Here’s an update. I set up atop on my VPS and waited until the issue occurred again. Here’s the atop log from the event.

ATOP - ip-172-31-7-27   2023/07/22  18:40:02   -----------------   10m0s elapsed
PRC | sys    9m49s | user  12.66s | #proc    134 | #zombie    0 | #exit      3 |
CPU | sys      99% | user      0% | irq       0% | idle      0% | wait      0% |
MEM | tot   957.1M | free   49.8M | buff    0.1M | slab   95.1M | numnode    1 |
SWP | tot     0.0M | free    0.0M | swcac   0.0M | vmcom   2.4G | vmlim 478.6M |
PAG | numamig    0 | migrate    0 | swin       0 | swout      0 | oomkill    0 |
PSI | cpusome  63% | memsome  99% | memfull  88% | iosome   99% | iofull    0% |
DSK |         xvda | busy    100% | read  461505 | write    171 | avio 1.30 ms |
DSK |        xvda1 | busy    100% | read  461505 | write    171 | avio 1.30 ms |
NET | transport    | tcpi    2004 | tcpo    1477 | udpi       9 | udpo      11 |
NET | network      | ipi     2035 | ipo     1521 | ipfrw     20 | deliv   2015 |
NET | eth0    ---- | pcki    2028 | pcko    1500 | si    4 Kbps | so    1 Kbps |

    PID SYSCPU USRCPU  VGROW  RGROW  RDDSK  WRDSK  CPU CMD            
     41  5m17s  0.00s     0B     0B     0B     0B  53% kswapd0        
      1 21.87s  0.00s     0B -80.0K   1.2G     0B   4% systemd        
  21681 20.28s  0.00s     0B   4.0K   4.2G     0B   3% lemmy          
    435 18.00s  0.00s     0B 392.0K 163.1M     0B   3% snapd          
  21576 17.20s  0.00s     0B     0B   4.2G     0B   3% pict-rs        

The culprit seems to be kswapd0 trying to move memory to swap space, although there is no swap space.

I set memory swappiness to 0 on the system for now, I’ll check if that makes a difference.