Error during installation of Dedalus on COSMA7

[Manohar Teja]

Hi,

I am trying to install Dedalus v3 on COSMA. There is an error coming up during testing (python3 -m dedalus test). However I am sure that the dedalus folder is up-to-date. I went into dedalus folder and tried git pull and it shows Already up to date. I am unsure why this error is coming up. Could someone help me with this?

Error:

(dedalus3) [dc-kall1@login7a [cosma7] dedalus]$ python3 -m dedalus test
--------------------------------------------------------------------------
WARNING: There was an error initializing an OpenFabrics device.

  Local host:   login7a
  Local device: mlx5_1
--------------------------------------------------------------------------
/cosma/home/dp050/dc-kall1/miniforge3/envs/dedalus3/lib/python3.12/multiprocessing/popen_fork.py:66: DeprecationWarning: This process (pid=119575) is multi-threaded, use of fork() may lead to deadlocks in the child.
  self.pid = os.fork()
/cosma/home/dp050/dc-kall1/miniforge3/envs/dedalus3/lib/python3.12/site-packages/pytest_parallel/__init__.py:221: PytestDeprecationWarning: The hookimpl ParallelRunner.pytest_sessionstart uses old-style configuration options (marks or attributes).
Please use the pytest.hookimpl(tryfirst=True) decorator instead
 to configure the hooks.
 See https://docs.pytest.org/en/latest/deprecations.html#configuring-hook-specs-impls-using-markers
  @pytest.mark.tryfirst
======================================== test session starts ========================================
platform linux -- Python 3.12.0, pytest-7.4.3, pluggy-1.3.0
benchmark: 4.0.0 (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: /cosma/home/dp050/dc-kall1/dedalus
plugins: benchmark-4.0.0, cov-4.1.0, parallel-0.1.1
collected 0 items / 22 errors                                                                      

============================================== ERRORS ===============================================
_______________________ ERROR collecting dedalus/tests/test_cartesian_ncc.py ________________________
ImportError while importing test module '/cosma/home/dp050/dc-kall1/dedalus/dedalus/tests/test_cartesian_ncc.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
../miniforge3/envs/dedalus3/lib/python3.12/importlib/__init__.py:90: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
dedalus/tests/test_cartesian_ncc.py:6: in <module>
    import dedalus.public as d3
dedalus/public.py:4: in <module>
    from .core.coords import *
dedalus/core/__init__.py:2: in <module>
    from . import distributor
dedalus/core/distributor.py:23: in <module>
    from .transposes import FFTWTranspose as TransposePlanner
E   ModuleNotFoundError: No module named 'dedalus.core.transposes'
____________________ ERROR collecting dedalus/tests/test_cartesian_operators.py _____________________
ImportError while importing test module '/cosma/home/dp050/dc-kall1/dedalus/dedalus/tests/test_cartesian_operators.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
../miniforge3/envs/dedalus3/lib/python3.12/importlib/__init__.py:90: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
dedalus/tests/test_cartesian_operators.py:6: in <module>
    import dedalus.public as d3
dedalus/public.py:4: in <module>
    from .core.coords import *
dedalus/core/__init__.py:2: in <module>
    from . import distributor
dedalus/core/distributor.py:23: in <module>
    from .transposes import FFTWTranspose as TransposePlanner
E   ModuleNotFoundError: No module named 'dedalus.core.transposes'
____________________________ ERROR collecting dedalus/tests/test_cfl.py _____________________________
ImportError while importing test module '/cosma/home/dp050/dc-kall1/dedalus/dedalus/tests/test_cfl.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
../miniforge3/envs/dedalus3/lib/python3.12/importlib/__init__.py:90: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
dedalus/tests/test_cfl.py:5: in <module>
    import dedalus.public as d3
dedalus/public.py:4: in <module>
    from .core.coords import *
dedalus/core/__init__.py:2: in <module>
    from . import distributor
dedalus/core/distributor.py:23: in <module>
    from .transposes import FFTWTranspose as TransposePlanner
E   ModuleNotFoundError: No module named 'dedalus.core.transposes'
__________________________ ERROR collecting dedalus/tests/test_clenshaw.py __________________________
ImportError while importing test module '/cosma/home/dp050/dc-kall1/dedalus/dedalus/tests/test_clenshaw.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
../miniforge3/envs/dedalus3/lib/python3.12/importlib/__init__.py:90: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
dedalus/tests/test_clenshaw.py:7: in <module>
    import dedalus.public as d3
dedalus/public.py:4: in <module>
    from .core.coords import *
dedalus/core/__init__.py:2: in <module>
    from . import distributor
dedalus/core/distributor.py:23: in <module>
    from .transposes import FFTWTranspose as TransposePlanner
E   ModuleNotFoundError: No module named 'dedalus.core.transposes'
____________________________ ERROR collecting dedalus/tests/test_evp.py _____________________________
ImportError while importing test module '/cosma/home/dp050/dc-kall1/dedalus/dedalus/tests/test_evp.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
../miniforge3/envs/dedalus3/lib/python3.12/importlib/__init__.py:90: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
dedalus/tests/test_evp.py:6: in <module>
    import dedalus.public as d3
dedalus/public.py:4: in <module>
    from .core.coords import *
dedalus/core/__init__.py:2: in <module>
    from . import distributor
dedalus/core/distributor.py:23: in <module>
    from .transposes import FFTWTranspose as TransposePlanner
E   ModuleNotFoundError: No module named 'dedalus.core.transposes'
_____________________ ERROR collecting dedalus/tests/test_fourier_operators.py ______________________
ImportError while importing test module '/cosma/home/dp050/dc-kall1/dedalus/dedalus/tests/test_fourier_operators.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
../miniforge3/envs/dedalus3/lib/python3.12/importlib/__init__.py:90: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
dedalus/tests/test_fourier_operators.py:5: in <module>
    import dedalus.public as d3
dedalus/public.py:4: in <module>
    from .core.coords import *
dedalus/core/__init__.py:2: in <module>
    from . import distributor
dedalus/core/distributor.py:23: in <module>
    from .transposes import FFTWTranspose as TransposePlanner
E   ModuleNotFoundError: No module named 'dedalus.core.transposes'
_______________________ ERROR collecting dedalus/tests/test_grid_operators.py _______________________
ImportError while importing test module '/cosma/home/dp050/dc-kall1/dedalus/dedalus/tests/test_grid_operators.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
../miniforge3/envs/dedalus3/lib/python3.12/importlib/__init__.py:90: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
dedalus/tests/test_grid_operators.py:5: in <module>
    import dedalus.public as d3
dedalus/public.py:4: in <module>
    from .core.coords import *
dedalus/core/__init__.py:2: in <module>
    from . import distributor
dedalus/core/distributor.py:23: in <module>
    from .transposes import FFTWTranspose as TransposePlanner
E   ModuleNotFoundError: No module named 'dedalus.core.transposes'
____________________________ ERROR collecting dedalus/tests/test_ivp.py _____________________________
ImportError while importing test module '/cosma/home/dp050/dc-kall1/dedalus/dedalus/tests/test_ivp.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
../miniforge3/envs/dedalus3/lib/python3.12/importlib/__init__.py:90: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
dedalus/tests/test_ivp.py:5: in <module>
    import dedalus.public as d3
dedalus/public.py:4: in <module>
    from .core.coords import *
dedalus/core/__init__.py:2: in <module>
    from . import distributor
dedalus/core/distributor.py:23: in <module>
    from .transposes import FFTWTranspose as TransposePlanner
E   ModuleNotFoundError: No module named 'dedalus.core.transposes'
______________________ ERROR collecting dedalus/tests/test_jacobi_operators.py ______________________
ImportError while importing test module '/cosma/home/dp050/dc-kall1/dedalus/dedalus/tests/test_jacobi_operators.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
../miniforge3/envs/dedalus3/lib/python3.12/importlib/__init__.py:90: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
dedalus/tests/test_jacobi_operators.py:5: in <module>
    import dedalus.public as d3
dedalus/public.py:4: in <module>
    from .core.coords import *
dedalus/core/__init__.py:2: in <module>
    from . import distributor
dedalus/core/distributor.py:23: in <module>
    from .transposes import FFTWTranspose as TransposePlanner
E   ModuleNotFoundError: No module named 'dedalus.core.transposes'
____________________________ ERROR collecting dedalus/tests/test_lbvp.py ____________________________
ImportError while importing test module '/cosma/home/dp050/dc-kall1/dedalus/dedalus/tests/test_lbvp.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
../miniforge3/envs/dedalus3/lib/python3.12/importlib/__init__.py:90: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
dedalus/tests/test_lbvp.py:6: in <module>
    import dedalus.public as d3
dedalus/public.py:4: in <module>
    from .core.coords import *
dedalus/core/__init__.py:2: in <module>
    from . import distributor
dedalus/core/distributor.py:23: in <module>
    from .transposes import FFTWTranspose as TransposePlanner
E   ModuleNotFoundError: No module named 'dedalus.core.transposes'
___________________________ ERROR collecting dedalus/tests/test_nlbvp.py ____________________________
ImportError while importing test module '/cosma/home/dp050/dc-kall1/dedalus/dedalus/tests/test_nlbvp.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
../miniforge3/envs/dedalus3/lib/python3.12/importlib/__init__.py:90: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
dedalus/tests/test_nlbvp.py:6: in <module>
    import dedalus.public as d3
dedalus/public.py:4: in <module>
    from .core.coords import *
dedalus/core/__init__.py:2: in <module>
    from . import distributor
dedalus/core/distributor.py:23: in <module>
    from .transposes import FFTWTranspose as TransposePlanner
E   ModuleNotFoundError: No module named 'dedalus.core.transposes'
___________________________ ERROR collecting dedalus/tests/test_output.py ___________________________
ImportError while importing test module '/cosma/home/dp050/dc-kall1/dedalus/dedalus/tests/test_output.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
../miniforge3/envs/dedalus3/lib/python3.12/importlib/__init__.py:90: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
dedalus/tests/test_output.py:6: in <module>
    import dedalus.public as d3
dedalus/public.py:4: in <module>
    from .core.coords import *
dedalus/core/__init__.py:2: in <module>
    from . import distributor
dedalus/core/distributor.py:23: in <module>
    from .transposes import FFTWTranspose as TransposePlanner
E   ModuleNotFoundError: No module named 'dedalus.core.transposes'
_______________________ ERROR collecting dedalus/tests/test_polar_calculus.py _______________________
ImportError while importing test module '/cosma/home/dp050/dc-kall1/dedalus/dedalus/tests/test_polar_calculus.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
../miniforge3/envs/dedalus3/lib/python3.12/importlib/__init__.py:90: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
dedalus/tests/test_polar_calculus.py:5: in <module>
    from dedalus.core import coords, distributor, basis, field, operators, arithmetic
dedalus/core/__init__.py:2: in <module>
    from . import distributor
dedalus/core/distributor.py:23: in <module>
    from .transposes import FFTWTranspose as TransposePlanner
E   ModuleNotFoundError: No module named 'dedalus.core.transposes'
_________________________ ERROR collecting dedalus/tests/test_polar_ncc.py __________________________
ImportError while importing test module '/cosma/home/dp050/dc-kall1/dedalus/dedalus/tests/test_polar_ncc.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
../miniforge3/envs/dedalus3/lib/python3.12/importlib/__init__.py:90: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
dedalus/tests/test_polar_ncc.py:4: in <module>
    from dedalus.core import coords, distributor, basis, field, operators, problems, solvers, arithmetic
dedalus/core/__init__.py:2: in <module>
    from . import distributor
dedalus/core/distributor.py:23: in <module>
    from .transposes import FFTWTranspose as TransposePlanner
E   ModuleNotFoundError: No module named 'dedalus.core.transposes'
______________________ ERROR collecting dedalus/tests/test_polar_operators.py _______________________
ImportError while importing test module '/cosma/home/dp050/dc-kall1/dedalus/dedalus/tests/test_polar_operators.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
../miniforge3/envs/dedalus3/lib/python3.12/importlib/__init__.py:90: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
dedalus/tests/test_polar_operators.py:5: in <module>
    from dedalus.core import coords, distributor, basis, field, operators, arithmetic, problems, solvers
dedalus/core/__init__.py:2: in <module>
    from . import distributor
dedalus/core/distributor.py:23: in <module>
    from .transposes import FFTWTranspose as TransposePlanner
E   ModuleNotFoundError: No module named 'dedalus.core.transposes'
______________________ ERROR collecting dedalus/tests/test_sphere_calculus.py _______________________
ImportError while importing test module '/cosma/home/dp050/dc-kall1/dedalus/dedalus/tests/test_sphere_calculus.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
../miniforge3/envs/dedalus3/lib/python3.12/importlib/__init__.py:90: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
dedalus/tests/test_sphere_calculus.py:5: in <module>
    from dedalus.core import coords, distributor, basis, field, operators, arithmetic, problems, solvers
dedalus/core/__init__.py:2: in <module>
    from . import distributor
dedalus/core/distributor.py:23: in <module>
    from .transposes import FFTWTranspose as TransposePlanner
E   ModuleNotFoundError: No module named 'dedalus.core.transposes'
_________________________ ERROR collecting dedalus/tests/test_sphere_ncc.py _________________________
ImportError while importing test module '/cosma/home/dp050/dc-kall1/dedalus/dedalus/tests/test_sphere_ncc.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
../miniforge3/envs/dedalus3/lib/python3.12/importlib/__init__.py:90: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
dedalus/tests/test_sphere_ncc.py:4: in <module>
    from dedalus.core import coords, distributor, basis, field, operators, problems, solvers, arithmetic
dedalus/core/__init__.py:2: in <module>
    from . import distributor
dedalus/core/distributor.py:23: in <module>
    from .transposes import FFTWTranspose as TransposePlanner
E   ModuleNotFoundError: No module named 'dedalus.core.transposes'
____________________ ERROR collecting dedalus/tests/test_spherical_arithmetic.py ____________________
ImportError while importing test module '/cosma/home/dp050/dc-kall1/dedalus/dedalus/tests/test_spherical_arithmetic.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
../miniforge3/envs/dedalus3/lib/python3.12/importlib/__init__.py:90: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
dedalus/tests/test_spherical_arithmetic.py:4: in <module>
    from dedalus.core import coords, distributor, basis, field, operators, arithmetic
dedalus/core/__init__.py:2: in <module>
    from . import distributor
dedalus/core/distributor.py:23: in <module>
    from .transposes import FFTWTranspose as TransposePlanner
E   ModuleNotFoundError: No module named 'dedalus.core.transposes'
_____________________ ERROR collecting dedalus/tests/test_spherical_calculus.py _____________________
ImportError while importing test module '/cosma/home/dp050/dc-kall1/dedalus/dedalus/tests/test_spherical_calculus.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
../miniforge3/envs/dedalus3/lib/python3.12/importlib/__init__.py:90: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
dedalus/tests/test_spherical_calculus.py:5: in <module>
    from dedalus.core import coords, distributor, basis, field, operators, arithmetic
dedalus/core/__init__.py:2: in <module>
    from . import distributor
dedalus/core/distributor.py:23: in <module>
    from .transposes import FFTWTranspose as TransposePlanner
E   ModuleNotFoundError: No module named 'dedalus.core.transposes'
_______________________ ERROR collecting dedalus/tests/test_spherical_ncc.py ________________________
ImportError while importing test module '/cosma/home/dp050/dc-kall1/dedalus/dedalus/tests/test_spherical_ncc.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
../miniforge3/envs/dedalus3/lib/python3.12/importlib/__init__.py:90: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
dedalus/tests/test_spherical_ncc.py:4: in <module>
    import dedalus.public as d3
dedalus/public.py:4: in <module>
    from .core.coords import *
dedalus/core/__init__.py:2: in <module>
    from . import distributor
dedalus/core/distributor.py:23: in <module>
    from .transposes import FFTWTranspose as TransposePlanner
E   ModuleNotFoundError: No module named 'dedalus.core.transposes'
____________________ ERROR collecting dedalus/tests/test_spherical_operators.py _____________________
ImportError while importing test module '/cosma/home/dp050/dc-kall1/dedalus/dedalus/tests/test_spherical_operators.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
../miniforge3/envs/dedalus3/lib/python3.12/importlib/__init__.py:90: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
dedalus/tests/test_spherical_operators.py:5: in <module>
    from dedalus.core import coords, distributor, basis, field, operators, arithmetic, problems, solvers
dedalus/core/__init__.py:2: in <module>
    from . import distributor
dedalus/core/distributor.py:23: in <module>
    from .transposes import FFTWTranspose as TransposePlanner
E   ModuleNotFoundError: No module named 'dedalus.core.transposes'
_________________________ ERROR collecting dedalus/tests/test_transforms.py _________________________
ImportError while importing test module '/cosma/home/dp050/dc-kall1/dedalus/dedalus/tests/test_transforms.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
../miniforge3/envs/dedalus3/lib/python3.12/importlib/__init__.py:90: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
dedalus/tests/test_transforms.py:4: in <module>
    from dedalus.core import coords, distributor, basis, field, operators
dedalus/core/__init__.py:2: in <module>
    from . import distributor
dedalus/core/distributor.py:23: in <module>
    from .transposes import FFTWTranspose as TransposePlanner
E   ModuleNotFoundError: No module named 'dedalus.core.transposes'
====================================== short test summary info ======================================
ERROR dedalus/tests/test_cartesian_ncc.py
ERROR dedalus/tests/test_cartesian_operators.py
ERROR dedalus/tests/test_cfl.py
ERROR dedalus/tests/test_clenshaw.py
ERROR dedalus/tests/test_evp.py
ERROR dedalus/tests/test_fourier_operators.py
ERROR dedalus/tests/test_grid_operators.py
ERROR dedalus/tests/test_ivp.py
ERROR dedalus/tests/test_jacobi_operators.py
ERROR dedalus/tests/test_lbvp.py
ERROR dedalus/tests/test_nlbvp.py
ERROR dedalus/tests/test_output.py
ERROR dedalus/tests/test_polar_calculus.py
ERROR dedalus/tests/test_polar_ncc.py
ERROR dedalus/tests/test_polar_operators.py
ERROR dedalus/tests/test_sphere_calculus.py
ERROR dedalus/tests/test_sphere_ncc.py
ERROR dedalus/tests/test_spherical_arithmetic.py
ERROR dedalus/tests/test_spherical_calculus.py
ERROR dedalus/tests/test_spherical_ncc.py
ERROR dedalus/tests/test_spherical_operators.py
ERROR dedalus/tests/test_transforms.py
!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Interrupted: 22 errors during collection !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
======================================== 22 errors in 1.65s =========================================

Regards.

Manohar Teja Kalluri

CGAFD, Univ of Exeter

[Keaton Burns]

Hi Manojar,

Did you try to make an editable install from the clone of the v3 repository, or to pip install it into the conda environment?

-Keaton

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[Manohar Teja]

Hi Keaton,

Sorry for the delay in reply. I cloned the dedalus from the git repository. Probably I messed up the installation a bit. So I have deleted the dedalus3 environment and all the files and started from scratch with custom conda installation, loading MPI, HDF5, FFTW modules and providing their path on conda_install_dedalus3.sh script. I have now ended with the error below. What should I do?

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

  ERROR: Failed building wheel for dedalus

Failed to build dedalus

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

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'

Regards

Manohar

CGAFD, Univ of Exeter

To view this discussion on the web visit https://groups.google.com/d/msgid/dedalus-users/CADZXxBjgpAiFsQSUAgZ6-1njJL7f2LP96MPHLv9euhWbOf%3DB4g%40mail.gmail.com.

[Keaton Burns]

Hi Manohar,

This doesn’t include the part of the error message showing the failure, so it’s impossible to tell from this. Please send a copy of the full error / output.

-Keaton

To view this discussion on the web visit https://groups.google.com/d/msgid/dedalus-users/CAGuRpfSAsREiz9ZN07%2BtnP1f-nKB%2BAmQmZG%2BQbYcSti-_-5iFQ%40mail.gmail.com.

[Manohar Teja]

Here is a more detailed error message mentioned above:

mpicc -fno-strict-overflow -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /cosma/home/dp050/dc-kall1/miniforge3/envs/dedalus3/include -fPIC -O2 -isystem /cosma/home/dp050/dc-kall1/miniforge3/envs/dedalus3/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /cosma/home/dp050/dc-kall1/miniforge3/envs/dedalus3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /cosma/home/dp050/dc-kall1/miniforge3/envs/dedalus3/include -fPIC -I/cosma/home/dp050/dc-kall1/miniforge3/envs/dedalus3/lib/python3.12/site-packages/numpy/core/include -I/cosma/home/dp050/dc-kall1/miniforge3/envs/dedalus3/lib/python3.12/site-packages/mpi4py/include -I/cosma/local/Modules/modulefiles/mpi/openmpi/3.0.1/include -Idedalus/libraries/fftw/ -I/cosma/local/Modules/modulefiles/libraries/fftw/3.3.7/include -I/cosma/home/dp050/dc-kall1/miniforge3/envs/dedalus3/include/python3.12 -c dedalus/core/transposes.c -o build/temp.linux-x86_64-cpython-312/dedalus/core/transposes.o -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -Wno-unused-function -fopenmp
      cc1: error: /cosma/local/Modules/modulefiles/mpi/openmpi/3.0.1/include: Not a directory
      cc1: error: /cosma/local/Modules/modulefiles/libraries/fftw/3.3.7/include: Not a directory
      error: command '/cosma/local/openmpi/gnu_7.3.0/3.0.1/bin/mpicc' 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
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'

From what I understand the error is due to a faulty directory (/cosma/local/Modules/modulefiles/mpi/openmpi/3.0.1/include). But the path '/cosma/local/Modules/modulefiles/mpi/openmpi/' leads to file 3.0.1. And I have set this in conda_install_dedalus3.sh script at export MPI_PATH. Is that the correct procedure?

Regards

Manohar

CGAFD, Univ of Exeter

[Manohar Teja]

Hi, Hope the screenshot attached helps

Regards

Manohar

CGAFD, Univ of Exeter

To view this discussion on the web visit https://groups.google.com/d/msgid/dedalus-users/CADZXxBjcbQCwSo0VWvYiabo6QwtRM%3DT%2BpL50kCm4u%3DOqUS-jcg%40mail.gmail.com.

[Keaton Burns]

I’m not sure what you mean by “leads to” here. The error is stating that the PATH + “/include” is not a directory. You should find the actual location with the header files, and set the PATH to the prefix of that (the part without “/include” at the end).

To view this discussion on the web visit https://groups.google.com/d/msgid/dedalus-users/CAGuRpfQp55MW94x-NepbZfFYjLXXjLERfQwNoQTV89MZFn%3D4SQ%40mail.gmail.com.

[Manohar Teja]

Hi Keaton,

Got it. Thank you. I got the issue sorted out.

Regards

Manohar

CGAFD, Univ of Exeter

To view this discussion on the web visit https://groups.google.com/d/msgid/dedalus-users/CADZXxBhdapan4A9cgb2UhAkCg33EjXeXOOMRCgOAdLkCyCOGQg%40mail.gmail.com.

[Manohar Teja]

The Dedalus test (python3 -m dedalus test) gives the following message:

========================================= warnings summary ==========================================
miniforge3/envs/dedalus3/lib/python3.12/site-packages/dateutil/tz/tz.py:37
  /cosma/home/dp050/dc-kall1/miniforge3/envs/dedalus3/lib/python3.12/site-packages/dateutil/tz/tz.py:37: DeprecationWarning: datetime.datetime.utcfromtimestamp() is deprecated and scheduled for removal in a future version. Use timezone-aware objects to represent datetimes in UTC: datetime.datetime.fromtimestamp(timestamp, datetime.UTC).
    EPOCH = datetime.datetime.utcfromtimestamp(0)

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
== 5416 passed, 16 skipped, 613 deselected, 134 xfailed, 18 xpassed, 1 warning in 65.58s (0:01:05) ==

I assume this is fine since there are only warnings and not errors. Moving on to installing Dedalus directly from GitHub using pip (CC=mpicc pip3 install --no-cache --no-build-isolation http://github.com/dedalusproject/dedalus/zipball/master/), and updating it, which also didn't throw any errors. But when I enter into python in the dedalus3 environment I am unable to import dedalus.public. The error can be seen below. (Please note that the modules are still loaded and I can see all the modules being loaded when I enter module list command)

(dedalus3) [dc-kall1@login7a [cosma7] ~]$ python
Python 3.12.0 | packaged by conda-forge | (main, Oct  3 2023, 08:43:22) [GCC 12.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy
>>> import dedalus.public

--------------------------------------------------------------------------
WARNING: There was an error initializing an OpenFabrics device.

  Local host:   login7a
  Local device: mlx5_1
--------------------------------------------------------------------------

Regards

Manohar

CGAFD, Univ of Exeter

[Keaton Burns]

Hi Manohar,

I think you should contact the cluster support about this. The issue looks related to how the MPI environment is being set up or something, not really a Dedalus issue.

-Keaton

To view this discussion on the web visit https://groups.google.com/d/msgid/dedalus-users/CAGuRpfSC84xTk6OVKeHiYKEnpBpW48FQ%3DykJFre-SbTmp1fVxg%40mail.gmail.com.

[Manohar Teja]

Sure, thanks for this. Good to know that it has nothing to do with the Dedalus installation. I'll contact the COSMA support team regarding this issue.

Regards

Manohar

CGAFD, Univ of Exeter

To view this discussion on the web visit https://groups.google.com/d/msgid/dedalus-users/CADZXxBhc3fznP5NZyR_LXqxTkOmGz3w-8_1NOok%3DW10OSoAAPQ%40mail.gmail.com.

[Manohar Teja]

Hi,

I am encountering a problem while running a job. I am unsure if this is to do with COSMA or Dedalus. Could you please look into this?

I have successfully installed Dedalus on COSMA and submitted a job on a single node and the runs without any errors. However when I run the job on multiple nodes, it throws an error and the output is not printed on log file no matter how long I let it run. The error with multiple nodes is as follows:

[m7352][[59694,1],16][btl_tcp_endpoint.c:625:mca_btl_tcp_endpoint_recv_connect_ack] received unexpected process identifier [[59694,1],24]

Is this something to do with Dedalus?

I have googled about this and found one of the posts (https://github.com/horovod/horovod/issues/1516) saying they solved the problem adding '-mca btl_tcp_if_include ib0' to the mpirun command line solved their issue. Do you have an idea what this is? I tried doing the same  with command line as follows:

mpiexec -np 32 -mca btl_tcp_if_include ib0 python3 ./run_script_3D_1.py > log

This leads to Exception raised in Dedalus

2023-12-07 14:49:31,288 __main__ 22/32 ERROR :: Exception raised, triggering end of main loop.

What exception is this exactly? Any clue?

Regards

Manohar

CGAFD, Univ of Exeter

[Keaton Burns]

Hi Manohar,

No I don’t think this is a Dedalus issue. Please contact your cluster support staff for details regarding the system's MPI environment and settings. 

-Keaton

To view this discussion on the web visit https://groups.google.com/d/msgid/dedalus-users/CAGuRpfTOEFOixk%3D%3DNMejV8ZAYwp3_rcgRWXcpkDJh%2BcbbcGorA%40mail.gmail.com.

[C Wareing]

Hello Manohar,

I used the COSMA machines some time in the distant past and this looks sort of familiar - and clearly relates to the MPI and the infiniband connection.

I would suggest trying different permutations of modules for the compiler and MPI until you find a combination that works, probably starting from GNU and OpenMPI.

https://www.dur.ac.uk/icc/cosma/support/modules/

The support team (old friends, acquaintances and colleagues) will help you.

Apologies if this has already been suggested.

Best,

Chris