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everything is literally everything including scrolling , switching apps , typing even moving pointer is very laggy , i'm using Debian Stretch with GNOME and nautilus (obviously)

Here's top output

root@www:~# top

top - 19:27:05 up 1 day,  3:15,  1 user,  load average: 5.53, 5.61, 3.84
Tasks: 229 total,   1 running, 228 sleeping,   0 stopped,   0 zombie
%Cpu(s):  0.8 us,  2.0 sy,  0.0 ni, 25.0 id, 72.1 wa,  0.0 hi,  0.2 si,  0.0 st
KiB Mem :  7945316 total,   102772 free,  2399920 used,  5442624 buff/cache
KiB Swap:  8152572 total,  8152572 free,        0 used.  4927412 avail Mem 

  PID USER      PR  NI    VIRT    RES    SHR S  %CPU %MEM     TIME+ COMMAND                     
 7627 root      20   0   13168   2452   1856 S   4.7  0.0   0:32.63 mount.ntfs                  
 7609 rahman    20   0  980360  51112  36556 S   1.3  0.6   0:20.01 nautilus                    
12419 rahman    20   0 1510144  80536  32580 S   1.3  1.0   6:57.26 transmission-gt             
 5139 root      20   0  266576   5448   4592 S   0.7  0.1   8:46.92 iio-sensor-prox             
 5340 root      20   0       0      0      0 S   0.7  0.0   0:01.31 kworker/u16:9               
 7647 root      20   0   13356   2516   1816 S   0.7  0.0   0:04.50 mount.ntfs                  
 7844 rahman    20   0 2509544 283260  66824 S   0.7  3.6  50:20.60 gnome-shell                 
    3 root      20   0       0      0      0 S   0.3  0.0   0:00.87 ksoftirqd/0                 
   16 root      20   0       0      0      0 S   0.3  0.0   0:05.33 ksoftirqd/1                 
   28 root      20   0       0      0      0 S   0.3  0.0   0:06.55 ksoftirqd/3                 
   47 root      20   0       0      0      0 D   0.3  0.0   0:04.99 kswapd0                     
  217 root      20   0       0      0      0 S   0.3  0.0   0:05.00 jbd2/sda8-8                 
 7877 root      20   0       0      0      0 D   0.3  0.0   0:00.11 kworker/2:2                 
 8160 root      20   0   45032   3800   3044 R   0.3  0.0   0:00.04 top                         
    1 root      20   0  204824   7144   5256 S   0.0  0.1   0:08.84 systemd                     
    2 root      20   0       0      0      0 S   0.0  0.0   0:00.08 kthreadd                    
    5 root       0 -20       0      0      0 S   0.0  0.0   0:00.00 kworker/0:0H 

my xorg intel configuration file is : (i use intel hd graphics ironlake)

root@www:~# cat /etc/X11/xorg.conf.d/20-intel.conf 
Section "Device"
   Identifier  "Intel Graphics"
   Driver      "intel"
   Option      "AccelMethod" "sna"
   Option      "DRI"         "3"
EndSection

if you need some sort of more info please leave a comment below, don't ignore.

3

The clue is here:

%Cpu(s):  0.8 us,  2.0 sy,  0.0 ni, 25.0 id, 72.1 wa,  0.0 hi,  0.2 si,  0.0 st

72% of your CPU power is stuck waiting for I/O operations to complete. If I had to guess, your USB medium is connected to a port running directly from the motherboard's chipset rather than a PCI card, and it's jumping to the front of the line.

  • i guess you're right,i tried another port and wa is almost same so i guess all of my USB ports run directly from the motherboard's chip-set , is there any way to fix that even a little bit ? – A.Rahman Mahmoud Oct 9 '17 at 18:00
  • Beside, I had 25% idle CPU so why did it act like its stuck at 100% – A.Rahman Mahmoud Oct 9 '17 at 18:42
  • Not shown: the number of cores; if your GUI composter thread was on the same core as the USB I/O thread, for instance, that might cause this sort of thing. – DopeGhoti Oct 9 '17 at 20:00
  • That 72% of power is not stuck, really. It's just the percentage of time spent waiting for I/O doing nothing, basically a different type of idle. – Ferenc Wágner Oct 11 '17 at 12:57
  • If it's committed to waiting for an I/O operation to complete and cannot be allocated to other processes, that's close enough to 'stuck' or at the very least 'unavailable' for the purposes of this question, in my opinion. – DopeGhoti Oct 11 '17 at 17:40

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