search

DedalusProject / dedalus

A flexible framework for solving PDEs with modern spectral methods.
http://dedalus-project.org/
GNU General Public License v3.0
513 stars 121 forks source link

Pip install fails #228

Closed tomass2077 closed 2 years ago

tomass2077 commented 2 years ago

pip3 install dedalus output:

`Defaulting to user installation because normal site-packages is not writeable Collecting dedalus Using cached dedalus-2.2207.1.tar.gz (124 kB) Installing build dependencies ... done Getting requirements to build wheel ... done Preparing metadata (pyproject.toml) ... done Requirement already satisfied: h5py>=2.10.0 in /home/tomass/.local/lib/python3.10/site-packages (from dedalus) (3.7.0) Requirement already satisfied: scipy>=1.4.0 in /home/tomass/.local/lib/python3.10/site-packages (from dedalus) (1.9.2) Collecting pytest Using cached pytest-7.1.3-py3-none-any.whl (298 kB) Requirement already satisfied: numpy>=1.20.0 in /home/tomass/.local/lib/python3.10/site-packages (from dedalus) (1.23.3) Collecting pytest-cov Using cached pytest_cov-4.0.0-py3-none-any.whl (21 kB) Collecting docopt Using cached docopt-0.6.2-py2.py3-none-any.whl Collecting pytest-benchmark Using cached pytest_benchmark-3.4.1-py2.py3-none-any.whl (50 kB) Requirement already satisfied: mpi4py>=2.0.0 in /usr/local/lib/python3.10/dist-packages (from dedalus) (3.1.3) Collecting pytest-parallel Using cached pytest_parallel-0.1.1-py3-none-any.whl (7.0 kB) Requirement already satisfied: matplotlib in /home/tomass/.local/lib/python3.10/site-packages (from dedalus) (3.6.1) Requirement already satisfied: python-dateutil>=2.7 in /home/tomass/.local/lib/python3.10/site-packages (from matplotlib->dedalus) (2.8.2) Requirement already satisfied: packaging>=20.0 in /usr/lib/python3/dist-packages (from matplotlib->dedalus) (21.3) Requirement already satisfied: cycler>=0.10 in /home/tomass/.local/lib/python3.10/site-packages (from matplotlib->dedalus) (0.11.0) Requirement already satisfied: kiwisolver>=1.0.1 in /home/tomass/.local/lib/python3.10/site-packages (from matplotlib->dedalus) (1.4.4) Requirement already satisfied: pyparsing>=2.2.1 in /usr/lib/python3/dist-packages (from matplotlib->dedalus) (2.4.7) Requirement already satisfied: pillow>=6.2.0 in /usr/lib/python3/dist-packages (from matplotlib->dedalus) (9.0.1) Requirement already satisfied: fonttools>=4.22.0 in /home/tomass/.local/lib/python3.10/site-packages (from matplotlib->dedalus) (4.37.4) Requirement already satisfied: contourpy>=1.0.1 in /home/tomass/.local/lib/python3.10/site-packages (from matplotlib->dedalus) (1.0.5) Collecting iniconfig Using cached iniconfig-1.1.1-py2.py3-none-any.whl (5.0 kB) Requirement already satisfied: attrs>=19.2.0 in /home/tomass/.local/lib/python3.10/site-packages (from pytest->dedalus) (22.1.0) Collecting py>=1.8.2 Using cached py-1.11.0-py2.py3-none-any.whl (98 kB) Requirement already satisfied: tomli>=1.0.0 in /home/tomass/.local/lib/python3.10/site-packages (from pytest->dedalus) (2.0.1) Collecting pluggy<2.0,>=0.12 Using cached pluggy-1.0.0-py2.py3-none-any.whl (13 kB) Collecting py-cpuinfo Using cached py_cpuinfo-8.0.0-py3-none-any.whl Collecting coverage[toml]>=5.2.1 Using cached coverage-6.5.0-cp310-cp310-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (213 kB) Collecting tblib Using cached tblib-1.7.0-py2.py3-none-any.whl (12 kB) Requirement already satisfied: six>=1.5 in /usr/lib/python3/dist-packages (from python-dateutil>=2.7->matplotlib->dedalus) (1.16.0) Building wheels for collected packages: dedalus Building wheel for dedalus (pyproject.toml) ... error ERROR: Command errored out with exit status 1: command: /usr/bin/python3 /home/tomass/.local/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py build_wheel /tmp/tmpqcq1b0nl cwd: /tmp/pip-install-weap5xss/dedalus_3a40a1332ca6438ab6e7b55a01153cc2 Complete output (90 lines): Looking for mpi include path Cannot find env var MPI_INCLUDE_PATH Looking for mpi prefix Found matching library in /usr/lib Looking for fftw include path Cannot find env var FFTW_INCLUDE_PATH Looking for fftw prefix Found matching library in /usr/lib Looking for fftw library path Cannot find env var FFTW_LIBRARY_PATH Looking for fftw prefix Found matching library in /usr/lib Looking for mpi library path Cannot find env var MPI_LIBRARY_PATH Looking for mpi prefix Found matching library in /usr/lib running bdist_wheel running build running build_py creating build creating build/lib.linux-x86_64-3.10 creating build/lib.linux-x86_64-3.10/dedalus copying dedalus/public.py -> build/lib.linux-x86_64-3.10/dedalus copying dedalus/main.py -> build/lib.linux-x86_64-3.10/dedalus copying dedalus/dev.py -> build/lib.linux-x86_64-3.10/dedalus copying dedalus/init.py -> build/lib.linux-x86_64-3.10/dedalus creating build/lib.linux-x86_64-3.10/dedalus/extras copying dedalus/extras/flow_tools.py -> build/lib.linux-x86_64-3.10/dedalus/extras copying dedalus/extras/atmospheres.py -> build/lib.linux-x86_64-3.10/dedalus/extras copying dedalus/extras/plot_tools.py -> build/lib.linux-x86_64-3.10/dedalus/extras copying dedalus/extras/init.py -> build/lib.linux-x86_64-3.10/dedalus/extras creating build/lib.linux-x86_64-3.10/dedalus/libraries copying dedalus/libraries/matsolvers.py -> build/lib.linux-x86_64-3.10/dedalus/libraries copying dedalus/libraries/init.py -> build/lib.linux-x86_64-3.10/dedalus/libraries creating build/lib.linux-x86_64-3.10/dedalus/core copying dedalus/core/basis.py -> build/lib.linux-x86_64-3.10/dedalus/core copying dedalus/core/problems.py -> build/lib.linux-x86_64-3.10/dedalus/core copying dedalus/core/solvers.py -> build/lib.linux-x86_64-3.10/dedalus/core copying dedalus/core/pencil.py -> build/lib.linux-x86_64-3.10/dedalus/core copying dedalus/core/distributor.py -> build/lib.linux-x86_64-3.10/dedalus/core copying dedalus/core/field.py -> build/lib.linux-x86_64-3.10/dedalus/core copying dedalus/core/domain.py -> build/lib.linux-x86_64-3.10/dedalus/core copying dedalus/core/metadata.py -> build/lib.linux-x86_64-3.10/dedalus/core copying dedalus/core/operators.py -> build/lib.linux-x86_64-3.10/dedalus/core copying dedalus/core/evaluator.py -> build/lib.linux-x86_64-3.10/dedalus/core copying dedalus/core/future.py -> build/lib.linux-x86_64-3.10/dedalus/core copying dedalus/core/init.py -> build/lib.linux-x86_64-3.10/dedalus/core copying dedalus/core/timesteppers.py -> build/lib.linux-x86_64-3.10/dedalus/core copying dedalus/core/system.py -> build/lib.linux-x86_64-3.10/dedalus/core creating build/lib.linux-x86_64-3.10/dedalus/tools copying dedalus/tools/dispatch.py -> build/lib.linux-x86_64-3.10/dedalus/tools copying dedalus/tools/plot_op.py -> build/lib.linux-x86_64-3.10/dedalus/tools copying dedalus/tools/progress.py -> build/lib.linux-x86_64-3.10/dedalus/tools copying dedalus/tools/array.py -> build/lib.linux-x86_64-3.10/dedalus/tools copying dedalus/tools/parsing.py -> build/lib.linux-x86_64-3.10/dedalus/tools copying dedalus/tools/sparse.py -> build/lib.linux-x86_64-3.10/dedalus/tools copying dedalus/tools/cache.py -> build/lib.linux-x86_64-3.10/dedalus/tools copying dedalus/tools/config.py -> build/lib.linux-x86_64-3.10/dedalus/tools copying dedalus/tools/logging.py -> build/lib.linux-x86_64-3.10/dedalus/tools copying dedalus/tools/post.py -> build/lib.linux-x86_64-3.10/dedalus/tools copying dedalus/tools/parallel.py -> build/lib.linux-x86_64-3.10/dedalus/tools copying dedalus/tools/init.py -> build/lib.linux-x86_64-3.10/dedalus/tools copying dedalus/tools/general.py -> build/lib.linux-x86_64-3.10/dedalus/tools copying dedalus/tools/exceptions.py -> build/lib.linux-x86_64-3.10/dedalus/tools creating build/lib.linux-x86_64-3.10/dedalus/tests copying dedalus/tests/test_bvp.py -> build/lib.linux-x86_64-3.10/dedalus/tests copying dedalus/tests/test_nlbvp.py -> build/lib.linux-x86_64-3.10/dedalus/tests copying dedalus/tests/test_output.py -> build/lib.linux-x86_64-3.10/dedalus/tests copying dedalus/tests/test_evp.py -> build/lib.linux-x86_64-3.10/dedalus/tests copying dedalus/tests/init.py -> build/lib.linux-x86_64-3.10/dedalus/tests copying dedalus/tests/test_ivp.py -> build/lib.linux-x86_64-3.10/dedalus/tests copying dedalus/tests/test_matsolvers.py -> build/lib.linux-x86_64-3.10/dedalus/tests creating build/lib.linux-x86_64-3.10/dedalus/libraries/fftw copying dedalus/libraries/fftw/init.py -> build/lib.linux-x86_64-3.10/dedalus/libraries/fftw creating build/lib.linux-x86_64-3.10/dedalus/tests/special_functions copying dedalus/tests/special_functions/bessel.py -> build/lib.linux-x86_64-3.10/dedalus/tests/special_functions copying dedalus/tests/special_functions/airy.py -> build/lib.linux-x86_64-3.10/dedalus/tests/special_functions copying dedalus/tests/special_functions/init.py -> build/lib.linux-x86_64-3.10/dedalus/tests/special_functions copying dedalus/dedalus.cfg -> build/lib.linux-x86_64-3.10/dedalus copying dedalus/examples.tar.gz -> build/lib.linux-x86_64-3.10/dedalus running build_ext creating build/temp.linux-x86_64-3.10 creating build/temp.linux-x86_64-3.10/dedalus creating build/temp.linux-x86_64-3.10/dedalus/libraries creating build/temp.linux-x86_64-3.10/dedalus/libraries/fftw x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idedalus/libraries/fftw/ -I/tmp/pip-build-env-bvx5qepg/overlay/local/lib/python3.10/dist-packages/numpy/core/include -I/tmp/pip-build-env-bvx5qepg/overlay/local/lib/python3.10/dist-packages/mpi4py/include -I/usr/include -I/usr/include -I/usr/include/python3.10 -c dedalus/libraries/fftw/fftw_wrappers.c -o build/temp.linux-x86_64-3.10/dedalus/libraries/fftw/fftw_wrappers.o -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -Wno-unused-function dedalus/libraries/fftw/fftw_wrappers.c:1514:3: error: unknown type name ‘MPI_Message’ 1514 | MPI_Message ob_mpi; | ^~~ error: command '/usr/bin/x86_64-linux-gnu-gcc' failed with exit code 1

ERROR: Failed building wheel for dedalus Failed to build dedalus ERROR: Could not build wheels for dedalus, which is required to install pyproject.toml-based projects`

kburns commented 2 years ago

The nightly build which follows the conda installation instructions is still succeeding, so it looks like there is probably an issue with the python environment you're trying to install to. I'd recommend trying the conda installation, and if issues remain please get in touch on the mailing list with the full info of how you've built the python environment, etc.