Ubuntu 20.04 freezes after 1-2 days even when cpu and ram usage is very low

Question

I have installed ubuntu 20.04.02 LTS on my system. My system has 63 GB RAM and 48 cpu. I was running a python program for 2-3 days which consumes RAM around 11 GB and 3-4 cpu. Ubuntu 20 freezes even when most part of RAM and cpu is empty.

I changed the graphicx driver from propriety(tested) to Xorg, but still I can feel some lagging is there. Rebooting the system is a temporary solution but I can't reboot every time as some program runs most of the time.

It would be great if someone can tell where the actual problem lies? Since I am new to ubuntu so I have included the output of lscpu if that helps

Architecture:                    x86_64
CPU op-mode(s):                  32-bit, 64-bit
Byte Order:                      Little Endian
Address sizes:                   46 bits physical, 48 bits virtual
CPU(s):                          48
On-line CPU(s) list:             0-47
Thread(s) per core:              2
Core(s) per socket:              12
Socket(s):                       2
NUMA node(s):                    2
Vendor ID:                       GenuineIntel
CPU family:                      6
Model:                           63
Model name:                      Intel(R) Xeon(R) CPU E5-2670 v3 @ 2.30GHz
Stepping:                        2
CPU MHz:                         1197.247
CPU max MHz:                     3100.0000
CPU min MHz:                     1200.0000
BogoMIPS:                        4589.03
Virtualization:                  VT-x
L1d cache:                       768 KiB
L1i cache:                       768 KiB
L2 cache:                        6 MiB
L3 cache:                        60 MiB
NUMA node0 CPU(s):               0-11,24-35
NUMA node1 CPU(s):               12-23,36-47
Vulnerability Itlb multihit:     KVM: Mitigation: VMX disabled
Vulnerability L1tf:              Mitigation; PTE Inversion; VMX conditional cach
                                 e flushes, SMT vulnerable
Vulnerability Mds:               Mitigation; Clear CPU buffers; SMT vulnerable
Vulnerability Meltdown:          Mitigation; PTI
Vulnerability Spec store bypass: Mitigation; Speculative Store Bypass disabled v
                                 ia prctl and seccomp
Vulnerability Spectre v1:        Mitigation; usercopy/swapgs barriers and __user
                                  pointer sanitization
Vulnerability Spectre v2:        Mitigation; Full generic retpoline, IBPB condit
                                 ional, IBRS_FW, STIBP conditional, RSB filling
Vulnerability Srbds:             Not affected
Vulnerability Tsx async abort:   Not affected
Flags:                           fpu vme de pse tsc msr pae mce cx8 apic sep mtr
                                 r pge mca cmov pat pse36 clflush dts acpi mmx f
                                 xsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rd
                                 tscp lm constant_tsc arch_perfmon pebs bts rep_
                                 good nopl xtopology nonstop_tsc cpuid aperfmper
                                 f pni pclmulqdq dtes64 monitor ds_cpl vmx smx e
                                 st tm2 ssse3 sdbg fma cx16 xtpr pdcm pcid dca s
                                 se4_1 sse4_2 x2apic movbe popcnt tsc_deadline_t
                                 imer aes xsave avx f16c rdrand lahf_lm abm cpui
                                 d_fault epb invpcid_single pti intel_ppin ssbd 
                                 ibrs ibpb stibp tpr_shadow vnmi flexpriority ep
                                 t vpid ept_ad fsgsbase tsc_adjust bmi1 avx2 sme
                                 p bmi2 erms invpcid cqm xsaveopt cqm_llc cqm_oc
                                 cup_llc dtherm ida arat pln pts md_clear flush_
                                 l1d

Ouput of lspci | grep VGA

03:00.0 VGA compatible controller: NVIDIA Corporation GK110GL [Quadro K5200] (rev a1)

EDIT I was running 10 python3 using jupyter notebook in mozilla firefox, all involves calculations and file handling i.e. writing and saving.

free -h

              total        used        free      shared  buff/cache   available
Mem:           62Gi       1.6Gi        58Gi        43Mi       2.5Gi        60Gi
Swap:         2.0Gi          0B       2.0Gi

grep -i swap /etc/fstab

/swapfile                                 none            swap    sw              0       0

sysctl vm.swappiness

vm.swappiness = 60

I checked the log just 1-2 hrs before I noticed freeze. Here is the some output lines of journalctl --since "2021-03-03 15:10:00"

Mar 03 15:10:00 santanu-Precision-Tower-7810 /usr/lib/gdm3/gdm-x-session[1942]: (--) NVIDIA(GPU-0): DFP-3: disconnected
Mar 03 15:10:00 santanu-Precision-Tower-7810 /usr/lib/gdm3/gdm-x-session[1942]: (--) NVIDIA(GPU-0): DFP-3: Internal TMDS
Mar 03 15:10:00 santanu-Precision-Tower-7810 /usr/lib/gdm3/gdm-x-session[1942]: (--) NVIDIA(GPU-0): DFP-3: 330.0 MHz maximum pixel clock
Mar 03 15:10:00 santanu-Precision-Tower-7810 /usr/lib/gdm3/gdm-x-session[1942]: (--) NVIDIA(GPU-0):
Mar 03 15:10:00 santanu-Precision-Tower-7810 /usr/lib/gdm3/gdm-x-session[1942]: (--) NVIDIA(GPU-0): DELL P2414H (DFP-4): connected
Mar 03 15:10:00 santanu-Precision-Tower-7810 /usr/lib/gdm3/gdm-x-session[1942]: (--) NVIDIA(GPU-0): DELL P2414H (DFP-4): Internal DisplayPort
Mar 03 15:10:00 santanu-Precision-Tower-7810 /usr/lib/gdm3/gdm-x-session[1942]: (--) NVIDIA(GPU-0): DELL P2414H (DFP-4): 960.0 MHz maximum pixel clock
Mar 03 15:10:00 santanu-Precision-Tower-7810 /usr/lib/gdm3/gdm-x-session[1942]: (--) NVIDIA(GPU-0):
Mar 03 15:10:00 santanu-Precision-Tower-7810 /usr/lib/gdm3/gdm-x-session[1942]: (--) NVIDIA(GPU-0): DFP-5: disconnected
Mar 03 15:10:00 santanu-Precision-Tower-7810 /usr/lib/gdm3/gdm-x-session[1942]: (--) NVIDIA(GPU-0): DFP-5: Internal DisplayPort
Mar 03 15:10:00 santanu-Precision-Tower-7810 /usr/lib/gdm3/gdm-x-session[1942]: (--) NVIDIA(GPU-0): DFP-5: 960.0 MHz maximum pixel clock
Mar 03 15:10:00 santanu-Precision-Tower-7810 /usr/lib/gdm3/gdm-x-session[1942]: (--) NVIDIA(GPU-0):
Mar 03 15:10:03 santanu-Precision-Tower-7810 gnome-shell[2080]: JS ERROR: TypeError: windowActor is null
                                                                _addWindowEffect@resource:///org/gnome/shell/ui/closeDialog.js:90:28
                                                                vfunc_show@resource:///org/gnome/shell/ui/closeDialog.js:162:14
Mar 03 15:10:08 santanu-Precision-Tower-7810 gnome-shell[2080]: JS ERROR: TypeError: windowActor is null
                                                                _addWindowEffect@resource:///org/gnome/shell/ui/closeDialog.js:90:28
                                                                vfunc_show@resource:///org/gnome/shell/ui/closeDialog.js:162:14
Mar 03 15:10:13 santanu-Precision-Tower-7810 gnome-shell[2080]: JS ERROR: TypeError: windowActor is null
                                                                _addWindowEffect@resource:///org/gnome/shell/ui/closeDialog.js:90:28
                                                                vfunc_show@resource:///org/gnome/shell/ui/closeDialog.js:162:14
Mar 03 15:10:23 santanu-Precision-Tower-7810 gnome-shell[2080]: JS ERROR: TypeError: windowActor is null
                                                                _addWindowEffect@resource:///org/gnome/shell/ui/closeDialog.js:90:28
                                                                vfunc_show@resource:///org/gnome/shell/ui/closeDialog.js:162:14

One more issue is there, its not a problem but it might be helpful. Icons are highlighted just by the mouse movement. I attached a picture to better describe it.Destop Icon Highlight

Edit 2:

python command not working.

Output of python3 --version is Python 3.8.5.

No gnome-shell extension,

root@santanu-Precision-Tower-7810:/home/santanu/.local/share/gnome-shell# ls
application_state  gnome-overrides-migrated

Output of ls -al /usr/share/gnome-shell/extensions

total 20
drwxr-xr-x 5 root root 4096 Feb  4 08:04 .
drwxr-xr-x 7 root root 4096 Feb  4 08:05 ..
drwxr-xr-x 2 root root 4096 Feb  4 08:04 desktop-icons@csoriano
drwxr-xr-x 3 root root 4096 Feb  4 08:04 ubuntu-appindicators@ubuntu.com
drwxr-xr-x 3 root root 4096 Feb  4 08:04 ubuntu-dock@ubuntu.com

Nvidia card information: NVIDIA Corporation GK110GL [Quadro K5200] Nvidia Driver information: nvidia driver 400 (propriety, tested)

Driver Version: 460.39

Bios Version A10 Its quit old machine, I couldn't change bios as there is a risk of damaging the hardware.

Product:
Product Name  Precision Tower 7810
Vendor        Dell Inc
Board:
Name:         OGWHMW
Version:      A02

Should I switch back to ubuntu 18 as the machine hardware is quite old?

Thanks

Unfortunately you haven’t provided any clues about what is the cause. One way to diagnose this is to look at error logs. You can do this with a command of the form journalctl -p 3 -b1. The trick is the b1 bit. b1 means the boot before the current boot. You can use journalctl --list-boots to list recent boots. Then you need to identify a boot when this problem occurred and use the number you found in the -b# bit. You may have some errors every time you boot. You can see those in the latest boot with journalctl -p 3 -b0. Any errors here are probably not causing the freeze — PonJar, Mar 04 '21 at 13:55
Update your question with any errors in the log just before the freeze — PonJar, Mar 04 '21 at 13:58
Edit your question and show me the output of free -h and grep -i swap /etc/fstab and sysctl vm.swappiness. Start comments to me with @heynnema or I'll miss them. — heynnema, Mar 04 '21 at 15:06
@heynnema I updated the output of the commands you provided. Please check. — ABCD, Mar 05 '21 at 09:56
@PonJar I put the output of journalctl --since "2021-03-03 15:10:00". Please check, there is some error related to gnome-shell that I can't figure it out. — ABCD, Mar 05 '21 at 10:24
What do you mean by freezing? Has the computer completely hung or just the graphical interface? Can you switch to a terminal window and do something? If you can and if your program isn't a graphical program (is it?), perhaps you can consider not using xorg and just run your program in a terminal? Looking at your problem description, I see that you've tagged it as 'nvidia' and 'xorg' and I wonder why you think they're relevant? Perhaps you can edit your question and clarify some of this? — Ray, Mar 05 '21 at 10:41
@Ray Freezing means I could not select anything either through keyboard or mouse in desktop but using ssh I can access terminal. After reboot it becomes okay but it happens 2-3 times. I reinstalled ubuntu twice. Regarding python3 program it is mostly calculations and file handling. I thought Its related to graphics driver thats why I tagged nvidia and xorg as I switched from propriety to xorg after freezing. — ABCD, Mar 05 '21 at 10:47
@heynnema answered a question recently with a similar windowActor error here https://askubuntu.com/questions/1312512/what-is-this-js-error-from-gnome-shell-keeps-happening-and-not-finding-answers. Would be worth a look — PonJar, Mar 05 '21 at 14:12
@SatyamMishra Edit your question and show me python --version, and ls -al ~/.local/share/gnome-shell/extensions and ls -al /usr/share/gnome-shell/extensions. Tell me what Nvidia card you have, and what version driver. Show me sudo dmidecode -s bios-version and tell me the make/model of your motherboard or computer. — heynnema, Mar 05 '21 at 14:44
@SatyamMishra I see. I would avoid tagging future questions if you aren't sure. Some people follow certain tags and you could miss out on certain points of view. Maybe you could consider switching back to the proprietary driver to confirm that problem doesn't occur any more. Such information can help others help you better. Also, does Alt + F2 work? If so, try R to restore Gnome. See this. — Ray, Mar 05 '21 at 15:01
@SatyamMishra And this is a terrible solution, but if no one else can offer you a better solution, it's something to consider... It could be that xorg doesn't support your system and with another release (i.e., 20.10 or 21.04), the problem goes away. Yes, you would be stepping away from LTS; I'm just saying this has happened to me before -- a future version "solves" my graphics problems. — Ray, Mar 05 '21 at 15:04
@heynnema I updated the output as you asked. Please check. Is my system compatible with python3 and ubuntu 20? — ABCD, Mar 05 '21 at 18:45
You don’t seem to have provided the second set of information requested by @heynnema. There’s a good chance your issue is with a gnome extension. The information requested will help identify this. It’s very likely your system is compatible — PonJar, Mar 05 '21 at 21:04
@SatyamMishra Please see my answer. If it solve your problem(s), please remember to accept it by clicking on the checkmark icon that appears just to the left of my answer. Thanks! — heynnema, Mar 05 '21 at 21:33
@PonJar There is not any gnome shell extension at this location /.local/share/gnome-shell. As output of ls -al ~/.local/share/gnome-shell/extensions returns no such file or directory. — ABCD, Mar 06 '21 at 12:42

heynnema · Accepted Answer · 2021-03-05T21:34:55.567

0

BIOS

Dell Precision Tower 7810

Intel(R) Xeon(R) CPU E5-2670 v3 @ 2.30GHz

You have a very old BIOS. There's a newer BIOS available that should work on your machine (but see the CPU notes, below), version A34, dated Nov 17, 2020 and can be downloaded here.

Note: Confirm that I have the correct web page for your model.

Note: Have good backups before updating the BIOS.

vm.swappiness

With 64G RAM, you can change vm.swappiness=10 to reduce swapping. Add this to the bottom of /etc/sysctl.conf and reboot.

SWAP

A 2G /swapfile might just be a little small for your configuration. Let's increase it to 4G...

Note: Incorrect use of the dd command can cause data loss. Suggest copy/paste.

In the terminal...

sudo swapoff -a           # turn off swap
sudo rm -i /swapfile      # remove old /swapfile
sudo dd if=/dev/zero of=/swapfile bs=1M count=4096
sudo chmod 600 /swapfile  # set proper file protections
sudo mkswap /swapfile     # init /swapfile
sudo swapon /swapfile     # turn on swap
free -h                   # confirm 64G RAM and 4G swap

Confirm this /swapfile line at the end of /etc/fstab... and confirm no other “swap” lines...

To edit, use sudo -H gedit /etc/fstab or sudo pico /etc/fstab

/swapfile  none  swap  sw  0  0

reboot                    # reboot and verify operation

gnome-shell and desktop icon problems

See my answer at What is this? JS ERROR from gnome-shell keeps happening, and not finding answers

NVIDIA

NVIDIA Corporation GK110GL [Quadro K5200]

Driver Version: 460.39

Note: We still may have a problem here that we'll need to discuss, if need be.

edited Mar 05 '21 at 21:34

answered Mar 05 '21 at 21:29

heynnema

70,711

Thanks for your help. As of now I reduce swappiness and increase swap space. Regarding bios update, since this system is a workstation for 2-3 people and updating bios has a risk of damaging the hardware so I can't update the bios. Is there any alternative solution like switching back to older version of ubuntu? can you tell which ubuntu version would be perfect for this bios version? And regarding NVIDIA I switched back the driver from xorg to propriety(tested). As of now no lagging is there. But that desktop icon highlight(picture in question) issue is still there. – ABCD Mar 06 '21 at 12:18
Regarding NVIDIA driver which issue you are talking about? Is it about selecting the correct driver? – ABCD Mar 06 '21 at 12:30
@SatyamMishra Without doing a good backup, and updating the BIOS, nothing else matters. The desktop icons problem, did you follow the link I gave in my answer? The Nvidia thing... I couldn't find that model # at https://www.nvidia.com/en-us/geforce/drivers/ – heynnema Mar 06 '21 at 13:30
Yes I followed the link you gave on JS error and typed grep -i gnome-shell /var/log/syslog* | grep -i extensions but it gives no output. Also there is no any extension at https://extensions.gnome.org/local/. So there is no extension to reinstall. – ABCD Mar 06 '21 at 16:25
@SatyamMishra In my linked answer, you only need to do the "Do the work" portion of that answer. You'll be replacing a gnome-shell extension in /usr/share/gnome-shell/extensions. – heynnema Mar 06 '21 at 16:29
Thanks it solved my desktop icon problem, I installed the extension Desktop Icons NG (DING) by rastersoft version 3.38 Extension Version. – ABCD Mar 07 '21 at 09:47
@SatyamMishra Great news! Thanks for the update. – heynnema Mar 07 '21 at 14:11

Ubuntu 20.04 freezes after 1-2 days even when cpu and ram usage is very low

1 Answers1