[SOLVED] Where is all my disk space?

[mathieu]

Hi all,

When I open my Disk Usage Analyser, the following picture is shown:

As you see, it says I have 8.8GB available of my 53.4 GB allocated to this partition in total. I conclude from this, that 53.4 - 8.8 = 44.6 GB must be used up somewhere.

However, when I open mathieu-PC or the home folder, I get the following:

This adds up to 14.1 + 5.5 = 19.6 GB.

Where are the other 44.6 - 19.6 = 25.0 GB? And may I be able to safely delete what's in there? (I'm pretty confident I am wasting unnecessary space somewhere, I just don't know where). Could this be the space that Linux Mint itself is taking up?

Thanks in advance!
Matt

[SMG]

Maybe this will help you How to Clean Linux Mint Safely.

[linux-rox]

Where are you saving Timeshift snapshots? Are you willing to try diagnosing this with Terminal commands?

[ajgreeny]

It is much easier to see details with the output of terminal command

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df -hT

which will show the size of your partitions and how much of that space is used.

[mathieu]

I have tried most of the things indicated in the post you sent SMG, thanks. Unfortunately it didn't do much. In fact while I was using my PC, not downloading anything big, I "lost" another GB of storage, it now says I have 7.0 GB available.

ajgreeny, I have run this command and can't conclude much from it, but I've attached it in case that helps, thanks. (note that I now have my HDD attached and previously didn't, it's the Elements thing)

linux-rox, yes I would be willing to diagnose via Terminal and would be super grateful for any guidance in that. I am currently saving my timeshifts on an external HDD, or so I think at least. I guess it's still possible that timeshift is the culprit and I am misunderstanding something. Thanks for that hint.

[SMG]

I have tried most of the things indicated in the post you sent SMG, thanks. Unfortunately it didn't do much. In fact while I was using my PC, not downloading anything big, I "lost" another GB of storage, it now says I have 7.0 GB available.

It could be a runaway log. Looking at the first image you posted, /var is quite large. My /var (which I never clean) is 1.9 GB and yours is 7.1 GB.

[linux-rox]

Notice df says the home partition is only 7 GB. Also that / has 44 GB used, which is huge if Timeshift snapshots are stored elsewhere. And, as SMG says, /var looks suspicious. Let's try a few different ways of getting at this:

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inxi -SMpo
sudo parted --list
sudo du -m -d 1 / | sort -n -r
sudo du -m -d 1 /var | sort -n -r 
sudo du -m -d 1 /home | sort -n -r

Please use copy-and-paste for Terminal outputs, rather than screenshots. Place the output for each command in a separate code box (that's what the thing above is called). For each, type [code], paste in from clipboard, then type [/code]. Or you can copy in from clipboard, select with mouse, and click the </> button above the text entry window (which will automatically insert the code tags).

[cliffcoggin]

Another possible culprit for filling var is Flatpaks.

[mathieu]

I just ran the commands linux-rox recommended. I had to abort the one for / (it didn't load, maybe it would have eventually?). Here's the output:

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(base) mathieu@mathieu-PC:~$ inxi -SMpo
System:    Host: mathieu-PC Kernel: 5.4.0-37-generic x86_64 bits: 64 Desktop: Cinnamon 4.4.8 
           Distro: Linux Mint 19.3 Tricia 
Machine:   Type: Convertible System: ASUSTeK product: UX370UAR v: 1.0 serial: <root required> 
           Mobo: ASUSTeK model: UX370UAR v: 1.0 serial: <root required> UEFI: American Megatrends 
           v: UX370UAR.300 date: 09/07/2017 
Partition: ID-1: / size: 49.73 GiB used: 43.25 GiB (87.0%) fs: ext4 dev: /dev/sda5 
           ID-2: /boot/efi size: 256.0 MiB used: 31.8 MiB (12.4%) fs: vfat dev: /dev/sda1 
           ID-3: /home size: 6.94 GiB used: 5.12 GiB (73.8%) fs: ext4 dev: /dev/sda6 
           ID-4: /media/mathieu/b69ce86b-607b-4a55-b4a6-4857ac1fac9c size: 86.01 GiB used: 40.62 GiB (47.2%) 
           fs: ext4 dev: /dev/sdb2 
Unmounted: ID-1: /dev/sda2 size: 16.0 MiB fs: <root required> label: N/A uuid: N/A 
           ID-2: /dev/sda3 size: 179.66 GiB fs: ntfs label: N/A uuid: N/A 
           ID-3: /dev/sda4 size: 800.0 MiB fs: ntfs label: N/A uuid: 74C6E2E7C6E2A896 
           ID-4: /dev/sdb1 size: 843.59 GiB fs: ntfs label: Elements uuid: EEEE8C05EE8BC475 
(base) mathieu@mathieu-PC:~$ sudo parted --list
Model: ATA SanDisk SD8SN8U2 (scsi)
Disk /dev/sda: 256GB
Sector size (logical/physical): 512B/512B
Partition Table: gpt
Disk Flags: 

Number  Start   End    Size    File system  Name                          Flags
 1      1049kB  274MB  273MB   fat32        EFI system partition          boot, esp
 2      274MB   290MB  16,8MB               Microsoft reserved partition  msftres
 3      290MB   193GB  193GB                Basic data partition          msftdata
 5      193GB   248GB  54,4GB  ext4
 6      248GB   255GB  7642MB  ext4
 4      255GB   256GB  839MB   ntfs         Basic data partition          hidden, diag


Model: WD Elements 2621 (scsi)
Disk /dev/sdb: 1000GB
Sector size (logical/physical): 512B/512B
Partition Table: gpt
Disk Flags: 

Number  Start   End     Size    File system  Name      Flags
 1      1049kB  906GB   906GB   ntfs         Elements  msftdata
 2      906GB   1000GB  94,4GB  ext4


(base) mathieu@mathieu-PC:~$ sudo du -m -d 1 / | sort -n -r
du: cannot read directory '/proc/1588/task/1588/net': Invalid argument
du: cannot read directory '/proc/1588/net': Invalid argument
du: cannot access '/proc/7531': No such file or directory
du: cannot access '/proc/7532': No such file or directory
du: cannot access '/proc/7533': No such file or directory
du: cannot access '/proc/7535': No such file or directory
du: cannot access '/proc/7536': No such file or directory
du: cannot access '/proc/7537': No such file or directory
du: cannot access '/proc/7538': No such file or directory
du: cannot access '/proc/7545/task/7545/fd/4': No such file or directory
du: cannot access '/proc/7545/task/7545/fdinfo/4': No such file or directory
du: cannot access '/proc/7545/fd/3': No such file or directory
du: cannot access '/proc/7545/fdinfo/3': No such file or directory
du: cannot access '/run/user/1000/gvfs': Permission denied
^C
(base) mathieu@mathieu-PC:~$ sudo du -m -d 1 /var | sort -n -r
8689	/var
6382	/var/lib
2094	/var/tmp
147	/var/cache
56	/var/log
12	/var/backups
1	/var/spool
1	/var/opt
1	/var/mail
1	/var/local
(base) mathieu@mathieu-PC:~$ sudo du -m -d 1 /home | sort -n -r
5208	/home/mathieu
5208	/home
1	/home/lost+found

As far as I can tell, var/log is very modest in size with 56MB. Instead, /var/lib seems to be way too large and also /var/tmp given what you said about the typical size of /var SMG.

But also, I still don't understand where all the other space is? Is it not available because the home partition is too big and I could just make it smaller? Or are there files filling it up? Is that what you meant linux-rox?

Regarding Flatpak, cliffcoggin, as far as I can tell, it only takes up about 1GB. Or am I drawing the wrong conclusion from the following command.

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(base) mathieu@mathieu-PC:~$  du -s --si /var/lib/flatpak/*/*
1,1G	/var/lib/flatpak/app/com.jetbrains.PyCharm-Community
39M	/var/lib/flatpak/appstream/flathub
8,2k	/var/lib/flatpak/exports/bin
168k	/var/lib/flatpak/exports/share
4,1k	/var/lib/flatpak/repo/config
4,1k	/var/lib/flatpak/repo/extensions
4,1k	/var/lib/flatpak/repo/flathub.trustedkeys.gpg
5,2G	/var/lib/flatpak/repo/objects
197k	/var/lib/flatpak/repo/refs
4,1k	/var/lib/flatpak/repo/state
5,2M	/var/lib/flatpak/repo/tmp
12M	/var/lib/flatpak/runtime/org.freedesktop.Platform
312k	/var/lib/flatpak/runtime/org.freedesktop.Platform.GL.default
148k	/var/lib/flatpak/runtime/org.freedesktop.Platform.html5-codecs
9,0M	/var/lib/flatpak/runtime/org.freedesktop.Platform.Locale
3,4M	/var/lib/flatpak/runtime/org.freedesktop.Platform.openh264
144k	/var/lib/flatpak/runtime/org.freedesktop.Platform.VAAPI.Intel
24M	/var/lib/flatpak/runtime/org.freedesktop.Sdk
9,1M	/var/lib/flatpak/runtime/org.freedesktop.Sdk.Locale
58k	/var/lib/flatpak/runtime/org.gtk.Gtk3theme.Mint-Y

Again, thanks to all of you for your help!

[SMG]

Just as an FYI, the latest 5.4.0 kernel is 5.4.0-70. Given your full root partition, I would not install any until the problem is sorted, but keep updating in mind for later.
System:
Host: mathieu-PC Kernel: 5.4.0-37-generic x86_64 bits: 64 Desktop: Cinnamon 4.4.8
Distro: Linux Mint 19.3 Tricia

As far as I can tell, var/log is very modest in size with 56MB. Instead, /var/lib seems to be way too large and also /var/tmp given what you said about the typical size of /var SMG.

I do not know what is "typical", but my install is a rather basic Mint install. (I do not have any flatpaks installed.)

But also, I still don't understand where all the other space is? Is it not available because the home partition is too big and I could just make it smaller?

Your /home is the tiniest I've ever seen. Normally, one would not have a separate /home if /home is not going to be larger in size than the root partition. Just make one larger root partition and not have a separate /home.

Partition: ID-1: / size: 49.73 GiB used: 43.25 GiB (87.0%) fs: ext4 dev: /dev/sda5
ID-2: /boot/efi size: 256.0 MiB used: 31.8 MiB (12.4%) fs: vfat dev: /dev/sda1
ID-3: /home size: 6.94 GiB used: 5.12 GiB (73.8%) fs: ext4 dev: /dev/sda6
ID-4: /media/mathieu/b69ce86b-607b-4a55-b4a6-4857ac1fac9c size: 86.01 GiB used: 40.62 GiB (47.2%)
fs: ext4 dev: /dev/sdb2

[linux-rox]

I agree with SMG, there was little advantage to splitting out /home to its own partition with so little space available. Unfortunately, lots of sources act like it's essential (it's not) and/or don't bother to discuss when it's not a good idea. Anyway, the good news for purposes of this thread is that we've answered the original question. The Devices & Locations screenshot does not reflect space which should be available on the home partition.

This still leaves the question of why / is so full. I'm puzzled the du command wouldn't run. Does the ^C mean you terminated the command? Try again, letting it squawk about the directories it can't read. When done, you should get a report which looks something like this:

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5113	/usr
1435	/var
1394	/lib
839	/home
334	/boot
19	/sbin
19	/opt
16	/bin
15	/etc
2	/run
1	/tmp
1	/srv
1	/root
1	/mnt
1	/lost+found
1	/lib64
1	/cdrom
0	/sys
0	/proc
0	/dev

That's a VirtualBox VM, with a basic as-installed system. I've omitted the /media folder (mostly shared from the internal hard drive) and /timeshift (which you're saving elsewhere). Those values are size in MB. So /var, for example, is 1435 MB or 1.435 GB.

Note: When you report the output, please copy only the lines with the folders and their size. Don't bother with the squawks, which will merely clutter up the report and aren't relevant to the inquiry.

[ajgreeny]

Note that the du output for the root partition can take quite a long time to show, maybe a minute or two depending on your hardware.

Also I suggest that you use the -h option instead of the -m option; it makes the sizes of partitions much more easily readable to my eyes at least.

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sudo du -h -d 1 / | sort -n -r

It's a minor point but try it, and wait until the terminal prompt returns in case du is still in action.

[Flemur]

Also I suggest that you use the -h option instead of the -m option; it makes the sizes of partitions much more easily readable to my eyes at least.

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sudo du -h -d 1 / | sort -n -r

That will include other partitions mounted under "/", namely it can easily give the wrong answer. It also returns the results in a weirdly unsorted order; here's what I got.

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988K	/run
252K	/root
98G	/
95G	/mnt
50M	/var
...

/mnt = a data partition. Also note the bad output order. Note that it says there's 95G used on "/", which is a partition of about 30G.


This command (-x = stay on partition):

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sudo du -xhd1 / | sort -h

doesn't include other partitions, and puts the directories of interest at the end:

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4.0K	/lost+found
...
50M	/var
3.7G	/usr
3.8G	/

[ajgreeny]

Flippin heck!

I'd never noticed that before; it sorts on the numerical digits and ignores the letters indicating megabytes, M, gigabytes, G and kilobytes, K.
Thanks for that Flemur. I will stick with -m in future to keep everything in megabytes.

We learn something new every day!

[linux-rox]

I also like Flemur's form of the command. Let's use that, mathieu. As a bonus, no squawks.

As we're sharing tips, this form of the df command strips out a lot of cruft: df -hT -x squashfs -x tmpfs -x devtmpfs.
By the way, I've formulated none of these, including the ones I gave above. I merely notice things of this sort in my travels and save the ones which seem useful.

[mathieu]

Big thanks to all of you for helping me here! It's so amazing to me that I can ask a question on a forum and people I've never met will answer me, just to help out. I mean it when I say you have my fullest admiration.

Given all that I know now (that I should never have separated / and /home, that something somewhere is wrong with my var folder and others and that my root is generally way bigger than expected etc.), I've decided to just delete and reinstall linux-mint. I'll save a back-up, just in case. I think it will be cleaner. I don't have much on here anyway (yet! ).

I'm super glad you guys found the answer to that original question.

You are right linux-rox and ajgreeny: I had interrupted the du command via keyboard, bc it wouldn't load, but when I gave it more time, it did.

FYI, here's what I get with Flemur's command:

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(base) mathieu@mathieu-PC:~$ sudo du -xhd1 / | sort -h
[sudo] password for mathieu:              
4,0K	/cdrom
4,0K	/lib64
4,0K	/mnt
4,0K	/opt
4,0K	/srv
16K	/lost+found
32K	/timeshift
40K	/media
524K	/tmp
15M	/etc
16M	/bin
19M	/sbin
164M	/boot
869M	/lib
4,3G	/usr
8,7G	/var
29G	/root
44G	/

[linux-rox]

FYI, here's the answer to the mystery:

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29G	/root

That's the home folder of user root, not to be confused with the root directory (which is /). Normally, /root has almost nothing in it. My guess would be that you deleted a bunch of stuff as root and it ended up in /root's trash bin (/root/.local/share/Trash).

[senjoz]

That's the home folder of user root, not to be confused with the root directory (which is /). Normally, /root has almost nothing in it. My guess would be that you deleted a bunch of stuff as root and it ended up in /root's trash bin (/root/.local/share/Trash).

@mathieu, you can empty root's trash with trash-cli. Install it with Synaptic Package Manager. Terminal command trash-list lists files in the trash for logged in user, command sudo trash-list lists files in root's trash. Command trash-empty empties logged in user's trash, sudo trash-empty empties root's trash. Read man trash.

Regards, Jože