[Python 3.9] Overhaul RMG-RMS Python-Julia dependencies (`juliaup` and `pythoncall`), Add Tests for Arkane Network Algorithms #2687

JacksonBurns · 2024-06-27T13:37:46Z

Replace #2635, targeting a smaller improvement in Python minor version to keep better compatibility with our dependencies.

JacksonBurns · 2024-06-27T13:43:21Z

I'll update this comment with the path forward for each platform as the errors roll in.

All Platforms

There are Cython errors all over the place, namely because we have incremented Cython to:
cython 3.0.10
from
cython 0.29.33
...oh boy

M1 Macs

The following packages are outright missing, but without any conflicts:

    - nothing provides requested rmg::symmetry
    - nothing provides requested rmg::pyrms
    - nothing provides requested rmg::pydqed >=1.0.3
    - nothing provides requested rmg::pydas >=1.0.3
    - nothing provides requested conda-forge::muq
    - nothing provides requested conda-forge::julia =1.9.1*
    - nothing provides requested rmg::diffeqpy
    - nothing provides julia >=1.5.0 needed by pyjulia-0.6.0-pyhd8ed1ab_0

Anything in the RMG channel we can build for M1 macs, if it comes to that. muq and julia and pyjulia are out of our hands, though.

Ubuntu

We will need to rebuild the rmg channel packages (or just rebase this branch onto #2640, to at least remove a couple of them)

Intel Macs

Same as Ubuntu.

rwest · 2024-06-27T19:55:34Z

Julia and Pyjulia would be taken care of by #2640 (which would be unblocked if we could get past Python 3.7), so that leave muq? (and the ones that are our responsibility)

rwest · 2024-06-27T19:56:45Z

Is this faring any better than 3.10 or 3.11? at least it solved the boost - rdkit - muq issue? or do we need to await results on non-M1-platforms?

JacksonBurns · 2024-06-27T20:12:26Z

Local testing shows that this resolves the muq + rdkit issue. I tried leaving in our packages (rmg channel) to see if the conflict resolution would work, to no avail. I have removed them now to let it (hopefully) suggest solutions to conflicts (if there are any) and then we should have an idea of the path forward.

JacksonBurns · 2024-06-27T20:22:05Z

@rwest initial tests are done. M1 macs are missing a number of packages that are outside of our control. I think that is a dead end.

Ubuntu and MacOS need the rmg channel packages. If we rebase this on #2640 we can avoid building those we plan to immediately remove afterward (I want to do this).

All platforms will need Cython errors fixed.

JacksonBurns · 2024-06-28T15:27:18Z

Following some offline discussion, @hwpang and I have agreed that I will rebase this PR onto #2640 and then merge it into the same. This will:

prevent me having to build packages which we will immediately remove, simplifying this PR: Complete conda-recipes Overhaul conda-recipes#18
require resolving the Cython compilation errors. This may or may not be very difficult - subsequent work in this PR will focus on addressing the scope of these changes.
still require building pydas and pydqed, which may or not be difficult, but will handled in separate PRs on their respective repositories.

…ator/RMG-Py into feat/py39

hwpang · 2024-07-03T19:05:45Z

I'm running the test after relaxing the python version requirement in RMS from version="3.9" to version=">=3.9" to see if this was the problem. I wasn't aware that version="3.9" doesn't imply version="3.9*".

Ah yeah this is a quirk of conda I think

The latest CI has an interessting array of failures:

Intel Mac is timing out during the Julia install (like it always did)

M1 Mac is trying to install RMG-molecule for some reason ?? and failing because there are no M1 binaries for that package, see https://github.com/ReactionMechanismGenerator/RMG-Py/actions/runs/9764305750/job/26952342727?pr=2687#step:11:1113 worth nothing too that the Linux build isn't doing this: https://github.com/ReactionMechanismGenerator/RMG-Py/actions/runs/9764305750/job/26952342727?pr=2687#step:11:1113

Linux is seg faulting during the tests, specifically while running 'test_find_error_canceling_reaction'. This doesn't directly touch any of the code I have changed, but does use lpsolve, which is:

lp_solve 5.5.2.11 hd590300_0 conda-forge
lpsolve55 5.5 py37hda87dfa_1005 conda-forge
on main but

lp_solve 5.5.2.11 hd590300_0 conda-forge
lpsolve55 5.5 py39h44dd56e_1007 conda-forge on this branch.

Going to push a commit to just try and get a better stacktrace and maybe some output during the failure

I was able to make the MacOS to not install rmgmolecule. However, now we run into a new error:

ERROR: LoadError: InitError: ReadOnlyMemoryError()
during initialization of module PythonPlot
in expression starting at /Users/runner/miniconda3/envs/rmg_env/.julia/packages/ReactionMechanismSimulator/C6833/src/Plotting.jl:1
in expression starting at /Users/runner/miniconda3/envs/rmg_env/.julia/packages/ReactionMechanismSimulator/C6833/src/ReactionMechanismSimulator.jl:1
Matplotlib is building the font cache; this may take a moment.

JacksonBurns · 2024-07-04T19:24:58Z

Ok so interesting developments - the Linux build continues to fail when calling out to Lpsolve but the Intel Mac (which didn't use to even install RMS at all, so this is surprising) passes that test, later failing during this unit test because of something I did with Cython, I think:

 >   def same_object(object1, object2, _check_identical, _only_check_label,
                 _generate_initial_map, _strict, _save_order):
E                TypeError: same_object() takes exactly 7 positional arguments (2 given)

rmgpy/reaction.py:1545: TypeError

The M1 error... no idea. Our current docs tell users to just have the M1 hardware emulate the old arch so that they can run old arch binaries - perhaps we do the same in the CI?

hwpang · 2024-07-04T20:17:06Z

Ok so interesting developments - the Linux build continues to fail when calling out to Lpsolve but the Intel Mac (which didn't use to even install RMS at all, so this is surprising) passes that test, later failing during this unit test because of something I did with Cython, I think:
 >   def same_object(object1, object2, _check_identical, _only_check_label,
                 _generate_initial_map, _strict, _save_order):
E                TypeError: same_object() takes exactly 7 positional arguments (2 given)

rmgpy/reaction.py:1545: TypeError
The M1 error... no idea. Our current docs tell users to just have the M1 hardware emulate the old arch so that they can run old arch binaries - perhaps we do the same in the CI?

Yeah that sounds fine to me.

for some reason `functools.partial` is allowed, but not `lambda`

…ator/RMG-Py into feat/py39

JacksonBurns · 2024-07-08T15:26:28Z

@hwpang ARM mac is now installing Intel packages, but this error pops up during RMS installation:

Looking for: ["matplotlib[version='>=1']", "conda-forge::python[version='>=3.8,<4',build=*cpython*]"]


Downloading and Extracting Packages: ...working... done
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Python path configuration:
  PYTHONHOME = '/Users/runner/miniconda3/envs/rmg_env:/Users/runner/miniconda3/envs/rmg_env'
  PYTHONPATH = '/Users/runner/work/RMG-Py/RMG-Py/RMG-Py:'
  program name = '/Users/runner/miniconda3/envs/rmg_env/bin/python'
  isolated = 0
  environment = 1
  user site = 1
  safe_path = 0
  import site = 1
  is in build tree = 0
  stdlib dir = '/Users/runner/miniconda3/envs/rmg_env/lib/python3.12'
  sys._base_executable = '/Users/runner/miniconda3/envs/rmg_env/bin/python'
  sys.base_prefix = '/Users/runner/miniconda3/envs/rmg_env'
  sys.base_exec_prefix = '/Users/runner/miniconda3/envs/rmg_env'
  sys.platlibdir = 'lib'
  sys.executable = '/Users/runner/miniconda3/envs/rmg_env/bin/python'
  sys.prefix = '/Users/runner/miniconda3/envs/rmg_env'
  sys.exec_prefix = '/Users/runner/miniconda3/envs/rmg_env'
  sys.path = [
    '/Users/runner/work/RMG-Py/RMG-Py/RMG-Py',
    '/Users/runner/miniconda3/envs/rmg_env/.julia/packages/ReactionMechanismSimulator/NVrJU/deps',
    '/Users/runner/miniconda3/envs/rmg_env/lib/python312.zip',
    '/Users/runner/miniconda3/envs/rmg_env/lib/python3.12',
    '/Users/runner/miniconda3/envs/rmg_env/lib/python3.12/lib-dynload',
  ]
Fatal Python error: init_fs_encoding: failed to get the Python codec of the filesystem encoding
Python runtime state: core initialized
ModuleNotFoundError: No module named 'encodings'

JacksonBurns · 2024-07-08T15:27:15Z

Stack overflow says it's because we are setting PYTHONPATH https://stackoverflow.com/a/65740883

hwpang · 2024-07-08T18:03:59Z

Stack overflow says it's because we are setting PYTHONPATH https://stackoverflow.com/a/65740883

Thanks. The only PYTHONPATH it has is the PYTHONPATH we set for the RMG-Py, and we didn't set any other PYTHONPATH. Any ideas on what we could try?

Python path configuration:
  PYTHONHOME = '/Users/runner/miniconda3/envs/rmg_env:/Users/runner/miniconda3/envs/rmg_env'
  PYTHONPATH = '/Users/runner/work/RMG-Py/RMG-Py/RMG-Py:'

hwpang · 2024-07-08T18:42:31Z

So unsetting the PYTHONPATH didn't solve the problem we encountered with ARM mac. It failed with the same error:

Downloading and Extracting Packages: ...working... done
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Python path configuration:
  PYTHONHOME = '/Users/runner/miniconda3/envs/rmg_env:/Users/runner/miniconda3/envs/rmg_env'
  PYTHONPATH = (not set)
  program name = '/Users/runner/miniconda3/envs/rmg_env/bin/python'
  isolated = 0
  environment = 1
  user site = 1
  safe_path = 0
  import site = 1
  is in build tree = 0
  stdlib dir = '/Users/runner/miniconda3/envs/rmg_env/lib/python3.12'
  sys._base_executable = '/Users/runner/miniconda3/envs/rmg_env/bin/python'
  sys.base_prefix = '/Users/runner/miniconda3/envs/rmg_env'
  sys.base_exec_prefix = '/Users/runner/miniconda3/envs/rmg_env'
  sys.platlibdir = 'lib'
  sys.executable = '/Users/runner/miniconda3/envs/rmg_env/bin/python'
  sys.prefix = '/Users/runner/miniconda3/envs/rmg_env'
  sys.exec_prefix = '/Users/runner/miniconda3/envs/rmg_env'
  sys.path = [
    '/Users/runner/miniconda3/envs/rmg_env/lib/python312.zip',
    '/Users/runner/miniconda3/envs/rmg_env/lib/python3.12',
    '/Users/runner/miniconda3/envs/rmg_env/lib/python3.12/lib-dynload',
  ]
Fatal Python error: init_fs_encoding: failed to get the Python codec of the filesystem encoding
Python runtime state: core initialized
ModuleNotFoundError: No module named 'encodings'

Current thread 0x00000001fe960c00 (most recent call first):
  <no Python frame>
Stacktrace:
  [1] pkgerror(msg::String)
    @ Pkg.Types ~/miniconda3/envs/rmg_env/.julia/juliaup/julia-1.10.4+0.aarch64.apple.darwin14/share/julia/stdlib/v1.10/Pkg/src/Types.jl:70
  [2] (::Pkg.Operations.var"#67#74"{Bool, Pkg.Types.Context, String, Pkg.Types.PackageSpec, String})()
    @ Pkg.Operations ~/miniconda3/envs/rmg_env/.julia/juliaup/julia-1.10.4+0.aarch64.apple.darwin14/share/julia/stdlib/v1.10/Pkg/src/Operations.jl:1157
  [3] withenv(::Pkg.Operations.var"#67#74"{Bool, Pkg.Types.Context, String, Pkg.Types.PackageSpec, String}, ::Pair{String, String}, ::Vararg{Pair{String}})
    @ Base ./env.jl:257
  [4] (::Pkg.Operations.var"#117#122"{String, Bool, Bool, Bool, Pkg.Operations.var"#67#74"{Bool, Pkg.Types.Context, String, Pkg.Types.PackageSpec, String}, Pkg.Types.PackageSpec})()
    @ Pkg.Operations ~/miniconda3/envs/rmg_env/.julia/juliaup/julia-1.10.4+0.aarch64.apple.darwin14/share/julia/stdlib/v1.10/Pkg/src/Operations.jl:1825
  [5] with_temp_env(fn::Pkg.Operations.var"#117#122"{String, Bool, Bool, Bool, Pkg.Operations.var"#67#74"{Bool, Pkg.Types.Context, String, Pkg.Types.PackageSpec, String}, Pkg.Types.PackageSpec}, temp_env::String)
    @ Pkg.Operations ~/miniconda3/envs/rmg_env/.julia/juliaup/julia-1.10.4+0.aarch64.apple.darwin14/share/julia/stdlib/v1.10/Pkg/src/Operations.jl:1706
  [6] (::Pkg.Operations.var"#115#120"{Dict{String, Any}, Bool, Bool, Bool, Pkg.Operations.var"#67#74"{Bool, Pkg.Types.Context, String, Pkg.Types.PackageSpec, String}, Pkg.Types.Context, Pkg.Types.PackageSpec, String, Pkg.Types.Project, String})(tmp::String)
    @ Pkg.Operations ~/miniconda3/envs/rmg_env/.julia/juliaup/julia-1.10.4+0.aarch64.apple.darwin14/share/julia/stdlib/v1.10/Pkg/src/Operations.jl:1[795](https://github.com/ReactionMechanismGenerator/RMG-Py/actions/runs/9844707391/job/27178685242?pr=2687#step:12:796)
  [7] mktempdir(fn::Pkg.Operations.var"#115#120"{Dict{String, Any}, Bool, Bool, Bool, Pkg.Operations.var"#67#74"{Bool, Pkg.Types.Context, String, Pkg.Types.PackageSpec, String}, Pkg.Types.Context, Pkg.Types.PackageSpec, String, Pkg.Types.Project, String}, parent::String; prefix::String)
    @ Base.Filesystem ./file.jl:766
  [8] mktempdir(fn::Function, parent::String)
    @ Base.Filesystem ./file.jl:762
  [9] mktempdir
    @ ./file.jl:762 [inlined]
 [10] sandbox(fn::Function, ctx::Pkg.Types.Context, target::Pkg.Types.PackageSpec, target_path::String, sandbox_path::String, sandbox_project_override::Pkg.Types.Project; preferences::Dict{String, Any}, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool)
    @ Pkg.Operations ~/miniconda3/envs/rmg_env/.julia/juliaup/julia-1.10.4+0.aarch64.apple.darwin14/share/julia/stdlib/v1.10/Pkg/src/Operations.jl:1753
 [11] build_versions(ctx::Pkg.Types.Context, uuids::Set{Base.UUID}; verbose::Bool)
    @ Pkg.Operations ~/miniconda3/envs/rmg_env/.julia/juliaup/julia-1.10.4+0.aarch64.apple.darwin14/share/julia/stdlib/v1.10/Pkg/src/Operations.jl:1138
 [12] build_versions
    @ ~/miniconda3/envs/rmg_env/.julia/juliaup/julia-1.10.4+0.aarch64.apple.darwin14/share/julia/stdlib/v1.10/Pkg/src/Operations.jl:1056 [inlined]
 [13] add(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}, new_git::Set{Base.UUID}; preserve::Pkg.Types.PreserveLevel, platform::Base.BinaryPlatforms.Platform)
    @ Pkg.Operations ~/miniconda3/envs/rmg_env/.julia/juliaup/julia-1.10.4+0.aarch64.apple.darwin14/share/julia/stdlib/v1.10/Pkg/src/Operations.jl:1399
 [14] add
    @ ~/miniconda3/envs/rmg_env/.julia/juliaup/julia-1.10.4+0.aarch64.apple.darwin14/share/julia/stdlib/v1.10/Pkg/src/Operations.jl:1377 [inlined]
 [15] add(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; preserve::Pkg.Types.PreserveLevel, platform::Base.BinaryPlatforms.Platform, kwargs::@Kwargs{io::Base.PipeEndpoint})
    @ Pkg.API ~/miniconda3/envs/rmg_env/.julia/juliaup/julia-1.10.4+0.aarch64.apple.darwin14/share/julia/stdlib/v1.10/Pkg/src/API.jl:278
 [16] add(pkgs::Vector{Pkg.Types.PackageSpec}; io::Base.PipeEndpoint, kwargs::@Kwargs{})
    @ Pkg.API ~/miniconda3/envs/rmg_env/.julia/juliaup/julia-1.10.4+0.aarch64.apple.darwin14/share/julia/stdlib/v1.10/Pkg/src/API.jl:159
 [17] add(pkgs::Vector{Pkg.Types.PackageSpec})
    @ Pkg.API ~/miniconda3/envs/rmg_env/.julia/juliaup/julia-1.10.4+0.aarch64.apple.darwin14/share/julia/stdlib/v1.10/Pkg/src/API.jl:148
 [18] add(pkg::Pkg.Types.PackageSpec)
    @ Pkg.API ~/miniconda3/envs/rmg_env/.julia/juliaup/julia-1.10.4+0.aarch64.apple.darwin14/share/julia/stdlib/v1.10/Pkg/src/API.jl:146
 [19] top-level scope
    @ none:1
Error: Process completed with exit code 1.

It has also caused the previously working Ubuntu installation to fail. So I'm gonna drop that commit. Would appreciate any ideas to try. @JacksonBurns

rwest · 2024-07-09T17:01:20Z

This looks promising, right? What @hwpang pushed yesterday compiled and installed everything and started to run all the unit tests?
Then it seg-faulted on a line status = lpsolve('solve', lp)?
(But maybe that's just where we were last week?)

Update: it could feasibly be the underlying lp_solve package causing issues not just the lpsolve55 which is the wrapper/API.

JacksonBurns · 2024-07-14T22:15:19Z

Apologies for the delay, travel and also @hwpang is Dr. @hwpang now 🎉!

I am not sure what else to try RE: ARM Mac is busted. Running ARM Packages natively failed at the Julia installation, emulating Intel packages failed during Julia installation also but for a different, possibly PYTHONPATH related reason. I will be back in front of an ARM Mac a week from now, which might make debugging easier, but I would appreciate help here.

Intel Mac is broken on GitHub because it is too slow to install RMS (except when sometimes it does, for some reason, only to fail due to a Cython error I think I caused). Ubuntu is failing because lpsolve crashes the whole test run, and frustratingly refuses to even give a helpful trace.

For now, maybe we try and figure out why lpsolve is failing?

rwest · 2024-07-22T16:05:54Z

How hard is it to remove the need for LPSolve?.... #2623 and #2596 (comment)

hwpang · 2024-07-22T20:43:47Z

How hard is it to remove the need for LPSolve?.... #2623 and #2596 (comment)

@rwest This is sort of a chicken and egg problem, because replacing lpsolve with scipy.optimize.milp requires python 3.9, and this PR that upgrades RMG to python 3.9 is failing due to lpsolve :(

hwpang · 2024-07-22T20:45:05Z

An alternative thought, maybe we can rebase #2623 on this PR and see if that resolves the lpsolve issue?

rwest · 2024-07-23T07:13:41Z

Worth a try. We have both the chickens and the eggs as open PRs. We should try putting them together.

JacksonBurns · 2024-07-24T18:08:52Z

I will (1) make a copy of @xiaoruiDong's branch in #2623 and push it to ReactionMechanismGenerator/RMG-Py and then (2) rebase that branch on this branch and then (3) open a PR from that branch into this one

JacksonBurns · 2024-07-24T18:19:24Z

@hwpang's #2596 is also required in combination with #2694 in order to completely remove lpsolve. I will (1) make a copy of that branch on RMG-Py (2) rebase it onto #2694 (3) tack on a commit to remove lpsolve (4) open a PR into #2694

Merge order would then be Isodesmic into CLAR, CLAR into this, and this into main.

rwest · 2024-07-29T17:19:23Z

I lost track of the other PRs. Is this idea of removing lpsolve looking promising?

JacksonBurns · 2024-08-04T20:40:16Z

I lost track of the other PRs. Is this idea of removing lpsolve looking promising?

Yes - the combination of #2694 and #2695 will allow us to remove lpsolve (as well as roll in some bug fixes), which should allow merging this PR.

JacksonBurns · 2024-10-30T19:04:13Z

Don't fix merge conflicts in this PR, I have already done so in #2694

hwpang added 24 commits June 28, 2024 11:32

switch to branch

798a1b0

Use pyjuliacall instead of pyjulia

8b4f136

No need to install julia from conda

b3796da

update

d4c539e

update

e8faefb

Swap the order

f52d0d7

update

c1f2017

doc

a11a96d

Use the preexisting mamba

05d1772

Use JULIA_CONDAPKG_EXE=$CONDA/condabin/conda

6f5612c

Add channels

be3e424

skip make for now for debugging

a812cab

Trying to use juliaup

0a165ee

Don't need to install diffeqpy

bf7017b

Uncomment make step

b312ca1

Don't need julia plug in

c4fc809

Use mamba

3ce04fd

No need to add channels

17f397b

import juliacall

f65d07d

Don't track coverage

d52efbf

debug

c7c0632

debug

7e770fb

convert empty list

29e6c43

Add additional test file for sls

7a473df

hwpang added 2 commits July 3, 2024 14:39

Consolidate the export of Julia paths

f45f7bd

Merge branch 'feat/py39' of https://github.com/ReactionMechanismGener…

7d3a765

…ator/RMG-Py into feat/py39

JacksonBurns and others added 3 commits July 8, 2024 10:51

add step to make ARM mac use intel mac packages

bff1865

passthrough args to same_object

0f87f76

for some reason `functools.partial` is allowed, but not `lambda`

Merge branch 'feat/py39' of https://github.com/ReactionMechanismGener…

7b2296d

…ator/RMG-Py into feat/py39

hwpang force-pushed the feat/py39 branch from bf2295c to 7b2296d Compare July 8, 2024 18:42

This was referenced Jul 24, 2024

Run Complete CI on MacOS and Ubuntu #2648

Closed

[Python 3.9] Reimplement Clar Optimization with Scipy MILP #2694

Draft

JacksonBurns mentioned this pull request Jul 24, 2024

[Python 3.9] Improve isodesmic and add element balance constraints #2695

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JacksonBurns mentioned this pull request Aug 21, 2024

updating 'rotconsts' ref to be compatible with cclib v1.8+ #2639

Merged

JacksonBurns mentioned this pull request Nov 13, 2024

Juliaup interferes with PATH preventing python-jl from using rmg_env conda environment. #2730

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[Python 3.9] Overhaul RMG-RMS Python-Julia dependencies (`juliaup` and `pythoncall`), Add Tests for Arkane Network Algorithms #2687

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JacksonBurns commented Oct 30, 2024

[Python 3.9] Overhaul RMG-RMS Python-Julia dependencies (`juliaup` and `pythoncall`), Add Tests for Arkane Network Algorithms #2687

[Python 3.9] Overhaul RMG-RMS Python-Julia dependencies (`juliaup` and `pythoncall`), Add Tests for Arkane Network Algorithms #2687

JacksonBurns commented Jun 27, 2024 •

edited

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JacksonBurns commented Jun 27, 2024 •

edited

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rwest commented Jul 9, 2024 •

edited

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hwpang commented Jul 22, 2024 •

edited

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