Category: Linux System

Move your /home to a new LVM partition

To have better control and security over your Linux OS, you might want to move your say /home or/var to another LVM partition. The advantage is that you can easily increase/decrease the size at a future stage.


On this article, I will take an example of the /home directory and we will move it to a fresh disk on Virtual Box. Here is an example of a df -h on my Virtual Machine.

We will now add a new disk [sdc] by creating another VG.

Screenshot from 2015-10-21 19:22:05

Start with the following steps:

    • pvcreate /dev/sdc
    • vgcreate vghome /dev/sdc
    • lvcreate -l 100%FREE vghome
  • lvrename /dev/vghome/lvol0 /dev/vghome/lvhome

Screenshot from 2015-10-21 19:27:38

Once you have successfully created the lvhome, you will need to edit your /etc/fstab before mounting the partition so that each time you reboot your machine, it will render the same configuration.



I have inserted the following parameters:

  • /dev/mapper/vghome-lvhome /home ext4 defaults,noatime 1 2

Screenshot from 2015-10-21 19:32:28



You will also need to format the partition before mounting the disk with this command :

  • mkfs.ext4 /dev/mapper/vghome-lvhome
Screenshot from 2015-10-21 19:35:49
  • You now need to mount the partition by using the following command mount /home
  • Here is now the results from a df -h
Screenshot from 2015-10-21 19:39:55
Tips:
  • You can also format your partition with ext3 when your /etc/fstab has been specified with the ext4 format as ext4 support ext3
    • You can also specify the name of the lv directly whilst creating it by using the command lvcreate -l 100%FREE -n lvhome vghome so that you don’t need to rename anew the lv. By default on Vbox and VMware, it uses lvol0
  • More articles I have posted on LVM are :

Add and extend disk on Virtual Box through LVM

Managing LVM with Pvmove – Part 1


Managing LVM with Pvmove – Part 2


Add and extend disk on Virtual Box through LVM

You can easily add and extend disk on Virtual Box through some LVM manipulations. LVM (Logical Volume Partitioning) is a device mapper target that provides logical volume management for the Linux kernel. – Wikipedia. However, I have written a brief introduction about LVM on a previous post – Managing LVM with pvmove – Part 1.

Add and extend disk on Virtual Box through LVM 1


Prior the extension is made you need to assure yourself there that you already know the actual state of the machine’ s hard disk.

Those commands are helpful to perform your analysis before the operation is carried out.

>> fdisk -l

> pvdisplay >> vgdisplay >> lvdisplay

>> vgs >> lvs >> vgs

>> lsblk

 

Here is the state of the disk before the operation is carried out.

centos6

Now, you can get into your Oracle VM VirtualBox Manager to add the new disk.

The steps are :

  • Click on the ‘Settings’ option on the VirtualBox Manager after having selected your virtual machine which you intend to perform a disk extension. In my case, it’s the ‘centos6’ one.
  • Then, on the ‘Storage’ option, next to the “Controller: SATA” there is an icon to “add new hard disk”.

Screenshot from 2015-10-16 07:25:41

  • Once you have click on the “add new hard disk” it will prompt you to “cancel” “choose existing disk” and “create new disk”. Choose “create new disk”. Of course, you can also choose an existing disk, but here we are adding a completely new fresh disk.
  • Afterward, it will prompt a “create Virtual Hard Drive” box. Choose “VDI”. Click on next, then on “dynamically allocated”. Give a new name to your hard disk. In my case, I am adding a new 2GB hard disk. Click on create and you are done.
  • Boot your machine if you are on VirtualBox, then fire the lsblk command to see your new hard disk. See screenshot below. You can also check with the fdisk -l command as well as the dmesg log which is really helpful.

centos6

  • Once the disk is detected, start by converting the disk to the PV using the command pvcreate /dev/sdb. You will notice that if you launch again a pvs the new disk is now on the PV but no part of the PV is allocated to any VG. As you can see in the picture below here is the new sdb which now forms part of the PV
  • Now we will extend the actual VG called vg_labo. Use the command vgextend vg_labo /dev/sdb

Screenshot from 2015-10-16 08:26:27


  • Once this is completed, you can now choose which LV you will extend. I am choosing the LV called lv_root. Use the command lvextend -l +100%FREE /dev/vg_labo/lv_root

Screenshot from 2015-10-16 08:34:42

The disk is now extended. You can also verify with the command df -h. You can also check out the following article on how to perform a pvmove.

Tips:

    • On Virtual Box, you cannot add a new disk if your machine is running compared to VMware. To be able to solve that issue, you will need to shut down the machine to be able to add the disk.
  • If ever after adding a new hard disk, you noticed that the disk is not being detected just stay cool, as you might need to troubleshoot between LUNs on VCenter. Use the following command:

ls /sys/class/scsi_host/ | while read host ; do echo “- – -” > /sys/class/scsi_host/$host/scan ; done


  • You can also use the script rescanscsibus.sh after having to install the sg3_utils package to troubleshoot for LUN detection.

Repair your Kernel Panic with Dracut

If you have encountered a Kernel Panic which usually happens after a major change in the Linux System, you can follow these procedures to rebuild the Kernel files with Dracut tools.

  1. Boot the server on rescue mode or simply through a live CD or ISO.
  2. To boot the server on rescue mode login on the Vsphere Interface and look for a live CD. In case of Kernel Panic on your own machine, you can boot your machine with a live CD.
  3. Once booted, create a directory in the folder /mnt
    mkdir /mnt/sysimage
  4. Use fdisk –l to find where is the /boot. However, you can also create another directory in mnt to mount different partitions. [sysimage is just a name given]
  5. Mount the disk into sysimage with the aim to mount the boot file. In my case, the sda1 is the boot partition
    mount /dev/sda2 /mnt/sysimage
    %MINIFYHTML74a49a25b154c1a7dc7302ca0464bd9624%
    %MINIFYHTML74a49a25b154c1a7dc7302ca0464bd9625%
    mount/dev/sda1 /mnt/sysimage/boot
  6. Once the disks are mounted mount the proc/dev/ and sys folders. Here are the commands:
    mount - -bind /proc /mnt/sysimage/proc
    
    mount - -bind /dev /mnt/sysimage/dev
    
    mount - -bind/sys /mnt/sysimage/sys
  7. After the mount operations have been carried out, you need to access the directory by chrooting into it.
    chroot /mnt/sysimage
  8. Get into the directory sysimage 
  9. You can back up the /boot to another location and use the command Dracut to regenerate anew the file initramfs. An example is as follows: 
    dracut -f /boot/initramfs-2.6.32-358.el6.x86_64.img 2.6.32-358.el6.x86_64
  10. You can umount all partitions and /or simply reboot the machine.
 

Repair your Kernel Panic with Dracut 2



Tips:

    • On Vcenter, you may need to boot go through the BIOS interface first before being able to boot through the ISO and force the BIOS screen to appear on your screen.
    • You may also use the Finnix ISO which is usually compatible with all UNIX system.
    • When firing the dracut command make sure you only paste the kernel version with the architecture. Do not use the file .img extension, otherwise, it won’t work – Step9
    • The last part ‘2.6.32-358.el6.x86_64’ is just the same version which needs to be regenerated. -Step9
    • To know which kernel version your machine is actually using, you need to get into the grub folder and look for the grub.conf. The first option is usually the kernel used by default.
    • Sometimes, you need to try with the same version of the OS, it may happen after you have boot your machine with a live CD, the ISO which you have used do not detect your disk or the data store. You may, for example, think the disk is not good or there is a problem in the SAN.
    • However, without doing a root cause analysis, you cannot be certain if by repairing the initrd the Kernel Panic might be the unique solution. There are circumstances where a mounted NFS is not the same version with the actual machine which can result in Kernel Panic. The Dracut solution is not a definite solution.
  • Always investigate on the Dmesg log if possible or the crash dump if same has been set up.

Managing LVM with PVMOVE – Part 2

After a little introduction about LVM from the article Managing LVM with PVMOVE – Part 1, its time to get into the details of the pvmove command. Based on the scenario and constraints described in part 1, that I will elaborate on the pvmove operation here.

Managing LVM with PVMOVE - Part 2 3

Before handling any operation, do your precheck tasks such as verification of the state of the server, URLs, services and application running,  the port they are listening etc.. This is done to be able to handle complicated tasks both at the system and application level. However, in respect of the pvmove operation, I would recommend you to fire the vgs, pvs and lvs commands as well as a fdisk -l to check for the physical disk state. Do a df -h and if possible; an lsblk to list all blocks for future references. On CentOS / RedHat you need to install the package util-linux to be able to use lsblk which is very interesting.


Screenshot from 2015-09-30 21:07:28

 

Let us say we have a disk of 100G [lets called it sdb] and we have to replace it with another disk of 20G [sdc]. We assume that there is 10G of data being used out of the 100G hard disk which looks reasonable and possible to be handled by the 20G hard disk that we have planned to shift to. On our Sdb we have 2 LV lets call it lvsql that is being used by MySQL having the database there and lvhome handling the rest of the server applications. See illustration from the diagram on the right. Both LVs are found in the same VG called VGNAME.

Managing LVM with PVMOVE - Part 2 4

 

So you might ask yourself how come if you perform a df -h on your machine you find that lvsql total size is 15G and that of lvhome is 80G making a total of 95G when the hard disk is a 100G [As described on the diagram above]. Is there 5G missing? The answer is no. When you fire the command pvdisplay, you will notice that the “PE Size” had consumed 5 GB. For example on this screenshot on the left, the PE Size is 4MB.

Usually, the 5Gb missing will be allocated there which means that the PE Size is used for a specific purpose for example in our situation a back up of the MySQL database or other processes. If the missing size is not found it means that it’s still in the VG and has not been allocated to the LV. It’s important to allocate some additional space there. So before start do a pvdisplay, lvdisplay, and vgdisplay as well which are important. We now have our sde hard disk as described in this picture below.

Screenshot from 2015-09-30 21:05:13

How to start? It’s up to you to decide which lv you want to allocate more space as you have control over the vg. You can also add another physical disk and extend the vgname and resize the lvsql since a database usually grows in size.

 

 

 

 

Do your pre-check tasks as described.

  1. Stop all applications running such as MySQL and Atop in our case. You can use the lsof command to check if there are still processes and application writing on the disk.
  2. Once all applications have been stopped you can type the mount command to check the presence of the partitions as well as you have to confirm that there is no application writing on the disk – use lsof or fuser.
  3. Comment the two lines related to the 2 vg partitions in the /etc/fstab file. Usually it would be the lines /dev/vgname/lvsql and /dev/vgname/lvhome. You can now umount the disk.
  4. You would notice that it would not be possible to umount the partitions if ever an application is writing on it. Another issue is that if you have ssh running on the machine, you need to stop it! Then, how do you ssh on the machine? Use the console from vSphere or if it’s a physical machine boot it with a live cd.
  5. Next step is to do a lvreduce of the lv if possible according to the size. In our case 5GB being used out of 80. Do a lvreduce -L 7GB –resizefs /dev/vgname/lvhome. This is done because when you will move the pv it will be faster.  The bigger the lv the more time it takes.
  6. Once all lv size has been reduced to the maximum, add the disk sdc. Make sure it gets detected if you are on VMware. Use the fdisk command to check and compare from your precheck test.
  7. Now create from the sdc a pv The command is pvcreate /dev/sdc. This means that you created a pv from the disk you have added.
  8. After the pv has been created extend the vg called vgname from the old disk (sdb) by using the disk sdc which you just added to the same old vg called vgname. Command is vgextend vgname /dev/sdc
  9. Now the magic starts, fire a pvmove /dev/sdb /dev/sdc – This means that you are moving the pv allocated to the vgname belonging to the PEs of hard disk sdb into sdc.
  10. When the pvmove is completed, you just need to do a vgreduce vgname /dev/sdb. When you launch the vgreduce it will throw out the old disk out from the VG as you have reduced it completely. You can now remove the old disk.
  11. Since you have reduced the lvhome you will notice that lvhome is at 7GB instead of 10G as we have reduced size in step 4 to accelerate the pvmove process. The step is to lvresize -l +100%FREE /dev/vgname/lvhome. You will notice that the PE Size is intact as we had not resized the lvsql.
  12. You can now do a /sbin/resize2fs /dev/vgname/lvhome. Uncomment back the lines on fstab, mount -av and restart your applications.


Congrats you just did a pvmove. Comments below so that we can clear any ambiguities.


Managing LVM with PVMOVE – Part 1

One of the challenging issues that I have encountered is the manipulation of LVM – Logical Volume Management on virtual servers. Whilst writing this article, I noticed that I have to split it into parts as it looks bulky in some sort. Once you have understood the logic of the LVM, things get pretty easy to deal with. I will elaborate some details of LVM, and will surely get into some brief real-life experience that is important to grasp. Let’s take an example of a disk where there are some applications running like MySQL, Apache, some monitoring tools like Atop and Htop which are writing on the disk and we have to shrink that very disk or replace it with another disk. Let’s also assume that the server is running on an ESX host and the operation will be carried out through the VMware  VCenter. How do you shrink a disk having its application generating IOs? How do you replace a disk with a smaller one having its data on an LVM?

In brief, here is what I have understood from what is LVM – Logical Volume Management.

We have Physical Volume (PV), Volume Groups (VG) and Logical Volume  (LV). These terms are a must to understand before proceeding with Logical Volume Management operations.

PV- These are hard disks or even Hard disk partitions. These PVs have logical unit numbers. Each PV is or can be composed of chunks called PEs (Physical Extents)

VG – The Volume Group is the highest level of abstraction used with the LVM. Does this term look complicated? I would say no. In the field of Software Engineering, there are two terms that are usually used that is modeling and meta-modeling. Just understand it like this if you are not familiar with software engineering. Modeling means one step or one level removed from reality whilst Meta-Modelling means modeling at a higher level of logic. So basically, it looks like some sort of higher modeling happened at the level of the VG. 

LV – The logical volume is a product of the VG. They are disks which are not restricted to the physical disk size and it can be resized or even move easily without even having your application to be stopped or having your system unmounted. Of course, I need to do more research to get into a more deeper explanation of the PV, PE, VG, and LV. Lets now see an explanation through my horrible drawing skills.


Screenshot from 2015-09-29 21:04:46From the Diagram we conclude that :

  • PVs looks like hard disks divided into chunks called PEs
  • The VGs are just a high level of abstraction that should look from the above.
  • VGs are created by combining PVs.

If you have access to a Linux machine having LVM configured and some VG have already been created, you can start firing these commands to have an overview of the PV, VG, and LV

  • pvs – Report information about physical volume
  • vgs – Information about volume groups
  • lvs – Information about logical volumes

Those physical disks can be picked up from the datastores, where RAID is configured. This act as another layer of security to be able to handle disk failures or loss of data at all cost.

Screenshot from 2015-09-29 21:37:28


On Linux, if you type vg or lv or pv press tab twice you will have an idea all the commands that exist and possibilities of manipulation. On part2 of this article, I will take an example of the pvmove command and actions that could be done to minimize impact before carrying out a pvmove operation.

Part2 of the article is on this link