leiden alg with igraph flavor causes out of bounds freezing #2969
Comments
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@RubenVanEsch Can you provide a more minimally reproducible example? For example, paring down a bit the above to just: import scanpy as sc
em_adata = sc.datasets.pbmc3k()
sc.pp.pca(em_adata, n_comps=50)
sc.pp.neighbors(em_adata)
sc.tl.umap(em_adata)
sc.tl.leiden(em_adata,flavor='igraph',n_iterations=2,random_state=1653,directed=False)does not yield any error. |
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@ilan-gold your minimal example causes the exact same error: Exception ignored in: <class 'ValueError'> if you are curious, it spits the error out 14.210 times (71050 lines of error message) EDIT: the random state does not seem to matter btw, also happens with different random states |
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Ok @RubenVanEsch we have to assume that this is a windows problem then. I think we will try to set up a test job and hopefully this catches the problem, although will likely catch others. What happens without a |
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@ilan-gold same thing without random state |
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@RubenVanEsch Yes, and the issue there is that we're not the ones calling |
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If the problem is windows, it's possible it will be solved by numpy 2.0. Not sure how easy the upgrade path to numpy 2.0 will be, however. |
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I got the test runner to do windows and while there were other errors, this one was seemingly not present: https://dev.azure.com/scverse/scanpy/_build/results?buildId=6287&view=logs&j=4eb20215-89fc-58e4-6218-2c2fa88ddf72&t=482e4b16-75d9-5f8c-9594-aadcd098d2cb&l=3977 We have a test that is strikingly similar to the more minimal example from above: https://github.com/scverse/scanpy/blob/main/scanpy/tests/notebooks/test_pbmc3k.py minus the umap. Could you try this test (which doesn't call In general there will be some back and forth here until we find someone near us with a windows machine since using CI to fix this problem isn't really feasible, but at least we can narrow the scope. |
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@RubenVanEsch, are you able to run this in WSL? Also, does the number you pass for random seed matter? |
From @RubenVanEsch :
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@ivirshup @ilan-gold just got back to this, thought i could not install wsl as I am on a somewhat company restricted laptop, but turns out i can. installing it now (and probably using that from here on out). will run the tester in a bit and let you know |
@melonora, would you mind running this on your windows machine with the latest scanpy release to see if you can reproduce it? |
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Yes I will and report back. Most likely in the evening. |
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I can reproduce, this is the error that I get: From a first glance it seems like the default for randint is used which is |
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I will see if I can reproduce on main and pinpoint where the problem arises. |
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Do you guys still want me to try and run the test from @ilan-gold ? Or is it fine now that it is reproduced on your side as well? |
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It is reproduced. It is due to the The part of the code that fails due to this is when using the context manager to perform the leiden clustering with igraph flavor. |
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In particular here is the piece of code: scanpy/scanpy/tools/_leiden.py Lines 184 to 185 in a33111f Though the |
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Where would you put the |
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It wouldn't be on our side. As far as I know the numpy random number generator is called from within c code within igraph itself. |
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Since we can’t test this without your help, could you check if passing your own RNG here makes it work? |
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I can test tomorrow |
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I can reproduce this bug on my machine as well. I can supply additional information or context if needed, and I can test fixes |
I can reproduce the error using Numpy 2.0.2. |
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@patrick-nicodemus What we need more than anything is someone to test out a fix and to confirm that using See #3041 The issue is that we don't have windows machines. |
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@ilan-gold If you want to try it out, I give instructions for how to reproduce the error with a Docker container for Windows in the cross-referenced issue. I also have tried it on WSL, and the problem is not present on WSL, so this is a workaround for Windows users. However, I am organizing a Python workshop in a few weeks, and I think it would add some additional administrative burden/overhead to the workshop to coordinate installing and setting up WSL (as we see in #3041, Ruben had trouble installing WSL and others might as well.) So, for me, using WSL is a suboptimal workaround. |
Yes please. I’m confused how Windows comes into play though since I thougt that Docker always runs on a Linux kernel – natively on Linux and in a VM on macOS and Windows. |
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Yes, this was my impression too. However there is a documented option
"Switch to Windows containers" which is available if you right click on the
Docker icon in the taskbar and this allows one to run vms using a Windows
kernel.
…On Fri, Sep 6, 2024, 3:36 AM Philipp A. ***@***.***> wrote:
If you want to try it out, I give instructions for how to reproduce the
error with a Docker container for Windows in the cross-referenced issue
Yes please. I’m confused how Windows comes into play though since I thougt
that Docker always runs on a Linux kernel – natively on Linux and in a VM
on macOS and Windows.
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Adding a link here for a comment I made in the |
Please make sure these conditions are met
What happened?
was running the standard pipeline on some data and when i run
sc.tl.leiden(em_adata,flavor='igraph',n_iterations=2,random_state=1653,directed=False)it spits out infinite lines of ignored exceptions. it does not actually crash the kernel, but does bog it down and causes everything to to take much more time than necesarry.
I am working in a conda env on a Win 10 , 64bit, x64 system
the problem also occurs using the pbmc3k dataset
Minimal code sample
Error output
Versions
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