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DaggyStyle
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PostPosted: Wed Apr 24, 2013 7:58 am    Post subject: raid not starting up not consistant in boots [solved] Reply with quote

hello all, I have a strange issue, I've reinstalled my system and for some reason my raid 5 doesn't starts up ok every boot.

my setup is as follows:
  • /boot on raid1 /dev/md1 (200mb) composed of /dev/sd[a-d]1
  • / on raid1 /dev/md2 (2Gb) composed of /dev/sd[a-d]2
  • /var, /opt and /usr among other things on raid5 /dev/md3 (200mb) composed of /dev/sd[a-d]3


for some reasons the raid5 doesn't boots in sum boots, here are some outputs:
dmesg from defunct boot: http://bpaste.net/show/93684/
dmesg from good boot: http://bpaste.net/show/93687/
mdadm --examine: http://bpaste.net/show/93685/

I'm not using initramfs althoguh the raid5 has metadata 1.2, afaik, because my root is metadata 0.9, autoraid detection works and raid1 and 5 are built in to the kernel.

that is how I worked before the reinstall and it didn't caused issue.
I'm using kernel 3.8.8 and my config can be found here: http://bpaste.net/show/93692/

any hints on why this is happening?

thanks.
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Last edited by DaggyStyle on Mon May 06, 2013 5:46 am; edited 1 time in total
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NeddySeagoon
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PostPosted: Wed Apr 24, 2013 7:08 pm    Post subject: Reply with quote

DaggyStyle,

Both dmesgs contain
Code:
[    2.487007] md: Autodetecting RAID arrays.
[    2.517127] md: invalid raid superblock magic on sda3
[    2.517163] md: sda3 does not have a valid v0.90 superblock, not importing!
[    2.521342] usb 1-1.6.1: new high-speed USB device number 9 using ehci-pci
[    2.548294] md: invalid raid superblock magic on sdb3
[    2.548330] md: sdb3 does not have a valid v0.90 superblock, not importing!
[    2.581454] md: invalid raid superblock magic on sdc3
[    2.581490] md: sdc3 does not have a valid v0.90 superblock, not importing!
[    2.615020] md: invalid raid superblock magic on sdd3
[    2.615056] md: sdd3 does not have a valid v0.90 superblock, not importing!

The one that work s also has
Code:
[    3.777733] md: bind<sdd3>
[    3.785956] md: bind<sdb3>
[    3.804730] md: bind<sdc3>
[    3.854603] md: bind<sda3>
[    3.872058] md/raid:md3: device sda3 operational as raid disk 0
[    3.872060] md/raid:md3: device sdc3 operational as raid disk 2
[    3.872061] md/raid:md3: device sdb3 operational as raid disk 1
[    3.872061] md/raid:md3: device sdd3 operational as raid disk 3
[    3.872211] md/raid:md3: allocated 4314kB
[    3.872225] md/raid:md3: raid level 5 active with 4 out of 4 devices, algorithm 2

Your 'everything else' md3 always fails to auto assemble, which is because
Code:
/dev/sda3:
          Magic : a92b4efc
        Version : 1.2
it has a raid version 1.2 superblock.

From this I surmise that mdadm sometimes assembles md3 ans sometimes not. A separate /usr not mounted before udev starts is no supported, are you using udev?
Changing the raid superblock version demands that you backup all the data, destroy the raid, fix it then restore your data.

Its time to learn to roll your own initrd.
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PostPosted: Thu Apr 25, 2013 7:07 am    Post subject: Reply with quote

NeddySeagoon wrote:
DaggyStyle,

Hello NeddySeagoon,

I've assumed you'll be the one answering me :)

NeddySeagoon wrote:

Both dmesgs contain
Code:
[    2.487007] md: Autodetecting RAID arrays.
[    2.517127] md: invalid raid superblock magic on sda3
[    2.517163] md: sda3 does not have a valid v0.90 superblock, not importing!
[    2.521342] usb 1-1.6.1: new high-speed USB device number 9 using ehci-pci
[    2.548294] md: invalid raid superblock magic on sdb3
[    2.548330] md: sdb3 does not have a valid v0.90 superblock, not importing!
[    2.581454] md: invalid raid superblock magic on sdc3
[    2.581490] md: sdc3 does not have a valid v0.90 superblock, not importing!
[    2.615020] md: invalid raid superblock magic on sdd3
[    2.615056] md: sdd3 does not have a valid v0.90 superblock, not importing!

The one that work s also has
Code:
[    3.777733] md: bind<sdd3>
[    3.785956] md: bind<sdb3>
[    3.804730] md: bind<sdc3>
[    3.854603] md: bind<sda3>
[    3.872058] md/raid:md3: device sda3 operational as raid disk 0
[    3.872060] md/raid:md3: device sdc3 operational as raid disk 2
[    3.872061] md/raid:md3: device sdb3 operational as raid disk 1
[    3.872061] md/raid:md3: device sdd3 operational as raid disk 3
[    3.872211] md/raid:md3: allocated 4314kB
[    3.872225] md/raid:md3: raid level 5 active with 4 out of 4 devices, algorithm 2

Your 'everything else' md3 always fails to auto assemble, which is because
Code:
/dev/sda3:
          Magic : a92b4efc
        Version : 1.2
it has a raid version 1.2 superblock.

From this I surmise that mdadm sometimes assembles md3 ans sometimes not. A separate /usr not mounted before udev starts is no supported, are you using udev?

yes, I'm using latest udev, I was using udev-174 (pre whole LP gone mad debacle) and with a almost identical setup (boot, root on raid1, 0.9 and rest on 1.2 raid5) and all worked well, at one point I've decided to check what is the status of separate /usr support on newer udevs, ssuominen answered me that it is supported, so I took the plunge and the system booted without a problem.

up until the new reinstall, I've never encountered scenario in which the raid5 didn't got assemble. if it isn't supported, why the auto assemble is in consistent?
NeddySeagoon wrote:

Changing the raid superblock version demands that you backup all the data, destroy the raid, fix it then restore your data.

I've assumed that.
NeddySeagoon wrote:
Its time to learn to roll your own initrd.

I usually refrain from using initrd, the two main reasons is the creation of it (not sure how complicated it) and the memory issue, I'm not willing to use initramfs because it stays in the memory post boot and this memory block cannot be used anymore. not sure if initrd is the same.
moreover, from what I understand initrd is deprecated and is due to be replaced by initramfs later on which is (again) something I'm not willing to do.

can you shed some more light on this?

Thanks.
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PostPosted: Thu Apr 25, 2013 6:06 pm    Post subject: Reply with quote

DaggyStyle,

You appear to have a race condition. When md3 is not started when the attempt to mount /usr happens, your boot fails.

As md3 cannot be auto assembled, it must be assembled by a call to mdadm during the boot process.
In which runlevel is mdadm ?
If its in default, move it to boot and see what happens.

Making an initrd for your case is fairly easy.
You need two files.
The first is a list of things to include in the initrd, the second is the init script to go in the initrd.
Then you feed the file list to a script that is provided in the kernel.
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PostPosted: Fri Apr 26, 2013 4:04 pm    Post subject: Reply with quote

NeddySeagoon wrote:
DaggyStyle,

You appear to have a race condition. When md3 is not started when the attempt to mount /usr happens, your boot fails.

As md3 cannot be auto assembled, it must be assembled by a call to mdadm during the boot process.
In which runlevel is mdadm ?
If its in default, move it to boot and see what happens.

it is in boot level
NeddySeagoon wrote:

Making an initrd for your case is fairly easy.
You need two files.
The first is a list of things to include in the initrd, the second is the init script to go in the initrd.
Then you feed the file list to a script that is provided in the kernel.

don't know what I need to include all I want it to assemble my raids and than continue to boot as normal, maybe add a rescue mode but no need to boot any special modules, the kernel already loads all.
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PostPosted: Fri Apr 26, 2013 5:42 pm    Post subject: Reply with quote

DaggyStyle,

Heres my /root/initrd directory contents. Its just two files init and initramfs_list.
initramfs_list contains the list of files to be included in the initrd.
Code:
# directory structure
dir /proc       755 0 0
dir /usr        755 0 0
dir /bin        755 0 0
dir /sys        755 0 0
dir /var        755 0 0
#dir /lib        755 0 0
dir /lib64      755 0 0
dir /sbin       755 0 0
dir /mnt        755 0 0
dir /mnt/root   755 0 0
dir /etc        755 0 0
dir /root       700 0 0
dir /dev        755 0 0

# busybox
file /bin/busybox /bin/busybox  755 0 0

# for raid on lvm
file /sbin/mdadm                /sbin/mdadm              755 0 0
file /sbin/lvm.static           /sbin/lvm.static         755 0 0

# libraries required by /sbin/fsck.ext4 and /sbin/fsck

slink   /lib                            /lib64                          777 0 0
file    /lib64/ld-linux-x86-64.so.2     /lib64/ld-linux-x86-64.so.2     755 0 0
file    /lib64/libext2fs.so.2           /lib64/libext2fs.so.2           755 0 0
file    /lib64/libcom_err.so.2          /lib64/libcom_err.so.2          755 0 0
file    /lib64/libpthread.so.0          /lib64/libpthread.so.0          755 0 0
file    /lib64/libblkid.so.1            /lib64/libblkid.so.1            755 0 0
file    /lib64/libuuid.so.1             /lib64/libuuid.so.1             755 0 0
file    /lib64/libe2p.so.2              /lib64/libe2p.so.2              755 0 0
file    /lib64/libc.so.6                /lib64/libc.so.6                755 0 0
file    /lib64/libmount.so.1            /lib64/libmount.so.1            755 0 0

file    /sbin/fsck              /sbin/fsck                      755 0 0
file    /sbin/fsck.ext4         /sbin/fsck.ext4                 755 0 0

# our init script
file    /init                   /root/initrd/init               755 0 0

Trap for the unwary, a few packages need the static USe flag. This is a bad thing to set globally.
Code:
# static bits and pieces for an initrd
sys-fs/lvm2 static
sys-fs/mdadm static
sys-apps/busybox static

The init script contains
Code:
#!/bin/busybox sh

rescue_shell() {
    echo "$@"
    echo "Something went wrong. Dropping you to a shell."
    /bin/busybox --install -s
    exec /bin/sh
}

# allow the use of UUIDs or filesystem lables
uuidlabel_root() {
    for cmd in $(cat /proc/cmdline) ; do
        case $cmd in
        root=*)
            type=$(echo $cmd | cut -d= -f2)
            echo "Mounting rootfs"
            if [ $type == "LABEL" ] || [ $type == "UUID" ] ; then
                uuid=$(echo $cmd | cut -d= -f3)
                mount -o ro $(findfs "$type"="$uuid") /mnt/root
            else
                mount -o ro $(echo $cmd | cut -d= -f2) /mnt/root
            fi
            ;;
        esac
    done
}

check_filesystem() {
    # most of code coming from /etc/init.d/fsck

    local fsck_opts= check_extra= RC_UNAME=$(uname -s)

    # FIXME : get_bootparam forcefsck
    if [ -e /forcefsck ]; then
        fsck_opts="$fsck_opts -f"
        check_extra="(check forced)"
    fi

    echo "Checking local filesystem $check_extra : $1"

    if [ "$RC_UNAME" = Linux ]; then
        fsck_opts="$fsck_opts -C0 -T"
    fi

    trap : INT QUIT

    # using our own fsck, not the builtin one from busybox
    /sbin/fsck -p $fsck_opts $1

    ret_val=$?


    case $ret_val in
        0)      return 0;;
        1)      echo "Filesystem repaired"; return 0;;
        2|3)    if [ "$RC_UNAME" = Linux ]; then
                        echo "Filesystem repaired, but reboot needed"
                        reboot -f
                else
                        rescue_shell "Filesystem still have errors; manual fsck required"
                fi;;
        4)      if [ "$RC_UNAME" = Linux ]; then
                        rescue_shell "Fileystem errors left uncorrected, aborting"
                else
                        echo "Filesystem repaired, but reboot needed"
                        reboot
                fi;;
        8)      echo "Operational error"; return 0;;
        16)     echo "Use or Syntax Error"; return 16;;
        32)     echo "fsck interrupted";;
        127)    echo "Shared Library Error"; sleep 20; return 0;;
        *)      echo $ret_val; echo "Some random fsck error - continuing anyway"; sleep 20; return 0;;
    esac

# rescue_shell can't find tty so its broken
    rescue_shell
}

# start for real here

# temporarily mount proc and sys
mount -t proc none /proc
mount -t sysfs none /sys
mount -t devtmpfs none /dev

# disable kernel messages from popping onto the screen
###echo 0 > /proc/sys/kernel/printk
# clear the screen
###clear

# assemble the raid set(s) - they got renumbered from md1, md5 and md6

# not needed on SSD but we may want to maintain it
# /boot
/sbin/mdadm --assemble /dev/md125 /dev/sda1 /dev/sdb1 /dev/sdc1 /dev/sdd1
# don't care if /boot fails to assemble

# not needed on SSD
# /  (root)  I wimped out of root on lvm for this box
/sbin/mdadm --assemble /dev/md126 /dev/sda5 /dev/sdb5 /dev/sdc5 /dev/sdd5 || rescue_shell
# if root won't assemble, we are stuck

# LVM for everything else
# /home and everything portge related
/sbin/mdadm --assemble /dev/md127 /dev/sda6 /dev/sdb6 /dev/sdc6 /dev/sdd6 || rescue_shell
# and if the LVM space won't assemble there is no /usr or /var so we are really in a mess
# TODO could auto cope with degraded raid operation

# lvm runs as whatever its called as
ln -s /sbin/lvm.static /sbin/vgchange

# everything on the SDD
/sbin/vgchange -ay ssd || rescue_shell

# start the vg volume group - /home and everything for portage - need not die here
/sbin/vgchange -ay vg || rescue_shell
# if this failed we have no /usr or /var

# get here with raid sets assembled and logical volumes available

# mounting rootfs on /mnt/root
uuidlabel_root || rescue_shell "Error with uuidlabel_root"

# space separated list of mountpoints that ...
mountpoints="/usr /var"

# ... we want to find in /etc/fstab ...
ln -s /mnt/root/etc/fstab /etc/fstab

# ... to check filesystems and mount our devices.
for m in $mountpoints ; do

#echo $m

    check_filesystem $m

    echo "Mounting $m"
    # mount the device and ...
    mount $m || rescue_shell "Error while mounting $m"

    # ... move the tree to its final location
    mount --move $m "/mnt/root"$m || rescue_shell "Error while moving $m"
done

echo "All done. Switching to real root."

# clean up. The init process will remount proc sys and dev later
umount /proc
umount /sys
umount /dev

# switch to the real root and execute init
exec switch_root /mnt/root /sbin/init

I have root on LVM, a separate /usr and /var, so you can trim it down quite a bit.

The hard bit is running
Code:
scripts/gen_initramfs_list.sh
in the kernel tree.

The good thing about this initrd, is that its kernel agnostic - there are no kernel modules so it rarely needs updating.
This is from a hew install but it has its origins in a 2009 initrd which still works.
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DaggyStyle
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PostPosted: Sat Apr 27, 2013 6:43 am    Post subject: Reply with quote

Thanks for the info.

three small question,

  • I assume that there is a pkg that creates the initrd, is it mkinitrd?
  • all I need is to assemble the raid, can I trim down the init script to do that (skip the check and mounts)?
  • I see that I need static mdadm, is it ok to hand compile is outside of the tree and copy the resulting and the config to the initrd?

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PostPosted: Sat Apr 27, 2013 8:02 am    Post subject: Reply with quote

DaggyStyle,

1) Its
NeddySeagoon wrote:
The hard bit is running
Code:
scripts/gen_initramfs_list.sh
in the kernel tree.


2) With the ongoing /usr merge, its only a matter of time until you are forced to mount /usr in the initrd.
Yo may as will do that now. You will also need to fsck /usr before you mount it.

3) Not really. The script that builds the initrd copies the system mdadm and busybox.
Put
Code:
sys-fs/mdadm static
sys-apps/busybox static
in your package.use and have those two packages static system wide.
If you do anything else, you will forget next time you build the initrd, which may be a long time away.
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PostPosted: Sat Apr 27, 2013 9:20 am    Post subject: Reply with quote

NeddySeagoon wrote:
DaggyStyle,

1) Its
NeddySeagoon wrote:
The hard bit is running
Code:
scripts/gen_initramfs_list.sh
in the kernel tree.

I see, btw, the output is initrd or initramfs?

NeddySeagoon wrote:

2) With the ongoing /usr merge, its only a matter of time until you are forced to mount /usr in the initrd.
Yo may as will do that now. You will also need to fsck /usr before you mount it.

ongoing /usr merge? can you please elaborate more?

NeddySeagoon wrote:

3) Not really. The script that builds the initrd copies the system mdadm and busybox.
Put
Code:
sys-fs/mdadm static
sys-apps/busybox static
in your package.use and have those two packages static system wide.
If you do anything else, you will forget next time you build the initrd, which may be a long time away.


actually I don't fancy building busybox and mdadm as static as part of the tree, that is why I'm thinking of compiling them by hand out of the tree.
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PostPosted: Sat Apr 27, 2013 9:34 am    Post subject: Reply with quote

DaggyStyle,

Code that was in /, /lib, /sbin and others is slowly being moved to the same places but in /usr.
There will be little left on /

udev somewhat unfairly got the blame for the breakage this causes when the devs dropped support for retrying things that failed because /usr was not yet mounted.
The real cause was the move of code from / to /usr, whih is nothing to do with udev. udev had been papering over the cracks, then stopped.
If a separate /usr works for you now, its only a matter of time until it fails.

The script builds an initramfs, its a cpio archive.

busybox should be static if its installed at all. Its a rescue toolkit. If your dynamic linking or any of its libs are broken, it won't work as rescue shell.
You only need build the initrd stuff with USE=static long enough to make the initrd. You can revert it after.
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PostPosted: Sat Apr 27, 2013 5:21 pm    Post subject: Reply with quote

NeddySeagoon wrote:
DaggyStyle,

Code that was in /, /lib, /sbin and others is slowly being moved to the same places but in /usr.
There will be little left on /

udev somewhat unfairly got the blame for the breakage this causes when the devs dropped support for retrying things that failed because /usr was not yet mounted.
The real cause was the move of code from / to /usr, whih is nothing to do with udev. udev had been papering over the cracks, then stopped.
If a separate /usr works for you now, its only a matter of time until it fails.

I understand, your script does it for all partitions, right?
will doing it to root and usr is enough?

NeddySeagoon wrote:
The script builds an initramfs, its a cpio archive.

mmm no good, I need initrd, lets assume the following, I want to detect the raids, have rescue shell, root is reiserfs and usr is ext4.
I need busybox, mdadm, ext4.fchk and reiserfs check fs all static.
as initramfs doesn't release the memory it takes, I'm loosing memory and I'm not willing to do that.
for me this is a bloatware that I'm not supporting, initrd will load the stuff I need and release the memory later on.
how can I generate an initrd?
NeddySeagoon wrote:
busybox should be static if its installed at all. Its a rescue toolkit. If your dynamic linking or any of its libs are broken, it won't work as rescue shell.
You only need build the initrd stuff with USE=static long enough to make the initrd. You can revert it after.

as said, I'd rather builds all the tools statically out of the tree (not install them anywhere, just compile) and copy it into the initrd

Thanks.
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PostPosted: Sat Apr 27, 2013 7:16 pm    Post subject: Reply with quote

DaggyStyle,

Root is checked after its mounted read only, since fsck, is stored on root and with no initrd, there is no way to check root until its mounted.
That does not change when you use and initrd, so you only need fsck for /usr

If you want to build the static stuff out of the tree, you may do so. Change the corresponding entries in initramfs_list to point to your static programs.
You can make an initrd if you wish too. Its an ext2 root filesystem in a file that is gzipped before being moved to /boot.
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PostPosted: Sun Apr 28, 2013 5:54 am    Post subject: Reply with quote

NeddySeagoon wrote:
DaggyStyle,

Root is checked after its mounted read only, since fsck, is stored on root and with no initrd, there is no way to check root until its mounted.
That does not change when you use and initrd, so you only need fsck for /usr

If you want to build the static stuff out of the tree, you may do so. Change the corresponding entries in initramfs_list to point to your static programs.
You can make an initrd if you wish too. Its an ext2 root filesystem in a file that is gzipped before being moved to /boot.


ok, what is the process of creating the initrd? I assume that creating the img, create the fs, mount it, create a root like structure, copy the files like you did and then?

Thanks.
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PostPosted: Sun Apr 28, 2013 10:59 am    Post subject: Reply with quote

DaggyStyle,

Either make the initrd in an empty file formatted with ext2, or make it in a spare ext2 formatted partiton.
Put all the files there in the right directory structure, with the right owners, groups and permissions, they are all listed in the _list file.
gzip the file and put the gzip version into /boot so you use your bootloader to load it.

Make sure your kernel has initrd and ext2 support. ext2 must be build in.
Tell the kernel that root=/dev/ram0 real_root=/dev/md...

Cross your fingers and reboot. Its not that bad.
As your kernel have everything in it to boot but not reliably, its easy enough to have another go without booting a live distro.
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PostPosted: Sun Apr 28, 2013 11:25 am    Post subject: Reply with quote

ok, thanks, btw, is it possible to run rm -rf on all unnecessary file before I run switchroot if I use initramfs?
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PostPosted: Sun Apr 28, 2013 11:53 am    Post subject: Reply with quote

DaggyStyle,

Probably - I've not tried.
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PostPosted: Sun Apr 28, 2013 11:54 am    Post subject: Reply with quote

DaggyStyle,

Probably - I've not tried.
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PostPosted: Sun Apr 28, 2013 1:33 pm    Post subject: Reply with quote

my problem with initramfs was the amount of memory that the initramfs takes as it says in the memory, if I can remove all rest of the files, I might be able to live with it.
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PostPosted: Sun Apr 28, 2013 1:55 pm    Post subject: Reply with quote

DaggyStyle,

I'm not sure if rm the files frees the RAM or not.

-- edit --

Interesting exercise ... read the initramfs_list file, determine the size of the initrd ext2 filesystem
make the initrd filesystem file, format it as ext2 copy everything over and gzip it to a destination file of your choice.

Late thought. mdadm and busybox need not be static as the dynamic loader is present in the initramfs for mount and fsck.
You would just need to add the libs identified by lddtree busybox and lddtree mdadm
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PostPosted: Mon Apr 29, 2013 7:58 am    Post subject: Reply with quote

Assuming you're using busybox's switch_root, it already does rm -f on the initramfs before the switch.
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PostPosted: Mon Apr 29, 2013 6:27 pm    Post subject: Reply with quote

Goverp.

Code:
exec switch_root /mnt/root /sbin/init
so thats a yes.
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PostPosted: Tue Apr 30, 2013 11:42 am    Post subject: Reply with quote

I'm working on this, btw, how can I add disk/by-label support to the initramfs?
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PostPosted: Tue Apr 30, 2013 11:45 am    Post subject: Reply with quote

NeddySeagoon wrote:
DaggyStyle,

I'm not sure if rm the files frees the RAM or not.

-- edit --

Interesting exercise ... read the initramfs_list file, determine the size of the initrd ext2 filesystem
make the initrd filesystem file, format it as ext2 copy everything over and gzip it to a destination file of your choice.

Late thought. mdadm and busybox need not be static as the dynamic loader is present in the initramfs for mount and fsck.
You would just need to add the libs identified by lddtree busybox and lddtree mdadm


initramfs size if ~140mb I keeping 140 mb in memory just of boot is a bad practice imho.
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PostPosted: Tue Apr 30, 2013 6:21 pm    Post subject: Reply with quote

DaggyStyle,

The script I posted supports disk by lable and UUIDs.

140Mb for an initrd ?
That would be huge
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PostPosted: Tue Apr 30, 2013 6:51 pm    Post subject: Reply with quote

NeddySeagoon wrote:
DaggyStyle,

The script I posted supports disk by lable and UUIDs.

140Mb for an initrd ?
That would be huge


140 unpacked.

well I don't see the partitions of the raid 5 and I don't have /dev/disk/by-label so I've got an error there, any idea what I'm missing? I've took your script.
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