Memory leak in io.load_electron_counts

[ercius]

I often will use the same notebook to look through many datasets without restarting the kernel.

I often run ee = stio.load_electron_counts(fullPath) and each time I run this the memory increases.

Using del ee does not release the memory. Running garbage collection import gc;gc.collect() also does not release the memory.

Is there a way to release the memory?

[cjh1]

@ercius I will take a look, del ee should do it.

[cjh1]

Is it just with the stio.load_electron_counts(fullPath) call that you see the memory increase, as in is there anything else going on in the notebook?

[cjh1]

OK, I can recreate this in a simple notebook, will work out what is going on.

[cjh1]

So I was able to create a test case without stempy that shows the same behavior. It seems the problem only occur with the vlen type. I have raised an issue with h5py, we will see if they can shed any light on this, its possible its a bug in h5py.

[ercius]

Thanks for looking into this. Let's see what h5py says.

On Fri, Nov 6, 2020, 10:11 AM Chris Harris [email protected] wrote:

So I was able to create a test case without stempy that shows the same behavior. It seems the problem only occur with the vlen type. I have raised an issue with h5py, we will see if they can shed any light on this, its possible its a bug in h5py.

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[ercius]

this is tracked in https://github.com/h5py/h5py/issues/1747