[SOLVED] Partition 1 does not start on physical sector boundary.

miky76 · 2012-05-01 15:59:29

Hi All,
I've just installed from zero Arch linux,
during the standard installing process I've choosed "Manualy partition disk" and everything seemed to go till the end fine.

only after I've installed and configured many things I've realized that I have the message in the title when I check fdisk -l

[root@artemide ~]# fdisk -l

Disk /dev/sda: 3000.6 GB, 3000592982016 bytes
255 heads, 63 sectors/track, 364801 cylinders, total 5860533168 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 identifier: 0x00000000

   Device Boot      Start         End      Blocks   Id  System
/dev/sda1   *          63      192779       96358+  83  Linux
Partition 1 does not start on physical sector boundary.
/dev/sda2          192780     4096574     1951897+  82  Linux swap / Solaris
Partition 2 does not start on physical sector boundary.
/dev/sda3         4096575    52918109    24410767+  83  Linux
Partition 3 does not start on physical sector boundary.
/dev/sda4        52918110   111507164    29294527+  83  Linux
Partition 4 does not start on physical sector boundary.

what does this mean?
how can I fix it?

Last edited by miky76 (2012-05-28 21:32:40)

Strike0 · 2012-05-01 17:29:10

The first partition starting at sector 63 is done automatically by the partitioning program to optimize read/write performance.
You dont have to do anything. If your sector size would be different to 512 bytes, it would be different.
(http://en.wikipedia.org/wiki/Cylinder-head-sector)

edit: In fact I was wrong, the physical sector size of your disk is 4096 bytes, not 512. In this case the disk should (theoretically) loose performance in some situations (e.g. small data blocks read/writes) I guess. But any change would involve re-partitioning. Personally I would not worry about it, if it is a desktop.

Last edited by Strike0 (2012-05-01 17:44:33)

miky76 · 2012-05-02 08:21:53

yes it's a desktop, but I do not like the idea to lose performance...

repartitioning do you think it will be a big issue?
how do you think I can do it?

Strike0 · 2012-05-02 19:28:18

The partition tools (e.g. fdisk) let you specify parameters when you setup the partitions. You may want to cross-check which should be optimum settings for your harddisk. Keep in mind most users don't change those parameters when installing.
Big issue or not depends on your setup really; it is to re-do the partitioning...

Roken · 2012-05-02 23:17:56

Personally - I'd go with Strike0 - the performance hit is negligible, and only apparent in specific situations. defining non-standard parameters to the partition could, ultimately, lead to more problems if you get any kind of FS corruption etc. What you may lose if you encounter a specific situation is not likely to even register to you as things are.

nomorewindows · 2012-05-03 01:23:18

Try the automatic partitioning, it might just give suitable partitions (especially if you're going to use the whole disk).

miky76 · 2012-05-03 08:43:37

Hi All,
thanks for you reply.

at the moment I have 3 primary partitions, (I've accidentally deleted the swap one ) all of them have the problem in the title
Also I would like to create more than 4 partitions, and at the moment cfdisk allow me to create only another extended partition not bigger than 750GB leaving most of the 3TB disk not allocated.

Do you think, if I change from MBR to GPT following this
https://wiki.archlinux.org/index.php/GP … MBR_to_GPT

I will solve both problems (the physical sector boundary and the number of partitions)?

thanks

Lone_Wolf · 2012-05-03 11:32:38

While MBR can have more then 4 partitions ( an extended partition can hold 100+ 'logical partitions' that for most purposes are treated the same as primary partitions), there are other limitations in MBR that imo make it unsuitable for a 3 TB disk.

Whether converting the partitions to GPT will fix the boundary issue, will depend on how smart the GPT gdisk command is.

miky76 · 2012-05-03 22:08:26

I've converted to GPT following this https://wiki.archlinux.org/index.php/GP … MBR_to_GPT
and this https://wiki.archlinux.org/index.php/GRUB2

after reboot everything seem still working

but, if I go in cgdisk for the disk /dev/sda

                                  cgdisk 0.8.4

                              Disk Drive: /dev/sda
                           Size: 5860533168, 2.7 TiB

Part. #     Size        Partition Type            Partition Name
----------------------------------------------------------------
            14.5 KiB    free space
   1        94.1 MiB    Linux filesystem          Linux filesystem
            1.9 GiB     free space
   3        23.3 GiB    Linux filesystem          Linux filesystem
   4        27.9 GiB    Linux filesystem          Linux filesystem
            2.7 TiB     free space

    [ Align  ]  [ Backup ]  [  Help  ]  [  Load  ]  [  New   ]  [  Quit  ]
    [ Verify ]  [ Write  ]

if I select Verify

Caution: Partition 1 doesn't begin on a 8-sector boundary. This may
result in degraded performance on some modern (2009 and later) hard disks.

Caution: Partition 3 doesn't begin on a 8-sector boundary. This may
result in degraded performance on some modern (2009 and later) hard disks.

Caution: Partition 4 doesn't begin on a 8-sector boundary. This may
result in degraded performance on some modern (2009 and later) hard disks.

Consult http://www.ibm.com/developerworks/linux/library/l-4kb-sector-disks/
for information on disk alignment.

No problems found. 5752929794 free sectors (2.7 TiB) available in 3
segments, the largest of which is 5749025970 (2.7 TiB) in size.

Press the <Enter> key to continue:

if I play with "align" and the partition, after I select "write" this message appear

The kernel may be using the old partition table. Reboot to use the new
partition table!

i reboot, but nothing seem to be changed..

what can I do?

DSpider · 2012-05-03 22:38:02

miky76 wrote:

I've converted to GPT following this https://wiki.archlinux.org/index.php/GP … MBR_to_GPT

"One of the best features of gdisk is its ability to convert MBR and BSD disklabels to GPT without data loss."

So in other words, you didn't repartition at all and you're wondering why nothing has changed.

Last edited by DSpider (2012-05-03 23:45:08)

miky76 · 2012-05-03 22:45:24

mmm I'm not sure to understand

from here:

[root@artemide ~]# gdisk
GPT fdisk (gdisk) version 0.8.4

Type device filename, or press <Enter> to exit: /dev/sda
Partition table scan:
  MBR: protective
  BSD: not present
  APM: not present
  GPT: present

Found valid GPT with protective MBR; using GPT.

I understand that it's not MBR anymore but is GPT, right?

I've tryed to use the "Align" function in cgdisk, but when I save the changes appear the message

The kernel may be using the old partition table. Reboot to use the new
partition table!

I reboot, and I'm with the same error message "Caution: Partition 1 doesn't begin on a 8-sector boundary. This may
result in degraded performance on some modern (2009 and later) hard disks."

what am I supposed to do?
It's th first time I face this kind of error, and I'm quite new in Linux, so probably I'm missing something

DSpider · 2012-05-03 22:51:55

Using a "live" Linux distribution like GParted Live, Parted Magic, Ubuntu, etc, do a Full System Backup with rsync ("rsync -av source destination" without /dev, /proc, /sys, /tmp) and use gparted or something like that to delete and create new partitions. Then put the files back exactly the same way you backed them up.

Last edited by DSpider (2012-05-03 22:54:58)

nomorewindows · 2012-05-03 23:02:49

DSpider wrote:

miky76 wrote:
I've converted to GPT following this https://wiki.archlinux.org/index.php/GP … MBR_to_GPT
"One of the best features of gdisk is its ability to convert MBR and BSD disklabels to GPT without data loss."
So in other words, you didn't repartition at all and you're wondering why nothing has changed.

I don't see anything for OpenBSD disklabels, there is for FreeBSD and NetBSD.
Hopefully you don't need UEFI to boot it.
Can you actually use gparted on GPT?

cfr · 2012-05-03 23:38:45

nomorewindows wrote:

Can you actually use gparted on GPT?

yes

DSpider · 2012-05-03 23:44:33

nomorewindows wrote:

Can you actually use gparted on GPT?

I thinks so.

If you go to Device - Create Partition Table - Advanced, you can choose "gpt" instead of "msdos".

But I'm not exactly sure what this means: https://wiki.archlinux.org/index.php/GPT#GNU_Parted

"GNU Parted 3.0 has all its FS related code removed. Filesystem specific tools are recommended to do all the FS operations.
GUI wrappers are available for parted."

Does it mean that you have to use something like "mkfs.ext4 /dev/sda1" to format a partition because "the FS related code was removed" (ie. not available for GPT partitions)? I don't know, maybe since parted 3.0 was released a year ago, that's just an older wiki entry. Parted is now at 3.1.

nomorewindows · 2012-05-04 01:04:49

DSpider wrote:

nomorewindows wrote:
Can you actually use gparted on GPT?
I thinks so.
If you go to Device - Create Partition Table - Advanced, you can choose "gpt" instead of "msdos".

But I'm not exactly sure what this means: https://wiki.archlinux.org/index.php/GPT#GNU_Parted
"GNU Parted 3.0 has all its FS related code removed. Filesystem specific tools are recommended to do all the FS operations.
GUI wrappers are available for parted."
Does it mean that you have to use something like "mkfs.ext4 /dev/sda1" to format a partition because "the FS related code was removed" (ie. not available for GPT partitions)? I don't know, maybe since parted 3.0 was released a year ago, that's just an older wiki entry. Parted is now at 3.1.

That's like ntfsprogs/ntfs-3g xfsprogs...etc.

cfr · 2012-05-04 02:37:41

It just means it relies on external tools.

miky76 · 2012-05-19 07:27:38

Hi all,
sorry for my VERY late answer to you, but I had many troubles in making a new arch installation on an USB stick

now, before destroy everything

I've booted with the new arch in a USB stick
I've created a new partition on a HD called /dev/sdb2

I've mounted that partition under /media

I've mounted the partition /dev/sdb3 under /mnt

and I've run the rsync as in the link https://wiki.archlinux.org/index.php/Fu … with_rsync

the code of the 2 files are:

rbackup.sh #!/bin/sh
# rsync backup script

su -c sh -c "
    rsync -av --delete-excluded --exclude-from=backup.lst /mnt /media;
    touch /media
"

backup.lst # Include
+ /mnt/dev/console
+ /mnt/dev/initctl
+ /mnt//dev/null
+ /mnt//dev/zero

# Exclude
- /mnt/dev/*
- /mnt/proc/*
- /mnt/sys/*
- /mnt/tmp/*
- /mnt/lost+found/
- /media/*
- /mnt/mnt/*

Do you think it is correct?

was I supposed to mount and then backup something else and not only the sdb3?

the fstab of the OS I want to backup is

#
# /etc/fstab: static file system information
#
# <file system> <dir>   <type>  <options>       <dump>  <pass>
tmpfs           /tmp    tmpfs   nodev,nosuid    0       0
sdb1 /boot ext2 defaults 0 1
sdb3 /home ext4 defaults 0 1
sdb4 / ext4 defaults 0 1

if you confirm me that nothing is wrong, I will destroy the partitions and make them again

thanks

cfr · 2012-05-20 00:59:43

So you are planning to back up sdb3 to sdb2? But those are partitions on the same disk, right? I thought you planned to repartition?

Whether you need to back anything else up depends on what you want to restore. If you only backup /home obviously you'll have to reinstall everything else on the disk in some other way e.g. by reinstalling arch etc.

But whatever you need to backup, you need to back it up to a different HD if you plan to repartition the first one.

nomorewindows · 2012-05-20 01:16:48

You're taking the 1.21 Gigawatts (1.9) of free space and partitioning it to use up that space! How did you get 1.9 GB of free space in between two other partitions?
If you use /dev/sdb2 in this way, the rest of the drive is not available (some 2.7TB!)
Scrap it and start over. The way you get the physical sector boundary problem licked is you may have to change the size of the partition so that there is no extra waste at the front or the end. Sometimes you can use gparted to resize these and fix them, but it is a lot of trouble to do this, when you are using a fresh disk.
If you come back later to fix something there will likely be slops. Due to sector sizes and such, if I want 100MB partition I may have to settle for 92MB or 125MB or something like this just to prevent the slop over. Work on that problem first. A fresh installation shouldn't have the problem of slop over if done right. Since the filesystem uses physical sector boundaries to align with this is somewhat important.

miky76 · 2012-05-21 21:04:06

cfr wrote:

So you are planning to back up sdb3 to sdb2? But those are partitions on the same disk, right? I thought you planned to repartition?
Whether you need to back anything else up depends on what you want to restore. If you only backup /home obviously you'll have to reinstall everything else on the disk in some other way e.g. by reinstalling arch etc.
But whatever you need to backup, you need to back it up to a different HD if you plan to repartition the first one.

OPS, I've just realized I did something stupid!!

ok I've moved everything on a different HD
thanks for telling me this

so now i'll try to install the grafic enviroment and gparted

thanks

miky76 · 2012-05-21 22:54:50

i've installed gnome and after that gparted

when I double click on Gparted in the gnome enviroment

I'm asked about root password and after that a small window open saying "scanning for partition"

after 20 sec scanning, the windows close and nothing seem to happen.
in the logs, i didn't find any errors just this one:

gpartedbin[801] trap int3 ip:7f31622285e1 sp:7f31560bd730 error:0

how can I make it works?

nomorewindows · 2012-05-22 04:07:02

miky76 wrote:

i've installed gnome and after that gparted
when I double click on Gparted in the gnome enviroment
I'm asked about root password and after that a small window open saying "scanning for partition"
after 20 sec scanning, the windows close and nothing seem to happen.
in the logs, i didn't find any errors just this one:
gpartedbin[801] trap int3 ip:7f31622285e1 sp:7f31560bd730 error:0
how can I make it works?

Using gparted on your working/installed OS won't work because the partitions you are working on are mounted at the time that you are trying to move them around. You have to use a Gparted or Ubuntu Live CD. You might be able to use parted on archlinux CD. If it is the new disk, you can just modify the partitions with whichever partiton editor, (fdisk) you have. You wouldn't necessarily need gnome just to run gparted, you could run it from twm. But it can't modify the active disks. Not sure why you really need gparted at the moment, just when you create the partitions themselves from scratch choose a size that doesn't leave slop or lie off of a sector boundary (takes a little playing around with, although the track/sector/heads could be calculated).

Last edited by nomorewindows (2012-05-22 04:07:59)

miky76 · 2012-05-22 08:51:45

nomorewindows wrote:

Using gparted on your working/installed OS won't work because the partitions you are working on are mounted at the time that you are trying to move them around.

I've buit a new Arch linux OS on a USB key
I've booted with this one the system and not with the one I want to rebuild.

in the Arch on USB Key, I've installed rsync, gnome, and gparted (i can send you the list of installed packages if needed)

i've copied with rsync the root to a third disk (not the usb, and not the HD with the originale OS)

than I've launched gnome, and inside it, gparted, but as I said it is not starting.

I did not mount the disk os the original OS yet, I'm just trying to start Gparted, but without success

nomorewindows · 2012-05-22 22:05:53

miky76 wrote:

nomorewindows wrote:
Using gparted on your working/installed OS won't work because the partitions you are working on are mounted at the time that you are trying to move them around.
I've buit a new Arch linux OS on a USB key
I've booted with this one the system and not with the one I want to rebuild.
in the Arch on USB Key, I've installed rsync, gnome, and gparted (i can send you the list of installed packages if needed)
i've copied with rsync the root to a third disk (not the usb, and not the HD with the originale OS)
than I've launched gnome, and inside it, gparted, but as I said it is not starting.
I did not mount the disk os the original OS yet, I'm just trying to start Gparted, but without success

If you are just partitioning the new disk you don't really need gparted. If you have gparted on the old installation, you could use it to partition the new drive.

Last edited by nomorewindows (2012-05-22 22:10:21)

Arch Linux

#1 2012-05-01 15:59:29

[SOLVED] Partition 1 does not start on physical sector boundary.

#2 2012-05-01 17:29:10

Re: [SOLVED] Partition 1 does not start on physical sector boundary.

#3 2012-05-02 08:21:53

Re: [SOLVED] Partition 1 does not start on physical sector boundary.

#4 2012-05-02 19:28:18

Re: [SOLVED] Partition 1 does not start on physical sector boundary.

#5 2012-05-02 23:17:56

Re: [SOLVED] Partition 1 does not start on physical sector boundary.

#6 2012-05-03 01:23:18

Re: [SOLVED] Partition 1 does not start on physical sector boundary.

#7 2012-05-03 08:43:37

Re: [SOLVED] Partition 1 does not start on physical sector boundary.

#8 2012-05-03 11:32:38

Re: [SOLVED] Partition 1 does not start on physical sector boundary.

#9 2012-05-03 22:08:26

Re: [SOLVED] Partition 1 does not start on physical sector boundary.

#10 2012-05-03 22:38:02

Re: [SOLVED] Partition 1 does not start on physical sector boundary.

#11 2012-05-03 22:45:24

Re: [SOLVED] Partition 1 does not start on physical sector boundary.

#12 2012-05-03 22:51:55

Re: [SOLVED] Partition 1 does not start on physical sector boundary.

#13 2012-05-03 23:02:49

Re: [SOLVED] Partition 1 does not start on physical sector boundary.

#14 2012-05-03 23:38:45

Re: [SOLVED] Partition 1 does not start on physical sector boundary.

#15 2012-05-03 23:44:33

Re: [SOLVED] Partition 1 does not start on physical sector boundary.

#16 2012-05-04 01:04:49

Re: [SOLVED] Partition 1 does not start on physical sector boundary.

#17 2012-05-04 02:37:41

Re: [SOLVED] Partition 1 does not start on physical sector boundary.

#18 2012-05-19 07:27:38

Re: [SOLVED] Partition 1 does not start on physical sector boundary.

#19 2012-05-20 00:59:43

Re: [SOLVED] Partition 1 does not start on physical sector boundary.

#20 2012-05-20 01:16:48

Re: [SOLVED] Partition 1 does not start on physical sector boundary.

#21 2012-05-21 21:04:06

Re: [SOLVED] Partition 1 does not start on physical sector boundary.

#22 2012-05-21 22:54:50

Re: [SOLVED] Partition 1 does not start on physical sector boundary.

#23 2012-05-22 04:07:02

Re: [SOLVED] Partition 1 does not start on physical sector boundary.

#24 2012-05-22 08:51:45

Re: [SOLVED] Partition 1 does not start on physical sector boundary.

#25 2012-05-22 22:05:53

Re: [SOLVED] Partition 1 does not start on physical sector boundary.

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