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Memory leak #142
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Thanks @Floreuzan. I also need a more clean code that cost fewer memroy. But it seems require a little bit effort to refactor the code. |
any up comming release of GSEApy which re-written in Rust will fix the problem here !!! Stay tune |
The Rust binding of GSEApy (v0.11.0) has been released. Close the issue now |
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Setup
I am reporting a problem with GSEApy version, Python version, and operating
system as follows:
3.7.11 (default, Jul 27 2021, 09:42:29) [MSC v.1916 64 bit (AMD64)]
CPython
Windows-10-10.0.19041-SP0
0.10.5
Expected behaviour
I want to run the gp.prerank() function.
Actual behaviour
I choose the C2 geneset from the MSigDB website, it has approximatively 6300 genesets.
Even though I call the function on a system with ~80 GB of RAM with swap space, it appears to be a memory leak because using swap space does not slow the calculation down -it's not going back to the memory it has used previously.
Attempted fix
To solve this issue, I modified the fie GSEApy/gseapy/algorithm.py, in the function gsea_compute(), it calls for the function Parallel() from the joblib package, then you can rermove the require=’sharedmen’ option (line 509).
In other words,
becomes:
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