RMS error after commit 437739 #2290

alirmg · 2022-04-02T20:25:03Z

I have just pulled the most recent RMG-Py and RMG-Database from git. when I run the superminimal example, I get the following error (full text below). (for both superminimal example and any other input files I generated) NameError: name 'rms' is not defined

The text was updated successfully, but these errors were encountered:

mjohnson541 · 2022-04-02T20:31:44Z

The environment has been updated. You need to reinstall see: http://reactionmechanismgenerator.github.io/RMG-Py/users/rmg/installation/anacondaDeveloper.html

IannLiu · 2022-04-03T07:29:22Z

The environment has been updated. You need to reinstall see: http://reactionmechanismgenerator.github.io/RMG-Py/users/rmg/installation/anacondaDeveloper.html

Hi, I got the same error after running the superminimal example. However, another error,
AttributeError: module 'julia.ReactionMechanismSimulator' has no attribute 'EmptyHenryLawConstant' occurred after installing and linking Julia dependencies.

mjohnson541 · 2022-04-03T13:22:34Z

Okay, in the environment run julia to open julia and then run

] add ReactionMechanismSimulator#main

The ] will disappear after you type it.

xiaoruiDong · 2022-04-06T18:53:32Z

@ChrisBNEU Hi Chris, I remembered you brought up this (or something similar) during the developer hour this week (Apr 4, 2022). Can you update here with what you found and what troubleshooting you have done? If there is a PR related please link it as well. Many thanks!

ChrisBNEU · 2022-04-06T19:51:38Z

So far, the problem appears to be that the ReactionMechanismSimulator package in julia does not update with the main branch of the RMS github repo, despite it being specified in the pyrms wrapper. Have not started a PR, the farthest I have gotten with it is it is we could solve it in the install step for julia:

julia -e 'using Pkg; Pkg.add(PackageSpec(name="ReactionMechanismSimulator",version="0.4")); ...'

I think we can specify this instead:

julia -e 'using Pkg; Pkg.add(PackageSpec(name="ReactionMechanismSimulator",rev="main")); ...'

although we should not need to do this, again since the repo is specified in pyrms. I have not gotten to the root cause of that yet.

Pegah-B · 2022-04-25T09:13:40Z

Hi, I have the similar issue on my mac 10.14.6 after installing the latest version of RMG (3.1.0) by pulling the most recent RMG-Py and RMG-Database from git. just according to the updated instruction as mentioned in "#2290 (comment)".
Running the minimal example of Ethane pyrolysis or any other input result in the error "NameError: name 'rms' is not defined". How should I fix the error?

mjohnson541 · 2022-04-25T14:53:52Z

If inside the rmg_env you run conda list and pyrms isn't in the dependencies you need to rebuild the rmg_env environment, there are faster ways to do this than entirely reinstalling, but entirely reinstalling is probably the easiest and least prone to error.
You should be launching RMG with python-jl now rather than python.
If the issue is none of the above activate the RMG environment and run:
julia -e 'using Pkg; Pkg.add(PackageSpec(name="ReactionMechanismSimulator",rev="main"));

Pegah-B · 2022-04-25T16:29:23Z

1- What I see in the list at the moment is:
pyrms 0.1.2 no_rmg_dep rmg
I did entirely reinstall it on the weekend and I still got the same error NameError: name 'rms' is not defined afterwards.
2- I already used python-jl.
3- I've just done it, but the same error still pops up for me.

mjohnson541 · 2022-04-25T16:34:10Z

Run
python-jl -c "from pyrms import rms"
and post the error trace you get.

Pegah-B · 2022-04-25T16:42:45Z

This is the result:

(rmg_env) Pegahs-MacBook-Pro:~ Pegah$ python-jl -c "from pyrms import rms"
Traceback (most recent call last):
  File "/Users/Pegah/opt/anaconda3/envs/rmg_env/lib/python3.7/site-packages/julia/pseudo_python_cli.py", line 308, in main
    python(**vars(ns))
  File "/Users/Pegah/opt/anaconda3/envs/rmg_env/lib/python3.7/site-packages/julia/pseudo_python_cli.py", line 52, in python
    exec(command, scope)
  File "<string>", line 1, in <module>
  File "/Users/Pegah/opt/anaconda3/envs/rmg_env/lib/python3.7/site-packages/pyrms/rms.py", line 6, in <module>
    from julia import Main
  File "<frozen importlib._bootstrap>", line 983, in _find_and_load
  File "<frozen importlib._bootstrap>", line 967, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 668, in _load_unlocked
  File "<frozen importlib._bootstrap>", line 638, in _load_backward_compatible
  File "/Users/Pegah/opt/anaconda3/envs/rmg_env/lib/python3.7/site-packages/julia/core.py", line 246, in load_module
    JuliaMainModule(self, fullname))
  File "/Users/Pegah/opt/anaconda3/envs/rmg_env/lib/python3.7/site-packages/julia/core.py", line 148, in __init__
    self._julia = loader.julia
  File "/Users/Pegah/opt/anaconda3/envs/rmg_env/lib/python3.7/site-packages/julia/core.py", line 238, in julia
    self.__class__.julia = julia = Julia()
  File "/Users/Pegah/opt/anaconda3/envs/rmg_env/lib/python3.7/site-packages/julia/core.py", line 471, in __init__
    self.api = LibJulia.from_juliainfo(jlinfo)
  File "/Users/Pegah/opt/anaconda3/envs/rmg_env/lib/python3.7/site-packages/julia/libjulia.py", line 195, in from_juliainfo
    sysimage=juliainfo.sysimage,
  File "/Users/Pegah/opt/anaconda3/envs/rmg_env/lib/python3.7/site-packages/julia/libjulia.py", line 217, in __init__
    setup_libjulia(self.libjulia)
  File "/Users/Pegah/opt/anaconda3/envs/rmg_env/lib/python3.7/site-packages/julia/libjulia.py", line 34, in setup_libjulia
    libjulia.jl_.argtypes = [c_void_p]
  File "/Users/Pegah/opt/anaconda3/envs/rmg_env/lib/python3.7/ctypes/__init__.py", line 377, in __getattr__
    func = self.__getitem__(name)
  File "/Users/Pegah/opt/anaconda3/envs/rmg_env/lib/python3.7/ctypes/__init__.py", line 382, in __getitem__
    func = self._FuncPtr((name_or_ordinal, self))
AttributeError: dlsym(0x11512df80, jl_): symbol not found

mjohnson541 · 2022-04-25T22:25:16Z

Hmm...I'm not sure what's happening there. It looks like it's erroring on from julia import Main in pyjulia so it doesn't look like an inherent pyrms issue. Can you try python-jl -c "from julia import Main"?

Pegah-B · 2022-04-25T22:43:59Z

Still the same:

(rmg_env) Pegahs-MBP:~ Pegah$ python-jl -c "from julia import Main"
Traceback (most recent call last):
  File "/Users/Pegah/opt/anaconda3/envs/rmg_env/lib/python3.7/site-packages/julia/pseudo_python_cli.py", line 308, in main
    python(**vars(ns))
  File "/Users/Pegah/opt/anaconda3/envs/rmg_env/lib/python3.7/site-packages/julia/pseudo_python_cli.py", line 52, in python
    exec(command, scope)
  File "<string>", line 1, in <module>
  File "<frozen importlib._bootstrap>", line 983, in _find_and_load
  File "<frozen importlib._bootstrap>", line 967, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 668, in _load_unlocked
  File "<frozen importlib._bootstrap>", line 638, in _load_backward_compatible
  File "/Users/Pegah/opt/anaconda3/envs/rmg_env/lib/python3.7/site-packages/julia/core.py", line 246, in load_module
    JuliaMainModule(self, fullname))
  File "/Users/Pegah/opt/anaconda3/envs/rmg_env/lib/python3.7/site-packages/julia/core.py", line 148, in __init__
    self._julia = loader.julia
  File "/Users/Pegah/opt/anaconda3/envs/rmg_env/lib/python3.7/site-packages/julia/core.py", line 238, in julia
    self.__class__.julia = julia = Julia()
  File "/Users/Pegah/opt/anaconda3/envs/rmg_env/lib/python3.7/site-packages/julia/core.py", line 471, in __init__
    self.api = LibJulia.from_juliainfo(jlinfo)
  File "/Users/Pegah/opt/anaconda3/envs/rmg_env/lib/python3.7/site-packages/julia/libjulia.py", line 195, in from_juliainfo
    sysimage=juliainfo.sysimage,
  File "/Users/Pegah/opt/anaconda3/envs/rmg_env/lib/python3.7/site-packages/julia/libjulia.py", line 217, in __init__
    setup_libjulia(self.libjulia)
  File "/Users/Pegah/opt/anaconda3/envs/rmg_env/lib/python3.7/site-packages/julia/libjulia.py", line 34, in setup_libjulia
    libjulia.jl_.argtypes = [c_void_p]
  File "/Users/Pegah/opt/anaconda3/envs/rmg_env/lib/python3.7/ctypes/__init__.py", line 377, in __getattr__
    func = self.__getitem__(name)
  File "/Users/Pegah/opt/anaconda3/envs/rmg_env/lib/python3.7/ctypes/__init__.py", line 382, in __getitem__
    func = self._FuncPtr((name_or_ordinal, self))
AttributeError: dlsym(0x1104f8f80, jl_): symbol not found

mjohnson541 · 2022-04-26T16:18:10Z

It must a Julia or pyjulia issue. What Julia version are you using?

Pegah-B · 2022-04-26T17:31:15Z

It is Julia Version 1.7.2 (2022-02-06).
How could I fix that then?

mjohnson541 · 2022-04-26T17:39:26Z

I'm not sure, are you on an M1 mac? We've had a lot of trouble with installs on those.

You can try installing the latest Julia 1.6 instead, which we've tested a lot more than Julia 1.7. If that doesn't work, I'm not sure what to do beyond opening an issue on pyjulia. If you have access to a linux computer or kernel the install for linux is pretty reliable since we package our own julia conda binaries with it.

Pegah-B · 2022-04-27T20:33:33Z

Thanks a lot. As you suggested, uninstalling Julia 1.7 and following the process again with Julia 1.6 this time, I did not get the error NameError: name 'rms' is not defined anymore. I just faced the error AttributeError: module 'julia.ReactionMechanismSimulator' has no attribute 'EmptyHenryLawConstant' which got fixed at once by what you commented earlier at #2290 (comment). Everything works pretty well now. I wanted to share my experience here and thank you again for your help.

ChrisBNEU · 2022-05-09T17:27:19Z

I tried a clean install using the developer instructions, with the modification to the rms install step:

julia -e 'using Pkg; Pkg.add(PackageSpec(name="ReactionMechanismSimulator",rev="main")); using ReactionMechanismSimulator;'

It worked fine when I did that, I opened PR #2305 to discuss this change. maybe it would be good to also include a caveat for V1.7 of julia, not sure if that is just a Mac/M1 chip issue.

xiaoruiDong added Type: Error Priority: High Should be addressed within 1 week RMS Type: Testing labels Apr 6, 2022

ChrisBNEU mentioned this issue May 9, 2022

update developer installation instructions to use the main rms branch #2305

Merged

alongd mentioned this issue Oct 11, 2022

AttributeError: henry_law_constant_data #2339

Closed

JacksonBurns mentioned this issue Jan 12, 2023

RMS compile issue during installation #2353

Closed

JacksonBurns mentioned this issue May 12, 2023

CI.yml and environment.yml updates to run CI on MacOS and Ubuntu #2415

Merged

JacksonBurns linked a pull request May 12, 2023 that will close this issue

CI.yml and environment.yml updates to run CI on MacOS and Ubuntu #2415

Merged

rwest closed this as completed in #2415 May 18, 2023

rwest mentioned this issue Jun 2, 2023

AttributeError: module 'julia.ReactionMechanismSimulator' has no attribute 'EmptyHenryLawConstant' #2451

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RMS error after commit 437739 #2290

RMS error after commit 437739 #2290

alirmg commented Apr 2, 2022 •

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IannLiu commented Apr 3, 2022 •

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RMS error after commit 437739 #2290

RMS error after commit 437739 #2290

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