spyder: `numpy.load` slows `runcell`

demo.mp4

Despite last command printing 0.0, runcell(3, ...) took several seconds. Strangely, shape = (2, ...) & dtype='float64', which is same size in memory, doesn’t yield this effect; haven’t tested with 'float32'. Also, IPython commands aren’t slowed.

Using spyder 4.2.1 as conda doesn’t have 4.2.2 yet; Win 10 x64, Python 3.7.9, numpy 1.19.2.

Code:

import numpy as np

X = np.random.randn(16, 16, 240, 24000).astype('float16')
np.save('arr.npy', X)

Restart kernel

import numpy as np
from time import time
out = np.load('arr.npy')

#%%
t0 = time()
t1 = time()

#%% 
print(t1 - t0)

About this issue

Original URL
State: open
Created 3 years ago
Comments: 21 (19 by maintainers)

Most upvoted comments

Maybe we should add a message saying: “Computing min/max for the current variables took more than 2 seconds. Do you want to disable automatic variable explorer refreshing?”

impact27 on Mar 15, 2021

I can confirm that this is due to min max in the variable explorer. X takes 30 seconds to compute on my box and X.max() takes about 13 seconds. It seems that variable explorer is recomputing the min max of every variable in the explorer when it gets the call to refresh after runcell or runfile. If the variable explorer is busy when runcell or runfile is

@OverLordGoldDragon @sawtw thanks for helping get to the bottom of this! Here is a work around: Open variable explorer, right click on the table and uncheck “show arrays min/max” wait for a while for the explorer to refresh and then it should be speedy again.

Debugging

Issue 1: Varible Exporer updates every variable regardless of change

With one array in the variable explorer and min/max enabled, it takes about 26 seconds to refresh the variable explorer. This is regardless of whether the array has changed. Just just running t0 = time() in either IPython directly of through runcell it takes ~26 s for the variable explorer to update.

I don’t know if there is much to be done here. Perhaps we check the array size and don’t give min/max past a certain size.

Issue 2: `Runcell` and `runfile` seem to wait for comms from variable explorer.

The issue for this bug is that runcell gets stuck in comms if variable explorer is already updating. If you use runcell and variable explorer is finished updating, runcell work just fine. I only gets stuck when you are running one cell right after the other. The first cell you run will return normally while the next cell waits until the update in the variable explorer to from the previous cell is finished.

Does the variable explorer need to respond to runcell or is it good enough to just assume it will update.

bcolsen on Mar 12, 2021