Dear community,
I followed the references in the site in order to install FEniCSx through ubuntu. I’m able to run script both in 3D and 2D with mesh created in python. I can’t run script in which the mesh is created and imported. There’s no errors in the script, in fact i’m able to run with an editor like pycharm, but when i run in ubuntu i get the following error and I’m stuck. Thanks for any help
How did you install
- FEniCSx (through apt-Get?)
- h5py (through pip?)
If you installed h5py through pip3 you need to make sure you do not install another binary, i.e.
pip3 install —no-binary=h5py h5py as DOLFINx already depends on hdf5.
Yes, FEniCSx is installed through apt-get, for h5py i follow this documentation but nothing works, always the same error appear. Installation — h5py 3.7.0 documentation
Any suggestion?
You Need to first uninstall h5py, as you now have it installed with wheels, as noted in: Installation — h5py 3.10.0 documentation
Then you should call the command
Could also just use apt and not use pip after uninstalling, in order to avoid the clash
apt-get install python3-h5py python3-h5py-mpi
1 Like
Unfortunately there’s no way to install. I’ll post the message error, I’m a new user of ubuntu but it seems no way solution 
As it says here, you already have h5py installed. You need to uninstall the current version
pip3 uninstall h5py
prior to trying to reinstall it with no binary.
Instead of putting in pictures of error messages, it would be better if you could format the input/output of terminal messages as:
```bash
Insert command here
```
In the last picture you supplied, it seems like you have sucessfully uninstalled h5py.
What happens if you now try to re-install it?
simulator@DESKTOP-CL4ID9R:~$ pip3 install --no-binary=h5py h5py
Defaulting to user installation because normal site-packages is not writeable
Collecting h5py
Using cached h5py-3.7.0.tar.gz (392 kB)
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... done
Requirement already satisfied: numpy>=1.14.5 in ./.local/lib/python3.8/site-packages (from h5py) (1.23.1)
Building wheels for collected packages: h5py
Building wheel for h5py (pyproject.toml) ... error
error: subprocess-exited-with-error
× Building wheel for h5py (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [130 lines of output]
running bdist_wheel
running build
running build_py
creating build
creating build/lib.linux-x86_64-cpython-38
creating build/lib.linux-x86_64-cpython-38/h5py
copying h5py/h5py_warnings.py -> build/lib.linux-x86_64-cpython-38/h5py
copying h5py/version.py -> build/lib.linux-x86_64-cpython-38/h5py
copying h5py/ipy_completer.py -> build/lib.linux-x86_64-cpython-38/h5py
copying h5py/__init__.py -> build/lib.linux-x86_64-cpython-38/h5py
creating build/lib.linux-x86_64-cpython-38/h5py/_hl
copying h5py/_hl/datatype.py -> build/lib.linux-x86_64-cpython-38/h5py/_hl
copying h5py/_hl/selections.py -> build/lib.linux-x86_64-cpython-38/h5py/_hl
copying h5py/_hl/group.py -> build/lib.linux-x86_64-cpython-38/h5py/_hl
copying h5py/_hl/vds.py -> build/lib.linux-x86_64-cpython-38/h5py/_hl
copying h5py/_hl/base.py -> build/lib.linux-x86_64-cpython-38/h5py/_hl
copying h5py/_hl/dims.py -> build/lib.linux-x86_64-cpython-38/h5py/_hl
copying h5py/_hl/files.py -> build/lib.linux-x86_64-cpython-38/h5py/_hl
copying h5py/_hl/dataset.py -> build/lib.linux-x86_64-cpython-38/h5py/_hl
copying h5py/_hl/attrs.py -> build/lib.linux-x86_64-cpython-38/h5py/_hl
copying h5py/_hl/__init__.py -> build/lib.linux-x86_64-cpython-38/h5py/_hl
copying h5py/_hl/compat.py -> build/lib.linux-x86_64-cpython-38/h5py/_hl
copying h5py/_hl/selections2.py -> build/lib.linux-x86_64-cpython-38/h5py/_hl
copying h5py/_hl/filters.py -> build/lib.linux-x86_64-cpython-38/h5py/_hl
creating build/lib.linux-x86_64-cpython-38/h5py/tests
copying h5py/tests/test_dataset_swmr.py -> build/lib.linux-x86_64-cpython-38/h5py/tests
copying h5py/tests/test_dataset.py -> build/lib.linux-x86_64-cpython-38/h5py/tests
copying h5py/tests/test_file.py -> build/lib.linux-x86_64-cpython-38/h5py/tests
copying h5py/tests/test_attribute_create.py -> build/lib.linux-x86_64-cpython-38/h5py/tests
copying h5py/tests/test_dims_dimensionproxy.py -> build/lib.linux-x86_64-cpython-38/h5py/tests
copying h5py/tests/test_slicing.py -> build/lib.linux-x86_64-cpython-38/h5py/tests
copying h5py/tests/test_datatype.py -> build/lib.linux-x86_64-cpython-38/h5py/tests
copying h5py/tests/test_dtype.py -> build/lib.linux-x86_64-cpython-38/h5py/tests
copying h5py/tests/test_file2.py -> build/lib.linux-x86_64-cpython-38/h5py/tests
copying h5py/tests/test_filters.py -> build/lib.linux-x86_64-cpython-38/h5py/tests
copying h5py/tests/test_objects.py -> build/lib.linux-x86_64-cpython-38/h5py/tests
copying h5py/tests/test_file_alignment.py -> build/lib.linux-x86_64-cpython-38/h5py/tests
copying h5py/tests/test_h5f.py -> build/lib.linux-x86_64-cpython-38/h5py/tests
copying h5py/tests/test_h5d_direct_chunk.py -> build/lib.linux-x86_64-cpython-38/h5py/tests
copying h5py/tests/test_dataset_getitem.py -> build/lib.linux-x86_64-cpython-38/h5py/tests
copying h5py/tests/test_base.py -> build/lib.linux-x86_64-cpython-38/h5py/tests
copying h5py/tests/common.py -> build/lib.linux-x86_64-cpython-38/h5py/tests
copying h5py/tests/conftest.py -> build/lib.linux-x86_64-cpython-38/h5py/tests
copying h5py/tests/test_attrs.py -> build/lib.linux-x86_64-cpython-38/h5py/tests
copying h5py/tests/test_h5p.py -> build/lib.linux-x86_64-cpython-38/h5py/tests
copying h5py/tests/test_h5o.py -> build/lib.linux-x86_64-cpython-38/h5py/tests
copying h5py/tests/test_selections.py -> build/lib.linux-x86_64-cpython-38/h5py/tests
copying h5py/tests/test_completions.py -> build/lib.linux-x86_64-cpython-38/h5py/tests
copying h5py/tests/test_errors.py -> build/lib.linux-x86_64-cpython-38/h5py/tests
copying h5py/tests/test_h5.py -> build/lib.linux-x86_64-cpython-38/h5py/tests
copying h5py/tests/test_dimension_scales.py -> build/lib.linux-x86_64-cpython-38/h5py/tests
copying h5py/tests/test_attrs_data.py -> build/lib.linux-x86_64-cpython-38/h5py/tests
copying h5py/tests/test_group.py -> build/lib.linux-x86_64-cpython-38/h5py/tests
copying h5py/tests/test_big_endian_file.py -> build/lib.linux-x86_64-cpython-38/h5py/tests
copying h5py/tests/test_h5pl.py -> build/lib.linux-x86_64-cpython-38/h5py/tests
copying h5py/tests/test_h5t.py -> build/lib.linux-x86_64-cpython-38/h5py/tests
copying h5py/tests/test_file_image.py -> build/lib.linux-x86_64-cpython-38/h5py/tests
copying h5py/tests/__init__.py -> build/lib.linux-x86_64-cpython-38/h5py/tests
creating build/lib.linux-x86_64-cpython-38/h5py/tests/data_files
copying h5py/tests/data_files/__init__.py -> build/lib.linux-x86_64-cpython-38/h5py/tests/data_files
creating build/lib.linux-x86_64-cpython-38/h5py/tests/test_vds
copying h5py/tests/test_vds/test_highlevel_vds.py -> build/lib.linux-x86_64-cpython-38/h5py/tests/test_vds
copying h5py/tests/test_vds/test_lowlevel_vds.py -> build/lib.linux-x86_64-cpython-38/h5py/tests/test_vds
copying h5py/tests/test_vds/test_virtual_source.py -> build/lib.linux-x86_64-cpython-38/h5py/tests/test_vds
copying h5py/tests/test_vds/__init__.py -> build/lib.linux-x86_64-cpython-38/h5py/tests/test_vds
copying h5py/tests/data_files/vlen_string_dset.h5 -> build/lib.linux-x86_64-cpython-38/h5py/tests/data_files
copying h5py/tests/data_files/vlen_string_dset_utc.h5 -> build/lib.linux-x86_64-cpython-38/h5py/tests/data_files
copying h5py/tests/data_files/vlen_string_s390x.h5 -> build/lib.linux-x86_64-cpython-38/h5py/tests/data_files
running build_ext
Loading library to get build settings and version: /usr/lib/x86_64-linux-gnu/hdf5/openmpi/libhdf5.so
********************************************************************************
Summary of the h5py configuration
HDF5 include dirs: [
'/usr/include/openmpi'
'/usr/include/hdf5/openmpi'
]
HDF5 library dirs: [
'/usr/lib/x86_64-linux-gnu/hdf5/openmpi'
'/usr/lib/openmpi/lib'
]
HDF5 Version: (1, 10, 4)
MPI Enabled: False
ROS3 VFD Enabled: False
DIRECT VFD Enabled: False
Rebuild Required: True
********************************************************************************
Executing api_gen rebuild of defs
Updated /tmp/pip-install-bqu6x3ax/h5py_a7dd5fe2c98e42768689ec1d3af25ff5/h5py/config.pxi
Executing cythonize()
[ 1/24] Cythonizing /tmp/pip-install-bqu6x3ax/h5py_a7dd5fe2c98e42768689ec1d3af25ff5/h5py/_conv.pyx
[ 2/24] Cythonizing /tmp/pip-install-bqu6x3ax/h5py_a7dd5fe2c98e42768689ec1d3af25ff5/h5py/_errors.pyx
[ 3/24] Cythonizing /tmp/pip-install-bqu6x3ax/h5py_a7dd5fe2c98e42768689ec1d3af25ff5/h5py/_objects.pyx
[ 4/24] Cythonizing /tmp/pip-install-bqu6x3ax/h5py_a7dd5fe2c98e42768689ec1d3af25ff5/h5py/_proxy.pyx
[ 5/24] Cythonizing /tmp/pip-install-bqu6x3ax/h5py_a7dd5fe2c98e42768689ec1d3af25ff5/h5py/_selector.pyx
[ 6/24] Cythonizing /tmp/pip-install-bqu6x3ax/h5py_a7dd5fe2c98e42768689ec1d3af25ff5/h5py/defs.pyx
[ 7/24] Cythonizing /tmp/pip-install-bqu6x3ax/h5py_a7dd5fe2c98e42768689ec1d3af25ff5/h5py/h5.pyx
[ 8/24] Cythonizing /tmp/pip-install-bqu6x3ax/h5py_a7dd5fe2c98e42768689ec1d3af25ff5/h5py/h5a.pyx
[ 9/24] Cythonizing /tmp/pip-install-bqu6x3ax/h5py_a7dd5fe2c98e42768689ec1d3af25ff5/h5py/h5ac.pyx
[10/24] Cythonizing /tmp/pip-install-bqu6x3ax/h5py_a7dd5fe2c98e42768689ec1d3af25ff5/h5py/h5d.pyx
[11/24] Cythonizing /tmp/pip-install-bqu6x3ax/h5py_a7dd5fe2c98e42768689ec1d3af25ff5/h5py/h5ds.pyx
[12/24] Cythonizing /tmp/pip-install-bqu6x3ax/h5py_a7dd5fe2c98e42768689ec1d3af25ff5/h5py/h5f.pyx
[13/24] Cythonizing /tmp/pip-install-bqu6x3ax/h5py_a7dd5fe2c98e42768689ec1d3af25ff5/h5py/h5fd.pyx
[14/24] Cythonizing /tmp/pip-install-bqu6x3ax/h5py_a7dd5fe2c98e42768689ec1d3af25ff5/h5py/h5g.pyx
[15/24] Cythonizing /tmp/pip-install-bqu6x3ax/h5py_a7dd5fe2c98e42768689ec1d3af25ff5/h5py/h5i.pyx
[16/24] Cythonizing /tmp/pip-install-bqu6x3ax/h5py_a7dd5fe2c98e42768689ec1d3af25ff5/h5py/h5l.pyx
[17/24] Cythonizing /tmp/pip-install-bqu6x3ax/h5py_a7dd5fe2c98e42768689ec1d3af25ff5/h5py/h5o.pyx
[18/24] Cythonizing /tmp/pip-install-bqu6x3ax/h5py_a7dd5fe2c98e42768689ec1d3af25ff5/h5py/h5p.pyx
[19/24] Cythonizing /tmp/pip-install-bqu6x3ax/h5py_a7dd5fe2c98e42768689ec1d3af25ff5/h5py/h5pl.pyx
[20/24] Cythonizing /tmp/pip-install-bqu6x3ax/h5py_a7dd5fe2c98e42768689ec1d3af25ff5/h5py/h5r.pyx
[21/24] Cythonizing /tmp/pip-install-bqu6x3ax/h5py_a7dd5fe2c98e42768689ec1d3af25ff5/h5py/h5s.pyx
[22/24] Cythonizing /tmp/pip-install-bqu6x3ax/h5py_a7dd5fe2c98e42768689ec1d3af25ff5/h5py/h5t.pyx
[23/24] Cythonizing /tmp/pip-install-bqu6x3ax/h5py_a7dd5fe2c98e42768689ec1d3af25ff5/h5py/h5z.pyx
[24/24] Cythonizing /tmp/pip-install-bqu6x3ax/h5py_a7dd5fe2c98e42768689ec1d3af25ff5/h5py/utils.pyx
building 'h5py.defs' extension
creating build/temp.linux-x86_64-cpython-38
creating build/temp.linux-x86_64-cpython-38/tmp
creating build/temp.linux-x86_64-cpython-38/tmp/pip-install-bqu6x3ax
creating build/temp.linux-x86_64-cpython-38/tmp/pip-install-bqu6x3ax/h5py_a7dd5fe2c98e42768689ec1d3af25ff5
creating build/temp.linux-x86_64-cpython-38/tmp/pip-install-bqu6x3ax/h5py_a7dd5fe2c98e42768689ec1d3af25ff5/h5py
x86_64-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 -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-bqu6x3ax/h5py_a7dd5fe2c98e42768689ec1d3af25ff5/lzf -I/tmp/pip-install-bqu6x3ax/h5py_a7dd5fe2c98e42768689ec1d3af25ff5/lzf/lzf -I/tmp/pip-build-env-_pqefzyh/overlay/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c /tmp/pip-install-bqu6x3ax/h5py_a7dd5fe2c98e42768689ec1d3af25ff5/h5py/defs.c -o build/temp.linux-x86_64-cpython-38/tmp/pip-install-bqu6x3ax/h5py_a7dd5fe2c98e42768689ec1d3af25ff5/h5py/defs.o
In file included from /usr/include/hdf5/openmpi/hdf5.h:22,
from /tmp/pip-install-bqu6x3ax/h5py_a7dd5fe2c98e42768689ec1d3af25ff5/h5py/api_compat.h:27,
from /tmp/pip-install-bqu6x3ax/h5py_a7dd5fe2c98e42768689ec1d3af25ff5/h5py/defs.c:803:
/usr/include/hdf5/openmpi/H5public.h:60:13: fatal error: mpi.h: No such file or directory
60 | # include <mpi.h>
| ^~~~~~~
compilation terminated.
error: command '/usr/bin/x86_64-linux-gnu-gcc' failed with exit code 1
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for h5py
Failed to build h5py
ERROR: Could not build wheels for h5py, which is required to install pyproject.toml-based projects
simulator@DESKTOP-CL4ID9R:~$
This is the complete output message.
Could you try with:
HDF5_MPI="ON" pip3 install --no-cache-dir --no-binary=h5py h5py --upgrade
There are also several suggestions at: c++ - fatal error: mpi.h: No such file or directory #include <mpi.h> - Stack Overflow
It gives the same error. I succesfully installed
sudo apt install libopenmpi-dev
pip install mpi4py
then i run
HDF5_MPI="ON" pip3 install --no-cache-dir --no-binary=h5py h5py --upgrade
and i got the same error.
This solved the problem in ubuntu 22.04.1 after reinstalling all packages and dependencies. Thanks a lot
Looks like you had an old version of Ubuntu. python3-h5py on its own will have to do on older releases where python3-h5py-mpi is not available. Glad you found ubuntu 22.04. Installation is usually simpler with the most recent release.
1 Like