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May 10, 2021 02:01
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| (base) Davids-MacBook-Pro-4:~ dpsanders$ conda activate base | |
| (base) Davids-MacBook-Pro-4:~ dpsanders$ bash install_conda.sh | |
| Setting up conda with 'source /usr/local/Caskroom/miniconda/base/etc/profile.d/conda.sh' | |
| Preventing conda from looking in ~/.local with 'export PYTHONNOUSERSITE=1' | |
| Preventing conda from looking in PYTHONPATH with 'unset PYTHONPATH' | |
| Building new conda environment 'dedalus' | |
| Collecting package metadata (current_repodata.json): ...working... done | |
| Solving environment: ...working... done | |
| ## Package Plan ## | |
| environment location: /usr/local/Caskroom/miniconda/base/envs/dedalus | |
| added / updated specs: | |
| - python=3.8 | |
| The following packages will be downloaded: | |
| package | build | |
| ---------------------------|----------------- | |
| ca-certificates-2020.12.5 | h033912b_0 138 KB conda-forge | |
| certifi-2020.12.5 | py38h50d1736_1 143 KB conda-forge | |
| libcxx-11.1.0 | habf9029_0 1.0 MB conda-forge | |
| libffi-3.3 | h046ec9c_2 45 KB conda-forge | |
| ncurses-6.2 | h2e338ed_4 881 KB conda-forge | |
| openssl-1.1.1k | h0d85af4_0 1.9 MB conda-forge | |
| pip-21.1.1 | pyhd8ed1ab_0 1.1 MB conda-forge | |
| python-3.8.8 |h4e93d89_0_cpython 12.4 MB conda-forge | |
| python_abi-3.8 | 1_cp38 4 KB conda-forge | |
| readline-8.1 | h05e3726_0 266 KB conda-forge | |
| setuptools-49.6.0 | py38h50d1736_3 931 KB conda-forge | |
| sqlite-3.35.5 | h44b9ce1_0 1.7 MB conda-forge | |
| tk-8.6.10 | h0419947_1 3.3 MB conda-forge | |
| wheel-0.36.2 | pyhd3deb0d_0 31 KB conda-forge | |
| xz-5.2.5 | haf1e3a3_1 228 KB conda-forge | |
| zlib-1.2.11 | h7795811_1010 102 KB conda-forge | |
| ------------------------------------------------------------ | |
| Total: 24.1 MB | |
| The following NEW packages will be INSTALLED: | |
| ca-certificates conda-forge/osx-64::ca-certificates-2020.12.5-h033912b_0 | |
| certifi conda-forge/osx-64::certifi-2020.12.5-py38h50d1736_1 | |
| libcxx conda-forge/osx-64::libcxx-11.1.0-habf9029_0 | |
| libffi conda-forge/osx-64::libffi-3.3-h046ec9c_2 | |
| ncurses conda-forge/osx-64::ncurses-6.2-h2e338ed_4 | |
| openssl conda-forge/osx-64::openssl-1.1.1k-h0d85af4_0 | |
| pip conda-forge/noarch::pip-21.1.1-pyhd8ed1ab_0 | |
| python conda-forge/osx-64::python-3.8.8-h4e93d89_0_cpython | |
| python_abi conda-forge/osx-64::python_abi-3.8-1_cp38 | |
| readline conda-forge/osx-64::readline-8.1-h05e3726_0 | |
| setuptools conda-forge/osx-64::setuptools-49.6.0-py38h50d1736_3 | |
| sqlite conda-forge/osx-64::sqlite-3.35.5-h44b9ce1_0 | |
| tk conda-forge/osx-64::tk-8.6.10-h0419947_1 | |
| wheel conda-forge/noarch::wheel-0.36.2-pyhd3deb0d_0 | |
| xz conda-forge/osx-64::xz-5.2.5-haf1e3a3_1 | |
| zlib conda-forge/osx-64::zlib-1.2.11-h7795811_1010 | |
| Preparing transaction: ...working... done | |
| Verifying transaction: ...working... done | |
| Executing transaction: ...working... done | |
| Updating conda-forge pip, wheel, setuptools, cython | |
| Collecting package metadata (current_repodata.json): ...working... done | |
| Solving environment: ...working... done | |
| ## Package Plan ## | |
| environment location: /usr/local/Caskroom/miniconda/base/envs/dedalus | |
| added / updated specs: | |
| - cython | |
| - pip | |
| - setuptools | |
| - wheel | |
| The following packages will be downloaded: | |
| package | build | |
| ---------------------------|----------------- | |
| cython-0.29.23 | py38ha048514_0 2.0 MB conda-forge | |
| ------------------------------------------------------------ | |
| Total: 2.0 MB | |
| The following NEW packages will be INSTALLED: | |
| cython conda-forge/osx-64::cython-0.29.23-py38ha048514_0 | |
| Preparing transaction: ...working... done | |
| Verifying transaction: ...working... done | |
| Executing transaction: ...working... done | |
| Installing conda-forge openblas, numpy, scipy | |
| Collecting package metadata (current_repodata.json): ...working... done | |
| Solving environment: ...working... done | |
| ## Package Plan ## | |
| environment location: /usr/local/Caskroom/miniconda/base/envs/dedalus | |
| added / updated specs: | |
| - libblas[build=*openblas] | |
| - numpy | |
| - scipy | |
| The following packages will be downloaded: | |
| package | build | |
| ---------------------------|----------------- | |
| libblas-3.9.0 | 9_openblas 11 KB conda-forge | |
| libcblas-3.9.0 | 9_openblas 11 KB conda-forge | |
| libgfortran-5.0.0 |9_3_0_h6c81a4c_22 19 KB conda-forge | |
| libgfortran5-9.3.0 | h6c81a4c_22 1.7 MB conda-forge | |
| liblapack-3.9.0 | 9_openblas 11 KB conda-forge | |
| libopenblas-0.3.15 |openmp_h5e1b9a4_0 8.7 MB conda-forge | |
| llvm-openmp-11.1.0 | hda6cdc1_1 268 KB conda-forge | |
| numpy-1.20.2 | py38had91d27_0 5.5 MB conda-forge | |
| scipy-1.6.3 | py38h431c0a8_0 18.6 MB conda-forge | |
| ------------------------------------------------------------ | |
| Total: 34.8 MB | |
| The following NEW packages will be INSTALLED: | |
| libblas conda-forge/osx-64::libblas-3.9.0-9_openblas | |
| libcblas conda-forge/osx-64::libcblas-3.9.0-9_openblas | |
| libgfortran conda-forge/osx-64::libgfortran-5.0.0-9_3_0_h6c81a4c_22 | |
| libgfortran5 conda-forge/osx-64::libgfortran5-9.3.0-h6c81a4c_22 | |
| liblapack conda-forge/osx-64::liblapack-3.9.0-9_openblas | |
| libopenblas conda-forge/osx-64::libopenblas-0.3.15-openmp_h5e1b9a4_0 | |
| llvm-openmp conda-forge/osx-64::llvm-openmp-11.1.0-hda6cdc1_1 | |
| numpy conda-forge/osx-64::numpy-1.20.2-py38had91d27_0 | |
| scipy conda-forge/osx-64::scipy-1.6.3-py38h431c0a8_0 | |
| kPreparing transaction: ...working... done | |
| Verifying transaction: ...working... ^R | |
| done | |
| Executing transaction: ...working... done | |
| Installing conda-forge openmpi, mpi4py | |
| Collecting package metadata (current_repodata.json): ...working... done | |
| Solving environment: ...working... done | |
| ## Package Plan ## | |
| environment location: /usr/local/Caskroom/miniconda/base/envs/dedalus | |
| added / updated specs: | |
| - mpi4py | |
| - openmpi | |
| - openmpi-mpicc | |
| The following packages will be downloaded: | |
| package | build | |
| ---------------------------|----------------- | |
| cctools_osx-64-949.0.1 | h6407bdd_21 1.8 MB conda-forge | |
| clang-11.1.0 | h694c41f_0 124 KB conda-forge | |
| clang-11-11.1.0 |default_he082bbe_0 686 KB conda-forge | |
| clang_osx-64-11.1.0 | hb91bd55_1 16 KB conda-forge | |
| clangxx-11.1.0 |default_he082bbe_0 124 KB conda-forge | |
| compiler-rt-11.1.0 | h654b07c_0 78 KB conda-forge | |
| compiler-rt_osx-64-11.1.0 | h8c5fa43_0 5.6 MB conda-forge | |
| ld64_osx-64-530 | he8994da_21 1.3 MB conda-forge | |
| ldid-2.1.2 | h7660a38_2 55 KB conda-forge | |
| libclang-cpp11.1-11.1.0 |default_he082bbe_0 12.6 MB conda-forge | |
| libllvm11-11.1.0 | hd011deb_2 22.5 MB conda-forge | |
| llvm-tools-11.1.0 | hd011deb_2 11.7 MB conda-forge | |
| mpi-1.0 | openmpi 4 KB conda-forge | |
| mpi4py-3.0.3 | py38h1087cf1_7 578 KB conda-forge | |
| openmpi-4.1.1 | hd3cd54c_0 3.2 MB conda-forge | |
| openmpi-mpicc-4.1.1 | h0d85af4_0 9 KB conda-forge | |
| tapi-1100.0.11 | h9ce4665_0 196 KB conda-forge | |
| ------------------------------------------------------------ | |
| Total: 60.5 MB | |
| The following NEW packages will be INSTALLED: | |
| cctools_osx-64 conda-forge/osx-64::cctools_osx-64-949.0.1-h6407bdd_21 | |
| clang conda-forge/osx-64::clang-11.1.0-h694c41f_0 | |
| clang-11 conda-forge/osx-64::clang-11-11.1.0-default_he082bbe_0 | |
| clang_osx-64 conda-forge/osx-64::clang_osx-64-11.1.0-hb91bd55_1 | |
| clangxx conda-forge/osx-64::clangxx-11.1.0-default_he082bbe_0 | |
| compiler-rt conda-forge/osx-64::compiler-rt-11.1.0-h654b07c_0 | |
| compiler-rt_osx-64 conda-forge/noarch::compiler-rt_osx-64-11.1.0-h8c5fa43_0 | |
| ld64_osx-64 conda-forge/osx-64::ld64_osx-64-530-he8994da_21 | |
| ldid conda-forge/osx-64::ldid-2.1.2-h7660a38_2 | |
| libclang-cpp11.1 conda-forge/osx-64::libclang-cpp11.1-11.1.0-default_he082bbe_0 | |
| libllvm11 conda-forge/osx-64::libllvm11-11.1.0-hd011deb_2 | |
| llvm-tools conda-forge/osx-64::llvm-tools-11.1.0-hd011deb_2 | |
| mpi conda-forge/osx-64::mpi-1.0-openmpi | |
| mpi4py conda-forge/osx-64::mpi4py-3.0.3-py38h1087cf1_7 | |
| openmpi conda-forge/osx-64::openmpi-4.1.1-hd3cd54c_0 | |
| openmpi-mpicc conda-forge/osx-64::openmpi-mpicc-4.1.1-h0d85af4_0 | |
| tapi conda-forge/osx-64::tapi-1100.0.11-h9ce4665_0 | |
| Preparing transaction: ...working... done | |
| Verifying transaction: ...working... done | |
| Executing transaction: ...working... done | |
| Installing conda-forge fftw | |
| Collecting package metadata (current_repodata.json): ...working... done | |
| Solving environment: ...working... done | |
| ## Package Plan ## | |
| environment location: /usr/local/Caskroom/miniconda/base/envs/dedalus | |
| added / updated specs: | |
| - fftw[build=*openmpi*] | |
| The following packages will be downloaded: | |
| package | build | |
| ---------------------------|----------------- | |
| fftw-3.3.9 |mpi_openmpi_hb67d103_1 5.4 MB conda-forge | |
| ------------------------------------------------------------ | |
| Total: 5.4 MB | |
| The following NEW packages will be INSTALLED: | |
| fftw conda-forge/osx-64::fftw-3.3.9-mpi_openmpi_hb67d103_1 | |
| Preparing transaction: ...working... done | |
| Verifying transaction: ...working... done | |
| Executing transaction: ...working... done | |
| Installing conda-forge hdf5, h5py | |
| Collecting package metadata (current_repodata.json): ...working... done | |
| Solving environment: ...working... done | |
| ## Package Plan ## | |
| environment location: /usr/local/Caskroom/miniconda/base/envs/dedalus | |
| added / updated specs: | |
| - h5py | |
| - hdf5 | |
| The following packages will be downloaded: | |
| package | build | |
| ---------------------------|----------------- | |
| c-ares-1.17.1 | h0d85af4_1 95 KB conda-forge | |
| cached-property-1.5.2 | hd8ed1ab_1 4 KB conda-forge | |
| cached_property-1.5.2 | pyha770c72_1 11 KB conda-forge | |
| h5py-3.2.1 |nompi_py38h9a16e60_100 1.1 MB conda-forge | |
| hdf5-1.10.6 |nompi_hc5d9132_1114 3.1 MB conda-forge | |
| krb5-1.17.2 | h60d9502_0 1.2 MB conda-forge | |
| libcurl-7.76.1 | h8ef9fac_1 309 KB conda-forge | |
| libedit-3.1.20191231 | h0678c8f_2 103 KB conda-forge | |
| libev-4.33 | haf1e3a3_1 99 KB conda-forge | |
| libnghttp2-1.43.0 | h07e645a_0 837 KB conda-forge | |
| libssh2-1.9.0 | h52ee1ee_6 214 KB conda-forge | |
| ------------------------------------------------------------ | |
| Total: 7.0 MB | |
| The following NEW packages will be INSTALLED: | |
| c-ares conda-forge/osx-64::c-ares-1.17.1-h0d85af4_1 | |
| cached-property conda-forge/noarch::cached-property-1.5.2-hd8ed1ab_1 | |
| cached_property conda-forge/noarch::cached_property-1.5.2-pyha770c72_1 | |
| h5py conda-forge/osx-64::h5py-3.2.1-nompi_py38h9a16e60_100 | |
| hdf5 conda-forge/osx-64::hdf5-1.10.6-nompi_hc5d9132_1114 | |
| krb5 conda-forge/osx-64::krb5-1.17.2-h60d9502_0 | |
| libcurl conda-forge/osx-64::libcurl-7.76.1-h8ef9fac_1 | |
| libedit conda-forge/osx-64::libedit-3.1.20191231-h0678c8f_2 | |
| libev conda-forge/osx-64::libev-4.33-haf1e3a3_1 | |
| libnghttp2 conda-forge/osx-64::libnghttp2-1.43.0-h07e645a_0 | |
| libssh2 conda-forge/osx-64::libssh2-1.9.0-h52ee1ee_6 | |
| Preparing transaction: ...working... done | |
| Verifying transaction: ...working... done | |
| Executing transaction: ...working... done | |
| Installing conda-forge docopt, matplotlib | |
| Collecting package metadata (current_repodata.json): ...working... done | |
| Solving environment: ...working... done | |
| ## Package Plan ## | |
| environment location: /usr/local/Caskroom/miniconda/base/envs/dedalus | |
| added / updated specs: | |
| - docopt | |
| - matplotlib | |
| The following packages will be downloaded: | |
| package | build | |
| ---------------------------|----------------- | |
| cycler-0.10.0 | py_2 9 KB conda-forge | |
| docopt-0.6.2 | py_1 14 KB conda-forge | |
| freetype-2.10.4 | h4cff582_1 890 KB conda-forge | |
| jpeg-9d | hbcb3906_0 250 KB conda-forge | |
| kiwisolver-1.3.1 | py38hd9c93a9_1 57 KB conda-forge | |
| lcms2-2.12 | h577c468_0 404 KB conda-forge | |
| libpng-1.6.37 | h7cec526_2 313 KB conda-forge | |
| libtiff-4.2.0 | h7c11950_1 623 KB conda-forge | |
| libwebp-base-1.2.0 | h0d85af4_2 700 KB conda-forge | |
| lz4-c-1.9.3 | h046ec9c_0 155 KB conda-forge | |
| matplotlib-3.4.2 | py38h50d1736_0 7 KB conda-forge | |
| matplotlib-base-3.4.2 | py38h6152e83_0 7.3 MB conda-forge | |
| olefile-0.46 | pyh9f0ad1d_1 32 KB conda-forge | |
| openjpeg-2.4.0 | h6cbf5cd_0 446 KB conda-forge | |
| pillow-8.1.2 | py38h83525de_1 657 KB conda-forge | |
| pyparsing-2.4.7 | pyh9f0ad1d_0 60 KB conda-forge | |
| python-dateutil-2.8.1 | py_0 220 KB conda-forge | |
| six-1.16.0 | pyh6c4a22f_0 14 KB conda-forge | |
| tornado-6.1 | py38h5406a74_1 643 KB conda-forge | |
| zstd-1.4.9 | h582d3a0_0 460 KB conda-forge | |
| ------------------------------------------------------------ | |
| Total: 13.1 MB | |
| The following NEW packages will be INSTALLED: | |
| cycler conda-forge/noarch::cycler-0.10.0-py_2 | |
| docopt conda-forge/noarch::docopt-0.6.2-py_1 | |
| freetype conda-forge/osx-64::freetype-2.10.4-h4cff582_1 | |
| jpeg conda-forge/osx-64::jpeg-9d-hbcb3906_0 | |
| kiwisolver conda-forge/osx-64::kiwisolver-1.3.1-py38hd9c93a9_1 | |
| lcms2 conda-forge/osx-64::lcms2-2.12-h577c468_0 | |
| libpng conda-forge/osx-64::libpng-1.6.37-h7cec526_2 | |
| libtiff conda-forge/osx-64::libtiff-4.2.0-h7c11950_1 | |
| libwebp-base conda-forge/osx-64::libwebp-base-1.2.0-h0d85af4_2 | |
| lz4-c conda-forge/osx-64::lz4-c-1.9.3-h046ec9c_0 | |
| matplotlib conda-forge/osx-64::matplotlib-3.4.2-py38h50d1736_0 | |
| matplotlib-base conda-forge/osx-64::matplotlib-base-3.4.2-py38h6152e83_0 | |
| olefile conda-forge/noarch::olefile-0.46-pyh9f0ad1d_1 | |
| openjpeg conda-forge/osx-64::openjpeg-2.4.0-h6cbf5cd_0 | |
| pillow conda-forge/osx-64::pillow-8.1.2-py38h83525de_1 | |
| pyparsing conda-forge/noarch::pyparsing-2.4.7-pyh9f0ad1d_0 | |
| python-dateutil conda-forge/noarch::python-dateutil-2.8.1-py_0 | |
| six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0 | |
| tornado conda-forge/osx-64::tornado-6.1-py38h5406a74_1 | |
| zstd conda-forge/osx-64::zstd-1.4.9-h582d3a0_0 | |
| Preparing transaction: ...working... done | |
| Verifying transaction: ...working... done | |
| Executing transaction: ...working... done | |
| Installing dedalus with pip | |
| Collecting dedalus | |
| Downloading dedalus-2.2006.tar.gz (123 kB) | |
| |████████████████████████████████| 123 kB 3.3 MB/s | |
| Preparing wheel metadata ... done | |
| Collecting pytest | |
| Downloading pytest-6.2.4-py3-none-any.whl (280 kB) | |
| |████████████████████████████████| 280 kB 4.2 MB/s | |
| Requirement already satisfied: numpy in /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages (from dedalus) (1.20.2) | |
| Requirement already satisfied: mpi4py>=2.0.0 in /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages (from dedalus) (3.0.3) | |
| Requirement already satisfied: h5py>=2.10.0 in /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages (from dedalus) (3.2.1) | |
| Collecting pytest-cov | |
| Downloading pytest_cov-2.11.1-py2.py3-none-any.whl (20 kB) | |
| Requirement already satisfied: matplotlib in /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages (from dedalus) (3.4.2) | |
| Collecting pytest-benchmark | |
| Downloading pytest_benchmark-3.4.1-py2.py3-none-any.whl (50 kB) | |
| |████████████████████████████████| 50 kB 5.0 MB/s | |
| Requirement already satisfied: docopt in /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages (from dedalus) (0.6.2) | |
| Requirement already satisfied: scipy>=0.13.0 in /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages (from dedalus) (1.6.3) | |
| Requirement already satisfied: python-dateutil>=2.7 in /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages (from matplotlib->dedalus) (2.8.1) | |
| Requirement already satisfied: cycler>=0.10 in /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages (from matplotlib->dedalus) (0.10.0) | |
| Requirement already satisfied: pyparsing>=2.2.1 in /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages (from matplotlib->dedalus) (2.4.7) | |
| Requirement already satisfied: kiwisolver>=1.0.1 in /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages (from matplotlib->dedalus) (1.3.1) | |
| Requirement already satisfied: pillow>=6.2.0 in /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages (from matplotlib->dedalus) (8.1.2) | |
| Requirement already satisfied: six in /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages (from cycler>=0.10->matplotlib->dedalus) (1.16.0) | |
| Collecting pluggy<1.0.0a1,>=0.12 | |
| Downloading pluggy-0.13.1-py2.py3-none-any.whl (18 kB) | |
| Collecting attrs>=19.2.0 | |
| Downloading attrs-21.2.0-py2.py3-none-any.whl (53 kB) | |
| |████████████████████████████████| 53 kB 12.4 MB/s | |
| Collecting packaging | |
| Downloading packaging-20.9-py2.py3-none-any.whl (40 kB) | |
| |████████████████████████████████| 40 kB 10.0 MB/s | |
| Collecting toml | |
| Downloading toml-0.10.2-py2.py3-none-any.whl (16 kB) | |
| Collecting iniconfig | |
| Downloading iniconfig-1.1.1-py2.py3-none-any.whl (5.0 kB) | |
| Collecting py>=1.8.2 | |
| Downloading py-1.10.0-py2.py3-none-any.whl (97 kB) | |
| |████████████████████████████████| 97 kB 10.8 MB/s | |
| Collecting py-cpuinfo | |
| Downloading py-cpuinfo-8.0.0.tar.gz (99 kB) | |
| |████████████████████████████████| 99 kB 9.3 MB/s | |
| Collecting coverage>=5.2.1 | |
| Downloading coverage-5.5-cp38-cp38-macosx_10_9_x86_64.whl (207 kB) | |
| |████████████████████████████████| 207 kB 12.9 MB/s | |
| Building wheels for collected packages: dedalus, py-cpuinfo | |
| Building wheel for dedalus (PEP 517) ... done | |
| Created wheel for dedalus: filename=dedalus-2.2006-cp38-cp38-macosx_10_9_x86_64.whl size=406087 sha256=17a3ab444f2ad8b7897377b9f326bc1ac9b14a130e6cde02da5d33d701773f7f | |
| Stored in directory: /private/var/folders/4d/hcl8czhx38nfdd_h2gm56v700000gn/T/pip-ephem-wheel-cache-clo4rx5m/wheels/2a/41/99/145eb206ab25b66ae61a36c3007b3adfb595349e057aa9dce8 | |
| Building wheel for py-cpuinfo (setup.py) ... done | |
| Created wheel for py-cpuinfo: filename=py_cpuinfo-8.0.0-py3-none-any.whl size=22245 sha256=a0fdeb5e6865eede3578e7ce2091075e49a6bbcf2d8d9f44ffff01c66f0ceb3b | |
| Stored in directory: /private/var/folders/4d/hcl8czhx38nfdd_h2gm56v700000gn/T/pip-ephem-wheel-cache-clo4rx5m/wheels/57/cb/6d/bab2257f26c5be4a96ff65c3d2a7122c96529b73773ee37f36 | |
| Successfully built dedalus py-cpuinfo | |
| Installing collected packages: toml, py, pluggy, packaging, iniconfig, attrs, pytest, py-cpuinfo, coverage, pytest-cov, pytest-benchmark, dedalus | |
| Successfully installed attrs-21.2.0 coverage-5.5 dedalus-2.2006 iniconfig-1.1.1 packaging-20.9 pluggy-0.13.1 py-1.10.0 py-cpuinfo-8.0.0 pytest-6.2.4 pytest-benchmark-3.4.1 pytest-cov-2.11.1 toml-0.10.2 | |
| Installation complete in conda environment 'dedalus' | |
| (base) Davids-MacBook-Pro-4:~ dpsanders$ conda activate dedalus | |
| (dedalus) Davids-MacBook-Pro-4:~ dpsanders$ python3 -m dedalus test | |
| ============================= test session starts ============================== | |
| platform darwin -- Python 3.8.8, pytest-6.2.4, py-1.10.0, pluggy-0.13.1 | |
| benchmark: 3.4.1 (defaults: timer=time.perf_counter disable_gc=False min_rounds=5 min_time=0.000005 max_time=1.0 calibration_precision=10 warmup=False warmup_iterations=100000) | |
| rootdir: /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/tests | |
| plugins: benchmark-3.4.1, cov-2.11.1 | |
| collected 201 items | |
| ../../usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/tests/test_bvp.py . [ 0%] | |
| ...............................FF.......................... [ 29%] | |
| ../../usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/tests/test_evp.py . [ 30%] | |
| ......F.... [ 35%] | |
| ../../usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/tests/test_ivp.py . [ 36%] | |
| ............................................... [ 59%] | |
| ../../usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/tests/test_matsolvers.py s [ 60%] | |
| ..s...ss...s..s...ss...s..s...ss..xs..s...ss...s..s...ss...s..s...ss..x [ 95%] | |
| ../../usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/tests/test_nlbvp.py . [ 96%] | |
| ....... [ 99%] | |
| ../../usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/tests/test_output.py . [100%] | |
| =================================== FAILURES =================================== | |
| ___________________ test_gaussian_free[Hermite-128-float64] ____________________ | |
| benchmark = None, x_basis_class = <class 'dedalus.core.basis.Hermite'>, Nx = 128 | |
| dtype = <class 'numpy.float64'> | |
| @pytest.mark.parametrize('dtype', [np.float64, np.complex128]) | |
| @pytest.mark.parametrize('Nx', [128]) | |
| @pytest.mark.parametrize('x_basis_class', [de.Hermite, DoubleLaguerre, LCCL]) | |
| @bench_wrapper | |
| def test_gaussian_free(benchmark, x_basis_class, Nx, dtype): | |
| # Stretch Laguerres | |
| if x_basis_class is de.Hermite: | |
| stretch = 1.0 | |
| else: | |
| stretch = 0.1 | |
| # Bases and domain | |
| x_basis = x_basis_class('x', Nx, center=0, stretch=stretch) | |
| domain = de.Domain([x_basis], grid_dtype=dtype) | |
| # Problem | |
| problem = de.LBVP(domain, variables=['u']) | |
| problem.parameters['pi'] = np.pi | |
| problem.add_equation("dx(u) + 2*x*u = 0", tau=True) | |
| problem.add_bc("integ(u) = sqrt(pi)") | |
| # Solver | |
| > solver = problem.build_solver() | |
| /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/tests/test_bvp.py:180: | |
| _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ | |
| /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/core/problems.py:313: in build_solver | |
| return self.solver_class(self, *args, **kw) | |
| /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/core/solvers.py:191: in __init__ | |
| pencil.build_matrices(self.pencils, problem, ['L']) | |
| /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/core/pencil.py:62: in build_matrices | |
| expr.operator_dict(test_index, vars, cacheid=cacheid, **problem.ncc_kw) | |
| /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/core/operators.py:440: in operator_dict | |
| op1 = self.args[1].operator_dict(index, vars, **kw) | |
| /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/core/operators.py:719: in operator_dict | |
| op0 = self.args[0].as_ncc_operator(frozen_arg1_basis_meta, **kw) | |
| /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/tools/cache.py:71: in __call__ | |
| self.cache[call] = result = self.function(*args, **kw) | |
| /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/core/future.py:208: in as_ncc_operator | |
| return ncc.as_ncc_operator(frozen_arg_basis_meta, cutoff, max_terms, cacheid=None) | |
| /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/tools/cache.py:71: in __call__ | |
| self.cache[call] = result = self.function(*args, **kw) | |
| /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/core/field.py:289: in as_ncc_operator | |
| return ncc.as_ncc_operator(frozen_arg_basis_meta, cutoff, max_terms, cacheid=None) | |
| /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/tools/cache.py:71: in __call__ | |
| self.cache[call] = result = self.function(*args, **kw) | |
| /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/core/field.py:556: in as_ncc_operator | |
| self.require_coeff_space() | |
| /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/core/field.py:440: in require_coeff_space | |
| self.towards_coeff_space() | |
| /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/core/field.py:423: in towards_coeff_space | |
| self.domain.dist.paths[index-1].decrement([self]) | |
| /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/core/distributor.py:372: in decrement | |
| self.decrement_single(*fields) | |
| /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/core/distributor.py:357: in decrement_single | |
| self.basis.forward(gdata, cdata, self.axis, field.meta[self.axis], field.scales[self.axis]) | |
| /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/core/basis.py:1090: in _forward_mmt | |
| forward_mat, _ = self._mmt_setup(gdata.shape[axis], cdata.shape[axis], meta['envelope']) | |
| /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/tools/cache.py:71: in __call__ | |
| self.cache[call] = result = self.function(*args, **kw) | |
| /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/core/basis.py:1081: in _mmt_setup | |
| N2 = np.sqrt(np.pi) * 2**n * special.factorial(n, exact=True) | |
| _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ | |
| n = array([[ 0.], | |
| [ 1.], | |
| [ 2.], | |
| [ 3.], | |
| [ 4.], | |
| [ 5.], | |
| [ 6.], | |
| [ 7.]... [121.], | |
| [122.], | |
| [123.], | |
| [124.], | |
| [125.], | |
| [126.], | |
| [127.]], dtype=float128) | |
| exact = True | |
| def factorial(n, exact=False): | |
| """ | |
| The factorial of a number or array of numbers. | |
| The factorial of non-negative integer `n` is the product of all | |
| positive integers less than or equal to `n`:: | |
| n! = n * (n - 1) * (n - 2) * ... * 1 | |
| Parameters | |
| ---------- | |
| n : int or array_like of ints | |
| Input values. If ``n < 0``, the return value is 0. | |
| exact : bool, optional | |
| If True, calculate the answer exactly using long integer arithmetic. | |
| If False, result is approximated in floating point rapidly using the | |
| `gamma` function. | |
| Default is False. | |
| Returns | |
| ------- | |
| nf : float or int or ndarray | |
| Factorial of `n`, as integer or float depending on `exact`. | |
| Notes | |
| ----- | |
| For arrays with ``exact=True``, the factorial is computed only once, for | |
| the largest input, with each other result computed in the process. | |
| The output dtype is increased to ``int64`` or ``object`` if necessary. | |
| With ``exact=False`` the factorial is approximated using the gamma | |
| function: | |
| .. math:: n! = \\Gamma(n+1) | |
| Examples | |
| -------- | |
| >>> from scipy.special import factorial | |
| >>> arr = np.array([3, 4, 5]) | |
| >>> factorial(arr, exact=False) | |
| array([ 6., 24., 120.]) | |
| >>> factorial(arr, exact=True) | |
| array([ 6, 24, 120]) | |
| >>> factorial(5, exact=True) | |
| 120 | |
| """ | |
| if exact: | |
| if np.ndim(n) == 0: | |
| if np.isnan(n): | |
| return n | |
| return 0 if n < 0 else math.factorial(n) | |
| else: | |
| n = asarray(n) | |
| un = np.unique(n).astype(object) | |
| # Convert to object array of long ints if np.int_ can't handle size | |
| if np.isnan(n).any(): | |
| dt = float | |
| elif un[-1] > 20: | |
| dt = object | |
| elif un[-1] > 12: | |
| dt = np.int64 | |
| else: | |
| dt = np.int_ | |
| out = np.empty_like(n, dtype=dt) | |
| # Handle invalid/trivial values | |
| # Ignore runtime warning when less operator used w/np.nan | |
| with np.errstate(all='ignore'): | |
| un = un[un > 1] | |
| out[n < 2] = 1 | |
| out[n < 0] = 0 | |
| # Calculate products of each range of numbers | |
| if un.size: | |
| > val = math.factorial(un[0]) | |
| E TypeError: 'numpy.float128' object cannot be interpreted as an integer | |
| /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/scipy/special/_basic.py:2352: TypeError | |
| ------------------------------ Captured log call ------------------------------- | |
| DEBUG domain:domain.py:55 Global coeff shape: [128] | |
| DEBUG distributor:distributor.py:92 Mesh: [] | |
| DEBUG problems:problems.py:127 Parsing Eqn 0 | |
| DEBUG problems:problems.py:146 Condition: True | |
| DEBUG problems:problems.py:147 LHS string form: dx(u) + 2*x*u | |
| DEBUG problems:problems.py:148 RHS string form: 0 | |
| DEBUG problems:problems.py:155 LHS object form: dx(u) + ((2*x)*u) | |
| DEBUG problems:problems.py:156 RHS object form: 0 | |
| DEBUG problems:problems.py:308 L linear form: dx(u) + ((2*x)*u) | |
| DEBUG problems:problems.py:127 Parsing Eqn 1 | |
| DEBUG problems:problems.py:146 Condition: True | |
| DEBUG problems:problems.py:147 LHS string form: integ(u) | |
| DEBUG problems:problems.py:148 RHS string form: sqrt(pi) | |
| DEBUG problems:problems.py:155 LHS object form: integ_x(u) | |
| DEBUG problems:problems.py:156 RHS object form: sqrt(pi) | |
| DEBUG problems:problems.py:308 L linear form: integ_x(u) | |
| DEBUG solvers:solvers.py:180 Beginning LBVP instantiation | |
| DEBUG basis:basis.py:1064 Building Hermite MMT matrices for (gsize, csize, env) = (128, 128, False) | |
| __________________ test_gaussian_free[Hermite-128-complex128] __________________ | |
| benchmark = None, x_basis_class = <class 'dedalus.core.basis.Hermite'>, Nx = 128 | |
| dtype = <class 'numpy.complex128'> | |
| @pytest.mark.parametrize('dtype', [np.float64, np.complex128]) | |
| @pytest.mark.parametrize('Nx', [128]) | |
| @pytest.mark.parametrize('x_basis_class', [de.Hermite, DoubleLaguerre, LCCL]) | |
| @bench_wrapper | |
| def test_gaussian_free(benchmark, x_basis_class, Nx, dtype): | |
| # Stretch Laguerres | |
| if x_basis_class is de.Hermite: | |
| stretch = 1.0 | |
| else: | |
| stretch = 0.1 | |
| # Bases and domain | |
| x_basis = x_basis_class('x', Nx, center=0, stretch=stretch) | |
| domain = de.Domain([x_basis], grid_dtype=dtype) | |
| # Problem | |
| problem = de.LBVP(domain, variables=['u']) | |
| problem.parameters['pi'] = np.pi | |
| problem.add_equation("dx(u) + 2*x*u = 0", tau=True) | |
| problem.add_bc("integ(u) = sqrt(pi)") | |
| # Solver | |
| > solver = problem.build_solver() | |
| /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/tests/test_bvp.py:180: | |
| _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ | |
| /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/core/problems.py:313: in build_solver | |
| return self.solver_class(self, *args, **kw) | |
| /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/core/solvers.py:191: in __init__ | |
| pencil.build_matrices(self.pencils, problem, ['L']) | |
| /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/core/pencil.py:62: in build_matrices | |
| expr.operator_dict(test_index, vars, cacheid=cacheid, **problem.ncc_kw) | |
| /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/core/operators.py:440: in operator_dict | |
| op1 = self.args[1].operator_dict(index, vars, **kw) | |
| /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/core/operators.py:719: in operator_dict | |
| op0 = self.args[0].as_ncc_operator(frozen_arg1_basis_meta, **kw) | |
| /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/tools/cache.py:71: in __call__ | |
| self.cache[call] = result = self.function(*args, **kw) | |
| /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/core/future.py:208: in as_ncc_operator | |
| return ncc.as_ncc_operator(frozen_arg_basis_meta, cutoff, max_terms, cacheid=None) | |
| /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/tools/cache.py:71: in __call__ | |
| self.cache[call] = result = self.function(*args, **kw) | |
| /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/core/field.py:289: in as_ncc_operator | |
| return ncc.as_ncc_operator(frozen_arg_basis_meta, cutoff, max_terms, cacheid=None) | |
| /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/tools/cache.py:71: in __call__ | |
| self.cache[call] = result = self.function(*args, **kw) | |
| /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/core/field.py:556: in as_ncc_operator | |
| self.require_coeff_space() | |
| /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/core/field.py:440: in require_coeff_space | |
| self.towards_coeff_space() | |
| /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/core/field.py:423: in towards_coeff_space | |
| self.domain.dist.paths[index-1].decrement([self]) | |
| /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/core/distributor.py:372: in decrement | |
| self.decrement_single(*fields) | |
| /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/core/distributor.py:357: in decrement_single | |
| self.basis.forward(gdata, cdata, self.axis, field.meta[self.axis], field.scales[self.axis]) | |
| /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/core/basis.py:1090: in _forward_mmt | |
| forward_mat, _ = self._mmt_setup(gdata.shape[axis], cdata.shape[axis], meta['envelope']) | |
| /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/tools/cache.py:71: in __call__ | |
| self.cache[call] = result = self.function(*args, **kw) | |
| /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/core/basis.py:1081: in _mmt_setup | |
| N2 = np.sqrt(np.pi) * 2**n * special.factorial(n, exact=True) | |
| _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ | |
| n = array([[ 0.], | |
| [ 1.], | |
| [ 2.], | |
| [ 3.], | |
| [ 4.], | |
| [ 5.], | |
| [ 6.], | |
| [ 7.]... [121.], | |
| [122.], | |
| [123.], | |
| [124.], | |
| [125.], | |
| [126.], | |
| [127.]], dtype=float128) | |
| exact = True | |
| def factorial(n, exact=False): | |
| """ | |
| The factorial of a number or array of numbers. | |
| The factorial of non-negative integer `n` is the product of all | |
| positive integers less than or equal to `n`:: | |
| n! = n * (n - 1) * (n - 2) * ... * 1 | |
| Parameters | |
| ---------- | |
| n : int or array_like of ints | |
| Input values. If ``n < 0``, the return value is 0. | |
| exact : bool, optional | |
| If True, calculate the answer exactly using long integer arithmetic. | |
| If False, result is approximated in floating point rapidly using the | |
| `gamma` function. | |
| Default is False. | |
| Returns | |
| ------- | |
| nf : float or int or ndarray | |
| Factorial of `n`, as integer or float depending on `exact`. | |
| Notes | |
| ----- | |
| For arrays with ``exact=True``, the factorial is computed only once, for | |
| the largest input, with each other result computed in the process. | |
| The output dtype is increased to ``int64`` or ``object`` if necessary. | |
| With ``exact=False`` the factorial is approximated using the gamma | |
| function: | |
| .. math:: n! = \\Gamma(n+1) | |
| Examples | |
| -------- | |
| >>> from scipy.special import factorial | |
| >>> arr = np.array([3, 4, 5]) | |
| >>> factorial(arr, exact=False) | |
| array([ 6., 24., 120.]) | |
| >>> factorial(arr, exact=True) | |
| array([ 6, 24, 120]) | |
| >>> factorial(5, exact=True) | |
| 120 | |
| """ | |
| if exact: | |
| if np.ndim(n) == 0: | |
| if np.isnan(n): | |
| return n | |
| return 0 if n < 0 else math.factorial(n) | |
| else: | |
| n = asarray(n) | |
| un = np.unique(n).astype(object) | |
| # Convert to object array of long ints if np.int_ can't handle size | |
| if np.isnan(n).any(): | |
| dt = float | |
| elif un[-1] > 20: | |
| dt = object | |
| elif un[-1] > 12: | |
| dt = np.int64 | |
| else: | |
| dt = np.int_ | |
| out = np.empty_like(n, dtype=dt) | |
| # Handle invalid/trivial values | |
| # Ignore runtime warning when less operator used w/np.nan | |
| with np.errstate(all='ignore'): | |
| un = un[un > 1] | |
| out[n < 2] = 1 | |
| out[n < 0] = 0 | |
| # Calculate products of each range of numbers | |
| if un.size: | |
| > val = math.factorial(un[0]) | |
| E TypeError: 'numpy.float128' object cannot be interpreted as an integer | |
| /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/scipy/special/_basic.py:2352: TypeError | |
| ------------------------------ Captured log call ------------------------------- | |
| DEBUG domain:domain.py:55 Global coeff shape: [128] | |
| DEBUG distributor:distributor.py:92 Mesh: [] | |
| DEBUG problems:problems.py:127 Parsing Eqn 0 | |
| DEBUG problems:problems.py:146 Condition: True | |
| DEBUG problems:problems.py:147 LHS string form: dx(u) + 2*x*u | |
| DEBUG problems:problems.py:148 RHS string form: 0 | |
| DEBUG problems:problems.py:155 LHS object form: dx(u) + ((2*x)*u) | |
| DEBUG problems:problems.py:156 RHS object form: 0 | |
| DEBUG problems:problems.py:308 L linear form: dx(u) + ((2*x)*u) | |
| DEBUG problems:problems.py:127 Parsing Eqn 1 | |
| DEBUG problems:problems.py:146 Condition: True | |
| DEBUG problems:problems.py:147 LHS string form: integ(u) | |
| DEBUG problems:problems.py:148 RHS string form: sqrt(pi) | |
| DEBUG problems:problems.py:155 LHS object form: integ_x(u) | |
| DEBUG problems:problems.py:156 RHS object form: sqrt(pi) | |
| DEBUG problems:problems.py:308 L linear form: integ_x(u) | |
| DEBUG solvers:solvers.py:180 Beginning LBVP instantiation | |
| DEBUG basis:basis.py:1064 Building Hermite MMT matrices for (gsize, csize, env) = (128, 128, False) | |
| __________________ test_qho_dense_evp[Hermite-128-complex128] __________________ | |
| benchmark = None, x_basis_class = <class 'dedalus.core.basis.Hermite'>, Nx = 128 | |
| dtype = <class 'numpy.complex128'> | |
| @pytest.mark.parametrize('dtype', [np.complex128]) | |
| @pytest.mark.parametrize('Nx', [128]) | |
| @pytest.mark.parametrize('x_basis_class', [de.Hermite]) | |
| @bench_wrapper | |
| def test_qho_dense_evp(benchmark, x_basis_class, Nx, dtype): | |
| n_comp = 10 | |
| # Stretch Laguerres | |
| if x_basis_class is de.Hermite: | |
| stretch = 1.0 | |
| else: | |
| stretch = 0.4 | |
| # Domain | |
| x_basis = x_basis_class('x', Nx, center=0, stretch=stretch) | |
| domain = de.Domain([x_basis], np.float64) | |
| # Problem | |
| problem = de.EVP(domain, variables=['ψ', 'ψx'], eigenvalue='E') | |
| problem.substitutions["V"] = "x**2 / 2" | |
| problem.substitutions["H(ψ,ψx)"] = "-dx(ψx)/2 + V*ψ" | |
| problem.add_equation("ψx - dx(ψ) = 0", tau=False) | |
| problem.add_equation("H(ψ,ψx) - E*ψ = 0", tau=False) | |
| # Solver | |
| solver = problem.build_solver() | |
| > solver.solve_dense(solver.pencils[0]) | |
| /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/tests/test_evp.py:128: | |
| _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ | |
| /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/core/solvers.py:95: in solve_dense | |
| pencil.build_matrices(self.problem, ['M', 'L'], cacheid=cacheid) | |
| /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/core/pencil.py:259: in _build_coupled_matrices | |
| Ei = eq_expr.operator_dict(global_index, eq_vars, cacheid=cacheid, **problem.ncc_kw) | |
| /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/core/operators.py:440: in operator_dict | |
| op1 = self.args[1].operator_dict(index, vars, **kw) | |
| /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/core/operators.py:719: in operator_dict | |
| op0 = self.args[0].as_ncc_operator(frozen_arg1_basis_meta, **kw) | |
| /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/tools/cache.py:71: in __call__ | |
| self.cache[call] = result = self.function(*args, **kw) | |
| /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/core/future.py:208: in as_ncc_operator | |
| return ncc.as_ncc_operator(frozen_arg_basis_meta, cutoff, max_terms, cacheid=None) | |
| /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/tools/cache.py:71: in __call__ | |
| self.cache[call] = result = self.function(*args, **kw) | |
| /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/core/field.py:289: in as_ncc_operator | |
| return ncc.as_ncc_operator(frozen_arg_basis_meta, cutoff, max_terms, cacheid=None) | |
| /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/tools/cache.py:71: in __call__ | |
| self.cache[call] = result = self.function(*args, **kw) | |
| /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/core/field.py:556: in as_ncc_operator | |
| self.require_coeff_space() | |
| /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/core/field.py:440: in require_coeff_space | |
| self.towards_coeff_space() | |
| /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/core/field.py:423: in towards_coeff_space | |
| self.domain.dist.paths[index-1].decrement([self]) | |
| /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/core/distributor.py:372: in decrement | |
| self.decrement_single(*fields) | |
| /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/core/distributor.py:357: in decrement_single | |
| self.basis.forward(gdata, cdata, self.axis, field.meta[self.axis], field.scales[self.axis]) | |
| /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/core/basis.py:1090: in _forward_mmt | |
| forward_mat, _ = self._mmt_setup(gdata.shape[axis], cdata.shape[axis], meta['envelope']) | |
| /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/tools/cache.py:71: in __call__ | |
| self.cache[call] = result = self.function(*args, **kw) | |
| /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/core/basis.py:1081: in _mmt_setup | |
| N2 = np.sqrt(np.pi) * 2**n * special.factorial(n, exact=True) | |
| _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ | |
| n = array([[ 0.], | |
| [ 1.], | |
| [ 2.], | |
| [ 3.], | |
| [ 4.], | |
| [ 5.], | |
| [ 6.], | |
| [ 7.]... [121.], | |
| [122.], | |
| [123.], | |
| [124.], | |
| [125.], | |
| [126.], | |
| [127.]], dtype=float128) | |
| exact = True | |
| def factorial(n, exact=False): | |
| """ | |
| The factorial of a number or array of numbers. | |
| The factorial of non-negative integer `n` is the product of all | |
| positive integers less than or equal to `n`:: | |
| n! = n * (n - 1) * (n - 2) * ... * 1 | |
| Parameters | |
| ---------- | |
| n : int or array_like of ints | |
| Input values. If ``n < 0``, the return value is 0. | |
| exact : bool, optional | |
| If True, calculate the answer exactly using long integer arithmetic. | |
| If False, result is approximated in floating point rapidly using the | |
| `gamma` function. | |
| Default is False. | |
| Returns | |
| ------- | |
| nf : float or int or ndarray | |
| Factorial of `n`, as integer or float depending on `exact`. | |
| Notes | |
| ----- | |
| For arrays with ``exact=True``, the factorial is computed only once, for | |
| the largest input, with each other result computed in the process. | |
| The output dtype is increased to ``int64`` or ``object`` if necessary. | |
| With ``exact=False`` the factorial is approximated using the gamma | |
| function: | |
| .. math:: n! = \\Gamma(n+1) | |
| Examples | |
| -------- | |
| >>> from scipy.special import factorial | |
| >>> arr = np.array([3, 4, 5]) | |
| >>> factorial(arr, exact=False) | |
| array([ 6., 24., 120.]) | |
| >>> factorial(arr, exact=True) | |
| array([ 6, 24, 120]) | |
| >>> factorial(5, exact=True) | |
| 120 | |
| """ | |
| if exact: | |
| if np.ndim(n) == 0: | |
| if np.isnan(n): | |
| return n | |
| return 0 if n < 0 else math.factorial(n) | |
| else: | |
| n = asarray(n) | |
| un = np.unique(n).astype(object) | |
| # Convert to object array of long ints if np.int_ can't handle size | |
| if np.isnan(n).any(): | |
| dt = float | |
| elif un[-1] > 20: | |
| dt = object | |
| elif un[-1] > 12: | |
| dt = np.int64 | |
| else: | |
| dt = np.int_ | |
| out = np.empty_like(n, dtype=dt) | |
| # Handle invalid/trivial values | |
| # Ignore runtime warning when less operator used w/np.nan | |
| with np.errstate(all='ignore'): | |
| un = un[un > 1] | |
| out[n < 2] = 1 | |
| out[n < 0] = 0 | |
| # Calculate products of each range of numbers | |
| if un.size: | |
| > val = math.factorial(un[0]) | |
| E TypeError: 'numpy.float128' object cannot be interpreted as an integer | |
| /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/scipy/special/_basic.py:2352: TypeError | |
| ----------------------------- Captured stdout call ----------------------------- | |
| 2021-05-09 21:46:33,367 problems 0/1 INFO :: Solving EVP with homogeneity tolerance of 1.000e-10 | |
| ------------------------------ Captured log call ------------------------------- | |
| DEBUG domain:domain.py:55 Global coeff shape: [128] | |
| DEBUG distributor:distributor.py:92 Mesh: [] | |
| INFO problems:problems.py:523 Solving EVP with homogeneity tolerance of 1.000e-10 | |
| DEBUG problems:problems.py:127 Parsing Eqn 0 | |
| DEBUG problems:problems.py:146 Condition: True | |
| DEBUG problems:problems.py:147 LHS string form: ψx - dx(ψ) | |
| DEBUG problems:problems.py:148 RHS string form: 0 | |
| DEBUG problems:problems.py:155 LHS object form: ψx + (-1*dx(ψ)) | |
| DEBUG problems:problems.py:156 RHS object form: 0 | |
| DEBUG problems:problems.py:308 M linear form: 0 | |
| DEBUG problems:problems.py:308 L linear form: ψx + (-1*dx(ψ)) | |
| DEBUG problems:problems.py:127 Parsing Eqn 1 | |
| DEBUG problems:problems.py:146 Condition: True | |
| DEBUG problems:problems.py:147 LHS string form: H(ψ,ψx) - E*ψ | |
| DEBUG problems:problems.py:148 RHS string form: 0 | |
| DEBUG problems:problems.py:155 LHS object form: (((-1*dx(ψx))*0.5) + (((x**2)*0.5)*ψ)) + (-1*(E*ψ)) | |
| DEBUG problems:problems.py:156 RHS object form: 0 | |
| DEBUG problems:problems.py:308 M linear form: -1*ψ | |
| DEBUG problems:problems.py:308 L linear form: (-0.5*dx(ψx)) + (((x**2)*0.5)*ψ) | |
| DEBUG solvers:solvers.py:58 Beginning EVP instantiation | |
| DEBUG solvers:solvers.py:73 Finished EVP instantiation | |
| DEBUG basis:basis.py:1064 Building Hermite MMT matrices for (gsize, csize, env) = (128, 128, False) | |
| =============================== warnings summary =============================== | |
| test_output.py::test_1d_output[Chebyshev-32-RK222-float64] | |
| /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/core/evaluator.py:496: DeprecationWarning: `np.int` is a deprecated alias for the builtin `int`. To silence this warning, use `int` by itself. Doing this will not modify any behavior and is safe. When replacing `np.int`, you may wish to use e.g. `np.int64` or `np.int32` to specify the precision. If you wish to review your current use, check the release note link for additional information. | |
| Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations | |
| ('iteration', np.int), | |
| test_output.py::test_1d_output[Chebyshev-32-RK222-float64] | |
| /usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/core/evaluator.py:497: DeprecationWarning: `np.int` is a deprecated alias for the builtin `int`. To silence this warning, use `int` by itself. Doing this will not modify any behavior and is safe. When replacing `np.int`, you may wish to use e.g. `np.int64` or `np.int32` to specify the precision. If you wish to review your current use, check the release note link for additional information. | |
| Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations | |
| ('write_number', np.int)]: | |
| -- Docs: https://docs.pytest.org/en/stable/warnings.html | |
| =========================== short test summary info ============================ | |
| FAILED ../../usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/tests/test_bvp.py::test_gaussian_free[Hermite-128-float64] | |
| FAILED ../../usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/tests/test_bvp.py::test_gaussian_free[Hermite-128-complex128] | |
| FAILED ../../usr/local/Caskroom/miniconda/base/envs/dedalus/lib/python3.8/site-packages/dedalus/tests/test_evp.py::test_qho_dense_evp[Hermite-128-complex128] | |
| ====== 3 failed, 172 passed, 24 skipped, 2 xfailed, 2 warnings in 11.68s ======= | |
| (dedalus) Davids-MacBook-Pro-4:~ dpsanders$ | |
| (dedalus) Davids-MacBook-Pro-4:~ dpsanders$ |
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