"Low Disk Space" (root filled by logs)

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stingray
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"Low Disk Space" (root filled by logs)

Post by stingray » Thu Aug 15, 2019 11:52 am

This morning I received an alert window:
Low Disk Space
The volume "filesystem root" has only 3.9 MB of disk space remaining.
I work from this computer so I typically have Firefox and Thunderbird and LibreOffice running simultaneously, along with several other programs. Now I'm limited in how much I can run at once before stuff starts crashing.

I am using two drives, a 250GB SSD (everything is installed here) and a 3TB HDD (purely a data disk, Timeshift saves here). The results of lsblk and df -h are included below.

The main culprit seems to be two log files in /var/log, "syslog" and "kern.log" each weighing in at 9.2 GB. There is also 850 MB in /var/log/journal but I'm less concerned about that (not a problem, right?). What's the deal with those log files? Is that normal? This was a clean install a few months ago.

Any help would be greatly appreciated.

lsblk

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NAME   MAJ:MIN RM   SIZE RO TYPE MOUNTPOINT
sda      8:0    0 232.9G  0 disk 
├─sda1   8:1    0   250M  0 part /boot/efi
├─sda2   8:2    0  31.8G  0 part /
└─sda3   8:3    0 200.9G  0 part /home
sdb      8:16   0   2.7T  0 disk 
└─sdb1   8:17   0   2.7T  0 part /media/data
sr0     11:0    1  1024M  0 rom  
df -h

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Filesystem      Size  Used Avail Use% Mounted on
udev            7.8G     0  7.8G   0% /dev
tmpfs           1.6G  1.5M  1.6G   1% /run
/dev/sda2        32G   29G  1.5G  96% /
tmpfs           7.8G  118M  7.7G   2% /dev/shm
tmpfs           5.0M  4.0K  5.0M   1% /run/lock
tmpfs           7.8G     0  7.8G   0% /sys/fs/cgroup
/dev/sda1       247M  6.1M  241M   3% /boot/efi
/dev/sda3       197G   24G  164G  13% /home
/dev/sdb1       2.8T  329G  2.5T  12% /media/data
tmpfs           1.6G   68K  1.6G   1% /run/user/1000
Last edited by stingray on Sat Aug 17, 2019 10:57 pm, edited 2 times in total.

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Re: "Low Disk Space" (root filled by logs)

Post by karlchen » Thu Aug 15, 2019 12:20 pm

Hello, stringray.

There always is a(n unpleasant) reason when logfiles like /var/log/syslog and /var/log/kern.log grow extremely fast and to enormous sizes.
More likely than not, one or several errors keep on being logged over and over again in very short intervals.

The solution is twofold:
  • To return your system to a usable state for a (short) period of time, boot from a Linux Mint live system.
    • Mount the internal harddisk device /dev/sda2 inside the live session.
    • Navigate to <dev_sda2_mountpoint>/var/log.
    • gzip the 2 files syslog and kern.log to an external device. Or simply copy them there.
    • Next truncate them by executing "cat /dev/null > syslog" and "cat /dev/null > kern.log" (Will require root privileges).
    • Inspect the gzipped / backed up syslog file in order to find out what makes it grow so large.
  • Boot your system normally. Fix the underlying root cause. Else you will be back to the "root filesystem full" situation.
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Re: "Low Disk Space" (root filled by logs)

Post by Larry78723 » Thu Aug 15, 2019 12:27 pm

Deleting those log files won't hurt anything, however steps should be taken to determine why those log files grew so large. Personally, I would go ahead and delete them then do a shutdown and restart. After the restart I would look for errors in those logs. Commands for deleting those logs follows:
Open a Terminal and paste (Ctrl-Shift-V) each command followed by Enter

Code: Select all

sudo rm /var/logs/kern.log

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sudo rm /var/logs/syslog
Hope this helps,
Larry
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Re: "Low Disk Space" (root filled by logs)

Post by stingray » Thu Aug 15, 2019 12:52 pm

Hmm, so you're saying I should actually look at the log files? What a radical concept...

Thanks, I'll look into it.

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Re: "Low Disk Space" (root filled by logs)

Post by stingray » Thu Aug 15, 2019 1:11 pm

The bad news is that there are so many errors that the log files maxed out the size limit. The good news is that new log files were created that are only 1.5 MB each so I can easily open and inspect them directly on this computer. These seem to be the key repeated errors. Is this just a log of disconnecting and reconnecting to wireless?

(I deleted my user name and MAC address from the output here, neither of which is probably that big of a deal. Anything else here I should be nervous about sharing publicly?)

kern.log

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Aug 11 23:36:22 ~user~ kernel: [405987.917783] [UFW BLOCK] IN=wlx64700225f629 OUT= MAC=xxREDACTEDxx SRC=192.168.1.254 DST=224.0.0.1 LEN=36 TOS=0x00 PREC=0xC0 TTL=1 ID=53193 DF PROTO=2 
Aug 11 23:38:27 ~user~ kernel: [406112.949673] [UFW BLOCK] IN=wlx64700225f629 OUT= MAC=xxREDACTEDxx SRC=192.168.1.254 DST=224.0.0.1 LEN=36 TOS=0x00 PREC=0xC0 TTL=1 ID=38905 DF PROTO=2 
Aug 11 23:40:32 ~user~ kernel: [406237.980623] [UFW BLOCK] IN=wlx64700225f629 OUT= MAC=xxREDACTEDxx SRC=192.168.1.254 DST=224.0.0.1 LEN=36 TOS=0x00 PREC=0xC0 TTL=1 ID=7920 DF PROTO=2 
Aug 11 23:44:42 ~user~ kernel: [406488.054046] [UFW BLOCK] IN=wlx64700225f629 OUT= MAC=xxREDACTEDxx SRC=192.168.1.254 DST=224.0.0.1 LEN=36 TOS=0x00 PREC=0xC0 TTL=1 ID=94 DF PROTO=2 
Aug 11 23:46:47 ~user~ kernel: [406613.095787] [UFW BLOCK] IN=wlx64700225f629 OUT= MAC=xxREDACTEDxx SRC=192.168.1.254 DST=224.0.0.1 LEN=36 TOS=0x00 PREC=0xC0 TTL=1 ID=11369 DF PROTO=2 
Aug 11 23:48:52 ~user~ kernel: [406738.127464] [UFW BLOCK] IN=wlx64700225f629 OUT= MAC=xxREDACTEDxx SRC=192.168.1.254 DST=224.0.0.1 LEN=36 TOS=0x00 PREC=0xC0 TTL=1 ID=50824 DF PROTO=2 
Aug 11 23:50:57 ~user~ kernel: [406862.857839] [UFW BLOCK] IN=wlx64700225f629 OUT= MAC=xxREDACTEDxx SRC=192.168.1.254 DST=224.0.0.1 LEN=36 TOS=0x00 PREC=0xC0 TTL=1 ID=948 DF PROTO=2 
Aug 11 23:53:02 ~user~ kernel: [406987.894576] [UFW BLOCK] IN=wlx64700225f629 OUT= MAC=xxREDACTEDxx SRC=192.168.1.254 DST=224.0.0.1 LEN=36 TOS=0x00 PREC=0xC0 TTL=1 ID=41865 DF PROTO=2 
syslog

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Aug 14 20:33:57 ~user~ kernel: [97916.979780] [UFW BLOCK] IN=wlx64700225f629 OUT= MAC=xxREDACTEDxx SRC=192.168.1.254 DST=224.0.0.1 LEN=36 TOS=0x00 PREC=0xC0 TTL=1 ID=36375 DF PROTO=2 
Aug 14 20:36:02 ~user~ kernel: [98042.013425] [UFW BLOCK] IN=wlx64700225f629 OUT= MAC=xxREDACTEDxx SRC=192.168.1.254 DST=224.0.0.1 LEN=36 TOS=0x00 PREC=0xC0 TTL=1 ID=21379 DF PROTO=2 
Aug 14 20:38:07 ~user~ kernel: [98167.050143] [UFW BLOCK] IN=wlx64700225f629 OUT= MAC=xxREDACTEDxx SRC=192.168.1.254 DST=224.0.0.1 LEN=36 TOS=0x00 PREC=0xC0 TTL=1 ID=4847 DF PROTO=2 
Aug 14 20:40:11 ~user~ kernel: [98291.471529] [UFW BLOCK] IN=wlx64700225f629 OUT= MAC=xxREDACTEDxx SRC=192.168.1.254 DST=224.0.0.1 LEN=36 TOS=0x00 PREC=0xC0 TTL=1 ID=16742 DF PROTO=2 
Aug 14 20:42:17 ~user~ kernel: [98417.122658] [UFW BLOCK] IN=wlx64700225f629 OUT= MAC=xxREDACTEDxx SRC=192.168.1.254 DST=224.0.0.1 LEN=36 TOS=0x00 PREC=0xC0 TTL=1 ID=5423 DF PROTO=2 
Aug 14 20:44:22 ~user~ kernel: [98542.159380] [UFW BLOCK] IN=wlx64700225f629 OUT= MAC=xxREDACTEDxx SRC=192.168.1.254 DST=224.0.0.1 LEN=36 TOS=0x00 PREC=0xC0 TTL=1 ID=35704 DF PROTO=2 
Aug 14 20:46:26 ~user~ kernel: [98666.589205] [UFW BLOCK] IN=wlx64700225f629 OUT= MAC=xxREDACTEDxx SRC=192.168.1.254 DST=224.0.0.1 LEN=36 TOS=0x00 PREC=0xC0 TTL=1 ID=37792 DF PROTO=2 
Aug 14 20:48:32 ~user~ kernel: [98792.232875] [UFW BLOCK] IN=wlx64700225f629 OUT= MAC=xxREDACTEDxx SRC=192.168.1.254 DST=224.0.0.1 LEN=36 TOS=0x00 PREC=0xC0 TTL=1 ID=2939 DF PROTO=2 

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Re: "Low Disk Space" (root filled by logs)

Post by smurphos » Thu Aug 15, 2019 1:20 pm

stingray wrote:
Thu Aug 15, 2019 12:52 pm
Hmm, so you're saying I should actually look at the log files? What a radical concept...
:)

Just for comparison so you know what you are seeing is definitely not normal my current kern.log is all of 1.4MB and syslog is 251kB
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Re: "Low Disk Space" (root filled by logs)

Post by smurphos » Thu Aug 15, 2019 1:25 pm

Temporarily disable the firewall's (ufw) logging

sudo ufw logging off

Then check your rules

sudo ufw status verbose
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Re: "Low Disk Space" (root filled by logs)

Post by stingray » Thu Aug 15, 2019 1:39 pm

Larry78723 wrote:
Thu Aug 15, 2019 12:27 pm
Deleting those log files won't hurt anything, however steps should be taken to determine why those log files grew so large. Personally, I would go ahead and delete them then do a shutdown and restart. After the restart I would look for errors in those logs. Commands for deleting those logs follows:
Open a Terminal and paste (Ctrl-Shift-V) each command followed by Enter

Code: Select all

sudo rm /var/logs/kern.log

Code: Select all

sudo rm /var/logs/syslog
Hope this helps,
Larry
Thanks, back to operational status. Now to actually fix the issue.
smurphos wrote:
Thu Aug 15, 2019 1:25 pm
Temporarily disable the firewall's (ufw) logging

sudo ufw logging off

Then check your rules

sudo ufw status verbose
Here is what I get:

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Status: active
Logging: off
Default: deny (incoming), allow (outgoing), disabled (routed)
New profiles: skip
Is this normal? (Ignore the "Free space" figure, this was pre-restart):
logs.png

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Re: "Low Disk Space" (root filled by logs)

Post by gm10 » Thu Aug 15, 2019 2:05 pm

Yes, that's the normal defaults, and those log messages are incoming IGMP messages from your router. You can just keep the firewall logging disabled and forget about it - unless you were planning on regularly reviewing that log it can get very spammy. Alternatively create a rule specifically for that and configure it to not get logged.
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Re: "Low Disk Space" (root filled by logs)

Post by karlchen » Thu Aug 15, 2019 2:19 pm

But I have got a doubt or two that ufw managed to make the 2 logfiles "explode". ufw logging is "on (low)" here, and the 2 files have never exceeded a few MB's, before the daily logrotate job came along and gzipped them.
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Re: "Low Disk Space" (root filled by logs)

Post by stingray » Thu Aug 15, 2019 3:00 pm

Alright, I'll try to take a look at those giant log files this evening. Any tips for looking at a 9+ GB text file?

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Re: "Low Disk Space" (root filled by logs)

Post by gm10 » Thu Aug 15, 2019 5:28 pm

stingray wrote:
Thu Aug 15, 2019 3:00 pm
Alright, I'll try to take a look at those giant log files this evening. Any tips for looking at a 9+ GB text file?
If it did get spammed then you won't have to search far. The last 100 lines will likely do:

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tail -n 100 /path/to/logfile
Otherwise for a graphical tool:

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apt install glogg
and then use glogg to open the file, it can handle it.
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Re: "Low Disk Space" (root filled by logs)

Post by stingray » Thu Aug 15, 2019 6:19 pm

Well, it wasn't just the firewall. There was a little bit of that at the top and bottom, but both 9 GB log files (glogg was great for this!) were mostly full of this thing repeated over the course of about 20 minutes this morning.

sdb1 is my 3TB HDD mounted at /media/data

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Aug 15 09:07:39 ~user~ kernel: [143140.874683] 
Aug 15 09:07:39 ~user~ kernel: [143140.874684] btstack dump:
Aug 15 09:07:39 ~user~ kernel: [143140.874685] bn = 0, index = 0
Aug 15 09:07:39 ~user~ kernel: [143140.874685] bn = b0d09f4, index = 0
Aug 15 09:07:39 ~user~ kernel: [143140.874686] bn = 0, index = 0
Aug 15 09:07:39 ~user~ kernel: [143140.874687] bn = b0d09f4, index = 0
Aug 15 09:07:39 ~user~ kernel: [143140.874688] bn = 0, index = 0
Aug 15 09:07:39 ~user~ kernel: [143140.874689] bn = b0d09f4, index = 0
Aug 15 09:07:39 ~user~ kernel: [143140.874689] bn = 0, index = 0
Aug 15 09:07:39 ~user~ kernel: [143140.874690] bn = ffff891a958387a0, index = 528
Aug 15 09:07:39 ~user~ kernel: [143140.874693] ERROR: (device sdb1): dtReadFirst [jfs]: btstack overrun
Aug 15 09:07:39 ~user~ kernel: [143140.874693] 
Aug 15 09:07:39 ~user~ kernel: [143140.874695] btstack dump:
Aug 15 09:07:39 ~user~ kernel: [143140.874695] bn = 0, index = 0
Aug 15 09:07:39 ~user~ kernel: [143140.874696] bn = b0d09f4, index = 0
Aug 15 09:07:39 ~user~ kernel: [143140.874696] bn = 0, index = 0
Aug 15 09:07:39 ~user~ kernel: [143140.874697] bn = b0d09f4, index = 0
Aug 15 09:07:39 ~user~ kernel: [143140.874698] bn = 0, index = 0
Aug 15 09:07:39 ~user~ kernel: [143140.874699] bn = b0d09f4, index = 0
Aug 15 09:07:39 ~user~ kernel: [143140.874700] bn = 0, index = 0
Aug 15 09:07:39 ~user~ kernel: [143140.874701] bn = ffff891a958387a0, index = 528
Aug 15 09:07:39 ~user~ kernel: [143140.874704] ERROR: (device sdb1): dtReadFirst [jfs]: btstack overrun
Aug 15 09:07:39 ~user~ kernel: [143140.874704] 

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Re: "Low Disk Space" (root filled by logs)

Post by gm10 » Thu Aug 15, 2019 6:36 pm

How is it formatted? I'm surprised to see JFS filesystem errors there. Are you really using that? I think some

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inxi -Fxz
output would be useful at this point.
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Re: "Low Disk Space" (root filled by logs)

Post by stingray » Thu Aug 15, 2019 7:22 pm

Aww, you don't gotta filesystem shame me, man. I know JFS is old but it's still fine, right? I use it for the data drive because it's very easy as far as wear and tear on hard drives compared to XFS and EXT. I thought about going BTRFS with everything but it wasn't compatible with something I wanted to do, can't remember what...

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System:
  Host: ~user~ Kernel: 4.15.0-58-generic x86_64 bits: 64 compiler: gcc 
  v: 7.4.0 Desktop: MATE 1.22.0 Distro: Linux Mint 19.2 Tina 
  base: Ubuntu 18.04 bionic 
Machine:
  Type: Desktop System: Gigabyte product: Z97X-UD3H-BK v: N/A 
  serial: <filter> 
  Mobo: Gigabyte model: Z97X-UD3H-BK-CF v: x.x serial: <filter> 
  UEFI: American Megatrends v: F6 date: 06/17/2014 
Battery:
  Device-1: hidpp_battery_0 model: Logitech Wireless Mouse M510 charge: 55% 
  status: Discharging 
CPU:
  Topology: Quad Core model: Intel Core i5-4690S bits: 64 type: MCP 
  arch: Haswell rev: 3 L2 cache: 6144 KiB 
  flags: lm nx pae sse sse2 sse3 sse4_1 sse4_2 ssse3 vmx bogomips: 25600 
  Speed: 800 MHz min/max: 800/3900 MHz Core speeds (MHz): 1: 800 2: 800 
  3: 800 4: 800 
Graphics:
  Device-1: Intel Xeon E3-1200 v3/4th Gen Core Processor Integrated Graphics 
  vendor: Gigabyte driver: i915 v: kernel bus ID: 00:02.0 
  Display: x11 server: X.Org 1.19.6 driver: modesetting unloaded: fbdev,vesa 
  resolution: 1920x1080~60Hz 
  OpenGL: renderer: Mesa DRI Intel Haswell Desktop v: 4.5 Mesa 19.0.8 
  direct render: Yes 
Audio:
  Device-1: Intel Xeon E3-1200 v3/4th Gen Core Processor HD Audio 
  driver: snd_hda_intel v: kernel bus ID: 00:03.0 
  Device-2: Intel 9 Series Family HD Audio vendor: Gigabyte 
  driver: snd_hda_intel v: kernel bus ID: 00:1b.0 
  Sound Server: ALSA v: k4.15.0-58-generic 
Network:
  Device-1: Intel Ethernet I217-V vendor: Gigabyte driver: e1000e v: 3.2.6-k 
  port: f080 bus ID: 00:19.0 
  IF: eno1 state: down mac: <filter> 
  Device-2: Atheros AR9271 802.11n type: USB driver: ath9k_htc 
  bus ID: 3-13:9 
  IF: wlx64700225f629 state: up mac: <filter> 
Drives:
  Local Storage: total: 2.96 TiB used: 380.13 GiB (12.6%) 
  ID-1: /dev/sda vendor: Samsung model: SSD 850 EVO 250GB size: 232.89 GiB 
  ID-2: /dev/sdb vendor: Western Digital model: WD30EZRZ-00WN9B0 
  size: 2.73 TiB 
Partition:
  ID-1: / size: 31.18 GiB used: 11.15 GiB (35.7%) fs: ext4 dev: /dev/sda2 
  ID-2: /home size: 196.68 GiB used: 23.25 GiB (11.8%) fs: ext4 
  dev: /dev/sda3 
Sensors:
  System Temperatures: cpu: 29.8 C mobo: 27.8 C 
  Fan Speeds (RPM): N/A 
Info:
  Processes: 194 Uptime: 5h 36m Memory: 15.53 GiB used: 2.14 GiB (13.8%) 
  Init: systemd runlevel: 5 Compilers: gcc: 7.4.0 Shell: bash v: 4.4.20 
  inxi: 3.0.32 
Last edited by stingray on Thu Aug 15, 2019 8:25 pm, edited 1 time in total.

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Re: "Low Disk Space" (root filled by logs)

Post by gm10 » Thu Aug 15, 2019 7:36 pm

Wasn't shaming you, just surprised (not something you see around these parts often) and wanting to make sure that was working as intended (and not you trying to mount ext4 as jfs and causing the errors that way - you never know until you ask).

Anyway, JFS should be fine in theory, but in this case clearly there are problems reading from it. Assuming the drive and cabling are fine that leaves file system corrupt, see if you can fix it with sudo fsck.jfs -f /dev/sdb1 I suppose (after unmounting it, but it doesn't seem mounted according to your inxi output, anyway).
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Re: "Low Disk Space" (root filled by logs)

Post by stingray » Thu Aug 15, 2019 8:24 pm

No, it's completely fine. I wasn't offended in the least. I should have added a winky face. This has been really helpful. Big thanks to everyone who has responded.

It's mounted at /media/data (with my fstab) but it's just storage. I have syslinks pointing there for a few of my profile directories like Music and Video. When I had to restart this morning the disk check ran and didn't come up with anything but maybe it only scanned sda? I'll check the cables and then run fsck.

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Re: "Low Disk Space" (root filled by logs)

Post by stingray » Thu Aug 15, 2019 9:38 pm

Nothing physical seemed loose. Ran fsck and I guess there were some issues. I'll keep an eye on the logs in the future and run fsck occasionally. Again, thanks for the help. I'm marking this as solved for now.

Code: Select all

fsck.jfs version 1.1.15, 04-Mar-2011
processing started: 8/15/2019 20:17:23
The current device is:  /dev/sdb1
Block size in bytes:  4096
Filesystem size in blocks:  732566272
**Phase 0 - Replay Journal Log
**Phase 1 - Check Blocks, Files/Directories, and  Directory Entries
**Phase 2 - Count links
Incorrect link counts have been detected. Will correct.
**Phase 3 - Duplicate Block Rescan and Directory Connectedness
**Phase 4 - Report Problems
File system object DF2656 is linked as: /lost+found
Errors detected in Directory Index Table. Will Fix.
**Phase 5 - Check Connectivity
**Phase 6 - Perform Approved Corrections
258 files reconnected to /lost+found/.
**Phase 7 - Rebuild File/Directory Allocation Maps
**Phase 8 - Rebuild Disk Allocation Maps
2930265088 kilobytes total disk space.
   894495 kilobytes in 443590 directories.
361173539 kilobytes in 382342 user files.
      364 kilobytes in extended attributes
  2461460 kilobytes reserved for system use.
2567524220 kilobytes are available for use.
Filesystem is clean.

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Re: "Low Disk Space" (root filled by logs)

Post by stingray » Sat Aug 17, 2019 11:09 pm

Things have taken a turn. Had the Low Disk Space error again this morning. syslog and kern.log were over 9 GB again. Couldn't even shut down gracefully. More importantly, I've been unable to boot to my install this time. Booted to a DVD live session and deleted one of the logs but I still can't boot at all. Tried disconnecting the HDD to no avail (I don't think it should be required to boot since it's just additional storage). Was able to get to a recovery command prompt as root but didn't want to mess around there. "Desktop" was the only thing that showed up with "ls".

I have a USB dock so I theoretically can access the SSD or HDD. No clue how to proceed. Please advise.

P.S. Should I keep this in the newbie forum or post elsewhere?

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Re: "Low Disk Space" (root filled by logs)

Post by Moem » Sun Aug 18, 2019 3:30 am

Probably best to start a new thread elsewhere, with a link to this one for reference. Good luck!
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If your issue is solved, kindly indicate that by editing the first post in the topic, and adding [SOLVED] to the title. Thanks!

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