System disk almost full error

Hi everyone.

Before I explain anything I simply just want everyone to know that I have no experience enough with the terminal, so the whole operation was partly done by me and some help from the internet.

I just want to ask about why my /mnt/apps a directory to mount my disk, is not existing. I created one using sudo mkdir /mnt/apps in the terminal. To clarify what I was doing was actually to create a new partition in my disk with over 1tb so I can transfer over half of my programs from my system disk (where fedora is) over to that disk. Since that didn’t work out cause to the issue of /mnt/apps not existing, or what dolphin file manager confirms and so does nautilus (gnome file manager) as well.

I made it also auto-mount to my disk using the nano etc/fstab command I think. In the disk I can see an option under the 4th partition I made that it says unmount. And I think that worked actually. But I could have a theory it’s some form of bug. Cause orignially I wanted to have more space on my system disk, because my brave browser I use, it kept crashing every 20 minutes or so. And the cause of that issue was due to partly of the disk being almost at it’s fullest capacity the error said.

I have a screenshot of the error on the 4th partition

Really appreciate if someone can help with this.

Before we can really assist we need more info.
Please post the output of mount and df and lsblk -f so we can see the config and hope to assist.

When posting what is copy & pasted please use the preformmatted text tags (the </> button on the toolbar) so we see the data as formatted on your screen.

It may help us if you explain the history of your installation and current Fedora version. A fresh install of Fedora 39 normally provides adequate space for the vast majority of users, and the current default btrfs configuration avoids some of the drawbacks of fixed partition sizes.

You will find it very useful to get comfortable with the terminal and either bash or zsh (most widey used shell programs). It can help when the GUI software fails and is import when posting on this forum as text is searchable so your posts can be found with text searches by others who have experience with similar problems. Today’s internet has become dominated by low-quality clickbait sites, so I recommend Linux Command, which has been around for years.

I thank you both for replying at first. First of all I have typed the following commands in the terminal as requested:

mount
/dev/nvme0n1p3 on / type btrfs (rw,relatime,seclabel,compress=zstd:1,ssd,discard=async,space_cache=v2,subvolid=257,subvol=/root)
devtmpfs on /dev type devtmpfs (rw,nosuid,seclabel,size=4096k,nr_inodes=6144635,mode=755,inode64)
tmpfs on /dev/shm type tmpfs (rw,nosuid,nodev,seclabel,inode64)
devpts on /dev/pts type devpts (rw,nosuid,noexec,relatime,seclabel,gid=5,mode=620,ptmxmode=000)
sysfs on /sys type sysfs (rw,nosuid,nodev,noexec,relatime,seclabel)
securityfs on /sys/kernel/security type securityfs (rw,nosuid,nodev,noexec,relatime)
cgroup2 on /sys/fs/cgroup type cgroup2 (rw,nosuid,nodev,noexec,relatime,seclabel,nsdelegate,memory_recursiveprot)
pstore on /sys/fs/pstore type pstore (rw,nosuid,nodev,noexec,relatime,seclabel)
efivarfs on /sys/firmware/efi/efivars type efivarfs (rw,nosuid,nodev,noexec,relatime)
bpf on /sys/fs/bpf type bpf (rw,nosuid,nodev,noexec,relatime,mode=700)
configfs on /sys/kernel/config type configfs (rw,nosuid,nodev,noexec,relatime)
proc on /proc type proc (rw,nosuid,nodev,noexec,relatime)
tmpfs on /run type tmpfs (rw,nosuid,nodev,seclabel,size=9847664k,nr_inodes=819200,mode=755,inode64)
selinuxfs on /sys/fs/selinux type selinuxfs (rw,nosuid,noexec,relatime)
systemd-1 on /proc/sys/fs/binfmt_misc type autofs (rw,relatime,fd=34,pgrp=1,timeout=0,minproto=5,maxproto=5,direct,pipe_ino=7414)
hugetlbfs on /dev/hugepages type hugetlbfs (rw,nosuid,nodev,relatime,seclabel,pagesize=2M)
mqueue on /dev/mqueue type mqueue (rw,nosuid,nodev,noexec,relatime,seclabel)
debugfs on /sys/kernel/debug type debugfs (rw,nosuid,nodev,noexec,relatime,seclabel)
tracefs on /sys/kernel/tracing type tracefs (rw,nosuid,nodev,noexec,relatime,seclabel)
fusectl on /sys/fs/fuse/connections type fusectl (rw,nosuid,nodev,noexec,relatime)
/dev/nvme0n1p3 on /home type btrfs (rw,relatime,seclabel,compress=zstd:1,ssd,discard=async,space_cache=v2,subvolid=256,subvol=/home)
tmpfs on /tmp type tmpfs (rw,nosuid,nodev,seclabel,size=24619156k,nr_inodes=1048576,inode64)
/dev/nvme0n1p2 on /boot type ext4 (rw,relatime,seclabel)
/dev/sda3 on /media/Backup type fuseblk (rw,relatime,user_id=0,group_id=0,allow_other,blksize=4096)
/dev/nvme0n1p1 on /boot/efi type vfat (rw,relatime,fmask=0077,dmask=0077,codepage=437,iocharset=ascii,shortname=winnt,errors=remount-ro)
/dev/sda4 on /mnt/apps type ext4 (rw,relatime,seclabel)
binfmt_misc on /proc/sys/fs/binfmt_misc type binfmt_misc (rw,nosuid,nodev,noexec,relatime)
sunrpc on /var/lib/nfs/rpc_pipefs type rpc_pipefs (rw,relatime)
overlay on /var/lib/docker/overlay2/205dca24e3c4e1d102f3860241cece95f7bcb56dc0114bbbcac518cfa5f5cf78/merged type overlay (rw,relatime,seclabel,lowerdir=/var/lib/docker/overlay2/l/IO5NTQFY5VEBF6UA7IYDESVUSK:/var/lib/docker/overlay2/l/62V3GWTD3BPW7GIIXC6YGBIIFH:/var/lib/docker/overlay2/l/353LKCQ3IAVH55BKZNFCCO2U46:/var/lib/docker/overlay2/l/DGEW3UTI74GWUPYNK7J2QN7CSK:/var/lib/docker/overlay2/l/SG6NSY6VFSMU3D566RM5LEHDAK,upperdir=/var/lib/docker/overlay2/205dca24e3c4e1d102f3860241cece95f7bcb56dc0114bbbcac518cfa5f5cf78/diff,workdir=/var/lib/docker/overlay2/205dca24e3c4e1d102f3860241cece95f7bcb56dc0114bbbcac518cfa5f5cf78/work)
nsfs on /run/docker/netns/9acd9e720844 type nsfs (rw)
tmpfs on /run/user/1000 type tmpfs (rw,nosuid,nodev,relatime,seclabel,size=4923828k,nr_inodes=1230957,mode=700,uid=1000,gid=1000,inode64)
gvfsd-fuse on /run/user/1000/gvfs type fuse.gvfsd-fuse (rw,nosuid,nodev,relatime,user_id=1000,group_id=1000)
portal on /run/user/1000/doc type fuse.portal (rw,nosuid,nodev,relatime,user_id=1000,group_id=1000)

df
Filesystem 1K-blocks Used Available Use% Mounted on
/dev/nvme0n1p3 486722560 478744408 4709000 100% /
devtmpfs 4096 0 4096 0% /dev
tmpfs 24619152 135388 24483764 1% /dev/shm
efivarfs 192 81 107 44% /sys/firmware/efi/efivars
tmpfs 9847664 2148 9845516 1% /run
/dev/nvme0n1p3 486722560 478744408 4709000 100% /home
tmpfs 24619156 28828 24590328 1% /tmp
/dev/nvme0n1p2 996780 418604 509364 46% /boot
/dev/sda3 605582332 473340984 132241348 79% /media/Backup
/dev/nvme0n1p1 613184 19528 593656 4% /boot/efi
/dev/sda4 364219208 2076 345642592 1% /mnt/apps
tmpfs 4923828 6308 4917520 1% /run/user/1000

lsblk -f
NAME FSTYPE FSVER LABEL UUID FSAVAIL FSUSE% MOUNTPOINTS
sda
├─sda1

├─sda2

├─sda3
│ ntfs Backup1 A69E5EFD9E5EC609 126.1G 78% /media/Backup
└─sda4
ext4 1.0 Programs2nd 4d9ee1d9-166a-49ad-a0a4-6e716bad1a64 329.6G 0% /mnt/apps
zram0
[SWAP]
nvme0n1

├─nvme0n1p1
│ vfat FAT32 7457-DDA1 579.7M 3% /boot/efi
├─nvme0n1p2
│ ext4 1.0 d8327c4f-66fe-4f99-a16e-f5c321f4d4d1 497.4M 42% /boot
└─nvme0n1p3
btrfs fedora 1e93772f-3b53-44bc-b667-ecd2eb7958b7 4.5G 98% /home
/

My current version of fedora is in fact fedora 39 and I have installed it approximately a month ago.

This is far from adequate free space for a fedora system. You must make more space available to use before you can do anything else with that system. Either by enlarging the device or identifying what is filling it up and removing what is unnecessary.

Please note that I suggested the following, and you did not do that. Readability is severely hampered with the lack of suitable formatting…

Your post becomes this with formatting.

mount
/dev/nvme0n1p3 on / type btrfs (rw,relatime,seclabel,compress=zstd:1,ssd,discard=async,space_cache=v2,subvolid=257,subvol=/root)
devtmpfs on /dev type devtmpfs (rw,nosuid,seclabel,size=4096k,nr_inodes=6144635,mode=755,inode64)
tmpfs on /dev/shm type tmpfs (rw,nosuid,nodev,seclabel,inode64)
devpts on /dev/pts type devpts (rw,nosuid,noexec,relatime,seclabel,gid=5,mode=620,ptmxmode=000)
sysfs on /sys type sysfs (rw,nosuid,nodev,noexec,relatime,seclabel)
securityfs on /sys/kernel/security type securityfs (rw,nosuid,nodev,noexec,relatime)
cgroup2 on /sys/fs/cgroup type cgroup2 (rw,nosuid,nodev,noexec,relatime,seclabel,nsdelegate,memory_recursiveprot)
pstore on /sys/fs/pstore type pstore (rw,nosuid,nodev,noexec,relatime,seclabel)
efivarfs on /sys/firmware/efi/efivars type efivarfs (rw,nosuid,nodev,noexec,relatime)
bpf on /sys/fs/bpf type bpf (rw,nosuid,nodev,noexec,relatime,mode=700)
configfs on /sys/kernel/config type configfs (rw,nosuid,nodev,noexec,relatime)
proc on /proc type proc (rw,nosuid,nodev,noexec,relatime)
tmpfs on /run type tmpfs (rw,nosuid,nodev,seclabel,size=9847664k,nr_inodes=819200,mode=755,inode64)
selinuxfs on /sys/fs/selinux type selinuxfs (rw,nosuid,noexec,relatime)
systemd-1 on /proc/sys/fs/binfmt_misc type autofs (rw,relatime,fd=34,pgrp=1,timeout=0,minproto=5,maxproto=5,direct,pipe_ino=7414)
hugetlbfs on /dev/hugepages type hugetlbfs (rw,nosuid,nodev,relatime,seclabel,pagesize=2M)
mqueue on /dev/mqueue type mqueue (rw,nosuid,nodev,noexec,relatime,seclabel)
debugfs on /sys/kernel/debug type debugfs (rw,nosuid,nodev,noexec,relatime,seclabel)
tracefs on /sys/kernel/tracing type tracefs (rw,nosuid,nodev,noexec,relatime,seclabel)
fusectl on /sys/fs/fuse/connections type fusectl (rw,nosuid,nodev,noexec,relatime)
/dev/nvme0n1p3 on /home type btrfs (rw,relatime,seclabel,compress=zstd:1,ssd,discard=async,space_cache=v2,subvolid=256,subvol=/home)
tmpfs on /tmp type tmpfs (rw,nosuid,nodev,seclabel,size=24619156k,nr_inodes=1048576,inode64)
/dev/nvme0n1p2 on /boot type ext4 (rw,relatime,seclabel)
/dev/sda3 on /media/Backup type fuseblk (rw,relatime,user_id=0,group_id=0,allow_other,blksize=4096)
/dev/nvme0n1p1 on /boot/efi type vfat (rw,relatime,fmask=0077,dmask=0077,codepage=437,iocharset=ascii,shortname=winnt,errors=remount-ro)
/dev/sda4 on /mnt/apps type ext4 (rw,relatime,seclabel)
binfmt_misc on /proc/sys/fs/binfmt_misc type binfmt_misc (rw,nosuid,nodev,noexec,relatime)
sunrpc on /var/lib/nfs/rpc_pipefs type rpc_pipefs (rw,relatime)
overlay on /var/lib/docker/overlay2/205dca24e3c4e1d102f3860241cece95f7bcb56dc0114bbbcac518cfa5f5cf78/merged type overlay (rw,relatime,seclabel,lowerdir=/var/lib/docker/overlay2/l/IO5NTQFY5VEBF6UA7IYDESVUSK:/var/lib/docker/overlay2/l/62V3GWTD3BPW7GIIXC6YGBIIFH:/var/lib/docker/overlay2/l/353LKCQ3IAVH55BKZNFCCO2U46:/var/lib/docker/overlay2/l/DGEW3UTI74GWUPYNK7J2QN7CSK:/var/lib/docker/overlay2/l/SG6NSY6VFSMU3D566RM5LEHDAK,upperdir=/var/lib/docker/overlay2/205dca24e3c4e1d102f3860241cece95f7bcb56dc0114bbbcac518cfa5f5cf78/diff,workdir=/var/lib/docker/overlay2/205dca24e3c4e1d102f3860241cece95f7bcb56dc0114bbbcac518cfa5f5cf78/work)
nsfs on /run/docker/netns/9acd9e720844 type nsfs (rw)
tmpfs on /run/user/1000 type tmpfs (rw,nosuid,nodev,relatime,seclabel,size=4923828k,nr_inodes=1230957,mode=700,uid=1000,gid=1000,inode64)
gvfsd-fuse on /run/user/1000/gvfs type fuse.gvfsd-fuse (rw,nosuid,nodev,relatime,user_id=1000,group_id=1000)
portal on /run/user/1000/doc type fuse.portal (rw,nosuid,nodev,relatime,user_id=1000,group_id=1000)

df
Filesystem     1K-blocks      Used Available Use% Mounted on
/dev/nvme0n1p3 486722560 478744408   4709000 100% /
devtmpfs            4096         0      4096   0% /dev
tmpfs           24619152    135388  24483764   1% /dev/shm
efivarfs             192        81       107  44% /sys/firmware/efi/efivars
tmpfs            9847664      2148   9845516   1% /run
/dev/nvme0n1p3 486722560 478744408   4709000 100% /home
tmpfs           24619156     28828  24590328   1% /tmp
/dev/nvme0n1p2    996780    418604    509364  46% /boot
/dev/sda3      605582332 473340984 132241348  79% /media/Backup
/dev/nvme0n1p1    613184     19528    593656   4% /boot/efi
/dev/sda4      364219208      2076 345642592   1% /mnt/apps
tmpfs            4923828      6308   4917520   1% /run/user/1000

lsblk -f
NAME FSTYPE FSVER LABEL       UUID                                 FSAVAIL FSUSE% MOUNTPOINTS
sda                                                                               
├─sda1
│                                                                                 
├─sda2
│                                                                                 
├─sda3
│    ntfs         Backup1     A69E5EFD9E5EC609                      126.1G    78% /media/Backup
└─sda4
     ext4   1.0   Programs2nd 4d9ee1d9-166a-49ad-a0a4-6e716bad1a64  329.6G     0% /mnt/apps
zram0
                                                                                  [SWAP]
nvme0n1
                                                                                  
├─nvme0n1p1
│    vfat   FAT32             7457-DDA1                             579.7M     3% /boot/efi
├─nvme0n1p2
│    ext4   1.0               d8327c4f-66fe-4f99-a16e-f5c321f4d4d1  497.4M    42% /boot
└─nvme0n1p3
     btrfs        fedora      1e93772f-3b53-44bc-b667-ecd2eb7958b7    4.5G    98% /home
                                                                                  /
1 Like

Please also post the output of sudo fdisk -l as well as sudo du -hs /* and du -hs ~/* so we can confirm the device sizes and exact partitioning as well as which paths are using the most space.

If I am reading the output of df correctly it seems that nvme01p3 should be almost 500 G and if so then it would appear that something is using an enormous amount of space for a system that was installed just a month ago.

I have now posted all the commands output in a preformatted text now. And thanks again for replying.
In the output there doesn’t seem to be programs that seem to have tremendous amount of space. But I just wanna know another thing as well. How much space should I have available on my system disk?

sudo fdisk -l

Disk /dev/sda: 931.51 GiB, 1000204886016 bytes, 1953525168 sectors
Disk model: WDC  WDS100T2B0A
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disklabel type: gpt
Disk identifier: 4CCFB2F5-8CFB-4E65-A9D3-7A5C0B475384

Device          Start        End    Sectors   Size Type
/dev/sda1          34       2081       2048     1M Microsoft LDM metadata
/dev/sda2        2082      32767      30686    15M Microsoft reserved
/dev/sda3       32768 1211197439 1211164672 577.5G Microsoft LDM data
/dev/sda4  1211197440 1953523711  742326272   354G Linux filesystem


Disk /dev/nvme0n1: 465.76 GiB, 500107862016 bytes, 976773168 sectors
Disk model: Samsung SSD 970 EVO Plus 500GB          
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disklabel type: gpt
Disk identifier: BDDCCC20-CBAD-4975-B8A2-5B5D8368ACFF

Device           Start       End   Sectors   Size Type
/dev/nvme0n1p1    2048   1230847   1228800   600M EFI System
/dev/nvme0n1p2 1230848   3327999   2097152     1G Linux filesystem
/dev/nvme0n1p3 3328000 976773119 973445120 464.2G Linux filesystem


Disk /dev/zram0: 8 GiB, 8589934592 bytes, 2097152 sectors
Units: sectors of 1 * 4096 = 4096 bytes
Sector size (logical/physical): 4096 bytes / 4096 bytes
I/O size (minimum/optimal): 4096 bytes / 4096 bytes

sudo du -hs /*

0	/afs
4.0K	/bin
428M	/boot
1.1M	/dev
35M	/etc
391G	/home
4.0K	/lib
4.0K	/lib64
0	/lost+found
452G	/media
20K	/mnt
2.7G	/opt
du: cannot access '/proc/6632/task/6632/fd/3': No such file or directory
du: cannot access '/proc/6632/task/6632/fdinfo/3': No such file or directory
du: cannot access '/proc/6632/fd/3': No such file or directory
du: cannot access '/proc/6632/fdinfo/3': No such file or directory
0	/proc
9.8M	/root
du: cannot access '/run/user/1000/gvfs': Permission denied
du: cannot access '/run/user/1000/doc': Permission denied
2.3M	/run
4.0K	/sbin
4.0K	/snap
0	/srv
0	/sys
4.0K	/tmp
12G	/usr
14G	/var

du -hs ~/*

16K	/home/anonymous/admin_settings.txt
0	/home/anonymous/AppImages
235M	/home/anonymous/Applications
373G	/home/anonymous/backup.tar.gz
3.2G	/home/anonymous/Desktop
235M	/home/anonymous/Discord-linux-x64
396K	/home/anonymous/Documents
1.1G	/home/anonymous/Downloads
8.0K	/home/anonymous/fedora.gpg
0	/home/anonymous/fmjvv-num42
8.0K	/home/anonymous/^G
27M	/home/anonymous/gnome-ext-hanabi
4.0K	/home/anonymous/gotify
0	/home/anonymous/hcpvd-ezjw6
0	/home/anonymous/hjkqe-zvxxb
4.0K	/home/anonymous/journalctl -xeu postgresql.service
4.0K	/home/anonymous/MOK.der
4.0K	/home/anonymous/MOK.priv
4.0K	/home/anonymous/mullvad-browser.desktop
4.0K	/home/anonymous/mullvad-browser.desktop.save
0	/home/anonymous/Music
0	/home/anonymous/my_disk
4.0K	/home/anonymous/nvidia.der
4.0K	/home/anonymous/nvidia.priv
3.4M	/home/anonymous/Pictures
8.0K	/home/anonymous/protonvpn-stable-release-1.0.1-2.noarch.rpm
0	/home/anonymous/Public
0	/home/anonymous/sdada
0	/home/anonymous/Sync
235M	/home/anonymous/Techlore.tech-linux-x64
0	/home/anonymous/Templates
4.0K	/home/anonymous/torbrowser.desktop
12K	/home/anonymous/user-settings.conf
0	/home/anonymous/Videos

The one taking up space is the archive:

373G /home/anonymous/backup.tar.gz

it appears to be created by backup software, which is not ideal as you are backing up to the same disk/partition, can you provide further details?

1 Like

Sorry for not responding. There is a story behind it:

So basically I wanted to backup all my files because I though they were encrypted. And then I learned about automounting and that was what I didn’t have done to my secondary disk also called backup as well as that file. I purposely made a tar file out of it to back it up. So I think that is what that file actually is.

Now I know for sure I can’t extract it to check it out, that will essentially create duplicate and that is not possible. But I am so sure that it’s a file I can remove, so that is what I am doing now.

Thanks a lot all of you.

Update:

I have permanently deleted the file.

What sometimes can happen is that the tar file itself gets included into the tar file. The tar program will then never reach the end of that file as the file keeps on growing while reading it.