can't conda install d3 in ubuntu because of wheel/gcc issue

Louis-Alexandre Couston

unread,

Mar 4, 2022, 6:39:31 AM3/4/22

to Dedalus Users

Hey,

I've tried various install routes and all failed because of wheel (possibly linked to gcc).

Sadly, I don't understand the error message.

Note that the problem is similar to that reported by Michel Ferre.

I am on ubuntu 20.04. I have anaconda3 with python 3.8.8. I already have dedalus (v2) conda installed and working fine.

The error message is this (all comments welcome!):

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

Building wheels for collected packages: dedalus, py-cpuinfo
Building wheel for dedalus (pyproject.toml) ... error
error: subprocess-exited-with-error

× Building wheel for dedalus (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [188 lines of output]
Looking for mpi include path
Cannot find env var MPI_INCLUDE_PATH
Looking for mpi prefix
Found matching library in /home/joseph/anaconda3/envs/dedalus3/lib
Looking for fftw include path
Cannot find env var FFTW_INCLUDE_PATH
Looking for fftw prefix
Found matching library in /home/joseph/anaconda3/envs/dedalus3/lib
Looking for fftw library path
Cannot find env var FFTW_LIBRARY_PATH
Looking for fftw prefix
Found matching library in /home/joseph/anaconda3/envs/dedalus3/lib
Looking for mpi library path
Cannot find env var MPI_LIBRARY_PATH
Looking for mpi prefix
Found matching library in /home/joseph/anaconda3/envs/dedalus3/lib
running bdist_wheel
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.8
creating build/lib.linux-x86_64-3.8/dedalus
copying dedalus/dev.py -> build/lib.linux-x86_64-3.8/dedalus
copying dedalus/public.py -> build/lib.linux-x86_64-3.8/dedalus
copying dedalus/__main__.py -> build/lib.linux-x86_64-3.8/dedalus
copying dedalus/__init__.py -> build/lib.linux-x86_64-3.8/dedalus
creating build/lib.linux-x86_64-3.8/d3_scratch
copying d3_scratch/sphere_rossby_waves.py -> build/lib.linux-x86_64-3.8/d3_scratch
copying d3_scratch/test_ball.py -> build/lib.linux-x86_64-3.8/d3_scratch
copying d3_scratch/test_disk_pipe.py -> build/lib.linux-x86_64-3.8/d3_scratch
copying d3_scratch/test_new_cartesian.py -> build/lib.linux-x86_64-3.8/d3_scratch
copying d3_scratch/test_BVP_shell.py -> build/lib.linux-x86_64-3.8/d3_scratch
copying d3_scratch/test_ball_2.py -> build/lib.linux-x86_64-3.8/d3_scratch
copying d3_scratch/test_coords_2.py -> build/lib.linux-x86_64-3.8/d3_scratch
copying d3_scratch/test_lbvp_2d.py -> build/lib.linux-x86_64-3.8/d3_scratch
copying d3_scratch/test_disk_helmholtz.py -> build/lib.linux-x86_64-3.8/d3_scratch
copying d3_scratch/chunk_s2.py -> build/lib.linux-x86_64-3.8/d3_scratch
copying d3_scratch/test_coords.py -> build/lib.linux-x86_64-3.8/d3_scratch
copying d3_scratch/test_new_marti_dynamo.py -> build/lib.linux-x86_64-3.8/d3_scratch
copying d3_scratch/test_new_rbc2d.py -> build/lib.linux-x86_64-3.8/d3_scratch
copying d3_scratch/sphere_jets.py -> build/lib.linux-x86_64-3.8/d3_scratch
copying d3_scratch/test_new_rbc2d_firstorder.py -> build/lib.linux-x86_64-3.8/d3_scratch
copying d3_scratch/test_scalar_advection_shell.py -> build/lib.linux-x86_64-3.8/d3_scratch
copying d3_scratch/test_shell_dynamo.py -> build/lib.linux-x86_64-3.8/d3_scratch
copying d3_scratch/test_new_marti_conv.py -> build/lib.linux-x86_64-3.8/d3_scratch
copying d3_scratch/chunk_cart.py -> build/lib.linux-x86_64-3.8/d3_scratch
copying d3_scratch/test_scalar_advection_shell_diff.py -> build/lib.linux-x86_64-3.8/d3_scratch
copying d3_scratch/test_shell_conv.py -> build/lib.linux-x86_64-3.8/d3_scratch
copying d3_scratch/test_jacobi_legendre.py -> build/lib.linux-x86_64-3.8/d3_scratch
copying d3_scratch/test_scalar_advection_ball.py -> build/lib.linux-x86_64-3.8/d3_scratch
copying d3_scratch/test_new_ball_ncc_diffusion.py -> build/lib.linux-x86_64-3.8/d3_scratch
copying d3_scratch/test_timings.py -> build/lib.linux-x86_64-3.8/d3_scratch
copying d3_scratch/test_timings2.py -> build/lib.linux-x86_64-3.8/d3_scratch
copying d3_scratch/test_new_rbc.py -> build/lib.linux-x86_64-3.8/d3_scratch
copying d3_scratch/test_arithmetic.py -> build/lib.linux-x86_64-3.8/d3_scratch
copying d3_scratch/test_jacobi_basics.py -> build/lib.linux-x86_64-3.8/d3_scratch
copying d3_scratch/scratch.py -> build/lib.linux-x86_64-3.8/d3_scratch
copying d3_scratch/__init__.py -> build/lib.linux-x86_64-3.8/d3_scratch
copying d3_scratch/test_marti_hydro.py -> build/lib.linux-x86_64-3.8/d3_scratch
copying d3_scratch/test_BVP.py -> build/lib.linux-x86_64-3.8/d3_scratch
copying d3_scratch/test_new_marti_hydro_sim.py -> build/lib.linux-x86_64-3.8/d3_scratch
copying d3_scratch/test_fourier_integrate_trigpoly.py -> build/lib.linux-x86_64-3.8/d3_scratch
copying d3_scratch/test_new_marti_hydro_ball_shell.py -> build/lib.linux-x86_64-3.8/d3_scratch
copying d3_scratch/test_new_marti_conv_potential.py -> build/lib.linux-x86_64-3.8/d3_scratch
copying d3_scratch/test_disk_convection.py -> build/lib.linux-x86_64-3.8/d3_scratch
copying d3_scratch/test_jacobi_integrate_poly.py -> build/lib.linux-x86_64-3.8/d3_scratch
creating build/lib.linux-x86_64-3.8/dedalus/core
copying dedalus/core/operators.py -> build/lib.linux-x86_64-3.8/dedalus/core
copying dedalus/core/domain.py -> build/lib.linux-x86_64-3.8/dedalus/core
copying dedalus/core/spaces.py -> build/lib.linux-x86_64-3.8/dedalus/core
copying dedalus/core/arithmetic.py -> build/lib.linux-x86_64-3.8/dedalus/core
copying dedalus/core/solvers.py -> build/lib.linux-x86_64-3.8/dedalus/core
copying dedalus/core/vectorspaces.py -> build/lib.linux-x86_64-3.8/dedalus/core
copying dedalus/core/problems.py -> build/lib.linux-x86_64-3.8/dedalus/core
copying dedalus/core/system.py -> build/lib.linux-x86_64-3.8/dedalus/core
copying dedalus/core/field.py -> build/lib.linux-x86_64-3.8/dedalus/core
copying dedalus/core/evaluator.py -> build/lib.linux-x86_64-3.8/dedalus/core
copying dedalus/core/future.py -> build/lib.linux-x86_64-3.8/dedalus/core
copying dedalus/core/basis.py -> build/lib.linux-x86_64-3.8/dedalus/core
copying dedalus/core/transforms.py -> build/lib.linux-x86_64-3.8/dedalus/core
copying dedalus/core/distributor.py -> build/lib.linux-x86_64-3.8/dedalus/core
copying dedalus/core/timesteppers.py -> build/lib.linux-x86_64-3.8/dedalus/core
copying dedalus/core/__init__.py -> build/lib.linux-x86_64-3.8/dedalus/core
copying dedalus/core/coords.py -> build/lib.linux-x86_64-3.8/dedalus/core
copying dedalus/core/subsystems.py -> build/lib.linux-x86_64-3.8/dedalus/core
creating build/lib.linux-x86_64-3.8/dedalus/tools
copying dedalus/tools/parallel.py -> build/lib.linux-x86_64-3.8/dedalus/tools
copying dedalus/tools/clenshaw.py -> build/lib.linux-x86_64-3.8/dedalus/tools
copying dedalus/tools/config.py -> build/lib.linux-x86_64-3.8/dedalus/tools
copying dedalus/tools/progress.py -> build/lib.linux-x86_64-3.8/dedalus/tools
copying dedalus/tools/logging.py -> build/lib.linux-x86_64-3.8/dedalus/tools
copying dedalus/tools/post.py -> build/lib.linux-x86_64-3.8/dedalus/tools
copying dedalus/tools/cache.py -> build/lib.linux-x86_64-3.8/dedalus/tools
copying dedalus/tools/general.py -> build/lib.linux-x86_64-3.8/dedalus/tools
copying dedalus/tools/parsing.py -> build/lib.linux-x86_64-3.8/dedalus/tools
copying dedalus/tools/random_arrays.py -> build/lib.linux-x86_64-3.8/dedalus/tools
copying dedalus/tools/exceptions.py -> build/lib.linux-x86_64-3.8/dedalus/tools
copying dedalus/tools/jacobi.py -> build/lib.linux-x86_64-3.8/dedalus/tools
copying dedalus/tools/__init__.py -> build/lib.linux-x86_64-3.8/dedalus/tools
copying dedalus/tools/array.py -> build/lib.linux-x86_64-3.8/dedalus/tools
copying dedalus/tools/dispatch.py -> build/lib.linux-x86_64-3.8/dedalus/tools
copying dedalus/tools/plot_op.py -> build/lib.linux-x86_64-3.8/dedalus/tools
creating build/lib.linux-x86_64-3.8/dedalus/extras
copying dedalus/extras/plot_tools.py -> build/lib.linux-x86_64-3.8/dedalus/extras
copying dedalus/extras/__init__.py -> build/lib.linux-x86_64-3.8/dedalus/extras
copying dedalus/extras/flow_tools.py -> build/lib.linux-x86_64-3.8/dedalus/extras
creating build/lib.linux-x86_64-3.8/dedalus/libraries
copying dedalus/libraries/matsolvers.py -> build/lib.linux-x86_64-3.8/dedalus/libraries
copying dedalus/libraries/__init__.py -> build/lib.linux-x86_64-3.8/dedalus/libraries
creating build/lib.linux-x86_64-3.8/dedalus/tests
copying dedalus/tests/test_spherical_ncc.py -> build/lib.linux-x86_64-3.8/dedalus/tests
copying dedalus/tests/test_nlbvp.py -> build/lib.linux-x86_64-3.8/dedalus/tests
copying dedalus/tests/test_clenshaw.py -> build/lib.linux-x86_64-3.8/dedalus/tests
copying dedalus/tests/test_sphere2D_calculus.py -> build/lib.linux-x86_64-3.8/dedalus/tests
copying dedalus/tests/ball_diffusion_analytical_eigenvalues.py -> build/lib.linux-x86_64-3.8/dedalus/tests
copying dedalus/tests/test_lbvp.py -> build/lib.linux-x86_64-3.8/dedalus/tests
copying dedalus/tests/test_grid_operators.py -> build/lib.linux-x86_64-3.8/dedalus/tests
copying dedalus/tests/test_fourier_operators.py -> build/lib.linux-x86_64-3.8/dedalus/tests
copying dedalus/tests/test_spherical3D_operators.py -> build/lib.linux-x86_64-3.8/dedalus/tests
copying dedalus/tests/test_spherical3D_calculus.py -> build/lib.linux-x86_64-3.8/dedalus/tests
copying dedalus/tests/test_evp.py -> build/lib.linux-x86_64-3.8/dedalus/tests
copying dedalus/tests/test_spherical3D_arithmetic.py -> build/lib.linux-x86_64-3.8/dedalus/tests
copying dedalus/tests/test_jacobi_operators.py -> build/lib.linux-x86_64-3.8/dedalus/tests
copying dedalus/tests/test_polar2D_operators.py -> build/lib.linux-x86_64-3.8/dedalus/tests
copying dedalus/tests/__init__.py -> build/lib.linux-x86_64-3.8/dedalus/tests
copying dedalus/tests/test_disk_ncc.py -> build/lib.linux-x86_64-3.8/dedalus/tests
copying dedalus/tests/test_cartesian_operators.py -> build/lib.linux-x86_64-3.8/dedalus/tests
copying dedalus/tests/test_transforms.py -> build/lib.linux-x86_64-3.8/dedalus/tests
copying dedalus/tests/test_polar2D_calculus.py -> build/lib.linux-x86_64-3.8/dedalus/tests
copying dedalus/tests/test_output.py -> build/lib.linux-x86_64-3.8/dedalus/tests
copying dedalus/tests/test_cartesian_ncc.py -> build/lib.linux-x86_64-3.8/dedalus/tests
copying dedalus/tests/test_ivp.py -> build/lib.linux-x86_64-3.8/dedalus/tests
creating build/lib.linux-x86_64-3.8/dedalus/libraries/fftw
copying dedalus/libraries/fftw/__init__.py -> build/lib.linux-x86_64-3.8/dedalus/libraries/fftw
creating build/lib.linux-x86_64-3.8/dedalus/libraries/dedalus_sphere
copying dedalus/libraries/dedalus_sphere/sphere_wrapper.py -> build/lib.linux-x86_64-3.8/dedalus/libraries/dedalus_sphere
copying dedalus/libraries/dedalus_sphere/operators.py -> build/lib.linux-x86_64-3.8/dedalus/libraries/dedalus_sphere
copying dedalus/libraries/dedalus_sphere/clenshaw.py -> build/lib.linux-x86_64-3.8/dedalus/libraries/dedalus_sphere
copying dedalus/libraries/dedalus_sphere/sphere.py -> build/lib.linux-x86_64-3.8/dedalus/libraries/dedalus_sphere
copying dedalus/libraries/dedalus_sphere/spin_operators.py -> build/lib.linux-x86_64-3.8/dedalus/libraries/dedalus_sphere
copying dedalus/libraries/dedalus_sphere/tuple_tools.py -> build/lib.linux-x86_64-3.8/dedalus/libraries/dedalus_sphere
copying dedalus/libraries/dedalus_sphere/annulus.py -> build/lib.linux-x86_64-3.8/dedalus/libraries/dedalus_sphere
copying dedalus/libraries/dedalus_sphere/zernike.py -> build/lib.linux-x86_64-3.8/dedalus/libraries/dedalus_sphere
copying dedalus/libraries/dedalus_sphere/jacobi.py -> build/lib.linux-x86_64-3.8/dedalus/libraries/dedalus_sphere
copying dedalus/libraries/dedalus_sphere/ball_wrapper.py -> build/lib.linux-x86_64-3.8/dedalus/libraries/dedalus_sphere
copying dedalus/libraries/dedalus_sphere/timesteppers.py -> build/lib.linux-x86_64-3.8/dedalus/libraries/dedalus_sphere
copying dedalus/libraries/dedalus_sphere/__init__.py -> build/lib.linux-x86_64-3.8/dedalus/libraries/dedalus_sphere
copying dedalus/libraries/dedalus_sphere/shell.py -> build/lib.linux-x86_64-3.8/dedalus/libraries/dedalus_sphere
copying dedalus/libraries/dedalus_sphere/old_intertwiner.py -> build/lib.linux-x86_64-3.8/dedalus/libraries/dedalus_sphere
creating build/lib.linux-x86_64-3.8/d3_scratch/special_functions
copying d3_scratch/special_functions/__init__.py -> build/lib.linux-x86_64-3.8/d3_scratch/special_functions
copying d3_scratch/special_functions/bessel.py -> build/lib.linux-x86_64-3.8/d3_scratch/special_functions
copying d3_scratch/special_functions/airy.py -> build/lib.linux-x86_64-3.8/d3_scratch/special_functions
copying dedalus/dedalus.cfg -> build/lib.linux-x86_64-3.8/dedalus
copying dedalus/examples.tar.gz -> build/lib.linux-x86_64-3.8/dedalus
running build_ext
building 'dedalus.libraries.fftw.fftw_wrappers' extension
creating build/temp.linux-x86_64-3.8
creating build/temp.linux-x86_64-3.8/dedalus
creating build/temp.linux-x86_64-3.8/dedalus/libraries
creating build/temp.linux-x86_64-3.8/dedalus/libraries/fftw
/home/joseph/anaconda3/envs/dedalus3/bin/x86_64-conda-linux-gnu-cc -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/joseph/anaconda3/envs/dedalus3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/joseph/anaconda3/envs/dedalus3/include -fPIC -Idedalus/libraries/fftw/ -I/tmp/pip-build-env-vxe64lg9/overlay/lib/python3.8/site-packages/numpy/core/include -I/tmp/pip-build-env-vxe64lg9/overlay/lib/python3.8/site-packages/mpi4py/include -I/home/joseph/anaconda3/envs/dedalus3/include -I/home/joseph/anaconda3/envs/dedalus3/include -I/home/joseph/anaconda3/envs/dedalus3/include/python3.8 -c dedalus/libraries/fftw/fftw_wrappers.c -o build/temp.linux-x86_64-3.8/dedalus/libraries/fftw/fftw_wrappers.o -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -Wno-unused-function
dedalus/libraries/fftw/fftw_wrappers.c: In function '__pyx_pf_7dedalus_9libraries_4fftw_13fftw_wrappers_16R2RTransformBase___init__':
dedalus/libraries/fftw/fftw_wrappers.c:6637:164: warning: passing argument 7 of 'fftw_plan_guru_r2r' from incompatible pointer type [-Wincompatible-pointer-types]
6637 | __pyx_v_self->forward_plan = fftw_plan_guru_r2r(__pyx_v_trans_rank, __pyx_v_trans_struct, __pyx_v_vec_rank, __pyx_v_vec_struct_f, __pyx_v_gdata, __pyx_v_cdata, (&__pyx_v_self->kind_f), (__pyx_v_intflags | __pyx_e_7dedalus_9libraries_4fftw_10fftw_c_api_FFTW_DESTROY_INPUT));
| ~^~~~~~~~~~~~~~~~~~~~~~
| |
| int *
In file included from dedalus/libraries/fftw/fftw_wrappers.c:741:
/home/joseph/anaconda3/envs/dedalus3/include/fftw3.h:465:1: note: expected 'const fftw_r2r_kind *' {aka 'const enum fftw_r2r_kind_do_not_use_me *'} but argument is of type 'int *'
465 | FFTW_DEFINE_API(FFTW_MANGLE_DOUBLE, double, fftw_complex)
| ^~~~~~~~~~~~~~~
dedalus/libraries/fftw/fftw_wrappers.c:6646:165: warning: passing argument 7 of 'fftw_plan_guru_r2r' from incompatible pointer type [-Wincompatible-pointer-types]
6646 | __pyx_v_self->backward_plan = fftw_plan_guru_r2r(__pyx_v_trans_rank, __pyx_v_trans_struct, __pyx_v_vec_rank, __pyx_v_vec_struct_b, __pyx_v_cdata, __pyx_v_gdata, (&__pyx_v_self->kind_b), (__pyx_v_intflags | __pyx_e_7dedalus_9libraries_4fftw_10fftw_c_api_FFTW_DESTROY_INPUT));
| ~^~~~~~~~~~~~~~~~~~~~~~
| |
| int *
In file included from dedalus/libraries/fftw/fftw_wrappers.c:741:
/home/joseph/anaconda3/envs/dedalus3/include/fftw3.h:465:1: note: expected 'const fftw_r2r_kind *' {aka 'const enum fftw_r2r_kind_do_not_use_me *'} but argument is of type 'int *'
465 | FFTW_DEFINE_API(FFTW_MANGLE_DOUBLE, double, fftw_complex)
| ^~~~~~~~~~~~~~~
gcc -pthread -shared -B /home/joseph/anaconda3/envs/dedalus3/compiler_compat -L/home/joseph/anaconda3/envs/dedalus3/lib -Wl,-rpath=/home/joseph/anaconda3/envs/dedalus3/lib -Wl,--no-as-needed -Wl,--sysroot=/ -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/home/joseph/anaconda3/envs/dedalus3/lib -Wl,-rpath-link,/home/joseph/anaconda3/envs/dedalus3/lib -L/home/joseph/anaconda3/envs/dedalus3/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/joseph/anaconda3/envs/dedalus3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/joseph/anaconda3/envs/dedalus3/include build/temp.linux-x86_64-3.8/dedalus/libraries/fftw/fftw_wrappers.o -L/home/joseph/anaconda3/envs/dedalus3/lib -L/home/joseph/anaconda3/envs/dedalus3/lib -Wl,--enable-new-dtags,-R/home/joseph/anaconda3/envs/dedalus3/lib -Wl,--enable-new-dtags,-R/home/joseph/anaconda3/envs/dedalus3/lib -lfftw3_mpi -lfftw3 -lm -o build/lib.linux-x86_64-3.8/dedalus/libraries/fftw/fftw_wrappers.cpython-38-x86_64-linux-gnu.so
/home/joseph/anaconda3/envs/dedalus3/compiler_compat/ld: cannot find /lib64/libpthread.so.0
/home/joseph/anaconda3/envs/dedalus3/compiler_compat/ld: cannot find /usr/lib64/libpthread_nonshared.a
collect2: error: ld returned 1 exit status
/tmp/pip-build-env-vxe64lg9/overlay/lib/python3.8/site-packages/setuptools/dist.py:505: UserWarning: Normalizing '3.0.0a' to '3.0.0a0'
warnings.warn(tmpl.format(**locals()))
error: command '/home/joseph/anaconda3/envs/dedalus3/bin/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 dedalus
Building wheel for py-cpuinfo (setup.py) ... done
Created wheel for py-cpuinfo: filename=py_cpuinfo-8.0.0-py3-none-any.whl size=22258 sha256=043f59096ce6d2f5f6cc8334d310627e9cc5870c03f632a5dc8f3645758cc3c7
Stored in directory: /tmp/pip-ephem-wheel-cache-k7t3c9cj/wheels/57/cb/6d/bab2257f26c5be4a96ff65c3d2a7122c96529b73773ee37f36
Successfully built py-cpuinfo
Failed to build dedalus
ERROR: Could not build wheels for dedalus, which is required to install pyproject.toml-based projects
Disabled threading by default in the environment
To make your changes take effect please reactivate your environment
To make your changes take effect please reactivate your environment

Installation complete in conda environment 'dedalus3'

Thanks !

Amey Varhade

unread,

Mar 8, 2022, 6:30:35 AM3/8/22

to Dedalus Users

I am facing the same issue, however, I did a fresh install in a fresh Ubuntu install. Wheels issue for mpi4py. I have tried all the installation methods but all of them fail in some way due to the wheels issue. Can someone please help ?

Amey Varhade

unread,

Mar 8, 2022, 6:41:57 AM3/8/22

to Dedalus Users

The exact error message on Ubuntu (Linux)

note: This error originates from a subprocess, and is likely not a problem with pip.

ERROR: Failed building wheel for mpi4py
Failed to build mpi4py
ERROR: Could not build wheels for mpi4py, which is required to install pyproject.toml-based projects

[end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.

error: subprocess-exited-with-error

× pip subprocess to install build dependencies did not run successfully.
│ exit code: 1
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.

Disabled threading by default in the environment

Keaton Burns

unread,

Mar 8, 2022, 7:03:17 PM3/8/22

to dedalu...@googlegroups.com

Hi everyone,

It looks like this is some upstream error with the conda compilers and python build. If you’re having this issue, can you try:

Delete the existing conda environment (conda env remove -n dedalus3)
Edit the “install_dedalus3_conda.sh” script to change the python version on line 35 from “3.8” to “3.9”
Try installing again.

-Keaton

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Louis-Alexandre Couston

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Mar 10, 2022, 7:55:24 AM3/10/22

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Hi Keaton,

Your fix solved the problem for me. I can run the disk libration problem alright.

Note that I had to end

python3 -m dedalus test

however, which I ran after the installation, because it was taking a really long time to finish--not sure whether there is a big problem with it (it also showed a bunch of errors).

Thank you !

eric.w....@gmail.com

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Apr 7, 2022, 1:13:33 PM4/7/22

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Hi all,

I'm running into a similar error, though now on on Mac OS 11.6.

Unfortunately, varying the python version in the install script (3.8, 3.9, 3.10) doesn't seem to change the error output, which I can provide if it will help.

Basically it fails at the same stage, when trying to build wheels for mpi4py after downloading d3 and trying to install with pip:

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

error: Cannot link MPI programs. Check your configuration!!!

[end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.

ERROR: Failed building wheel for mpi4py

Failed to build mpi4py

ERROR: Could not build wheels for mpi4py, which is required to install pyproject.toml-based projects

[end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.

error: subprocess-exited-with-error

Shafayat Shawqi

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Apr 7, 2022, 9:27:10 PM4/7/22

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I think my problem is similar trying to install on macOS Monterey Version 12.3.1.

Getting the error:

Installing build dependencies ... error

error: subprocess-exited-with-error

× pip subprocess to install build dependencies did not run successfully.

│ exit code: 1

╰─> [230 lines of output]

.

ERROR: Failed building wheel for mpi4py

Failed to build mpi4py

ERROR: Could not build wheels for mpi4py, which is required to install pyproject.toml-based projects

[end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.

error: subprocess-exited-with-error

× pip subprocess to install build dependencies did not run successfully.

│ exit code: 1

╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.

Any advice will be really appreciated. Thanks!

Shafayat

Keaton Burns

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Apr 9, 2022, 1:55:32 PM4/9/22

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It looks like this may have been an error with intel-based macs pulling compilers from anaconda defaults instead of conda-forge. I’ve tried to prevent this in the latest version of the install script — can you redownload the latest version and try again?

Thanks,

-Keaton

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Eric Hester

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Apr 10, 2022, 12:52:30 PM4/10/22

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After updating to Monterey Version 12.3.1 and reinstalling Xcode command line tools, the install script works great!

Thanks Keaton,

Eric

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Louis-Alexandre Couston

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Apr 11, 2022, 4:17:57 AM4/11/22

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Hi Keaton,

Your fix solved the issue running python3 -m dedalus test.

My final output was:

= 5301 passed, 16 skipped, 1618 deselected, 73 xfailed, 10 xpassed, 157 warnings in 102.65s (0:01:42)

Thanks!

Louis

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