Error with conda dedalus installation

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Simon Lance

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Jul 10, 2019, 5:14:23 AM7/10/19

to Dedalus Users

Hi all,

I'm attempting to install dedalus using the new conda installation method on my MacBook, however when running the install_conda.sh script the installation breaks down with some gcc errors resulting in the following errors:

gcc: error: unrecognized command line option ‘-Wl’; did you mean ‘-W’?

gcc: error: unrecognized command line option ‘-rpath’

error: command 'gcc' failed with exit status 1

----------------------------------------

ERROR: Failed building wheel for dedalus

Running setup.py clean for dedalus

Failed to build dedalus

ERROR: Could not build wheels for dedalus which use PEP 517 and cannot be installed directly

Installation complete in conda environment 'dedalus'

I couldn't see an installation log for the conda installation to upload for you so I've just copied the complete terminal output since initially running the install_conda.sh script to the end of the his post.

Thanks in advance for any guidance you can provide.

Kind regards,

Simon Lance

(base) pebblesastro:~ slance$ bash install_conda.sh

Setting up conda with 'source /Users/slance/anaconda3/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'

WARNING: The conda.compat module is deprecated and will be removed in a future release.

Collecting package metadata: ...working... done

Solving environment: ...working... done

## Package Plan ##

environment location: /Users/slance/anaconda3/envs/dedalus

added / updated specs:

- python=3.7

The following packages will be downloaded:

package | build

---------------------------|-----------------

python-3.7.3 | h93065d6_1 20.8 MB conda-forge

readline-8.0 | hcfe32e1_0 415 KB conda-forge

sqlite-3.28.0 | hb7d70f7_1 2.4 MB conda-forge

------------------------------------------------------------

Total: 23.6 MB

The following NEW packages will be INSTALLED:

bzip2 conda-forge/osx-64::bzip2-1.0.6-h1de35cc_1002

ca-certificates conda-forge/osx-64::ca-certificates-2019.6.16-hecc5488_0

certifi conda-forge/osx-64::certifi-2019.6.16-py37_0

libcxx conda-forge/osx-64::libcxx-8.0.0-4

libcxxabi conda-forge/osx-64::libcxxabi-8.0.0-4

libffi conda-forge/osx-64::libffi-3.2.1-h6de7cb9_1006

ncurses conda-forge/osx-64::ncurses-6.1-h0a44026_1002

openssl conda-forge/osx-64::openssl-1.1.1b-h01d97ff_2

pip conda-forge/osx-64::pip-19.1.1-py37_0

python conda-forge/osx-64::python-3.7.3-h93065d6_1

readline conda-forge/osx-64::readline-8.0-hcfe32e1_0

setuptools conda-forge/osx-64::setuptools-41.0.1-py37_0

sqlite conda-forge/osx-64::sqlite-3.28.0-hb7d70f7_1

tk conda-forge/osx-64::tk-8.6.9-h2573ce8_1002

wheel conda-forge/osx-64::wheel-0.33.4-py37_0

xz conda-forge/osx-64::xz-5.2.4-h1de35cc_1001

zlib conda-forge/osx-64::zlib-1.2.11-h1de35cc_1004

Preparing transaction: ...working... done

Verifying transaction: ...working... done

Executing transaction: ...working... done

Updating conda-forge pip, setuptools, cython

WARNING: The conda.compat module is deprecated and will be removed in a future release.

Collecting package metadata: ...working... done

Solving environment: ...working... done

## Package Plan ##

environment location: /Users/slance/anaconda3/envs/dedalus

added / updated specs:

- cython

- pip

- setuptools

The following packages will be downloaded:

package | build

---------------------------|-----------------

cython-0.29.12 | py37h6de7cb9_0 2.0 MB conda-forge

------------------------------------------------------------

Total: 2.0 MB

The following NEW packages will be INSTALLED:

cython conda-forge/osx-64::cython-0.29.12-py37h6de7cb9_0

Preparing transaction: ...working... done

Verifying transaction: ...working... done

Executing transaction: ...working... done

Installing conda-forge openblas, numpy, scipy

WARNING: The conda.compat module is deprecated and will be removed in a future release.

Collecting package metadata: ...working... done

Solving environment: ...working... done

## Package Plan ##

environment location: /Users/slance/anaconda3/envs/dedalus

added / updated specs:

- numpy[build=*openblas*]

- scipy[build=*openblas*]

The following NEW packages will be INSTALLED:

blas conda-forge/osx-64::blas-1.1-openblas

libgfortran conda-forge/osx-64::libgfortran-3.0.1-0

numpy conda-forge/osx-64::numpy-1.16.2-py37_blas_openblash486cb9f_0

openblas conda-forge/osx-64::openblas-0.3.3-hdc02c5d_1001

scipy conda-forge/osx-64::scipy-1.2.1-py37_blas_openblash486cb9f_0

Preparing transaction: ...working... done

Verifying transaction: ...working... done

Executing transaction: ...working... done

Installing conda-forge openmpi, mpi4py

WARNING: The conda.compat module is deprecated and will be removed in a future release.

Collecting package metadata: ...working... done

Solving environment: ...working... done

## Package Plan ##

environment location: /Users/slance/anaconda3/envs/dedalus

added / updated specs:

- mpi4py

- openmpi==3.1.0

The following NEW packages will be INSTALLED:

mpi conda-forge/osx-64::mpi-1.0-openmpi

mpi4py conda-forge/osx-64::mpi4py-3.0.1-py37h27a7d74_0

openmpi conda-forge/osx-64::openmpi-3.1.0-h26a2512_3

Preparing transaction: ...working... done

Verifying transaction: ...working... done

Executing transaction: ...working... done

Installing cryoem fftw-mpi

WARNING: The conda.compat module is deprecated and will be removed in a future release.

Collecting package metadata: ...working... done

Solving environment: ...working... done

## Package Plan ##

environment location: /Users/slance/anaconda3/envs/dedalus

added / updated specs:

- fftw-mpi

The following NEW packages will be INSTALLED:

fftw-mpi cryoem/osx-64::fftw-mpi-3.3.6-2

Preparing transaction: ...working... done

Verifying transaction: ...working... done

Executing transaction: ...working... done

Installing conda-forge hdf5, h5py

WARNING: The conda.compat module is deprecated and will be removed in a future release.

Collecting package metadata: ...working... done

Solving environment: ...working... done

## Package Plan ##

environment location: /Users/slance/anaconda3/envs/dedalus

added / updated specs:

- h5py

- hdf5

The following NEW packages will be INSTALLED:

h5py conda-forge/osx-64::h5py-2.9.0-nompi_py37h35dc34b_1102

hdf5 conda-forge/osx-64::hdf5-1.10.4-nompi_h0cbb7df_1106

six conda-forge/osx-64::six-1.12.0-py37_1000

Preparing transaction: ...working... done

Verifying transaction: ...working... done

Executing transaction: ...working... done

Installing conda-forge docopt, matplotlib

WARNING: The conda.compat module is deprecated and will be removed in a future release.

Collecting package metadata: ...working... done

Solving environment: ...working... done

## Package Plan ##

environment location: /Users/slance/anaconda3/envs/dedalus

added / updated specs:

- docopt

- matplotlib

The following NEW packages will be INSTALLED:

cycler conda-forge/noarch::cycler-0.10.0-py_1

docopt conda-forge/noarch::docopt-0.6.2-py_1

freetype conda-forge/osx-64::freetype-2.10.0-h24853df_0

kiwisolver conda-forge/osx-64::kiwisolver-1.1.0-py37h770b8ee_0

libpng conda-forge/osx-64::libpng-1.6.37-h2573ce8_0

matplotlib conda-forge/osx-64::matplotlib-3.1.1-py37_0

matplotlib-base conda-forge/osx-64::matplotlib-base-3.1.1-py37h3a684a6_0

pyparsing conda-forge/noarch::pyparsing-2.4.0-py_0

python-dateutil conda-forge/noarch::python-dateutil-2.8.0-py_0

tornado conda-forge/osx-64::tornado-6.0.3-py37h01d97ff_0

Preparing transaction: ...working... done

Verifying transaction: ...working... done

Executing transaction: ...working... done

Installing dedalus with pip

Collecting dedalus

Downloading https://files.pythonhosted.org/packages/ba/bc/fdd40d0bbab4c5d6e98f71e33b52022894daf6b702086c287e98e115419c/dedalus-2.1810.tar.gz (95kB)

|████████████████████████████████| 102kB 3.9MB/s

Installing build dependencies ... done

WARNING: Missing build requirements in pyproject.toml for dedalus from https://files.pythonhosted.org/packages/ba/bc/fdd40d0bbab4c5d6e98f71e33b52022894daf6b702086c287e98e115419c/dedalus-2.1810.tar.gz#sha256=ec8f4694f8b01e879a82707540149a0b4bf96e41e5b3083e408fcfb54742fcbc.

WARNING: The project does not specify a build backend, and pip cannot fall back to setuptools without 'wheel'.

Getting requirements to build wheel ... done

Installing backend dependencies ... done

Preparing wheel metadata ... done

Requirement already satisfied: docopt in ./anaconda3/envs/dedalus/lib/python3.7/site-packages (from dedalus) (0.6.2)

Requirement already satisfied: scipy>=0.13.0 in ./anaconda3/envs/dedalus/lib/python3.7/site-packages (from dedalus) (1.2.1)

Requirement already satisfied: numpy in ./anaconda3/envs/dedalus/lib/python3.7/site-packages (from dedalus) (1.16.2)

Requirement already satisfied: mpi4py>=2.0.0 in ./anaconda3/envs/dedalus/lib/python3.7/site-packages (from dedalus) (3.0.1)

Requirement already satisfied: matplotlib in ./anaconda3/envs/dedalus/lib/python3.7/site-packages (from dedalus) (3.1.1)

Requirement already satisfied: h5py>=2.6.0 in ./anaconda3/envs/dedalus/lib/python3.7/site-packages (from dedalus) (2.9.0)

Requirement already satisfied: cycler>=0.10 in ./anaconda3/envs/dedalus/lib/python3.7/site-packages (from matplotlib->dedalus) (0.10.0)

Requirement already satisfied: kiwisolver>=1.0.1 in ./anaconda3/envs/dedalus/lib/python3.7/site-packages (from matplotlib->dedalus) (1.1.0)

Requirement already satisfied: python-dateutil>=2.1 in ./anaconda3/envs/dedalus/lib/python3.7/site-packages (from matplotlib->dedalus) (2.8.0)

Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in ./anaconda3/envs/dedalus/lib/python3.7/site-packages (from matplotlib->dedalus) (2.4.0)

Requirement already satisfied: six in ./anaconda3/envs/dedalus/lib/python3.7/site-packages (from h5py>=2.6.0->dedalus) (1.12.0)

Requirement already satisfied: setuptools in ./anaconda3/envs/dedalus/lib/python3.7/site-packages (from kiwisolver>=1.0.1->matplotlib->dedalus) (41.0.1)

Building wheels for collected packages: dedalus

Building wheel for dedalus (PEP 517) ... error

ERROR: Complete output from command /Users/slance/anaconda3/envs/dedalus/bin/python3 /Users/slance/anaconda3/envs/dedalus/lib/python3.7/site-packages/pip/_vendor/pep517/_in_process.py build_wheel /var/folders/5p/0lzt36x55hb67svhplbdxdnc0013gz/T/tmpk900gg00:

ERROR: Looking for mpi include path

Cannot find env var MPI_INCLUDE_PATH

Looking for mpi prefix

Found matching library in /Users/slance/anaconda3/envs/dedalus/lib

Looking for fftw include path

Cannot find env var FFTW_INCLUDE_PATH

Looking for fftw prefix

Found matching library in /Users/slance/anaconda3/envs/dedalus/lib

Looking for fftw library path

Cannot find env var FFTW_LIBRARY_PATH

Looking for fftw prefix

Found matching library in /Users/slance/anaconda3/envs/dedalus/lib

Looking for mpi library path

Cannot find env var MPI_LIBRARY_PATH

Looking for mpi prefix

Found matching library in /Users/slance/anaconda3/envs/dedalus/lib

running bdist_wheel

running build

running build_py

creating build

creating build/lib.macosx-10.9-x86_64-3.7

creating build/lib.macosx-10.9-x86_64-3.7/dedalus

copying dedalus/__init__.py -> build/lib.macosx-10.9-x86_64-3.7/dedalus

copying dedalus/__main__.py -> build/lib.macosx-10.9-x86_64-3.7/dedalus

copying dedalus/dev.py -> build/lib.macosx-10.9-x86_64-3.7/dedalus

copying dedalus/public.py -> build/lib.macosx-10.9-x86_64-3.7/dedalus

creating build/lib.macosx-10.9-x86_64-3.7/dedalus/core

copying dedalus/core/__init__.py -> build/lib.macosx-10.9-x86_64-3.7/dedalus/core

copying dedalus/core/arithmetic.py -> build/lib.macosx-10.9-x86_64-3.7/dedalus/core

copying dedalus/core/basis.py -> build/lib.macosx-10.9-x86_64-3.7/dedalus/core

copying dedalus/core/distributor.py -> build/lib.macosx-10.9-x86_64-3.7/dedalus/core

copying dedalus/core/domain.py -> build/lib.macosx-10.9-x86_64-3.7/dedalus/core

copying dedalus/core/evaluator.py -> build/lib.macosx-10.9-x86_64-3.7/dedalus/core

copying dedalus/core/field.py -> build/lib.macosx-10.9-x86_64-3.7/dedalus/core

copying dedalus/core/future.py -> build/lib.macosx-10.9-x86_64-3.7/dedalus/core

copying dedalus/core/metadata.py -> build/lib.macosx-10.9-x86_64-3.7/dedalus/core

copying dedalus/core/operators.py -> build/lib.macosx-10.9-x86_64-3.7/dedalus/core

copying dedalus/core/pencil.py -> build/lib.macosx-10.9-x86_64-3.7/dedalus/core

copying dedalus/core/problems.py -> build/lib.macosx-10.9-x86_64-3.7/dedalus/core

copying dedalus/core/solvers.py -> build/lib.macosx-10.9-x86_64-3.7/dedalus/core

copying dedalus/core/system.py -> build/lib.macosx-10.9-x86_64-3.7/dedalus/core

copying dedalus/core/timesteppers.py -> build/lib.macosx-10.9-x86_64-3.7/dedalus/core

creating build/lib.macosx-10.9-x86_64-3.7/dedalus/extras

copying dedalus/extras/__init__.py -> build/lib.macosx-10.9-x86_64-3.7/dedalus/extras

copying dedalus/extras/atmospheres.py -> build/lib.macosx-10.9-x86_64-3.7/dedalus/extras

copying dedalus/extras/flow_tools.py -> build/lib.macosx-10.9-x86_64-3.7/dedalus/extras

copying dedalus/extras/plot_tools.py -> build/lib.macosx-10.9-x86_64-3.7/dedalus/extras

creating build/lib.macosx-10.9-x86_64-3.7/dedalus/libraries

copying dedalus/libraries/__init__.py -> build/lib.macosx-10.9-x86_64-3.7/dedalus/libraries

creating build/lib.macosx-10.9-x86_64-3.7/dedalus/tests

copying dedalus/tests/__init__.py -> build/lib.macosx-10.9-x86_64-3.7/dedalus/tests

creating build/lib.macosx-10.9-x86_64-3.7/dedalus/tools

copying dedalus/tools/__init__.py -> build/lib.macosx-10.9-x86_64-3.7/dedalus/tools

copying dedalus/tools/array.py -> build/lib.macosx-10.9-x86_64-3.7/dedalus/tools

copying dedalus/tools/cache.py -> build/lib.macosx-10.9-x86_64-3.7/dedalus/tools

copying dedalus/tools/config.py -> build/lib.macosx-10.9-x86_64-3.7/dedalus/tools

copying dedalus/tools/dispatch.py -> build/lib.macosx-10.9-x86_64-3.7/dedalus/tools

copying dedalus/tools/exceptions.py -> build/lib.macosx-10.9-x86_64-3.7/dedalus/tools

copying dedalus/tools/general.py -> build/lib.macosx-10.9-x86_64-3.7/dedalus/tools

copying dedalus/tools/logging.py -> build/lib.macosx-10.9-x86_64-3.7/dedalus/tools

copying dedalus/tools/parallel.py -> build/lib.macosx-10.9-x86_64-3.7/dedalus/tools

copying dedalus/tools/parsing.py -> build/lib.macosx-10.9-x86_64-3.7/dedalus/tools

copying dedalus/tools/plot_op.py -> build/lib.macosx-10.9-x86_64-3.7/dedalus/tools

copying dedalus/tools/post.py -> build/lib.macosx-10.9-x86_64-3.7/dedalus/tools

copying dedalus/tools/progress.py -> build/lib.macosx-10.9-x86_64-3.7/dedalus/tools

copying dedalus/tools/sparse.py -> build/lib.macosx-10.9-x86_64-3.7/dedalus/tools

creating build/lib.macosx-10.9-x86_64-3.7/dedalus/libraries/fftw

copying dedalus/libraries/fftw/__init__.py -> build/lib.macosx-10.9-x86_64-3.7/dedalus/libraries/fftw

creating build/lib.macosx-10.9-x86_64-3.7/dedalus/tests/special_functions

copying dedalus/tests/special_functions/__init__.py -> build/lib.macosx-10.9-x86_64-3.7/dedalus/tests/special_functions

copying dedalus/tests/special_functions/airy.py -> build/lib.macosx-10.9-x86_64-3.7/dedalus/tests/special_functions

copying dedalus/tests/special_functions/bessel.py -> build/lib.macosx-10.9-x86_64-3.7/dedalus/tests/special_functions

copying dedalus/dedalus.cfg -> build/lib.macosx-10.9-x86_64-3.7/dedalus

running build_ext

building 'dedalus.libraries.fftw.fftw_wrappers' extension

creating build/temp.macosx-10.9-x86_64-3.7

creating build/temp.macosx-10.9-x86_64-3.7/dedalus

creating build/temp.macosx-10.9-x86_64-3.7/dedalus/libraries

creating build/temp.macosx-10.9-x86_64-3.7/dedalus/libraries/fftw

gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/slance/anaconda3/envs/dedalus/include -arch x86_64 -I/Users/slance/anaconda3/envs/dedalus/include -arch x86_64 -I/usr/local/opt/llvm/include -Idedalus/libraries/fftw/ -I/private/var/folders/5p/0lzt36x55hb67svhplbdxdnc0013gz/T/pip-build-env-lab1d8uj/overlay/lib/python3.7/site-packages/numpy/core/include -I/private/var/folders/5p/0lzt36x55hb67svhplbdxdnc0013gz/T/pip-build-env-lab1d8uj/overlay/lib/python3.7/site-packages/mpi4py/include -I/Users/slance/anaconda3/envs/dedalus/include -I/Users/slance/anaconda3/envs/dedalus/include -I/Users/slance/anaconda3/envs/dedalus/include/python3.7m -c dedalus/libraries/fftw/fftw_wrappers.c -o build/temp.macosx-10.9-x86_64-3.7/dedalus/libraries/fftw/fftw_wrappers.o -Wno-error=declaration-after-statement

In file included from /private/var/folders/5p/0lzt36x55hb67svhplbdxdnc0013gz/T/pip-build-env-lab1d8uj/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822,

from /private/var/folders/5p/0lzt36x55hb67svhplbdxdnc0013gz/T/pip-build-env-lab1d8uj/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,

from /private/var/folders/5p/0lzt36x55hb67svhplbdxdnc0013gz/T/pip-build-env-lab1d8uj/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,

from dedalus/libraries/fftw/fftw_wrappers.c:639:

/private/var/folders/5p/0lzt36x55hb67svhplbdxdnc0013gz/T/pip-build-env-lab1d8uj/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]

#warning "Using deprecated NumPy API, disable it with " \

^~~~~~~

dedalus/libraries/fftw/fftw_wrappers.c:28986:18: warning: ‘__pyx_convert__to_py_fftw_iodim’ defined but not used [-Wunused-function]

static PyObject* __pyx_convert__to_py_fftw_iodim(fftw_iodim s) {

^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

gcc -bundle -undefined dynamic_lookup -L/Users/slance/anaconda3/envs/dedalus/lib -arch x86_64 -L/Users/slance/anaconda3/envs/dedalus/lib -arch x86_64 -L/usr/local/opt/llvm/lib -Wl -rpath /usr/local/opt/llvm/lib -I/usr/local/opt/llvm/include -arch x86_64 build/temp.macosx-10.9-x86_64-3.7/dedalus/libraries/fftw/fftw_wrappers.o -L/Users/slance/anaconda3/envs/dedalus/lib -L/Users/slance/anaconda3/envs/dedalus/lib -L/Users/slance/anaconda3/envs/dedalus/lib -L/Users/slance/anaconda3/envs/dedalus/lib -lfftw3_mpi -lfftw3 -lm -o build/lib.macosx-10.9-x86_64-3.7/dedalus/libraries/fftw/fftw_wrappers.cpython-37m-darwin.so

gcc: error: unrecognized command line option ‘-Wl’; did you mean ‘-W’?

gcc: error: unrecognized command line option ‘-rpath’

error: command 'gcc' failed with exit status 1

----------------------------------------

ERROR: Failed building wheel for dedalus

Running setup.py clean for dedalus

Failed to build dedalus

ERROR: Could not build wheels for dedalus which use PEP 517 and cannot be installed directly

Installation complete in conda environment 'dedalus'

Keaton Burns

unread,

Jul 10, 2019, 7:58:08 AM7/10/19

to dedalu...@googlegroups.com

Hi Simon,

Can you return the output of “gcc --version”? It looks like there’s maybe an issue with conda finding clang, which I think is what it expects for macs.

-Keaton

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Eric Mukherjee

unread,

Jul 10, 2019, 8:01:00 AM7/10/19

to Dedalus Users

Hi,

I recently dealt with this exact error message on my Mac Pro. What fixed it was installing (reinstalling?) Xcode command line tools.

You could enter 'gcc --version' at the command line to confirm this is the issue. I've forgotten what exactly it showed, but it should be vaguely similar to this:

Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include/c++/4.2.1

Apple LLVM version 10.0.1 (clang-1001.0.46.4)

Target: x86_64-apple-darwin18.6.0

Thread model: posix

InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin

Eric

Simon Lance

unread,

Jul 10, 2019, 10:10:12 AM7/10/19

to Dedalus Users

Thank you both for your quick responses! Frustratingly having some unrelated technical issues with my MacBook so unable to try your above suggestions just yet, but I will do so as soon as I get it back up and running again!