Partition 2 Does Not Start On The Physical Sector Boundary

Hi All;
Can someone give me some guidance on partitioning a 4TB drive into one partition ?

My goal is to align the partition for best performance. I searched the net for advice and I've found a lot of information on it but am still confused.

After setting the label to gpt,

I tried mkpart primary 0% 100%
and I get the warning that the partition isn't aligned

then I tried mkpart primary 1 -1 (which I really hoped would get me completed)

and when I do an align-check on partition 1, it reports 1 aligned

but then when I do an fdisk -l,
I get the warning that partition 1 does not start on a physical sector boundary

I read that sector size is usually 512 bytes but on some (or perhaps all) larger disks, the sector size is 4096.

I am really not knowledgable in this area and not sure if the above message about partition 1 not starting on a physical sector boundary is important or what impact this will have to my performance. Since these 4tb drives are being used in a media server, I'd like them to be as fast and efficient as possible.

Can you offer some guidance or perhaps some commands on how to partition my (full) 4tb drive into one partition so it is aligned and also so the partition table starts on a physical sector boundary ?

Also, is there a Ubuntu utility to display the sector size of a disk?

I have been researching this issue off and on for a few weeks and would like to finally get this partitioning completed this weekend so I can get on with setting up my system.

Thanks.

Tim

As I'm sure there are other posts for this, I'm terrified to mess with disks in Linux as I'm very green. I've looked at one other post which suggests to run the following so I'm going to do the same. The drive provisioned originally had 400 gb, but currently has 500 gb allocated in vmware. Thanks so much in advance!

Code:

fdisk -l
pvs
vgs
lvs
df -h

Code:

[root@uspk10splunk ~]# fdisk -l

Disk /dev/sda: 8589 MB, 8589934592 bytes
64 heads, 32 sectors/track, 8192 cylinders
Units = cylinders of 2048 * 512 = 1048576 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disk identifier: 0x000c255c

   Device Boot      Start         End      Blocks   Id  System
/dev/sda1   *           2         501      512000   83  Linux
Partition 1 does not end on cylinder boundary.
/dev/sda2             502        8192     7875584   8e  Linux LVM
Partition 2 does not end on cylinder boundary.

Disk /dev/sdb: 536.9 GB, 536870912000 bytes
255 heads, 63 sectors/track, 65270 cylinders
Units = cylinders of 16065 * 512 = 8225280 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disk identifier: 0x69437664

   Device Boot      Start         End      Blocks   Id  System
/dev/sdb1               1       52216   419424988+  8e  Linux LVM

Disk /dev/mapper/vg_uspk10vsp03-lv_root: 3833 MB, 3833593856 bytes
255 heads, 63 sectors/track, 466 cylinders
Units = cylinders of 16065 * 512 = 8225280 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disk identifier: 0x00000000


Disk /dev/mapper/vg_uspk10vsp03-lv_swap: 4227 MB, 4227858432 bytes
255 heads, 63 sectors/track, 514 cylinders
Units = cylinders of 16065 * 512 = 8225280 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disk identifier: 0x00000000


Disk /dev/mapper/vg_opt-lv_opt: 429.5 GB, 429488340992 bytes
255 heads, 63 sectors/track, 52215 cylinders
Units = cylinders of 16065 * 512 = 8225280 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disk identifier: 0x00000000

Code:

[root@uspk10splunk ~]# pvs
  PV         VG             Fmt  Attr PSize   PFree
  /dev/sda2  vg_uspk10vsp03 lvm2 a--    7.51g    0
  /dev/sdb1  vg_opt         lvm2 a--  399.99g    0

Code:

[root@uspk10splunk ~]# vgs
  VG             #PV #LV #SN Attr   VSize   VFree
  vg_opt           1   1   0 wz--n- 399.99g    0
  vg_uspk10vsp03   1   2   0 wz--n-   7.51g    0

Code:

[root@uspk10splunk ~]# lvs
  LV      VG             Attr      LSize   Pool Origin Data%  Move Log Cpy%Sync                     Convert
  lv_opt  vg_opt         -wi-ao--- 399.99g                                                          
  lv_root vg_uspk10vsp03 -wi-ao---   3.57g                                                          
  lv_swap vg_uspk10vsp03 -wi-ao---   3.94g

Code:

[root@uspk10splunk ~]# df -h
Filesystem            Size  Used Avail Use% Mounted on
/dev/mapper/vg_uspk10vsp03-lv_root
                      3.6G  1.5G  1.9G  45% /
tmpfs                 1.9G     0  1.9G   0% /dev/shm
/dev/mapper/vg_opt-lv_opt
                      394G  374G  422M 100% /opt
/dev/sda1             485M   32M  428M   7% /boot

UPDATED:
I installed a Deb 7 Srv w LVM w following partitions:
The end product should become a mail server (Citadel) and in time also a Web server.
Code:

 df -hT 
Filesystem                Type      Size  Used Avail Use% Mounted on
rootfs                    rootfs    322M  141M  165M  46% /
udev                      devtmpfs   10M     0   10M   0% /dev
tmpfs                     tmpfs     100M  260K  100M   1% /run
/dev/mapper/deb--srv-root ext4      322M  141M  165M  46% /
tmpfs                     tmpfs     5,0M     0  5,0M   0% /run/lock
tmpfs                     tmpfs     200M     0  200M   0% /run/shm
/dev/sda1                 ext2      228M   18M  199M   9% /boot
/dev/mapper/deb--srv-home ext4      233G  188M  221G   1% /home
/dev/mapper/deb--srv-tmp  ext4      368M   11M  339M   3% /tmp
/dev/mapper/deb--srv-usr  ext4      8,3G  481M  7,4G   6% /usr
/dev/mapper/deb--srv-var  ext4      2,8G  236M  2,4G   9% /var

 fdisk -l 
Disk /dev/sda: 268.4 GB, 268435456000 bytes
255 heads, 63 sectors/track, 32635 cylinders, total 524288000 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 identifier: 0x00064033

   Device Boot      Start         End      Blocks   Id  System
/dev/sda1   *        2048      499711      248832   83  Linux
/dev/sda2          501758   524285951   261892097    5  Extended
/dev/sda5          501760   524285951   261892096   8e  Linux LVM

Disk /dev/mapper/deb--srv-root: 348 MB, 348127232 bytes
255 heads, 63 sectors/track, 42 cylinders, total 679936 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 identifier: 0x00000000

Disk /dev/mapper/deb--srv-root doesn't contain a valid partition table

Disk /dev/mapper/deb--srv-swap_1: 2143 MB, 2143289344 bytes
255 heads, 63 sectors/track, 260 cylinders, total 4186112 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 identifier: 0x00000000

Disk /dev/mapper/deb--srv-swap_1 doesn't contain a valid partition table

Disk /dev/mapper/deb--srv-usr: 8996 MB, 8996782080 bytes
255 heads, 63 sectors/track, 1093 cylinders, total 17571840 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 identifier: 0x00000000

Disk /dev/mapper/deb--srv-usr doesn't contain a valid partition table

Disk /dev/mapper/deb--srv-var: 2998 MB, 2998927360 bytes
255 heads, 63 sectors/track, 364 cylinders, total 5857280 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 identifier: 0x00000000

Disk /dev/mapper/deb--srv-var doesn't contain a valid partition table

Disk /dev/mapper/deb--srv-tmp: 398 MB, 398458880 bytes
255 heads, 63 sectors/track, 48 cylinders, total 778240 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 identifier: 0x00000000

Disk /dev/mapper/deb--srv-tmp doesn't contain a valid partition table

Disk /dev/mapper/deb--srv-home: 253.3 GB, 253289824256 bytes
255 heads, 63 sectors/track, 30794 cylinders, total 494706688 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 identifier: 0x00000000

Disk /dev/mapper/deb--srv-home doesn't contain a valid partition table

 pvs 
PV         VG      Fmt  Attr PSize   PFree
/dev/sda5  deb-srv lvm2 a--  249,76g    0

 lvs 
LV     VG      Attr     LSize   Pool Origin Data%  Move Log Copy%  Convert
home   deb-srv -wi-ao-- 235,89g
root   deb-srv -wi-ao-- 332,00m
swap_1 deb-srv -wi-ao--   2,00g
tmp    deb-srv -wi-ao-- 380,00m
usr    deb-srv -wi-ao--   8,38g
var    deb-srv -wi-ao--   2,79g

Now i want to _shrink_ the HOME partition so I can expand my VAR partition. Looked for guides but haven't found any site useful so far

I tried to find a way to do it when I installed it but it didn't seem to offer me this at this time even I looked around for a while.

How do I do this shrinking of HOME and extending of VAR partition??
please be fairly specific as Im not a pro yet

Everything is working great on this server, however I am seeing Disk doesn't contain a valid partition table. I have no issue reading and writing, this something that can be ignored?


Disk /dev/xvda: 32.2 GB, 32212254720 bytes
255 heads, 63 sectors/track, 3916 cylinders, total 62914560 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 identifier: 0x00000000

Device Boot Start End Blocks Id System
/dev/xvda1 * 16065 62910539 31447237+ 83 Linux

Disk /dev/xvdf: 1099.5 GB, 1099511627776 bytes
255 heads, 63 sectors/track, 133674 cylinders, total 2147483648 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 identifier: 0x00000000

Disk /dev/xvdf doesn't contain a valid partition table

Disk /dev/xvdh: 1099.5 GB, 1099511627776 bytes
255 heads, 63 sectors/track, 133674 cylinders, total 2147483648 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 identifier: 0x00000000

Disk /dev/xvdh doesn't contain a valid partition table

Disk /dev/xvdg: 1099.5 GB, 1099511627776 bytes
255 heads, 63 sectors/track, 133674 cylinders, total 2147483648 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 identifier: 0x00000000

Disk /dev/xvdg doesn't contain a valid partition table

Disk /dev/xvdi: 1099.5 GB, 1099511627776 bytes
255 heads, 63 sectors/track, 133674 cylinders, total 2147483648 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 identifier: 0x00000000

Disk /dev/xvdi doesn't contain a valid partition table

Disk /dev/mapper/vgebs-lvebs: 4398.0 GB, 4398029733888 bytes
255 heads, 63 sectors/track, 534696 cylinders, total 8589901824 sectors
Units = sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 2097152 bytes / 4194304 bytes
Disk identifier: 0x00000000

Disk /dev/mapper/vgebs-lvebs doesn't contain a valid partition table

Disk /dev/xvdj: 32.2 GB, 32212254720 bytes
255 heads, 63 sectors/track, 3916 cylinders, total 62914560 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 identifier: 0x00000000

Disk /dev/xvdj doesn't contain a valid partition table

Hi all,

As you can probably tell I am new to Linux and new to the forum, I am using Kali and Mint both as live Linux environments on USB drives, all is good and I am finding my way around, the reason for the post is that I need to copy 15 CF cards that have multiple partitions, Windows isn't really an option as it can only see one partition on a removable drive, so here goes with Linux.

The CF cards contain Windows Embedded XP in one partition and a separate partition for user data which isn't protected, not that the contents matter, only the fact that it is bootable with multiple partitions, the object is to upgrade the old 2gb cards to 4gb cards to add an additional program on the embedded drive, but they are both full.

as long as I can copy both partitions over the partition size doesn't matter as I can resize that if necessary, but I need both partitions to copy over to the new drive.

I have read that dd command is the way to go but cant find much on multiple partitions which display in Linux as two drives, so how do I go about this, any pointers

Ideally I would like to automate the process as this is something that we could end up doing on a regular basis, I have seen a USB drive that was plugged into a PC and through a basic GUI allowed you to copy a HDD but I don't know If that would do both partitions, something for the future?

I got this configuration.

fdisk -l

Disk /dev/sda: 493.9 GB, 493921239040 bytes
255 heads, 63 sectors/track, 60049 cylinders
Units = cylinders of 16065 * 512 = 8225280 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disk identifier: 0x0002ac38

Device Boot Start End Blocks Id System
/dev/sda1 * 1 64 512000 83 Linux
Partition 1 does not end on cylinder boundary.
/dev/sda2 64 32636 261630976 8e Linux LVM

Disk /dev/mapper/vg_gazduire-lv_root: 53.7 GB, 53687091200 bytes
255 heads, 63 sectors/track, 6527 cylinders
Units = cylinders of 16065 * 512 = 8225280 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disk identifier: 0x00000000


Disk /dev/mapper/vg_gazduire-lv_swap: 5100 MB, 5100273664 bytes
255 heads, 63 sectors/track, 620 cylinders
Units = cylinders of 16065 * 512 = 8225280 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disk identifier: 0x00000000


Disk /dev/mapper/vg_gazduire-lv_home: 209.1 GB, 209119608832 bytes
255 heads, 63 sectors/track, 25424 cylinders
Units = cylinders of 16065 * 512 = 8225280 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disk identifier: 0x00000000


df -h

Filesystem Size Used Avail Use% Mounted on
/dev/mapper/vg_gazduire-lv_root
50G 21G 27G 44% /
tmpfs 2.4G 0 2.4G 0% /dev/shm
/dev/sda1 485M 161M 299M 35% /boot
/dev/mapper/vg_gazduire-lv_home
192G 17G 166G 9% /home
/usr/tmpDSK 2.0G 981M 955M 51% /tmp


I want to increase the /dev/sda1 with aproximativ 200 gb who remains ! My plans a i want to make /dev/sda3 and i want to put in
vg_gazduire!

VG Name vg_gazduire
System ID
Format lvm2
Metadata Areas 1
Metadata Sequence No 4
VG Access read/write
VG Status resizable
MAX LV 0
Cur LV 3
Open LV 3
Max PV 0
Cur PV 1
Act PV 1
VG Size 249.51 GiB
PE Size 4.00 MiB
Total PE 63874
Alloc PE / Size 63874 / 249.51 GiB
Free PE / Size 0 / 0



When i type fdisk /dev/sda3 the system give me Unable to open /dev/sda3!

Could anyone tell me the solution?

I'm setting up a new Linux server and trying to get the best performance from it, along with if any directory fills up, then I won't have to worry about the whole OS.

I want to split up /var into various partitions, such as the following:

/var/cache

/var/log

/var/software_install

Will there be a problem with having these separate partitions and still having a separate partition for /var too?

Or should I plan on just a separate partition only for /var only?

thanks

Booted my computer with 2 USB flash drives inserted. One of the drives turned out to be an MS-DOS boot drive. The PC booted in DOS and wiped out the partition table of the other flash drive with my data on it. This second (64Gb) drive had a single 64Gb type 83 (Linux) primary partition (ext4 file system).

Is there a way to recover the data that's on the second stick?

I've been told that all I have to do is repartition it exactly as it was and my data will be there. But I'd like to have advice from the pros here before I start messing with it.

For the time being, I dd-ed the entire stick, as is, onto a blank partition of my hard disk (dd if=/dev/sdb of=/dev/sda14). The process completed without errors but /dev/sda14 is unmountable for the moment.

Thanks for any help.

Hello!

TL;DR: Deleted Linux partition from Windows. Stuck at Grub rescue prompt.

I'm sorry to trouble you guys, because I'm an idiot.

So I'm wanting to dual-boot Kalilinux and Windows 8.
I went through the steps such as creating a bootable USB, changing the
boot order and so on. I get into Kali, start Gparted and try to partition stuff.

I'm far from an expert, so I wasn't sure what to do. Long-story short, I
didn't seem to get Kali installed correctly, due to something with an EFI
drive being required. So I boot into windows and then stupidly, because it said in the guide,try to "uninstall" Kali by removing it's partition, inside Win8 haha... So I did.

Now I simply get the Grub rescue command prompt when I boot from the same
USB and I have no idea how to fix it. I've run bootrec.exe/fixmbr in Windows haha,
for what it's worth. However Grub can't find any partition it says.

In windows, I have like... 2-3 Recovery partitions. Does anyone know how to remove
them??? I've tried to clear as much as I can, besides the C drive and Auxillary D drive.

Any advice would be very appreciated.

Did you find any way to get out with this error ? I've got the same with an extended partition...
Code:

# fdisk /dev/sda

Welcome to fdisk (util-linux 2.25.2).
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: 55,9 GiB, 60022480896 bytes, 117231408 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
Disklabel type: dos
Disk identifier: 0x00015c35

Device     Boot    Start       End  Sectors  Size Id Type
/dev/sda1  *        2048  19531775 19529728  9,3G 83 Linux
/dev/sda2       19533822 117229567 97695746 46,6G  5 Extended
/dev/sda5       19533824  23558143  4024320  1,9G 82 Linux swap / Solaris
/dev/sda6       23560192 117229567 93669376 44,7G 83 Linux

Code:

# dmesg|less
[   84.343741] EXT4-fs (sda2): unable to read superblock
[   84.348074] EXT4-fs (sda2): unable to read superblock
[   84.352391] EXT4-fs (sda2): unable to read superblock
[   84.357159] XFS (sda2): Invalid superblock magic number
[   84.373676] FAT-fs (sda2): utf8 is not a recommended IO charset for FAT filesystems, filesystem will be case sensitive!
[   84.373891] FAT-fs (sda2): bogus logical sector size 65535
[   84.373897] FAT-fs (sda2): Can't find a valid FAT filesystem
[   84.378220] FAT-fs (sda2): utf8 is not a recommended IO charset for FAT filesystems, filesystem will be case sensitive!
[   84.378444] FAT-fs (sda2): bogus logical sector size 65535
[   84.378449] FAT-fs (sda2): Can't find a valid FAT filesystem
[   84.386262] ntfs: (device sda2): is_boot_sector_ntfs(): Invalid boot sector checksum.
[   84.386270] ntfs: (device sda2): read_ntfs_boot_sector(): Primary boot sector is invalid.
[   84.386275] ntfs: (device sda2): read_ntfs_boot_sector(): Mount option errors=recover not used. Aborting without trying to recover.
[   84.386279] ntfs: (device sda2): ntfs_fill_super(): Not an NTFS volume.
[   84.390737] MINIX-fs: unable to read superblock
[   84.395176] attempt to access beyond end of device
[   84.395185] sda2: rw=16, want=3, limit=2
[   84.395191] hfsplus: unable to find HFS+ superblock
[   84.404204] qnx4: no qnx4 filesystem (no root dir).
[   84.408959] You didn't specify the type of your ufs filesystem

mount -t ufs -o ufstype=sun|sunx86|44bsd|ufs2|5xbsd|old|hp|nextstep|nextstep-cd|openstep ...

>>>WARNING<<< Wrong ufstype may corrupt your filesystem, default is ufstype=old
[   84.417367] hfs: can't find a HFS filesystem on dev sda2