System freeze. RAM and SWAP full? iowait goes high and processes all seem to want to read and write data at high speeds to hdd

Question

EDIT: I messed up the install below due to n00b and trying bleachbit and updating, probably not rebooting in between had that effect. Could fix most of it but didn't feel right. SO I moved to a clean install of 19.10. System has 6GB of ram, install chose, again, to allocate too little swapspace (still only 2GB, compared to 1GB in the previous install) HOWEVER in 19.10 physical RAM doesn't fill up nearly as fast and the swapspace that is being used is around 500MB after 10 hours of use while the 19.04 version would fill up both after an hour orso of use. Had to reboot after 3 hours. So, at least to me, it would seem that memory management in 19.10 has improved, or that there is something wrong in the 19.04 version. I still allocated 6GB of memory, just to be sure. Running conky I get to monitor stuff and I think this is the way Linux is supposed to function. So should I not be the only one out there with this problem on Disco Dingo, try moving to a newer version.

System does what I stated in the problem desc. I have been trying to find out what goes wrong where and via "glances" and "iotop" it has led me to this problem description. The swap and ram fills up, is able to stay at around 99% for a period of time (most often it takes a couple of hours before the system becomes unresponsive) and then iowait just goes through the roof. The moment that happens, hdd led starts burning full and disk read/writes of most, if not all, processes are shown to be anywhere from 0 to tens of MB/s in iotop. Which doesn't get the time to update anymore, nor does glances. The only thing that then works is a hard reset. I need to do this multiple times a day and is making my linux experience horrible.

The best I could find over the last couple of weeks was this problem description from someone who has been experiencing the same problem as I am experiencing on my laptop. https://unix.stackexchange.com/questions/373312/oom-killer-doesnt-work-properly-leads-to-a-frozen-os

This is a serious problem which more people, even very experienced ones, far more than me, seem to encounter quite a bit. Yet, no one seems to know where to turn to. To verify the above, please consult the link above and its links and comments.

Anyone? Any tips or advice? Somewhere to turn to perhaps?

Here are my systems' specs and output which I'll list for completeness. However, I am unsure if this will be of any benefit. If any other data is necessary, please provide me with the required commands and I will execute them gladly.

echo $MACHTYPE
x86_64-pc-linux-gnu

and

cat /etc/*-release
DISTRIB_ID=Ubuntu
DISTRIB_RELEASE=19.04
DISTRIB_CODENAME=disco
DISTRIB_DESCRIPTION="Ubuntu 19.04"
NAME="Ubuntu"
VERSION="19.04 (Disco Dingo)"
ID=ubuntu
ID_LIKE=debian
PRETTY_NAME="Ubuntu 19.04"
VERSION_ID="19.04"
HOME_URL="https://www.ubuntu.com/"
SUPPORT_URL="https://help.ubuntu.com/"
BUG_REPORT_URL="https://bugs.launchpad.net/ubuntu/"
PRIVACY_POLICY_URL="https://www.ubuntu.com/legal/terms-and-policies/privacy-policy"
VERSION_CODENAME=disco
UBUNTU_CODENAME=disco

and

sudo vmstat
procs -----------memory---------- ---swap-- -----io---- -system-- ------cpu-----
 r  b   swpd   free   buff  cache   si   so    bi    bo   in   cs us sy id wa st
 4  0 443648 1339308  19684 897180    1    9    48    41  674  536 22  7 66  5  0

and

lsblk -a
NAME                  MAJ:MIN RM   SIZE RO TYPE MOUNTPOINT
loop0                   7:0    0  35,3M  1 loop /snap/gtk-common-themes/1198
loop1                   7:1    0  54,4M  1 loop /snap/core18/1144
loop2                   7:2    0   2,3M  1 loop /snap/gotop/3
loop3                   7:3    0   4,2M  1 loop /snap/gnome-calculator/501
loop4                   7:4    0 117,2M  1 loop /snap/screencloud/2
loop5                   7:5    0     4M  1 loop /snap/gnome-calculator/406
loop6                   7:6    0 317,5M  1 loop /snap/pycharm-educational/14
loop7                   7:7    0  14,8M  1 loop /snap/gnome-characters/254
loop8                   7:8    0 140,7M  1 loop /snap/gnome-3-26-1604/92
loop9                   7:9    0  53,7M  1 loop /snap/core18/941
loop10                  7:10   0  12,6M  1 loop /snap/dmd/74
loop11                  7:11   0   956K  1 loop /snap/gnome-logs/73
loop12                  7:12   0 317,8M  1 loop /snap/pycharm-educational/16
loop13                  7:13   0    89M  1 loop /snap/core/7713
loop14                  7:14   0   6,5M  1 loop /snap/gnome-clocks/198
loop15                  7:15   0  65,9M  1 loop /snap/discord/93
loop16                  7:16   0   151M  1 loop /snap/gnome-3-28-1804/31
loop17                  7:17   0  52,2M  1 loop /snap/tvheadend/86
loop18                  7:18   0 149,9M  1 loop /snap/gnome-3-28-1804/71
loop19                  7:19   0   7,9M  1 loop /snap/amass/706
loop20                  7:20   0   6,9M  1 loop /snap/dub/37
loop21                  7:21   0  42,8M  1 loop /snap/gtk-common-themes/1313
loop22                  7:22   0 320,2M  1 loop /snap/pycharm-community/150
loop23                  7:23   0  26,7M  1 loop /snap/sickgear/486
loop24                  7:24   0  1008K  1 loop /snap/gnome-logs/61
loop25                  7:25   0 373,5M  1 loop /snap/anbox/158
loop26                  7:26   0  89,3M  1 loop /snap/core/6673
loop27                  7:27   0  14,8M  1 loop /snap/gnome-characters/317
loop28                  7:28   0 202,9M  1 loop /snap/vlc/1049
loop29                  7:29   0 320,9M  1 loop /snap/pycharm-community/155
loop30                  7:30   0 310,8M  1 loop 
loop31                  7:31   0     8M  1 loop /snap/amass/711
sda                     8:0    0  55,9G  0 disk 
└─sda1                  8:1    0  55,9G  0 part 
  ├─ubuntu--vg-root   253:0    0  54,9G  0 lvm  /
  └─ubuntu--vg-swap_1 253:1    0   976M  0 lvm  [SWAP]
sr0                    11:0    1  1024M  0 rom

and

sudo lshw -short
H/W path         Device      Class          Description
=======================================================
                             system         H36ST (To be filled by O.E.M.)
/0                           bus            H36ST
/0/0                         memory         64KiB BIOS
/0/4                         processor      Intel(R) Core(TM) i3 CPU       M 330  @ 2.13GHz
/0/4/5                       memory         32KiB L1 cache
/0/4/6                       memory         256KiB L2 cache
/0/4/7                       memory         3MiB L3 cache
/0/25                        memory         6GiB System Memory
/0/25/0                      memory         4GiB SODIMM DDR3 Synchronous 1067 MHz (0,9 ns)
/0/25/1                      memory         2GiB SODIMM DDR3 Synchronous 1067 MHz (0,9 ns)
/0/100                       bridge         Core Processor DRAM Controller
/0/100/1                     bridge         Core Processor PCI Express x16 Root Port
/0/100/1/0                   display        Madison [Mobility Radeon HD 5650/5750 / 6530M/6550M]
/0/100/1/0.1                 multimedia     Redwood HDMI Audio [Radeon HD 5000 Series]
/0/100/2                     display        Core Processor Integrated Graphics Controller
/0/100/16                    communication  5 Series/3400 Series Chipset HECI Controller
/0/100/1a                    bus            5 Series/3400 Series Chipset USB2 Enhanced Host Controller
/0/100/1a/1      usb1        bus            EHCI Host Controller
/0/100/1a/1/1                bus            Integrated Rate Matching Hub
/0/100/1a/1/1/5              communication  Bluetooth Module
/0/100/1b                    multimedia     5 Series/3400 Series Chipset High Definition Audio
/0/100/1c                    bridge         5 Series/3400 Series Chipset PCI Express Root Port 1
/0/100/1c.1                  bridge         5 Series/3400 Series Chipset PCI Express Root Port 2
/0/100/1c.1/0    wlp3s0      network        AR9285 Wireless Network Adapter (PCI-Express)
/0/100/1c.2                  bridge         5 Series/3400 Series Chipset PCI Express Root Port 3
/0/100/1c.5                  bridge         5 Series/3400 Series Chipset PCI Express Root Port 6
/0/100/1c.5/0    enp6s0      network        AR8131 Gigabit Ethernet
/0/100/1d                    bus            5 Series/3400 Series Chipset USB2 Enhanced Host Controller
/0/100/1d/1      usb2        bus            EHCI Host Controller
/0/100/1d/1/1                bus            Integrated Rate Matching Hub
/0/100/1d/1/1/1              input          Compact Optical Mouse 500
/0/100/1e                    bridge         82801 Mobile PCI Bridge
/0/100/1f                    bridge         HM55 Chipset LPC Interface Controller
/0/100/1f.2                  storage        5 Series/3400 Series Chipset 4 port SATA AHCI Controller
/0/100/1f.3                  bus            5 Series/3400 Series Chipset SMBus Controller
/0/100/1f.6                  generic        5 Series/3400 Series Chipset Thermal Subsystem
/0/101                       bridge         Core Processor QuickPath Architecture Generic Non-core Registers
/0/102                       bridge         Core Processor QuickPath Architecture System Address Decoder
/0/103                       bridge         Core Processor QPI Link 0
/0/104                       bridge         1st Generation Core i3/5/7 Processor QPI Physical 0
/0/105                       bridge         1st Generation Core i3/5/7 Processor Reserved
/0/106                       bridge         1st Generation Core i3/5/7 Processor Reserved
/0/1             scsi0       storage        
/0/1/0.0.0       /dev/sda    disk           60GB OCZ-VERTEX3
/0/1/0.0.0/1     /dev/sda1   volume         55GiB Linux LVM Physical Volume partition
/0/2             scsi1       storage        
/0/2/0.0.0       /dev/cdrom  disk           DVD A  DS8A4S
/1                           power          To Be Filled By O.E.M.

And

    lspci -k
00:00.0 Host bridge: Intel Corporation Core Processor DRAM Controller (rev 12)
    Subsystem: Pegatron Core Processor DRAM Controller
00:01.0 PCI bridge: Intel Corporation Core Processor PCI Express x16 Root Port (rev 12)
    Kernel driver in use: pcieport
00:02.0 VGA compatible controller: Intel Corporation Core Processor Integrated Graphics Controller (rev 12)
    Subsystem: Pegatron Core Processor Integrated Graphics Controller
    Kernel driver in use: i915
    Kernel modules: i915
00:16.0 Communication controller: Intel Corporation 5 Series/3400 Series Chipset HECI Controller (rev 06)
    Subsystem: Pegatron 5 Series/3400 Series Chipset HECI Controller
    Kernel driver in use: mei_me
    Kernel modules: mei_me
00:1a.0 USB controller: Intel Corporation 5 Series/3400 Series Chipset USB2 Enhanced Host Controller (rev 06)
    Subsystem: Pegatron 5 Series/3400 Series Chipset USB2 Enhanced Host Controller
    Kernel driver in use: ehci-pci
00:1b.0 Audio device: Intel Corporation 5 Series/3400 Series Chipset High Definition Audio (rev 06)
    Subsystem: Pegatron 5 Series/3400 Series Chipset High Definition Audio
    Kernel driver in use: snd_hda_intel
    Kernel modules: snd_hda_intel
00:1c.0 PCI bridge: Intel Corporation 5 Series/3400 Series Chipset PCI Express Root Port 1 (rev 06)
    Kernel driver in use: pcieport
00:1c.1 PCI bridge: Intel Corporation 5 Series/3400 Series Chipset PCI Express Root Port 2 (rev 06)
    Kernel driver in use: pcieport
00:1c.2 PCI bridge: Intel Corporation 5 Series/3400 Series Chipset PCI Express Root Port 3 (rev 06)
    Kernel driver in use: pcieport
00:1c.5 PCI bridge: Intel Corporation 5 Series/3400 Series Chipset PCI Express Root Port 6 (rev 06)
    Kernel driver in use: pcieport
00:1d.0 USB controller: Intel Corporation 5 Series/3400 Series Chipset USB2 Enhanced Host Controller (rev 06)
    Subsystem: Pegatron 5 Series/3400 Series Chipset USB2 Enhanced Host Controller
    Kernel driver in use: ehci-pci
00:1e.0 PCI bridge: Intel Corporation 82801 Mobile PCI Bridge (rev a6)
00:1f.0 ISA bridge: Intel Corporation HM55 Chipset LPC Interface Controller (rev 06)
    Subsystem: Pegatron HM55 Chipset LPC Interface Controller
    Kernel driver in use: lpc_ich
    Kernel modules: lpc_ich
00:1f.2 SATA controller: Intel Corporation 5 Series/3400 Series Chipset 4 port SATA AHCI Controller (rev 06)
    Subsystem: Pegatron 5 Series/3400 Series Chipset 4 port SATA AHCI Controller
    Kernel driver in use: ahci
    Kernel modules: ahci
00:1f.3 SMBus: Intel Corporation 5 Series/3400 Series Chipset SMBus Controller (rev 06)
    Subsystem: Pegatron 5 Series/3400 Series Chipset SMBus Controller
    Kernel driver in use: i801_smbus
    Kernel modules: i2c_i801
00:1f.6 Signal processing controller: Intel Corporation 5 Series/3400 Series Chipset Thermal Subsystem (rev 06)
    Subsystem: Pegatron 5 Series/3400 Series Chipset Thermal Subsystem
    Kernel driver in use: intel ips
    Kernel modules: intel_ips
01:00.0 VGA compatible controller: Advanced Micro Devices, Inc. [AMD/ATI] Madison [Mobility Radeon HD 5650/5750 / 6530M/6550M]
    Subsystem: Pegatron Madison [Mobility Radeon HD 5650/5750 / 6530M/6550M]
    Kernel driver in use: radeon
    Kernel modules: radeon
01:00.1 Audio device: Advanced Micro Devices, Inc. [AMD/ATI] Redwood HDMI Audio [Radeon HD 5000 Series]
    Subsystem: Pegatron Redwood HDMI Audio [Radeon HD 5000 Series]
    Kernel driver in use: snd_hda_intel
    Kernel modules: snd_hda_intel
03:00.0 Network controller: Qualcomm Atheros AR9285 Wireless Network Adapter (PCI-Express) (rev 01)
    Subsystem: AzureWave AW-NE785 / AW-NE785H 802.11bgn Wireless Full or Half-size Mini PCIe Card
    Kernel driver in use: ath9k
    Kernel modules: ath9k
06:00.0 Ethernet controller: Qualcomm Atheros AR8131 Gigabit Ethernet (rev c0)
    Subsystem: Pegatron AR8131 Gigabit Ethernet
    Kernel driver in use: atl1c
    Kernel modules: atl1c
3f:00.0 Host bridge: Intel Corporation Core Processor QuickPath Architecture Generic Non-core Registers (rev 02)
    Subsystem: Intel Corporation Core Processor QuickPath Architecture Generic Non-core Registers
3f:00.1 Host bridge: Intel Corporation Core Processor QuickPath Architecture System Address Decoder (rev 02)
    Subsystem: Intel Corporation Core Processor QuickPath Architecture System Address Decoder
3f:02.0 Host bridge: Intel Corporation Core Processor QPI Link 0 (rev 02)
    Subsystem: Intel Corporation Core Processor QPI Link 0
3f:02.1 Host bridge: Intel Corporation 1st Generation Core i3/5/7 Processor QPI Physical 0 (rev 02)
    Subsystem: Intel Corporation 1st Generation Core i3/5/7 Processor QPI Physical 0
3f:02.2 Host bridge: Intel Corporation 1st Generation Core i3/5/7 Processor Reserved (rev 02)
    Subsystem: Intel Corporation 1st Generation Core i3/5/7 Processor Reserved
3f:02.3 Host bridge: Intel Corporation 1st Generation Core i3/5/7 Processor Reserved (rev 02)
    Subsystem: Intel Corporation 1st Generation Core i3/5/7 Processor Reserved

And

Sudo free -h
              total        used        free      shared  buff/cache   available
Mem:          5,6Gi       3,6Gi       716Mi       542Mi       1,4Gi       1,3Gi
Swap:         975Mi          0B       975Mi

And

cat /etc/fstab
# /etc/fstab: static file system information.
#
# Use 'blkid' to print the universally unique identifier for a
# device; this may be used with UUID= as a more robust way to name devices
# that works even if disks are added and removed. See fstab(5).
#
# <file system> <mount point>   <type>  <options>       <dump>  <pass>
/dev/mapper/ubuntu--vg-root /               ext4    errors=remount-ro 0       1
/dev/mapper/ubuntu--vg-swap_1 none            swap    sw              0       0

And

sudo blkid
/dev/sda1: UUID="TJyyqj-69Oz-taq7-XNnr-Wa1c-KeQr-hE27gh" TYPE="LVM2_member" PARTUUID="d0b08d86-01"
/dev/mapper/ubuntu--vg-root: UUID="fec411bd-5ef0-46fa-8e9e-6dbe26ba91de" TYPE="ext4"
/dev/mapper/ubuntu--vg-swap_1: UUID="a8605c39-db25-47d2-99d3-b9ae97c59042" TYPE="swap"
/dev/loop0: TYPE="squashfs"
/dev/loop1: TYPE="squashfs"
/dev/loop2: TYPE="squashfs"
/dev/loop3: TYPE="squashfs"
/dev/loop4: TYPE="squashfs"
/dev/loop5: TYPE="squashfs"
/dev/loop6: TYPE="squashfs"
/dev/loop7: TYPE="squashfs"
/dev/loop8: TYPE="squashfs"
/dev/loop9: TYPE="squashfs"
/dev/loop10: TYPE="squashfs"
/dev/loop11: TYPE="squashfs"
/dev/loop12: TYPE="squashfs"
/dev/loop13: TYPE="squashfs"
/dev/loop14: TYPE="squashfs"
/dev/loop15: TYPE="squashfs"
/dev/loop16: TYPE="squashfs"
/dev/loop17: TYPE="squashfs"
/dev/loop18: TYPE="squashfs"
/dev/loop19: TYPE="squashfs"
/dev/loop20: TYPE="squashfs"
/dev/loop21: TYPE="squashfs"
/dev/loop22: TYPE="squashfs"
/dev/loop23: TYPE="squashfs"
/dev/loop24: TYPE="squashfs"
/dev/loop25: TYPE="squashfs"
/dev/loop26: TYPE="squashfs"
/dev/loop27: TYPE="squashfs"
/dev/loop28: TYPE="squashfs"
/dev/loop29: TYPE="squashfs"
/dev/loop30: TYPE="squashfs"
/dev/loop31: TYPE="squashfs"

Answer 1

From the comments...

With only 6G RAM, 1G swap is way too small. I'd recommend at least 6G swap. That's why you're having the freezing problem, and your disk is thrashing. Either increase the swap partition, or change over to using a /swapfile.

To create a /swapfile, you can use this as a guideline...

sudo swapoff -a
sudo rm /swapfile
sudo dd if=/dev/zero of=/swapfile bs=1M count=6144
sudo chmod 600 /swapfile
sudo mkswap /swapfile
sudo swapon /swapfile

Also, with only 6G RAM, vm.swappiness should be 60 or higher. With a larger swap partition, or /swapfile, I'd recommend setting this to 80.

To test various settings of vm.swappiness, use sudo sysctl vm.swappiness=80. vm.swappiness values greater than the default of 60 make more use of swap. Values less than 60 make more use of RAM.

To make it permanent, edit /etc/sysctl.conf and add vm.swappiness=80 at the end, then reboot.

In either case, you'll need to edit /etc/fstab...

comment out this...

/dev/mapper/ubuntu--vg-swap_1 none            swap    sw              0       0

and add this for a /swapfile...

/swapfile    none    swap    sw      0 0