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Run out of memory allocating stoichiometry matrix #5

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rwest opened this issue Oct 23, 2009 · 3 comments
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Run out of memory allocating stoichiometry matrix #5

rwest opened this issue Oct 23, 2009 · 3 comments
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Topic: Performance

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@rwest
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rwest commented Oct 23, 2009

This seems to be the limiting factor on how large a model you can build
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rwest commented Oct 23, 2009

Stoichiometry matrix is now sparse. This should help memory problems.

Had to replace a few calls to numpy.dot, but I think I got it working again.
Some info on sparse matrices in numpy can be found at
http://www.scipy.org/SciPy_Tutorial

Closed by 401aff2 (hopefully this linking to the issue tracker works!)

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rwest commented Nov 16, 2009

Reverted by e525b08 because creating the sparse lilmatrix was very very slow.
We need a better way to solve this

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rwest commented Mar 25, 2010

I think this is solved again by Josh, but I can't remember when.

@mjohnson541 mjohnson541 mentioned this issue Oct 20, 2017
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kblondal pushed a commit to kblondal/RMG-Py that referenced this issue Oct 17, 2018
@rwest
Run findCp0andCpInf when estimating thermo of surface species.
2cc2f37 
Addresses the comment in
cfgoldsmith#5 (comment)
but not actually issue ReactionMechanismGenerator#5.
@jimchu10 jimchu10 mentioned this issue Jun 12, 2019
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@hwpang hwpang mentioned this issue Aug 28, 2019
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@AH9316 AH9316 mentioned this issue Nov 23, 2019
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rwest added a commit that referenced this issue Jun 6, 2023
@rwest
Fix typo in environment.yml
a9b7a3d 
This is a combination of 12 commits, as we tried everything under the sun to debug the CI.
But they all cancelled out when merged (apart from fixing a typo in a comment)

- This is the 1st commit message:
CI: trying to force ubuntu-20.04 instead of ubuntu-latest (temporary)
While we figure out what's happening, let's try an older ubuntu.
- This is commit message #2:
fixup! CI: trying to force ubuntu-20.04 instead of ubuntu-latest (temporary)
- This is the commit message #3:
Switch back to ubuntu-latest
But leave a 20.04 in the matrix build
- This is the commit message #4:
Trying libstdcxx-ng < 13 in Conda environment.
Trying to debug. If this works it should be put in docker file too.
Or, better, the real cause found and fixed.
- This is the commit message #5:
fix typo in env, undo ubuntu os changes, set gcc version in CI to 6
this system object of this version is being provided by gcc, and the
runners no longer come prepackaged with it since its old (?)
- This is the commit message #6:
it wasn't the gcc version
- This is the commit message #7:
it was the julia version, 1.9.0 is brokey
as reported at conda-forge/julia-feedstock#253
the latest release of julia (1.9.0) is brokey, don't use it (put !=1.9.0 in the environment file)
- This is the commit message #8:
make mac and ubuntu use the same cxx library
- This is the commit message #9:
but what if it was rdkit all along?
- This is the commit message #10:
Revert "but what if it was rdkit all along?" because it wasn't
- This is the commit message #11:
Revert "make mac and ubuntu use the same cxx library" cos it didn't work
- This is the commit message #12:
Revert "it was the julia version, 1.9.0 is brokey" but it wasn't
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