Short periodic freezes every few seconds. Everything except the mouse

My computer freezes every 1 or 2 seconds for a short period as well. So 1 or 2 seconds working and 1 or 2 seconds not working. Everything stops working except for the mouse. ---------- The first time I discovered the problem was when I wanted to open a 1GB txt file with leafpad. The syslog (and other files) raised to 350MB with leafpad errors. I still don't really think it could be the cause but since then I have noticed it slow. I tried deleting those lines to make the files lighter but didn't work (ofc). The line was a repetition of: localhost leafpad: pango_tab_array_get_tab: assertion 'tab_index >= 0' failed ---------- **Gnome-shell debugging** (In the end I think the problem is not there) I have runned top to see the problem and my first guess was that gnome-shell. I have disabled all extensions on gnome and I have put Hidden=True on the gnome tracker. Reboot ofc but issue still continues. top - 11:37:47 up 16 min, 1 user, load average: 5.08, 4.53, 3.07 Tasks: 186 total, 1 running, 185 sleeping, 0 stopped, 0 zombie %Cpu(s): 5.4 us, 13.6 sy, 0.0 ni, 78.8 id, 2.2 wa, 0.0 hi, 0.0 si, 0.0 st MiB Mem : 11894.0 total, 9255.9 free, 884.7 used, 1753.4 buff/cache MiB Swap: 0.0 total, 0.0 free, 0.0 used. 10597.3 avail Mem PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND 1467 root 20 0 3828560 258004 73056 S 16.9 2.1 3:00.91 gnome-she+ 1627 root 20 0 384600 23668 17328 S 13.0 0.2 1:31.00 gsd-xsett+ 1732 root 20 0 1190848 66960 31648 S 11.6 0.5 1:21.92 gnome-sof+ 2371 root 20 0 239576 28532 22080 S 9.0 0.2 0:49.61 leafpad 2282 root 20 0 1397692 79500 38488 S 8.3 0.7 2:27.84 nautilus 1618 root 20 0 452484 40448 13752 S 7.6 0.3 1:01.97 packageki+ 1643 root 20 0 384156 24452 17428 S 5.3 0.2 1:16.62 gsd-keybo+ 1636 root 20 0 236512 22152 17128 S 3.0 0.2 1:16.76 gsd-clipb+ 1269 root 20 0 343084 47552 32060 S 0.7 0.4 0:19.31 Xorg 9 root 20 0 0 0 0 I 0.3 0.0 0:01.07 rcu_sched 1176 message+ 20 0 18272 5276 3476 S 0.3 0.0 0:01.51 dbus-daem+ 1640 root 20 0 550896 24776 19364 S 0.3 0.2 1:18.79 gsd-color 2850 root 20 0 527664 39564 28252 S 0.3 0.3 0:07.43 gnome-ter+ 3048 root 20 0 15804 3484 3040 R 0.3 0.0 0:00.01 top 1 root 20 0 192548 9036 6632 S 0.0 0.1 0:02.95 systemd 2 root 20 0 0 0 0 S 0.0 0.0 0:00.00 kthreadd 3 root 0 -20 0 0 0 I 0.0 0.0 0:00.00 rcu_gp I have used the following to know where the issue was and it seeams openat takes the majority. What also get's my attention is the amount of errors that function gets and I guess that might be the problem. strace -c -p 1467 strace: Process 1467 attached ^Cstrace: Process 1467 detached % time seconds usecs/call calls errors syscall ------ ----------- ----------- --------- --------- ---------------- 38.35 2.269925 65 34909 22415 openat 21.63 1.280485 1583 809 252 unlink 18.82 1.113966 4700 237 15 link 16.79 0.993957 4498 221 rename 0.96 0.056549 2 30633 21313 access 0.91 0.053897 3 20006 186 stat 0.47 0.027686 1 19059 read 0.42 0.024586 2 12498 close 0.33 0.019538 2 10852 fstat 0.28 0.016418 5 3083 munmap 0.21 0.012386 4 3099 mmap 0.18 0.010921 21 528 write 0.13 0.007561 1 7413 getuid So I killed the gnome-shell process and still the problem remains. I don't really see what the problem may be and I have a 4 cores intel i7 processor pc so it shouldn't be so demanded. ---------- iostat -h Linux 10/11/2018 _x86_64_ (4 CPU) avg-cpu: %user %nice %system %iowait %steal %idle 24.4% 0.4% 21.4% 10.8% 0.0% 43.0% tps kB_read/s kB_wrtn/s kB_read kB_wrtn Device 11.14 175.3k 0.0k 16.6M 0.0k sda 235.07 6.6M 2.9M 641.9M 286.4M sdb 769.76 789.5k 0.0k 75.0M 0.0k loop0