How to shrink lvm2 and add free space to /boot F38

oglop · August 18, 2023, 4:25pm

my /boot is not in lvm, I read that I need to

shrink logical volume
shrink physical volume
resize partition

I think I successfully did step 2, but stuck there, as Free PE seems disappears after a while, and I don’t understand why. Following commands are executed inside F38 live cd

[root@localhost-live liveuser]# parted /dev/sdb print
Model: ATA TS256GMTS400 (scsi)
Disk /dev/sdb: 256GB
Sector size (logical/physical): 512B/512B
Partition Table: gpt
Disk Flags: 

Number  Start   End    Size    File system  Name                  Flags
 1      1049kB  170GB  170GB                                      lvm
 3      170GB   170GB  345MB   fat32        Basic data partition  boot, esp
 4      170GB   170GB  268MB   ext4         Basic data partition  msftdata, no_automount
 5      170GB   256GB  85.8GB               No name


[root@localhost-live liveuser]# fdisk -l
Disk /dev/sda: 465.76 GiB, 500107862016 bytes, 976773168 sectors
Disk model: WDC WD5000LPLX-0
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 4096 bytes
I/O size (minimum/optimal): 4096 bytes / 4096 bytes
Disklabel type: dos
Disk identifier: 0x2efb7eca

Device     Boot Start       End   Sectors   Size Id Type
/dev/sda1  *     2048 976769023 976766976 465.8G  7 HPFS/NTFS/exFAT


Disk /dev/sdb: 238.47 GiB, 256060514304 bytes, 500118192 sectors
Disk model: TS256GMTS400    
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: 2251A347-06EB-4214-BAD1-0D779497D354

Device         Start       End   Sectors  Size Type
/dev/sdb1       2048 331298815 331296768  158G Linux LVM
/dev/sdb3  331298816 331972607    673792  329M EFI System
/dev/sdb4  331972608 332496895    524288  256M Microsoft basic data
/dev/sdb5  332496896 500117503 167620608 79.9G unknown


Disk /dev/mapper/fedora-root: 237.9 GiB, 255441502208 bytes, 498909184 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
GPT PMBR size mismatch (4100491 != 7856126) will be corrected by write.
The backup GPT table is not on the end of the device.


Disk /dev/sdc: 3.75 GiB, 4022337024 bytes, 7856127 sectors
Disk model: Cruzer Blade    
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: 596BFE18-6CFC-4880-BA94-298703C7C362

Device       Start     End Sectors  Size Type
/dev/sdc1       64 4075983 4075920  1.9G Microsoft basic data
/dev/sdc2  4075984 4099827   23844 11.6M EFI System
/dev/sdc3  4099828 4100427     600  300K Microsoft basic data


Disk /dev/loop0: 1.85 GiB, 1987653632 bytes, 3882136 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes


Disk /dev/loop1: 7.57 GiB, 8128561152 bytes, 15876096 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes


Disk /dev/loop2: 32 GiB, 34359738368 bytes, 67108864 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes


Disk /dev/mapper/live-rw: 7.57 GiB, 8128561152 bytes, 15876096 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes


Disk /dev/mapper/live-base: 7.57 GiB, 8128561152 bytes, 15876096 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes


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

[root@localhost-live liveuser]# lvresize -L -256M --resizefs /dev/mapper/fedora-root
fsck from util-linux 2.38.1
/dev/mapper/fedora-root: Inode 4195745 extent tree (at level 1) could be shorter.  IGNORED.
/dev/mapper/fedora-root: Inode 4200788 extent tree (at level 1) could be shorter.  IGNORED.
/dev/mapper/fedora-root: Inode 4328013 extent tree (at level 1) could be narrower.  IGNORED.
/dev/mapper/fedora-root: Inode 4365074 extent tree (at level 1) could be narrower.  IGNORED.
/dev/mapper/fedora-root: Inode 4719171 extent tree (at level 1) could be shorter.  IGNORED.
/dev/mapper/fedora-root: Inode 4719351 extent tree (at level 1) could be shorter.  IGNORED.
/dev/mapper/fedora-root: Inode 4721912 extent tree (at level 1) could be shorter.  IGNORED.
/dev/mapper/fedora-root: Inode 4744249 extent tree (at level 1) could be shorter.  IGNORED.
/dev/mapper/fedora-root: Inode 4981078 extent tree (at level 2) could be narrower.  IGNORED.
/dev/mapper/fedora-root: Inode 5112223 extent tree (at level 2) could be narrower.  IGNORED.
/dev/mapper/fedora-root: Inode 5113032 extent tree (at level 2) could be narrower.  IGNORED.
/dev/mapper/fedora-root: Inode 5113059 extent tree (at level 1) could be narrower.  IGNORED.
/dev/mapper/fedora-root: Inode 5113089 extent tree (at level 1) could be narrower.  IGNORED.
/dev/mapper/fedora-root: Inode 5113121 extent tree (at level 2) could be narrower.  IGNORED.
/dev/mapper/fedora-root: Inode 5113210 extent tree (at level 2) could be narrower.  IGNORED.
/dev/mapper/fedora-root: Inode 5118973 extent tree (at level 1) could be narrower.  IGNORED.
/dev/mapper/fedora-root: 1391744/15597568 files (1.4% non-contiguous), 25851215/62363648 blocks
resize2fs 1.46.5 (30-Dec-2021)
Resizing the filesystem on /dev/mapper/fedora-root to 62298112 (4k) blocks.
The filesystem on /dev/mapper/fedora-root is now 62298112 (4k) blocks long.

  Size of logical volume fedora/root changed from <237.90 GiB (60902 extents) to <237.65 GiB (60838 extents).
  Logical volume fedora/root successfully resized.

[root@localhost-live liveuser]# e2fsck -f /dev/sdb4
e2fsck 1.46.5 (30-Dec-2021)
Pass 1: Checking inodes, blocks, and sizes
Pass 2: Checking directory structure
Pass 3: Checking directory connectivity
Pass 4: Checking reference counts
Pass 5: Checking group summary information
boot: 102/65536 files (2.0% non-contiguous), 227467/262144 blocks
[root@localhost-live liveuser]# resize2fs /dev/sdb4
resize2fs 1.46.5 (30-Dec-2021)
The filesystem is already 262144 (1k) blocks long.  Nothing to do!

[root@localhost-live liveuser]# pvdisplay -v -m
  --- Physical volume ---
  PV Name               /dev/sdb5
  VG Name               fedora
  PV Size               <79.93 GiB / not usable 2.00 MiB
  Allocatable           yes (but full)
  PE Size               4.00 MiB
  Total PE              20461
  Free PE               0
  Allocated PE          20461
  PV UUID               QhFeDm-FZsC-ZThg-qbse-SKXv-yYuc-8obe87
   
  --- Physical Segments ---
  Physical extent 0 to 20460:
    Logical volume	/dev/fedora/root
    Logical extents	0 to 20460
   
  --- Physical volume ---
  PV Name               /dev/sdb1
  VG Name               fedora
  PV Size               157.97 GiB / not usable 2.00 MiB
  Allocatable           yes 
  PE Size               4.00 MiB
  Total PE              40441
  Free PE               64
  Allocated PE          40377
  PV UUID               JK7m9H-XWbv-MjT0-NId7-t2zo-wA3z-QIWdP7
   
  --- Physical Segments ---
  Physical extent 0 to 40376:
    Logical volume	/dev/fedora/root
    Logical extents	20461 to 60837
  Physical extent 40377 to 40440:
    FREE

[root@localhost-live liveuser]# pvresize /dev/sdb1 --setphysicalvolumesize 161512
/dev/sdb1: Requested size <157.73 GiB is less than real size 157.97 GiB. Proceed?  [y/n]: y
  WARNING: /dev/sdb1: Pretending size is 330776576 not 331296768 sectors.
  Physical volume "/dev/sdb1" changed
  1 physical volume(s) resized or updated / 0 physical volume(s) not resized

as you can see above , I have Free PE 64, but even though I have not done anything , I just opened gparted, blivet-gui and gnome disks to check info in a gui, the Free PE is 0 now, and I can not resize partition

latest info

# vgdisplay -v
  --- Volume group ---
  VG Name               fedora
  System ID             
  Format                lvm2
  Metadata Areas        2
  Metadata Sequence No  7
  VG Access             read/write
  VG Status             resizable
  MAX LV                0
  Cur LV                1
  Open LV               1
  Max PV                0
  Cur PV                2
  Act PV                2
  VG Size               <237.65 GiB
  PE Size               4.00 MiB
  Total PE              60838
  Alloc PE / Size       60838 / <237.65 GiB
  Free  PE / Size       0 / 0   
  VG UUID               cbwDRa-Grcd-H65X-l8ub-vbNc-y9aC-SO8H1X
   
  --- Logical volume ---
  LV Path                /dev/fedora/root
  LV Name                root
  VG Name                fedora
  LV UUID                eNmKl8-mo04-dGnf-I8lc-eSRt-wDFP-PWaWrg
  LV Write Access        read/write
  LV Creation host, time localhost.localdomain, 2017-04-06 18:27:50 -0700
  LV Status              available
  # open                 1
  LV Size                <237.65 GiB
  Current LE             60838
  Segments               2
  Allocation             inherit
  Read ahead sectors     auto
  - currently set to     256
  Block device           253:0
   
  --- Physical volumes ---
  PV Name               /dev/sdb5     
  PV UUID               QhFeDm-FZsC-ZThg-qbse-SKXv-yYuc-8obe87
  PV Status             allocatable
  Total PE / Free PE    20461 / 0
   
  PV Name               /dev/sdb1     
  PV UUID               JK7m9H-XWbv-MjT0-NId7-t2zo-wA3z-QIWdP7
  PV Status             allocatable
  Total PE / Free PE    40377 / 0

# pvdisplay 
  --- Physical volume ---
  PV Name               /dev/sdb5
  VG Name               fedora
  PV Size               <79.93 GiB / not usable 2.00 MiB
  Allocatable           yes (but full)
  PE Size               4.00 MiB
  Total PE              20461
  Free PE               0
  Allocated PE          20461
  PV UUID               QhFeDm-FZsC-ZThg-qbse-SKXv-yYuc-8obe87
   
  --- Physical volume ---
  PV Name               /dev/sdb1
  VG Name               fedora
  PV Size               <157.73 GiB / not usable 3.00 MiB
  Allocatable           yes (but full)
  PE Size               4.00 MiB
  Total PE              40377
  Free PE               0
  Allocated PE          40377
  PV UUID               JK7m9H-XWbv-MjT0-NId7-t2zo-wA3z-QIWdP7

# vgs
  VG     #PV #LV #SN Attr   VSize    VFree
  fedora   2   1   0 wz--n- <237.65g    0

# pvs
  PV         VG     Fmt  Attr PSize   PFree
  /dev/sdb1  fedora lvm2 a--  157.72g    0 
  /dev/sdb5  fedora lvm2 a--  <79.93g    0

barryascott · August 18, 2023, 6:29pm

Odd that you do not have the default 1GiB /boot.

I do not how easy it will be to do what you want.

Not only must you shrink LVM partition, but you have to move to up
the disk to free space at the end of the /boot.

It maybe safer to back up all the data and reinstall.

oglop · August 18, 2023, 6:50pm

I have a feeling next step is the dangerous part, use any partition tool to delete /dev/sdb1, recreate it the same way but with smaller size ( -256MB) ( would this cause data loss on /dev/sdb1 ?) , is my understanding correct ?

computersavvy · August 18, 2023, 6:57pm

I see 2 fedora LVM partitions. They may be part of the same PV arrangement, but from what you posted it seems /dev/sda1 is one PV and /dev/sda5 is the second PV.
The root LV seems to be in /dev/sda1 so it should be possible to do as you ask.

All these should be done when booted to a live media so the filesystems being modified are not in use.

shrink the root file system.
Shrink the root LV .
This can be done using lvreduce but read and follow the man page instructions or data loss may occur.
Once the LV has been reduced then the PV may be reduced using pvresize but make sure whatever LV is on that PV is shrunk first.
Finally, once there is free space on the drive after shrinking the PV and it is unallocated when using gparted, then the partitions (probably sdb5) can be moved to leave the open space adjacent to sdb4 and allow it to be expanded.

The previous suggestion about reinstalling might be much easier and less risky.

oglop · August 18, 2023, 8:45pm

I am stuck after step 3, from my log you can see ethat I have free PE, but I can’t see the free space, so I can’t do step 4

computersavvy · August 18, 2023, 8:53pm

Having the free PEs in the PV means they are still part of the PV. They must be removed from the PV before they are available for use on the disk. This is why the other steps must be done in order.

oglop · August 18, 2023, 9:39pm

they disappear even though I did not do anything, in “current” output, you can see that I have no free PE, but I still don’t know how to resize the partition, resize option in gparted ( booted from live media) is grayed out.