Resizing VM system disk - LVM Partition 1 does not start on physical sector boundary - CentOS 7

So you have a virtual machine and you've just expanded your virtual disk, log on to your CentOS Linux system and performed a fdisk -l to find this error:

# fdisk -l

Disk /dev/sda: 236.2 GB, 236223201280 bytes, 461373440 sectors
Units = sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 4096 bytes
I/O size (minimum/optimal): 4096 bytes / 4096 bytes
Disk label type: dos
Disk identifier: 0x00000000

   Device Boot      Start         End      Blocks   Id  System
/dev/sda1               1   209715199   104857599+  ee  GPT
Partition 1 does not start on physical sector boundary.

Disk /dev/mapper/centos-root: 34.4 GB, 34359738368 bytes, 67108864 sectors
Units = sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 4096 bytes
I/O size (minimum/optimal): 4096 bytes / 4096 bytes


Disk /dev/mapper/centos-swap: 4294 MB, 4294967296 bytes, 8388608 sectors
Units = sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 4096 bytes
I/O size (minimum/optimal): 4096 bytes / 4096 bytes


Disk /dev/mapper/centos-tmp: 4294 MB, 4294967296 bytes, 8388608 sectors
Units = sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 4096 bytes
I/O size (minimum/optimal): 4096 bytes / 4096 bytes


Disk /dev/mapper/centos-var: 34.4 GB, 34359738368 bytes, 67108864 sectors
Units = sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 4096 bytes
I/O size (minimum/optimal): 4096 bytes / 4096 bytes


Disk /dev/mapper/centos-opt: 21.5 GB, 21474836480 bytes, 41943040 sectors
Units = sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 4096 bytes
I/O size (minimum/optimal): 4096 bytes / 4096 bytes


Disk /dev/mapper/centos-home: 7507 MB, 7507804160 bytes, 14663680 sectors
Units = sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 4096 bytes
I/O size (minimum/optimal): 4096 bytes / 4096 bytes

Knowing that you have an /dev/sda2 and /dev/sda3 and want to create an /dev/sda4 but how? Install parted, and use this to fix the disk you've just expanded:

# parted
GNU Parted 3.1
Using /dev/sda
Welcome to GNU Parted! Type 'help' to view a list of commands.
(parted) p
Error: The backup GPT table is not at the end of the disk, as it should be.  This might mean that another operating system believes the disk is smaller.  Fix, by
moving the backup to the end (and removing the old backup)?
Fix/Ignore/Cancel? Fix
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 251658240 blocks) or continue with the
current setting?
Fix/Ignore? Fix
Model: Msft Virtual Disk (scsi)
Disk /dev/sda: 236GB
Sector size (logical/physical): 512B/4096B
Partition Table: gpt
Disk Flags:

Number  Start   End     Size   File system  Name                  Flags
 1      1049kB  538MB   537MB  ext4
 2      538MB   1075MB  537MB  fat16        EFI System Partition  boot
 3      1075MB  107GB   106GB                                     lvm

(parted) q

Now you can see all three partitions and so will be able to create the fourth:

# fdisk /dev/sda
WARNING: fdisk GPT support is currently new, and therefore in an experimental phase. Use at your own discretion.
Welcome to fdisk (util-linux 2.23.2).

Changes will remain in memory only, until you decide to write them.
Be careful before using the write command.


Command (m for help): p

Disk /dev/sda: 236.2 GB, 236223201280 bytes, 461373440 sectors
Units = sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 4096 bytes
I/O size (minimum/optimal): 4096 bytes / 4096 bytes
Disk label type: gpt


#         Start          End    Size  Type            Name
 1         2048      1050623    512M  Microsoft basic
 2      1050624      2099199    512M  EFI System      EFI System Partition
 3      2099200    209713151     99G  Linux LVM

Command (m for help): n
Partition number (4-128, default 4):
First sector (34-461373406, default 209713152):
Last sector, +sectors or +size{K,M,G,T,P} (209713152-461373406, default 461373406):
Created partition 4


Command (m for help): w
The partition table has been altered!

Calling ioctl() to re-read partition table.

WARNING: Re-reading the partition table failed with error 16: Device or resource busy.
The kernel still uses the old table. The new table will be used at
the next reboot or after you run partprobe(8) or kpartx(8)
Syncing disks.

Now you have created the forth partition, you can see it with the fdisk -l command:

[root@troi st14988]# fdisk -l
WARNING: fdisk GPT support is currently new, and therefore in an experimental phase. Use at your own discretion.

Disk /dev/sda: 236.2 GB, 236223201280 bytes, 461373440 sectors
Units = sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 4096 bytes
I/O size (minimum/optimal): 4096 bytes / 4096 bytes
Disk label type: gpt


#         Start          End    Size  Type            Name
 1         2048      1050623    512M  Microsoft basic
 2      1050624      2099199    512M  EFI System      EFI System Partition
 3      2099200    209713151     99G  Linux LVM
 4    209713152    461373406    120G  Linux filesyste

Disk /dev/mapper/centos-root: 34.4 GB, 34359738368 bytes, 67108864 sectors
Units = sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 4096 bytes
I/O size (minimum/optimal): 4096 bytes / 4096 bytes


Disk /dev/mapper/centos-swap: 4294 MB, 4294967296 bytes, 8388608 sectors
Units = sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 4096 bytes
I/O size (minimum/optimal): 4096 bytes / 4096 bytes


Disk /dev/mapper/centos-tmp: 4294 MB, 4294967296 bytes, 8388608 sectors
Units = sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 4096 bytes
I/O size (minimum/optimal): 4096 bytes / 4096 bytes


Disk /dev/mapper/centos-var: 34.4 GB, 34359738368 bytes, 67108864 sectors
Units = sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 4096 bytes
I/O size (minimum/optimal): 4096 bytes / 4096 bytes


Disk /dev/mapper/centos-opt: 21.5 GB, 21474836480 bytes, 41943040 sectors
Units = sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 4096 bytes
I/O size (minimum/optimal): 4096 bytes / 4096 bytes


Disk /dev/mapper/centos-home: 7507 MB, 7507804160 bytes, 14663680 sectors
Units = sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 4096 bytes
I/O size (minimum/optimal): 4096 bytes / 4096 bytes

Once you have rebooted for the new partition table to take effect, you can add the new partition to the LVM volume group to extend the logical volumes you need to grow/resize:

# vgs
  VG     #PV #LV #SN Attr   VSize  VFree
  centos   1   6   0 wz--n- 99.00g 4.00m

# vgextend centos /dev/sda4
  Physical volume "/dev/sda4" successfully created
  Volume group "centos" successfully extended

# vgs
  VG     #PV #LV #SN Attr   VSize   VFree
  centos   2   6   0 wz--n- 218.99g 120.00g

Now that you have more space, we can extend any of our logical volumes we want:

# lvs
  LV   VG     Attr       LSize  Pool Origin Data%  Meta%  Move Log Cpy%Sync Convert
  home centos -wi-ao----  6.99g
  opt  centos -wi-ao---- 20.00g
  root centos -wi-ao---- 32.00g
  swap centos -wi-ao----  4.00g
  tmp  centos -wi-ao----  4.00g
  var  centos -wi-ao---- 32.00g

# lvextend -L +100G centos/opt
  Size of logical volume centos/opt changed from 20.00 GiB (5120 extents) to 120.00 GiB (30720 extents).
  Logical volume opt successfully resized.

# lvs
  LV   VG     Attr       LSize   Pool Origin Data%  Meta%  Move Log Cpy%Sync Convert
  home centos -wi-ao----   6.99g
  opt  centos -wi-ao---- 120.00g
  root centos -wi-ao----  32.00g
  swap centos -wi-ao----   4.00g
  tmp  centos -wi-ao----   4.00g
  var  centos -wi-ao----  32.00g

# lvextend centos/home -l+100%FREE
  Size of logical volume centos/home changed from 6.99 GiB (1790 extents) to 26.99 GiB (6910 extents).
  Logical volume home successfully resized.

# lvs
  LV   VG     Attr       LSize   Pool Origin Data%  Meta%  Move Log Cpy%Sync Convert
  home centos -wi-ao----  26.99g
  opt  centos -wi-ao---- 120.00g
  root centos -wi-ao----  32.00g
  swap centos -wi-ao----   4.00g
  tmp  centos -wi-ao----   4.00g
  var  centos -wi-ao----  32.00g

MongoDB won't start - ERROR: dbpath (/data/db) does not exist.

For some reason - due to a bug probably - mongodb (or mongod) database won't start on default install because it is referencing the running direction /data/db to create a lock file. This error occurs even if you set the dbpath in /etc/mongod.conf to somewhere else (default installation says: /var/lib/mongodb). To fix this, simply create a simlink or the directory /data/db itself!

# service mongod start
Redirecting to /bin/systemctl start  mongod.service
Job for mongod.service failed because the control process exited with error code. See "systemctl status mongod.service" and "journalctl -xe" for details.
# systemctl status mongod.service
● mongod.service - High-performance, schema-free document-oriented database
   Loaded: loaded (/usr/lib/systemd/system/mongod.service; disabled; vendor preset: disabled)
   Active: failed (Result: exit-code) since Thu 2016-03-03 09:50:01 GMT; 6s ago
  Process: 21502 ExecStart=/usr/bin/mongod $OPTIONS run (code=exited, status=45)

Mar 03 09:50:01 p0 systemd[1]: Starting High-performance, schema-free document-oriented database...
Mar 03 09:50:01 p0 mongod[21502]: about to fork child process, waiting until server is ready for connections.
Mar 03 09:50:01 p0 mongod[21502]: forked process: 21504
Mar 03 09:50:01 p0 mongod[21502]: ERROR: child process failed, exited with error number 45
Mar 03 09:50:01 p0 systemd[1]: mongod.service: control process exited, code=exited status=45
Mar 03 09:50:01 p0 systemd[1]: Failed to start High-performance, schema-free document-oriented database.
Mar 03 09:50:01 p0 systemd[1]: Unit mongod.service entered failed state.
Mar 03 09:50:01 p0 systemd[1]: mongod.service failed.

# mongod --repair
2016-03-03T09:55:49.905+0000 [initandlisten] MongoDB starting : pid=21520 port=27017 dbpath=/data/db 64-bit host=comp-sscm-p0
2016-03-03T09:55:49.906+0000 [initandlisten] db version v2.6.11
2016-03-03T09:55:49.906+0000 [initandlisten] git version: nogitversion
2016-03-03T09:55:49.906+0000 [initandlisten] OpenSSL version: OpenSSL 1.0.1e-fips 11 Feb 2013
2016-03-03T09:55:49.906+0000 [initandlisten] build info: Linux buildvm-08.phx2.fedoraproject.org 4.1.4-100.fc21.x86_64 #1 SMP Tue Aug 4 03:25:05 UTC 2015 x86_64 BOOST_LIB_VERSION=1_53
2016-03-03T09:55:49.906+0000 [initandlisten] allocator: tcmalloc
2016-03-03T09:55:49.906+0000 [initandlisten] options: { repair: true }
2016-03-03T09:55:49.906+0000 [initandlisten] exception in initAndListen: 10296
*********************************************************************
 ERROR: dbpath (/data/db) does not exist.
 Create this directory or give existing directory in --dbpath.
 See http://dochub.mongodb.org/core/startingandstoppingmongo
*********************************************************************
, terminating
2016-03-03T09:55:49.906+0000 [initandlisten] dbexit:
2016-03-03T09:55:49.906+0000 [initandlisten] shutdown: going to close listening sockets...
2016-03-03T09:55:49.906+0000 [initandlisten] shutdown: going to flush diaglog...
2016-03-03T09:55:49.906+0000 [initandlisten] shutdown: going to close sockets...
2016-03-03T09:55:49.906+0000 [initandlisten] shutdown: waiting for fs preallocator...
2016-03-03T09:55:49.906+0000 [initandlisten] shutdown: closing all files...
2016-03-03T09:55:49.906+0000 [initandlisten] closeAllFiles() finished
2016-03-03T09:55:49.906+0000 [initandlisten] dbexit: really exiting now

# mkdir /data
# ln -s /var/lib/mongodb /data/db

or

# mkdir -p /data/db
# chown mongodb:mongodb /data/db

# service mongod start
Redirecting to /bin/systemctl start  mongod.service
# systemctl status mongod.service
● mongod.service - High-performance, schema-free document-oriented database
   Loaded: loaded (/usr/lib/systemd/system/mongod.service; disabled; vendor preset: disabled)
   Active: active (running) since Thu 2016-03-03 09:58:15 GMT; 55s ago
  Process: 21863 ExecStart=/usr/bin/mongod $OPTIONS run (code=exited, status=0/SUCCESS)
 Main PID: 21865 (mongod)
   CGroup: /system.slice/mongod.service
           └─21865 /usr/bin/mongod --quiet -f /etc/mongod.conf run

Mar 03 09:58:15 p0 systemd[1]: Starting High-performance, schema-free document-oriented database...
Mar 03 09:58:15 p0 mongod[21863]: about to fork child process, waiting until server is ready for connections.
Mar 03 09:58:15 p0 mongod[21863]: forked process: 21865
Mar 03 09:58:15 p0 systemd[1]: Started High-performance, schema-free document-oriented database.
Mar 03 09:58:58 p0 systemd[1]: Started High-performance, schema-free document-oriented database.