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

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

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.

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

1 Answers1