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Make and use a julia system image #2443

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Make and use a julia system image #2443

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b178895
Refactor julia importing in reactors.py
rwest May 18, 2023
7c005ff
Added instructions into the RMG website for creating system image of rms
calvinp0 Mar 2, 2023
ca36b62
Adjusted the reactors.py import of Julia to always look for rms.so
calvinp0 Mar 2, 2023
6110a5d
Use comments instead of inline string literals.
rwest May 19, 2023
cbc52e8
Use rmgpy.get_path to get the path to the rms.so system image
rwest May 19, 2023
613fb28
Print statements about using the Julia system image.
rwest May 19, 2023
c616741
TEMPORARY: A CI step that lets you connect to a shell to debug.
rwest May 19, 2023
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5 changes: 5 additions & 0 deletions .github/workflows/CI.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -134,6 +134,11 @@ jobs:
exit 1
fi

# For debugging
- name: Setup tmate session
uses: mxschmitt/action-tmate@v3
if: ${{ failure() }}

# Upload Regression Results as Failed if above step failed
- name: Upload Failed Results
if: failure()
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5 changes: 5 additions & 0 deletions documentation/source/users/rmg/installation/anacondaDeveloper.rst
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Expand Up @@ -151,6 +151,11 @@ Installation by Source Using Anaconda Environment for Unix-based Systems: Linux
python -c "import julia; julia.install(); import diffeqpy; diffeqpy.install()"


#. Create custom system image of Julia with RMS compiled,
to greatly accelerate launching::

python -m julia.sysimage rms.so

#. Finally, you can run RMG from any location by typing the following (given that you have prepared the input file as ``input.py`` in the current folder). ::

python-jl replace/with/path/to/rmg.py input.py
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49 changes: 31 additions & 18 deletions rmgpy/rmg/reactors.py
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Stylistically I think the "normal" case should come first in the if/elif/else.

I also think the failure to import pyrms, diffeqpy, or Julia should raise an exception not log a warning - not being able to simulate reactors should stop execution outright IMO. I am aware that other packages currently assume that this import fails and ignore it, but we are burying a significant runtime issue here. Other codes should do something like

try:
    from rmgpy import reactors
except JuliaImportError as jie:
    warnings.warn("Julia import failed as expected")

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Raising an exception to be handled by the calling code would mean the rest of this file would not get imported, which is what this "try/pass" thing is trying to achieve. I think the use case is code that needs to import this module, but doesn't actually execute anything important in it.
Not very satisfactory, I agree, (in more ways than one) but fixing is beyond scope of this PR.

Original file line number Diff line number Diff line change
Expand Up @@ -35,25 +35,38 @@
import sys
import logging
import itertools
import os
from rmgpy import get_path

try:
from julia.api import Julia
system_image_path = os.path.join(os.path.dirname(get_path()), "rms.so")
# Should be RMG-Py/rms.so for a normal install, alongside rmg.py
if os.path.exists(system_image_path):
print(f"Using system Julia system image at {system_image_path}")
jl = Julia(sysimage=system_image_path)
else:
print(f"Couldn't find Julia system image at {system_image_path}. "
"Using default Julia system image.")
if __debug__:
# This is the normal case (__debug__ is True by default)
jl = Julia(compiled_modules=False) # Disable incremental precompilation of modules.
else:
# This means that python was run with the -O flag.
# I don't know why or how often that is done
# (all it does usually is remove assert statements),
# nor why one would then need or wish to skip creating a Julia runtime,
# and allow incremental precompilation to be its default,
# but for now I'm trying to refactor without changing behaviour.
pass
from pyrms import rms
from diffeqpy import de
from julia import Main
except Exception as e:
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Bare exceptions are also considered bad practice. We should try to catch specific exceptions - failing to import Julia api could be because Julia is not installed, failed to load Julia with the image, specific imports fail, etc.

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I agree in principle, bare exceptions are a code smell. But I'm hoping that in future this whole thing can go away. I think it was introduced so ARC could pass nose tests or something - where this file is imported somewhere but nothing in it needs to actually run.
For this use case, all exceptions should be treated the same, so I'm going to leave it as is, until we get rid of it entirely.
At least I added some logging so we can see what the exception is.

logging.exception(e)
logging.warning("Could not import pyrms, RMS simulations will not be available")
pass

if __debug__:
try:
from os.path import dirname, abspath, join, exists
path_rms = dirname(dirname(dirname(abspath(__file__))))
from julia.api import Julia
jl = Julia(sysimage=join(path_rms,"rms.so")) if exists(join(path_rms,"rms.so")) else Julia(compiled_modules=False)
from pyrms import rms
from diffeqpy import de
from julia import Main
except:
pass
else:
try:
from pyrms import rms
from diffeqpy import de
from julia import Main
except:
pass

from rmgpy.species import Species
from rmgpy.reaction import Reaction
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