Error installing GIL

[james-vincent]

When trying to install with: $ python --version Python 3.11.8

get error in compile stage with cython. Seems to be code issue. Unclear how to proceed:

[10/12] Cythonizing mdtraj/geometry/src/_geometry.pyx performance hint: mdtraj/geometry/src/image_molecules.pxi:13:5: Exception check on 'make_whole' will always require the GIL to be acquired. Possible solutions:

1. Declare 'make_whole' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
2. Use an 'int' return type on 'make_whole' to allow an error code to be returned.

Error compiling Cython file:

... offset[k] += frame_unitcell_vectors[0, k]*roundf((delta[0]-offset[0])/frame_unitcell_vectors[0,0]) frame_positions[atom2, k] = frame_positions[atom2, k] - offset[k]

cdef void anchor_dists(float[:,::1] frame_positions, float[:,::1] frame_unitcell_vectors, vector[int[:]] anchor_molecules, ^

mdtraj/geometry/src/image_molecules.pxi:33:24: Reference-counted type 'int[:]' cannot be used as a template argument performance hint: mdtraj/geometry/src/image_molecules.pxi:31:5: Exception check on 'anchor_dists' will always require the GIL to be acquired.

[james-vincent]

Installing with python 3.9 also fails:

/tmp/easy_install-dqfcp_zc/mdtraj-1.9.9/./basesetup.py:451: UserWarning: Unrecognized setuptools command ('-q bdist_egg --dist-dir /tmp/easy_install-dqfcp_zc/mdtraj-1.9.9/egg-dist-tmp-af2lqfyp'), proceeding with generating Cython sources and expanding templates warnings.warn("Unrecognized setuptools command ('{}'), proceeding with " mdtrajs setup depends on Cython (>=0.29). Install it prior invoking setup.py No module named 'Cython'

and

python3.9/site-packages/setuptools/dist.py:476: SetuptoolsDeprecationWarning: Invalid dash-separated options !!

Is there a specific environment this can be installed with, OS version, exact python version, etc?

[TBGAnsell]

Hi James,

Apologies for the delay in getting back to you. I've starting a new job and am still getting established. The install error can be corrected by installing an older version of mdtraj. This results from the PyLipID install which has not been updated for newer mdtraj versions.

It on my list to address the install soon but please bear with me where I'm juggling bandwidth. Please do let me know if anything else that arrises.

Best wishes, Bertie

On Tue, Apr 30, 2024 at 12:12 PM james-vincent @.***> wrote:

Installing with python 3.9 also fails:

/tmp/easy_install-dqfcp_zc/mdtraj-1.9.9/./basesetup.py:451: UserWarning: Unrecognized setuptools command ('-q bdist_egg --dist-dir /tmp/easy_install-dqfcp_zc/mdtraj-1.9.9/egg-dist-tmp-af2lqfyp'), proceeding with generating Cython sources and expanding templates warnings.warn("Unrecognized setuptools command ('{}'), proceeding with " mdtrajs setup depends on Cython (>=0.29). Install it prior invoking setup.py No module named 'Cython'

and

python3.9/site-packages/setuptools/dist.py:476: SetuptoolsDeprecationWarning: Invalid dash-separated options !!

Is there a specific environment this can be installed with, OS version, exact python version, etc?

— Reply to this email directly, view it on GitHub https://github.com/TBGAnsell/LipIDens/issues/4#issuecomment-2086698105, or unsubscribe https://github.com/notifications/unsubscribe-auth/AN6N2Z7JP5QATU6C2F2EBVLY77UKRAVCNFSM6AAAAABGNPF5TKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAOBWGY4TQMJQGU . You are receiving this because you are subscribed to this thread.Message ID: @.***>

[james-vincent]

Thanks for the quick response. I was able to install by using mdtraj version 1.9.5.

Just for fun, I converted the requirements to a toml file for use with pixi  (https://pixi.sh/latest/). Pixi is a replacement for mamba, which is a replacement for conda. We’re using it more and more and like it very much.

I am not a user of lipidens but we’ve had a number of requests for it. We will curate in SBGrid and provide it for our users.

Thanks again, Jim

James Vincent, PhD Bioinformatics Software Curator Dept. of BCMP, Harvard Medical School — BioGrids.org --

On Apr 30, 2024 at 4:49 PM -0400, TBGAnsell @.***>, wrote:

Hi James,

Apologies for the delay in getting back to you. I've starting a new job and am still getting established. The install error can be corrected by installing an older version of mdtraj. This results from the PyLipID install which has not been updated for newer mdtraj versions.

It on my list to address the install soon but please bear with me where I'm juggling bandwidth. Please do let me know if anything else that arrises.

Best wishes, Bertie

On Tue, Apr 30, 2024 at 12:12 PM james-vincent @.***> wrote:

Installing with python 3.9 also fails:

/tmp/easy_install-dqfcp_zc/mdtraj-1.9.9/./basesetup.py:451: UserWarning: Unrecognized setuptools command ('-q bdist_egg --dist-dir /tmp/easy_install-dqfcp_zc/mdtraj-1.9.9/egg-dist-tmp-af2lqfyp'), proceeding with generating Cython sources and expanding templates warnings.warn("Unrecognized setuptools command ('{}'), proceeding with " mdtrajs setup depends on Cython (>=0.29). Install it prior invoking setup.py No module named 'Cython'

and

python3.9/site-packages/setuptools/dist.py:476: SetuptoolsDeprecationWarning: Invalid dash-separated options !!

Is there a specific environment this can be installed with, OS version, exact python version, etc?

— Reply to this email directly, view it on GitHub https://github.com/TBGAnsell/LipIDens/issues/4#issuecomment-2086698105, or unsubscribe https://github.com/notifications/unsubscribe-auth/AN6N2Z7JP5QATU6C2F2EBVLY77UKRAVCNFSM6AAAAABGNPF5TKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAOBWGY4TQMJQGU . You are receiving this because you are subscribed to this thread.Message ID: @.***>

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[TBGAnsell]

Thanks for the sign post to pixi Jim, much appreciated. I’ll have a look at this when I update the install.Best, Bertie On 1 May 2024, at 03:53, james-vincent @.***> wrote: Thanks for the quick response. I was able to install by using mdtraj version 1.9.5.

Just for fun, I converted the requirements to a toml file for use with pixi  (https://pixi.sh/latest/). Pixi is a replacement for mamba, which is a replacement for conda. We’re using it more and more and like it very much.

I am not a user of lipidens but we’ve had a number of requests for it. We will curate in SBGrid and provide it for our users.

Thanks again,

Jim

James Vincent, PhD

Bioinformatics Software Curator

Dept. of BCMP, Harvard Medical School

— BioGrids.org --

On Apr 30, 2024 at 4:49 PM -0400, TBGAnsell @.***>, wrote:

Hi James,

Apologies for the delay in getting back to you. I've starting a new job and

am still getting established.

The install error can be corrected by installing an older version of

mdtraj. This results from the PyLipID install which has not been updated

for newer mdtraj versions.

It on my list to address the install soon but please bear with me where I'm

juggling bandwidth. Please do let me know if anything else that arrises.

Best wishes,

Bertie

On Tue, Apr 30, 2024 at 12:12 PM james-vincent @.***>

wrote:

Installing with python 3.9 also fails:

/tmp/easy_install-dqfcp_zc/mdtraj-1.9.9/./basesetup.py:451: UserWarning:

Unrecognized setuptools command ('-q bdist_egg --dist-dir

/tmp/easy_install-dqfcp_zc/mdtraj-1.9.9/egg-dist-tmp-af2lqfyp'), proceeding

with generating Cython sources and expanding templates

warnings.warn("Unrecognized setuptools command ('{}'), proceeding with "

mdtrajs setup depends on Cython (>=0.29). Install it prior invoking

setup.py

No module named 'Cython'

and

python3.9/site-packages/setuptools/dist.py:476:

SetuptoolsDeprecationWarning: Invalid dash-separated options

!!

Is there a specific environment this can be installed with, OS version,

exact python version, etc?

—

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https://github.com/TBGAnsell/LipIDens/issues/4#issuecomment-2086698105,

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