Linux Tipps und Tricks: Difference between revisions

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[[Kategorie:Linux|Tipps und Tricks]]
[[Category:Linux|Tipps und Tricks]]
==Hard reboot==
==Hard reboot==
This is the hard way to kick your kernel into void. No filesystem sync is done, just and ugly fast direkt reboot!
This is the hard way to kick your kernel into void. No filesystem sync is done, just and ugly fast direkt reboot!
You should never do this...
You should never do this...
<source lang=bash>
<syntaxhighlight lang=bash>
# echo 1 > /proc/sys/kernel/sysrq
# echo 1 > /proc/sys/kernel/sysrq
# echo b > /proc/sysrq-trigger
# echo b > /proc/sysrq-trigger
</source>
</syntaxhighlight>
First line enables sysrq, second line sends the reboot request.
First line enables sysrq, second line sends the reboot request.


Line 12: Line 12:


==Scan all SCSI buses for new devices==
==Scan all SCSI buses for new devices==
<source lang=bash>
<syntaxhighlight lang=bash>
# for i in  /sys/class/scsi_host/host*/scan ; do echo "- - -" > $i ; done
# for i in  /sys/class/scsi_host/host*/scan ; do echo "- - -" > $i ; done
</source>
</syntaxhighlight>


==Scan all FC ports for new devices==
!!!Be CAREFUL!!!
This command line issues a Loop Initialization Protocol (LIP). This is a bus reset hat means that removed devices in the fabric will disappear and new ones will appear.
!!!BUT the connection might get lost for a moment!!!
The softer way is [[#Scan all SCSI buses for new devices|to scan the SCSI buses]].
<syntaxhighlight lang=bash>
# for i in  /sys/class/fc_host/*/issue_lip ; do echo "1" > $i ; done
</syntaxhighlight>


==Rescan a device (for example after changing a VMDK size)==
==Rescan a device (for example after changing a VMDK size)==
<source lang=bash>
<syntaxhighlight lang=bash>
# device=sda
# echo 1 > /sys/class/block/${device}/device/rescan
# echo 1 > /sys/class/block/${device}/device/rescan
</source>
</syntaxhighlight>


This is for device sda after changing the VMDK from 20GB to 25GB:
This is for device sda after changing the VMDK from 20GB to 25GB:
<source lang=bash>
<syntaxhighlight lang=bash>
# device=sda
# device=sda
# echo $[ 512 * $(cat /sys/block/${device}/size) / 1024 ** 3 ]
# echo "$[ 512 * $(</sys/block/${device}/size) / 1024 ** 3 ] GB"
20
20 GB
# echo 1 > /sys/class/block/${device}/device/rescan
# echo 1 > /sys/class/block/${device}/device/rescan
# echo $[ 512 * $(cat /sys/block/${device}/size) / 1024 ** 3 ]
# echo "$[ 512 * $(</sys/block/${device}/size) / 1024 ** 3 ] GB"
25
25 GB
# parted /dev/${device} "print free"
# parted /dev/${device} "print free"
Warning: Not all of the space available to /dev/sda appears to be used, you can fix the GPT to use all of the space (an extra 10485760 blocks) or
Warning: Not all of the space available to /dev/sda appears to be used, you can fix the GPT to use all of the space (an extra 10485760 blocks) or
Line 44: Line 54:
  1      1049kB  21,5GB  21,5GB  zfs
  1      1049kB  21,5GB  21,5GB  zfs
         21,5GB  26,8GB  5369MB  Free Space
         21,5GB  26,8GB  5369MB  Free Space
</source>
</syntaxhighlight>


I want to put the free space into partition 1 and resize the rpool:
I want to put the free space into partition 1 and resize the rpool:
<source lang=bash>
<syntaxhighlight lang=bash>
# parted /dev/${device} "resizepart 1 -1"
# parted /dev/${device} "resizepart 1 -1"
# parted /dev/${device} "print free"
# parted /dev/${device} "print free"
Line 78: Line 88:
rpool  24,9G  1,69G  23,2G        -    11%    6%  1.00x  ONLINE  -
rpool  24,9G  1,69G  23,2G        -    11%    6%  1.00x  ONLINE  -
# zpool set autoexpand=off rpool
# zpool set autoexpand=off rpool
</source>
</syntaxhighlight>
Done.
Done.


Line 86: Line 96:
Be careful! Like in this example the lowest SCSI-ID is not always the lowest device name!
Be careful! Like in this example the lowest SCSI-ID is not always the lowest device name!
Check it with <i>lsscsi</i> from the Ubuntu package lsscsi:
Check it with <i>lsscsi</i> from the Ubuntu package lsscsi:
<source lang=bash>
<syntaxhighlight lang=bash>
# lsscsi
# lsscsi
[2:0:0:0]    cd/dvd  NECVMWar VMware SATA CD00 1.00  /dev/sr0
[2:0:0:0]    cd/dvd  NECVMWar VMware SATA CD00 1.00  /dev/sr0
[32:0:0:0]  disk    VMware  Virtual disk    1.0  /dev/sdb
[32:0:0:0]  disk    VMware  Virtual disk    1.0  /dev/sdb
[32:0:1:0]  disk    VMware  Virtual disk    1.0  /dev/sda
[32:0:1:0]  disk    VMware  Virtual disk    1.0  /dev/sda
</source>
</syntaxhighlight>


Then check it is not longer in use:
Then check it is not longer in use:
Line 100: Line 110:


Then delete it:
Then delete it:
<source lang=bash>
<syntaxhighlight lang=bash>
# echo 1 >  /sys/bus/scsi/drivers/sd/32\:0\:0\:0/delete
# echo 1 >  /sys/bus/scsi/drivers/sd/32\:0\:0\:0/delete
</source>
</syntaxhighlight>
The 32:0:0:0 is the number reported from the lsscsi above.
The 32:0:0:0 is the number reported from the lsscsi above.


Et voila:
Et voila:
<source lang=bash>
<syntaxhighlight lang=bash>
# lsscsi
# lsscsi
[2:0:0:0]    cd/dvd  NECVMWar VMware SATA CD00 1.00  /dev/sr0
[2:0:0:0]    cd/dvd  NECVMWar VMware SATA CD00 1.00  /dev/sr0
[32:0:1:0]  disk    VMware  Virtual disk    1.0  /dev/sda
[32:0:1:0]  disk    VMware  Virtual disk    1.0  /dev/sda
</source>
</syntaxhighlight>


==Copy a GPT partition table==
==Copy a GPT partition table==


Copy partition table of sdX to sdY:
Copy partition table of sdX to sdY:
<source lang=bash>
<syntaxhighlight lang=bash>
# sgdisk /dev/sdX --replicate=/dev/sdY  
# sgdisk /dev/sdX --replicate=/dev/sdY  
# sgdisk --randomize-guids /dev/sdY
# sgdisk --randomize-guids /dev/sdY
</source>
</syntaxhighlight>
 
Or with:
<syntaxhighlight lang=bash>
# sgdisk --backup=sdX.table /dev/sdX
# sgdisk --load-backup=sdX.table /dev/sdY
# sgdisk -G /dev/sdY
</syntaxhighlight>


<pre>
<pre>
Line 129: Line 146:
               after cloning a disk in order to render all GUIDs once again unique.
               after cloning a disk in order to render all GUIDs once again unique.
</pre>
</pre>


==Resize a GPT partition==
==Resize a GPT partition==
Line 138: Line 154:


===Correct the GPT partition table===
===Correct the GPT partition table===
<source lang=bash>
<syntaxhighlight lang=bash>
root@mariadb:~# parted /dev/sdb                                 
root@mariadb:~# parted /dev/sdb                                 
GNU Parted 3.2
GNU Parted 3.2
Line 155: Line 171:
Number  Start  End    Size    File system  Name  Flags
Number  Start  End    Size    File system  Name  Flags
  1      1049kB  6442MB  6441MB  zfs
  1      1049kB  6442MB  6441MB  zfs
</source>
</syntaxhighlight>
===Resize the partition===
===Resize the partition===
<source lang=bash>
<syntaxhighlight lang=bash>
root@mariadb:~# parted /dev/sdb
root@mariadb:~# parted /dev/sdb
GNU Parted 3.2
GNU Parted 3.2
Line 186: Line 202:
(parted) q                                                                 
(parted) q                                                                 
Information: You may need to update /etc/fstab.
Information: You may need to update /etc/fstab.
</source>
</syntaxhighlight>


===Optional: Resize the ZPool in it===
===Optional: Resize the ZPool in it===
Check the actual values:
Check the actual values:
<source lang=bash>
<syntaxhighlight lang=bash>
root@mariadb:~# zpool list MYSQL-DATA
root@mariadb:~# zpool list MYSQL-DATA
NAME        SIZE  ALLOC  FREE  EXPANDSZ  FRAG    CAP  DEDUP  HEALTH  ALTROOT
NAME        SIZE  ALLOC  FREE  EXPANDSZ  FRAG    CAP  DEDUP  HEALTH  ALTROOT
Line 197: Line 213:
NAME        PROPERTY    VALUE  SOURCE
NAME        PROPERTY    VALUE  SOURCE
MYSQL-DATA  autoexpand  off    default
MYSQL-DATA  autoexpand  off    default
</source>
</syntaxhighlight>


Now inform ZPool to grow to the end of the partition.
Now inform ZPool to grow to the end of the partition.
Set autoexpand to on:
Set autoexpand to on:
<source lang=bash>
<syntaxhighlight lang=bash>
root@mariadb:~# zpool set autoexpand=on MYSQL-DATA
root@mariadb:~# zpool set autoexpand=on MYSQL-DATA
</source>
</syntaxhighlight>


Send an online to the already onlined device to force a recheck in the ZPool to resize it without export/import:
Send an online to the already onlined device to force a recheck in the ZPool to resize it without export/import:
<source lang=bash>
<syntaxhighlight lang=bash>
root@mariadb:~# zpool online  MYSQL-DATA /dev/sdb1
root@mariadb:~# zpool online  MYSQL-DATA /dev/sdb1
</source>
</syntaxhighlight>


Et voila:
Et voila:
<source lang=bash>
<syntaxhighlight lang=bash>
root@mariadb:~# zpool list MYSQL-DATA
root@mariadb:~# zpool list MYSQL-DATA
NAME        SIZE  ALLOC  FREE  EXPANDSZ  FRAG    CAP  DEDUP  HEALTH  ALTROOT
NAME        SIZE  ALLOC  FREE  EXPANDSZ  FRAG    CAP  DEDUP  HEALTH  ALTROOT
MYSQL-DATA  50,0G  994M  49,0G        -    5%    1%  1.00x  ONLINE  -
MYSQL-DATA  50,0G  994M  49,0G        -    5%    1%  1.00x  ONLINE  -
rpool      19,9G  3,36G  16,5G        -    19%    16%  1.00x  ONLINE  -
rpool      19,9G  3,36G  16,5G        -    19%    16%  1.00x  ONLINE  -
</source>
</syntaxhighlight>


Set autoexpand to off if you want prevent to autoexpand if partition grows:
Set autoexpand to off if you want prevent to autoexpand if partition grows:
<source lang=bash>
<syntaxhighlight lang=bash>
root@mariadb:~# zpool set autoexpand=off MYSQL-DATA
root@mariadb:~# zpool set autoexpand=off MYSQL-DATA
</source>
</syntaxhighlight>
===Optional: Resize the LVM physical volume===
===Optional: Resize the LVM physical volume===
Check the values:
Check the values:
<source lang=bash>
<syntaxhighlight lang=bash>
# parted /dev/${device} "print free"
# parted /dev/${device} "print free"
Model: VMware Virtual disk (scsi)
Model: VMware Virtual disk (scsi)
Line 239: Line 255:
   PV        VG      Fmt  Attr PSize  PFree
   PV        VG      Fmt  Attr PSize  PFree
   /dev/sda1  vg-root lvm2 a--  <35.00g    0  
   /dev/sda1  vg-root lvm2 a--  <35.00g    0  
</source>
</syntaxhighlight>
OK, we need to resize the physical volume
OK, we need to resize the physical volume
<source lang=bash>
<syntaxhighlight lang=bash>
# pvresize /dev/sda1
# pvresize /dev/sda1
   Physical volume "/dev/sda1" changed
   Physical volume "/dev/sda1" changed
   1 physical volume(s) resized / 0 physical volume(s) not resized
   1 physical volume(s) resized / 0 physical volume(s) not resized
</source>
</syntaxhighlight>
Check the values:
Check the values:
<source lang=bash>
<syntaxhighlight lang=bash>
# pvs
# pvs
   PV        VG      Fmt  Attr PSize  PFree  
   PV        VG      Fmt  Attr PSize  PFree  
   /dev/sda1  vg-root lvm2 a--  <45.00g 10.00g
   /dev/sda1  vg-root lvm2 a--  <45.00g 10.00g
</source>
</syntaxhighlight>
<syntaxhighlight lang=bash>
# lvextend -l +100%FREE /dev/vg-root/log
</syntaxhighlight>
 
Done.
Done.
==Find open but deleted files==
Sometimes you have a full filesystem, but cannot see files with ls.<br>
And the output of <i>du -sh <mountpoint></i> and <i>df -h <mountpoint></i> differ, because <i>du</i> just sums the files by traversing the directory.<br>
Then it is time to look for files that are open by any process but deleted in the filesystem.<br>
You can investigate the /proc kernel filesystem:
<syntaxhighlight lang=bash>
# find /proc/*/fd -ls | grep  '(deleted)'
91565697      0 lrwx------  1 mysql            mysql                  64 Nov 19 12:55 /proc/2118/fd/7 -> /tmp/ibNhVEnm\ (deleted)
91565698      0 lrwx------  1 mysql            mysql                  64 Nov 19 12:55 /proc/2118/fd/8 -> /tmp/ibhSEF8n\ (deleted)
91565699      0 lrwx------  1 mysql            mysql                  64 Nov 19 12:55 /proc/2118/fd/9 -> /tmp/ibADGDrl\ (deleted)
91565703      0 lrwx------  1 mysql            mysql                  64 Nov 19 12:55 /proc/2118/fd/13 -> /tmp/ibtl5efn\ (deleted)
</syntaxhighlight>
Or you can use <i>lsof</i>:
<syntaxhighlight lang=bash>
# lsof +aL1
COMMAND  PID  USER  FD  TYPE DEVICE SIZE/OFF NLINK  NODE NAME
mysqld  2118 mysql    7u  REG  0,27        0    0 32780 /tmp/ibNhVEnm (deleted)
mysqld  2118 mysql    8u  REG  0,27        0    0 32782 /tmp/ibhSEF8n (deleted)
mysqld  2118 mysql    9u  REG  0,27        0    0 32786 /tmp/ibADGDrl (deleted)
mysqld  2118 mysql  13u  REG  0,27        0    0 32796 /tmp/ibtl5efn (deleted)
</syntaxhighlight>
Or for a specific running command:
<syntaxhighlight lang=bash>
# lsof +aL1 -c mariadbd
COMMAND  PID  USER  FD  TYPE DEVICE SIZE/OFF NLINK NODE NAME
mariadbd 2821 mysql    7u  REG  0,36        0    0  50 /tmp/#50 (deleted)
mariadbd 2821 mysql    8u  REG  0,36        0    0  51 /tmp/#51 (deleted)
mariadbd 2821 mysql  10u  REG  0,36    5420    0  52 /tmp/#52 (deleted)
mariadbd 2821 mysql  13u  REG  0,36        0    0  53 /tmp/#53 (deleted)
</syntaxhighlight>
To truncate the files you can use the filedescriptor of the process that has the file open:<br>
<b>ATTENTION! Do this ONLY if you exactly know what you are doing!!! Restarting the process is often the much safer solution!!!</b>
<syntaxhighlight lang=bash>
# : > "/proc/<pid>/fd/<fd>"
</syntaxhighlight>

Latest revision as of 14:00, 19 November 2024

Hard reboot

This is the hard way to kick your kernel into void. No filesystem sync is done, just and ugly fast direkt reboot! You should never do this... 

# echo 1 > /proc/sys/kernel/sysrq
# echo b > /proc/sysrq-trigger

First line enables sysrq, second line sends the reboot request.

For more look at kernel.org!

Scan all SCSI buses for new devices

# for i in  /sys/class/scsi_host/host*/scan ; do echo "- - -" > $i ; done

Scan all FC ports for new devices

!!!Be CAREFUL!!! This command line issues a Loop Initialization Protocol (LIP). This is a bus reset hat means that removed devices in the fabric will disappear and new ones will appear. !!!BUT the connection might get lost for a moment!!! The softer way is to scan the SCSI buses. 

# for i in  /sys/class/fc_host/*/issue_lip ; do echo "1" > $i ; done

Rescan a device (for example after changing a VMDK size)

# device=sda
# echo 1 > /sys/class/block/${device}/device/rescan

This is for device sda after changing the VMDK from 20GB to 25GB: 

# device=sda
# echo "$[ 512 * $(</sys/block/${device}/size) / 1024 ** 3 ] GB"
20 GB
# echo 1 > /sys/class/block/${device}/device/rescan
# echo "$[ 512 * $(</sys/block/${device}/size) / 1024 ** 3 ] GB"
25 GB
# parted /dev/${device} "print free"
Warning: Not all of the space available to /dev/sda appears to be used, you can fix the GPT to use all of the space (an extra 10485760 blocks) or
continue with the current setting? 
Fix/Ignore? F                                                             
Model: VMware Virtual disk (scsi)
Disk /dev/sda: 26,8GB
Sector size (logical/physical): 512B/512B
Partition Table: gpt
Disk Flags: 

Number  Start   End     Size    File system  Name  Flags
 2      17,4kB  1049kB  1031kB                     bios_grub
 1      1049kB  21,5GB  21,5GB  zfs
        21,5GB  26,8GB  5369MB  Free Space

I want to put the free space into partition 1 and resize the rpool: 

# parted /dev/${device} "resizepart 1 -1"
# parted /dev/${device} "print free"
Model: VMware Virtual disk (scsi)
Disk /dev/sda: 26,8GB
Sector size (logical/physical): 512B/512B
Partition Table: gpt
Disk Flags: 

Number  Start   End     Size    File system  Name  Flags
 2      17,4kB  1049kB  1031kB                     bios_grub
 1      1049kB  26,8GB  26,8GB  zfs
        26,8GB  26,8GB  983kB   Free Space
# zpool list rpool
NAME    SIZE  ALLOC   FREE  EXPANDSZ   FRAG    CAP  DEDUP  HEALTH  ALTROOT
rpool  19,9G  1,68G  18,2G         -    14%     8%  1.00x  ONLINE  -
# zpool set autoexpand=on rpool
# zpool status rpool
  pool: rpool
 state: ONLINE
  scan: none requested
config:

	NAME        STATE     READ WRITE CKSUM
	rpool       ONLINE       0     0     0
	  sda1      ONLINE       0     0     0
# zpool online rpool sda1
# zpool list rpool
NAME    SIZE  ALLOC   FREE  EXPANDSZ   FRAG    CAP  DEDUP  HEALTH  ALTROOT
rpool  24,9G  1,69G  23,2G         -    11%     6%  1.00x  ONLINE  -
# zpool set autoexpand=off rpool

Done.

Remove a SCSI-device

Let us say we want to remove /dev/sdb.

Be careful! Like in this example the lowest SCSI-ID is not always the lowest device name! Check it with lsscsi from the Ubuntu package lsscsi: 

# lsscsi
[2:0:0:0]    cd/dvd  NECVMWar VMware SATA CD00 1.00  /dev/sr0
[32:0:0:0]   disk    VMware   Virtual disk     1.0   /dev/sdb
[32:0:1:0]   disk    VMware   Virtual disk     1.0   /dev/sda

Then check it is not longer in use:

  1. mount
  2. pvs
  3. zpool status
  4. etc.

Then delete it: 

# echo 1 >  /sys/bus/scsi/drivers/sd/32\:0\:0\:0/delete

The 32:0:0:0 is the number reported from the lsscsi above.

Et voila: 

# lsscsi
[2:0:0:0]    cd/dvd  NECVMWar VMware SATA CD00 1.00  /dev/sr0
[32:0:1:0]   disk    VMware   Virtual disk     1.0   /dev/sda

Copy a GPT partition table

Copy partition table of sdX to sdY: 

# sgdisk /dev/sdX --replicate=/dev/sdY 
# sgdisk --randomize-guids /dev/sdY

Or with: 

# sgdisk --backup=sdX.table /dev/sdX
# sgdisk --load-backup=sdX.table /dev/sdY
# sgdisk -G /dev/sdY

       -R, --replicate=second_device_filename
              Replicate  the  main device's partition table on the specified second device.  Note that the replicated partition table is an exact
              copy, including all GUIDs; if the device should have its own unique GUIDs, you should use the -G option on the new disk.

       -G, --randomize-guids
              Randomize the disk's GUID and all partitions' unique GUIDs (but not their partition type code GUIDs). This  function  may  be  used
              after cloning a disk in order to render all GUIDs once again unique.

Resize a GPT partition

The partition was resized in VMWare from ~6GB to ~50GB.

In the VM I did Remove a SCSI-device for the resized device and then Scan all SCSI buses for new devices after that parted saw the new size.

Correct the GPT partition table

root@mariadb:~# parted /dev/sdb                                
GNU Parted 3.2
Using /dev/sdb
Welcome to GNU Parted! Type 'help' to view a list of commands.
(parted) p                                                                
Warning: Not all of the space available to /dev/sdb appears to be used, you can fix the GPT to use all of the space (an extra 92274688 blocks) or continue with the
current setting? 
Fix/Ignore? F                                    <-- ! choose F                         
Model: VMware Virtual disk (scsi)
Disk /dev/sdb: 53,7GB                            <-- ! the new size is reported now
Sector size (logical/physical): 512B/512B
Partition Table: gpt
Disk Flags: 

Number  Start   End     Size    File system  Name  Flags
 1      1049kB  6442MB  6441MB  zfs

Resize the partition

root@mariadb:~# parted /dev/sdb
GNU Parted 3.2
Using /dev/sdb
Welcome to GNU Parted! Type 'help' to view a list of commands.
(parted) p                                                                
Model: VMware Virtual disk (scsi)
Disk /dev/sdb: 53,7GB
Sector size (logical/physical): 512B/512B
Partition Table: gpt
Disk Flags: 

Number  Start   End     Size    File system  Name  Flags
 1      1049kB  6442MB  6441MB  zfs

(parted) resizepart 1                                                     
End?  [6442MB]? 53,7GB                         <-- ! Put new size here                           
(parted) p                                     <-- ! Control if it worked                           
Model: VMware Virtual disk (scsi)
Disk /dev/sdb: 53,7GB
Sector size (logical/physical): 512B/512B
Partition Table: gpt
Disk Flags: 

Number  Start   End     Size    File system  Name  Flags
 1      1049kB  53,7GB  53,7GB  zfs

(parted) q                                                                
Information: You may need to update /etc/fstab.

Optional: Resize the ZPool in it

Check the actual values: 

root@mariadb:~# zpool list MYSQL-DATA
NAME         SIZE  ALLOC   FREE  EXPANDSZ   FRAG    CAP  DEDUP  HEALTH  ALTROOT
MYSQL-DATA  5,97G   994M  5,00G       44G    47%    16%  1.00x  ONLINE  -
root@mariadb:~# zpool get autoexpand MYSQL-DATA
NAME        PROPERTY    VALUE   SOURCE
MYSQL-DATA  autoexpand  off     default

Now inform ZPool to grow to the end of the partition. Set autoexpand to on: 

root@mariadb:~# zpool set autoexpand=on MYSQL-DATA

Send an online to the already onlined device to force a recheck in the ZPool to resize it without export/import: 

root@mariadb:~# zpool online  MYSQL-DATA /dev/sdb1

Et voila: 

root@mariadb:~# zpool list MYSQL-DATA
NAME         SIZE  ALLOC   FREE  EXPANDSZ   FRAG    CAP  DEDUP  HEALTH  ALTROOT
MYSQL-DATA  50,0G   994M  49,0G         -     5%     1%  1.00x  ONLINE  -
rpool       19,9G  3,36G  16,5G         -    19%    16%  1.00x  ONLINE  -

Set autoexpand to off if you want prevent to autoexpand if partition grows: 

root@mariadb:~# zpool set autoexpand=off MYSQL-DATA

Optional: Resize the LVM physical volume

Check the values: 

# parted /dev/${device} "print free"
Model: VMware Virtual disk (scsi)
Disk /dev/sda: 48.3GB
Sector size (logical/physical): 512B/512B
Partition Table: msdos
Disk Flags: 

Number  Start   End     Size    Type     File system  Flags
        32.3kB  1049kB  1016kB           Free Space
 1      1049kB  48.3GB  48.3GB  primary               boot
        48.3GB  48.3GB  999kB            Free Space
# pvs
  PV         VG      Fmt  Attr PSize   PFree
  /dev/sda1  vg-root lvm2 a--  <35.00g    0

OK, we need to resize the physical volume 

# pvresize /dev/sda1
  Physical volume "/dev/sda1" changed
  1 physical volume(s) resized / 0 physical volume(s) not resized

Check the values: 

# pvs
  PV         VG      Fmt  Attr PSize   PFree 
  /dev/sda1  vg-root lvm2 a--  <45.00g 10.00g

# lvextend -l +100%FREE /dev/vg-root/log

Done.

Find open but deleted files

Sometimes you have a full filesystem, but cannot see files with ls.
And the output of du -sh <mountpoint> and df -h <mountpoint> differ, because du just sums the files by traversing the directory.
Then it is time to look for files that are open by any process but deleted in the filesystem.
You can investigate the /proc kernel filesystem: 

# find /proc/*/fd -ls | grep  '(deleted)'
 91565697      0 lrwx------   1 mysql            mysql                  64 Nov 19 12:55 /proc/2118/fd/7 -> /tmp/ibNhVEnm\ (deleted)
 91565698      0 lrwx------   1 mysql            mysql                  64 Nov 19 12:55 /proc/2118/fd/8 -> /tmp/ibhSEF8n\ (deleted)
 91565699      0 lrwx------   1 mysql            mysql                  64 Nov 19 12:55 /proc/2118/fd/9 -> /tmp/ibADGDrl\ (deleted)
 91565703      0 lrwx------   1 mysql            mysql                  64 Nov 19 12:55 /proc/2118/fd/13 -> /tmp/ibtl5efn\ (deleted)

Or you can use lsof: 

# lsof +aL1 
COMMAND  PID  USER   FD   TYPE DEVICE SIZE/OFF NLINK  NODE NAME
mysqld  2118 mysql    7u   REG   0,27        0     0 32780 /tmp/ibNhVEnm (deleted)
mysqld  2118 mysql    8u   REG   0,27        0     0 32782 /tmp/ibhSEF8n (deleted)
mysqld  2118 mysql    9u   REG   0,27        0     0 32786 /tmp/ibADGDrl (deleted)
mysqld  2118 mysql   13u   REG   0,27        0     0 32796 /tmp/ibtl5efn (deleted)

Or for a specific running command: 

# lsof +aL1 -c mariadbd 
COMMAND   PID  USER   FD   TYPE DEVICE SIZE/OFF NLINK NODE NAME
mariadbd 2821 mysql    7u   REG   0,36        0     0   50 /tmp/#50 (deleted)
mariadbd 2821 mysql    8u   REG   0,36        0     0   51 /tmp/#51 (deleted)
mariadbd 2821 mysql   10u   REG   0,36     5420     0   52 /tmp/#52 (deleted)
mariadbd 2821 mysql   13u   REG   0,36        0     0   53 /tmp/#53 (deleted)

To truncate the files you can use the filedescriptor of the process that has the file open:
ATTENTION! Do this ONLY if you exactly know what you are doing!!! Restarting the process is often the much safer solution!!! 

# : > "/proc/<pid>/fd/<fd>"
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