install latest dedalus version using conda

[Louis-Alexandre Couston]

Hey,

For those who--like me--want to test some of the latest features available on the master branch, it is possible to install dedalus from master (clone the github master/main repo) using a conda env (which saves the trouble of finding the mpi and fftw prefix).

All you need to know is here: https://github.com/DedalusProject/dedalus_conda

However, I wanted to report that

python3 setup.py install

failed the first time I tried, returning the error that 'pytest' was missing (not sure why, as I had already successfully installed the dedalus_conda package in the past).

I corrected this by installing manually pytest, i.e. running

conda install -c conda-forge pytest

conda install -c conda-forge pytest-benchmark

conda install -c conda-forge pytest-cov

Best,

Louis

[Keaton Burns]

Hi Louis,

I think the easiest route is to just build the conda environment normally, and then follow the documentation on building dedalus from source   I think you’re right that you shouldn’t have to set the fftw/mpi paths, but using pip to install the package makes sure that all the dependencies are picked up and that dedalus actually gets updated (using “python setup.py install” seems to get confused when the version number on master is the same as the last release, and may not actually do the update).

It’s also pretty simple to directly update dedalus from the master branch (or another branch) with pip, without having to clone the repo (e.g. https://adamj.eu/tech/2019/03/11/pip-install-from-a-git-repository/).

Best,

-Keaton

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[Louis-Alexandre Couston]

Hi Keaton,

The procedure I followed and mentioned in my previous email worked for the master branch but not for the d3 branch, which is the one I actually want to play with. With d3, I got the error that the numpy version was too old. I used conda-forge to update numpy. The install worked fine it seems (all dependencies successfully created) but when I tried running the kdv example I got the error that 'scipy.fft' was missing.

I'm going to try using pip as you suggested before reporting more details on this error.

Best,

Louis

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[Louis-Alexandre Couston]

Hi again,

I got an error trying to install dedalus-d3. Somehow I wonder whether this is because I should install

conda install -c cryoem fftw-mpi

as my current fftw is 3.3.8-nompi_hfc0cae8_1114; is "nompi" worrying?

Here is everything I did on my linux ubuntu 20.04 system (note that it's a virtual machine I run on windows 10 with oracle VM):

- I downloaded the github repository, extracted and went into the local directory.

- I activated conda, which is version 4.10.3.

- I conda installed pip (as which pip or pip3 did not return a pip package in miniconda3 but in /home)

- ompi_info returned Open MPI: 4.0.4 with prefix /home/louiscouston/miniconda3, so I used this to set the paths, i.e.

export MPI_PATH=/home/louiscouston/miniconda3

export FFTW_PATH=/home/louiscouston/miniconda3

- I first got an error, which I thought suggested I don't have fftw, so I did

conda install -c conda-forge fftw

but realized it only updated 3.3.8-nompi_h7f3a6c3_1111 --> 3.3.8-nompi_hfc0cae8_1114

- On attempting again to install, I got the error (full error below):

  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
  gcc -pthread -B /home/louiscouston/miniconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Idedalus/libraries/fftw/ -I/tmp/pip-build-env-xrhgm_ft/overlay/lib/python3.8/site-packages/numpy/core/include -I/tmp/pip-build-env-xrhgm_ft/overlay/lib/python3.8/site-packages/mpi4py/include -I/home/louiscouston/miniconda3/include -I/home/louiscouston/miniconda3/include -I/home/louiscouston/miniconda3/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:675:10: fatal error: fftw3-mpi.h: No such file or directory
    675 | #include "fftw3-mpi.h"
        |          ^~~~~~~~~~~~~
  compilation terminated.
  error: command 'gcc' failed with exit status 1
  ----------------------------------------
  ERROR: Failed building wheel for dedalus
Failed to build dedalus
ERROR: Could not build wheels for dedalus which use PEP 517 and cannot be installed directly

Let me know if you see something I could change to make it work.

Thanks!

Louis

(base) louiscouston@louiscouston-VM:~/dedalus-d3$ pip3 install .
Processing /home/louiscouston/dedalus-d3
  DEPRECATION: A future pip version will change local packages to be built in-place without first copying to a temporary directory. We recommend you use --use-feature=in-tree-build to test your packages with this new behavior before it becomes the default.
   pip 21.3 will remove support for this functionality. You can find discussion regarding this at https://github.com/pypa/pip/issues/7555.
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
    Preparing wheel metadata ... done
Collecting docopt
  Using cached docopt-0.6.2-py2.py3-none-any.whl
Collecting pytest-benchmark
  Using cached pytest_benchmark-3.4.1-py2.py3-none-any.whl (50 kB)
Collecting pytest
  Using cached pytest-6.2.4-py3-none-any.whl (280 kB)
Collecting numexpr
  Using cached numexpr-2.7.3-cp38-cp38-manylinux2010_x86_64.whl (473 kB)
Requirement already satisfied: mpi4py>=2.0.0 in /home/louiscouston/miniconda3/lib/python3.8/site-packages (from dedalus==2.1905) (3.0.3)
Collecting pytest-cov
  Using cached pytest_cov-2.12.1-py2.py3-none-any.whl (20 kB)
Requirement already satisfied: numpy in /home/louiscouston/miniconda3/lib/python3.8/site-packages (from dedalus==2.1905) (1.20.3)
Requirement already satisfied: scipy>=1.4.0 in /home/louiscouston/miniconda3/lib/python3.8/site-packages (from dedalus==2.1905) (1.6.2)
Requirement already satisfied: matplotlib in /home/louiscouston/miniconda3/lib/python3.8/site-packages (from dedalus==2.1905) (3.3.4)
Collecting cython>=0.22
  Using cached Cython-0.29.24-cp38-cp38-manylinux1_x86_64.whl (1.9 MB)
Requirement already satisfied: h5py>=2.6.0 in /home/louiscouston/miniconda3/lib/python3.8/site-packages (from dedalus==2.1905) (3.2.1)
Requirement already satisfied: python-dateutil>=2.1 in /home/louiscouston/miniconda3/lib/python3.8/site-packages (from matplotlib->dedalus==2.1905) (2.8.2)
Requirement already satisfied: pillow>=6.2.0 in /home/louiscouston/miniconda3/lib/python3.8/site-packages (from matplotlib->dedalus==2.1905) (8.3.1)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.3 in /home/louiscouston/miniconda3/lib/python3.8/site-packages (from matplotlib->dedalus==2.1905) (2.4.7)
Requirement already satisfied: kiwisolver>=1.0.1 in /home/louiscouston/miniconda3/lib/python3.8/site-packages (from matplotlib->dedalus==2.1905) (1.3.1)
Requirement already satisfied: cycler>=0.10 in /home/louiscouston/miniconda3/lib/python3.8/site-packages (from matplotlib->dedalus==2.1905) (0.10.0)
Requirement already satisfied: six in /home/louiscouston/miniconda3/lib/python3.8/site-packages (from cycler>=0.10->matplotlib->dedalus==2.1905) (1.16.0)
Collecting packaging
  Using cached packaging-21.0-py3-none-any.whl (40 kB)
Collecting toml
  Using cached toml-0.10.2-py2.py3-none-any.whl (16 kB)
Collecting py>=1.8.2
  Using cached py-1.10.0-py2.py3-none-any.whl (97 kB)
Collecting pluggy<1.0.0a1,>=0.12
  Using cached pluggy-0.13.1-py2.py3-none-any.whl (18 kB)
Collecting attrs>=19.2.0
  Using cached attrs-21.2.0-py2.py3-none-any.whl (53 kB)
Collecting iniconfig
  Using cached iniconfig-1.1.1-py2.py3-none-any.whl (5.0 kB)
Collecting py-cpuinfo
  Using cached py_cpuinfo-8.0.0-py3-none-any.whl
Collecting coverage>=5.2.1
  Using cached coverage-5.5-cp38-cp38-manylinux2010_x86_64.whl (245 kB)
Building wheels for collected packages: dedalus
  Building wheel for dedalus (PEP 517) ... error
  ERROR: Command errored out with exit status 1:
   command: /home/louiscouston/miniconda3/bin/python3.8 /home/louiscouston/miniconda3/lib/python3.8/site-packages/pip/_vendor/pep517/in_process/_in_process.py build_wheel /tmp/tmpopmwy0if
       cwd: /tmp/pip-req-build-wgc4galr
  Complete output (116 lines):
  Looking for mpi include path
    Cannot find env var MPI_INCLUDE_PATH
  Looking for mpi prefix
    Found env var MPI_PATH = /home/louiscouston/miniconda3
  Looking for fftw include path
    Cannot find env var FFTW_INCLUDE_PATH
  Looking for fftw prefix
    Found env var FFTW_PATH = /home/louiscouston/miniconda3
  Looking for fftw library path
    Cannot find env var FFTW_LIBRARY_PATH
  Looking for fftw prefix
    Found env var FFTW_PATH = /home/louiscouston/miniconda3
  Looking for mpi library path
    Cannot find env var MPI_LIBRARY_PATH
  Looking for mpi prefix
    Found env var MPI_PATH = /home/louiscouston/miniconda3
  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/__init__.py -> build/lib.linux-x86_64-3.8/dedalus
  copying dedalus/public.py -> build/lib.linux-x86_64-3.8/dedalus
  creating 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_polar2D_operators.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_nlbvp.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_ncc_convo.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_spherical3D_arithmetic.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_spherical3D_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/__init__.py -> 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_ivp.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_fourier_operators.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_disk_ncc.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_evp.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_lbvp.py -> build/lib.linux-x86_64-3.8/dedalus/tests
  creating 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/parsing.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/post.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/general.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/array.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/parallel.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
  copying dedalus/tools/exceptions.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/clenshaw.py -> build/lib.linux-x86_64-3.8/dedalus/tools
  creating build/lib.linux-x86_64-3.8/dedalus/libraries
  copying dedalus/libraries/__init__.py -> build/lib.linux-x86_64-3.8/dedalus/libraries
  copying dedalus/libraries/matsolvers.py -> build/lib.linux-x86_64-3.8/dedalus/libraries
  creating 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/timesteppers.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/domain.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/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/distributor.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/arithmetic.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/problems.py -> 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/field.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/solvers.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/subsystems.py -> build/lib.linux-x86_64-3.8/dedalus/core
  creating 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/spin_operators.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
  copying dedalus/libraries/dedalus_sphere/shell.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/sphere_wrapper.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/zernike.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/jacobi.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/sphere.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
  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
  copying dedalus/dedalus.cfg -> 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
  gcc -pthread -B /home/louiscouston/miniconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Idedalus/libraries/fftw/ -I/tmp/pip-build-env-xrhgm_ft/overlay/lib/python3.8/site-packages/numpy/core/include -I/tmp/pip-build-env-xrhgm_ft/overlay/lib/python3.8/site-packages/mpi4py/include -I/home/louiscouston/miniconda3/include -I/home/louiscouston/miniconda3/include -I/home/louiscouston/miniconda3/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:675:10: fatal error: fftw3-mpi.h: No such file or directory
    675 | #include "fftw3-mpi.h"
        |          ^~~~~~~~~~~~~
  compilation terminated.
  error: command 'gcc' failed with exit status 1
  ----------------------------------------
  ERROR: Failed building wheel for dedalus
Failed to build dedalus
ERROR: Could not build wheels for dedalus which use PEP 517 and cannot be installed directly

[Keaton Burns]

Hi Louis,

Everything should be done in the conda environment built by the install_conda.sh script, not in the base environment.

-Keaton

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[Louis-Alexandre Couston]

Hey,

I tried various things but failed to get d3 working (the simple conda installation does work). Here is what I did:

- install latest anaconda: conda 4.10.1

- curl https://raw.githubusercontent.com/DedalusProject/dedalus_conda/master/install_conda.sh --output install_conda.sh

- conda activate base

- bash install_conda.sh

- conda activate dedalus

- python3 -m dedalus test

All this worked fine.

Then I wanted to "upgrade" to d3 by building from source. I downloaded and extracted d3 into /home/louiscouston/dedalus-d3

- cd dedalus-d3

- conda activate dedalus

- export MPI_PATH=/home/louiscouston/anaconda3/envs/dedalus

- export FFTW_PATH=/home/louiscouston/anaconda3/envs/dedalus

- pip3 install .

- output said successfully uninstalled dedalus 2.2006 and successfully installed dedalus 2.1905

What works

- after I conda install ipython while in the dedalus env, I can import numpy, matplotlib and dedalus

- I can also run "from dedalus import public as de"

What doesn't work

- when I run "python3 -m dedalus test", I get the error "No module named dedalus.__main__; 'dedalus' is a package and cannot be directly executed"

- I cannot run the kdv example, the error I get is

(dedalus2) louiscouston@louiscouston-VM:~/dedalus-d3/examples/ivp/1d_kdv_burgers$ python3 kdv_burgers.py
2021-07-22 12:27:48,708 numexpr.utils 0/1 INFO :: NumExpr defaulting to 8 threads.
Traceback (most recent call last):
  File "kdv_burgers.py", line 13, in <module>
    from dedalus.extras.plot_tools import quad_mesh, pad_limits
ModuleNotFoundError: No module named 'dedalus.extras'

- If I run in ipython "dedalus import public" and "x_basis = de.Fourier('x', 1024, interval=(-2, 8), dealias=3/2)" I get the error

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
<ipython-input-3-a29b2f20ad44> in <module>
----> 1 x_basis = de.Fourier('x', 1024, interval=(-2, 8), dealias=3/2)

AttributeError: module 'dedalus.public' has no attribute 'Fourier'

What I am unsure about is whether my MPI_PATH and FFTW_PATH are okay (ompi_info does points to this before and after pip3 install .).

Also, I don't really understand what pip3 install . is doing. Should I add the /home/louiscouston/dedalus-d3 path to PYTHONPATH? Or are all of the core routines in dedalus-d3 loaded into the dedalus environment directory?

Any help most welcome!

Thanks,

Louis