Today we ran into an issue where we had a one-off script that just needed to work, but it was just chewing threw memory like nothing.
Pre check the status of memory.
There are a number of ways that you can check the amount of memory on your system. The easiest is not necessarily my first go to is free... literally free.
check for free space
$ free -h
total used free shared buffers cached
Mem: 15G 15G 150M 0B 59M 8.7G
Generally my first go to is a bit more graphical, and not available on a stock stystem, but far more useful.... htop. htop is a terminal process explorer that shows cpu usage, mem usage, and running processes.
htop
sudo apt-get install htop # install it from your package repo
htop
First step throw more swap at it
Often before going through the process of getting a larger instance underneath the notebook you can hobble home with a bit more swap file. It may not be pretty or fast, but gets the job done in a pinch.
Check for free disk
$ du
Filesystem Size Used Avail Use% Mounted on
/dev/asdasd 200G 50G 150G 25% /
Make sure you check your free disk space first, filling both memory and disk can be bad news
make a swap file and activate it
SWAPFILE=~/swaps/swap1-50G
mkdir ~/swaps
sudo fallocate -l 50G $SWAPFILE
sudo chmod $SWAPFILE
sudo mkswap $SWAPFILE
sudo swapon $SWAPFILE
https://linuxize.com/post/how-to-add-swap-space-on-ubuntu-20-04/featured.jpg?ezimgfmt=ng:webp/ngcb30
More details on creating swapfiles checkout linuxize. It is my favorite linux tutorial site!
Refactor - functions
keep big datasets inside functions returning aggregations
Sometimes there is a clear quick and simple way to just let the python garbage collector. Often we pull in large datasets to create features then aggregate them down into smaller datasets that can be then joined into other datasets. This pattern of pulling in big_data, processing then aggregating can be a simple one.
let the garbage collector take care of big data
def process():
big_data = get_big_data()
smaller_data = <some aggregation>
return smaller_data
data = process()
If your notebook is following this type of pattern a simple del won't work because ipython adds extra references to your big_data that you didnt add. These are things that enable features like _, __, ___, umong others.
%reset
check out more on reset from the ipython docs
The last resort I would lean on here is an ipython specific feature %reset and %reset_selective. These will flush out all user define variables or selecive ones based on a regex respectively.
Following two example are directly from the ipython docs
%reset
In [6]: a = 1
In [7]: a
Out[7]: 1
In [8]: 'a' in get_ipython().user_ns
Out[8]: True
In [9]: %reset -f
In [1]: 'a' in get_ipython().user_ns
Out[1]: False
In [2]: %reset -f in
Flushing input history
In [3]: %reset -f dhist in
Flushing directory history
Flushing input history
_%reset_selective_
In [2]: a=1; b=2; c=3; b1m=4; b2m=5; b3m=6; b4m=7; b2s=8
In [3]: who_ls
Out[3]: ['a', 'b', 'b1m', 'b2m', 'b2s', 'b3m', 'b4m', 'c']
In [4]: %reset_selective -f b[2-3]m
In [5]: who_ls
Out[5]: ['a', 'b', 'b1m', 'b2s', 'b4m', 'c']
In [6]: %reset_selective -f d
In [7]: who_ls
Out[7]: ['a', 'b', 'b1m', 'b2s', 'b4m', 'c']
In [8]: %reset_selective -f c
In [9]: who_ls
Out[9]: ['a', 'b', 'b1m', 'b2s', 'b4m']
In [10]: %reset_selective -f b
In [11]: who_ls
Out[11]: ['a']
Develop faster utilizing autoreload in ipython
The above tips will help you reclaim used memory in ipython, but the following tip is one that single handedly is the reason I use Ipython for faster development over anything else.
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