h5py/tests
    copying h5py/tests/test_h5d_direct_chunk.py -> build/lib.linux-aarch64-3.6/h5py/tests
    copying h5py/tests/test_attrs.py -> build/lib.linux-aarch64-3.6/h5py/tests
    copying h5py/tests/test_threads.py -> build/lib.linux-aarch64-3.6/h5py/tests
    copying h5py/tests/test_completions.py -> build/lib.linux-aarch64-3.6/h5py/tests
    copying h5py/tests/test_h5f.py -> build/lib.linux-aarch64-3.6/h5py/tests
    copying h5py/tests/test_attrs_data.py -> build/lib.linux-aarch64-3.6/h5py/tests
    copying h5py/tests/test_h5t.py -> build/lib.linux-aarch64-3.6/h5py/tests
    copying h5py/tests/test_group.py -> build/lib.linux-aarch64-3.6/h5py/tests
    copying h5py/tests/test_file_image.py -> build/lib.linux-aarch64-3.6/h5py/tests
    copying h5py/tests/test_dims_dimensionproxy.py -> build/lib.linux-aarch64-3.6/h5py/tests
    copying h5py/tests/test_base.py -> build/lib.linux-aarch64-3.6/h5py/tests
    copying h5py/tests/test_dataset.py -> build/lib.linux-aarch64-3.6/h5py/tests
    copying h5py/tests/test_h5pl.py -> build/lib.linux-aarch64-3.6/h5py/tests
    copying h5py/tests/test_h5p.py -> build/lib.linux-aarch64-3.6/h5py/tests
    creating build/lib.linux-aarch64-3.6/h5py/tests/test_vds
    copying h5py/tests/test_vds/__init__.py -> build/lib.linux-aarch64-3.6/h5py/tests/test_vds
    copying h5py/tests/test_vds/test_virtual_source.py -> build/lib.linux-aarch64-3.6/h5py/tests/test_vds
    copying h5py/tests/test_vds/test_highlevel_vds.py -> build/lib.linux-aarch64-3.6/h5py/tests/test_vds
    copying h5py/tests/test_vds/test_lowlevel_vds.py -> build/lib.linux-aarch64-3.6/h5py/tests/test_vds
    running build_ext
    ----------------------------------------
ERROR: Command errored out with exit status -4: /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-req-build-jja5oowt/setup.py'"'"'; __file__='"'"'/tmp/pip-req-build-jja5oowt/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-record-zufa6fjz/install-record.txt --single-version-externally-managed --user --prefix= --compile --install-headers /home/jetson/.local/include/python3.6m/h5py Check the logs for full command output.

[simonfojtu]

I’ve seen the same error as OP, when I had numpy==1.19.5 installed. I managed to install h5py-2.10.0 when downgrading to numpy==1.19.3:

$ python3 -m venv-np1.19.3
$ pip install -U setuptools pip
...
Successfully installed pip-21.0.1 setuptools-56.0.0
$ pip install numpy==1.19.3
...
Successfully installed numpy-1.19.3
$ pip install h5py
Collecting h5py
  Using cached h5py-2.10.0.tar.gz (301 kB)
Requirement already satisfied: numpy>=1.7 in ./venv-np1.19.3/lib/python3.6/site-packages (from h5py) (1.19.3)
Collecting six
  Using cached six-1.15.0-py2.py3-none-any.whl (10 kB)
Using legacy 'setup.py install' for h5py, since package 'wheel' is not installed.
Installing collected packages: six, h5py
    Running setup.py install for h5py ... done
Successfully installed h5py-2.10.0 six-1.15.0

using python-3.6

[biswadipmaity]

Indeed it was related ! Thanks for the insight… Downgrading numpy (from 1.19.5) to 1.19.4 solved it for me.