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midway
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PostPosted: Mon Sep 17, 2012 2:50 pm    Post subject: grub missing from boot (vmware) Reply with quote

after upgrading the kernel, I get error (awk:fatal) about grub.conf and it asks me to create it manually.

genkernel works fine on its own:
http://pastebin.com/KCwTKgEh

However, I want the genkernel to automatically update my grub boot loader configuration but it fails (may be because it can not find grub).
http://pastebin.com/cU1MR8dU

this is odd but I dont have the grub configuration file:
Code:

~ # nano /boot/
System.map-genkernel-x86-3.3.8-gentoo  initramfs-genkernel-x86-3.3.8-gentoo   kernel-genkernel-x86-3.3.8-gentoo

~ # locate grub.conf
/usr/portage/sys-boot/grub/files/grub.conf.gentoo
/usr/share/doc/grub-0.97-r10/grub.conf.gentoo.bz2
/usr/share/doc/grub-0.97-r10/grub.conf.sample.bz2


More info:
Code:

~ # cd /boot/
System.map-genkernel-x86-3.3.8-gentoo  initramfs-genkernel-x86-3.3.8-gentoo   kernel-genkernel-x86-3.3.8-gentoo

~ # locate grub.conf
/usr/portage/sys-boot/grub/files/grub.conf.gentoo
/usr/share/doc/grub-0.97-r10/grub.conf.gentoo.bz2
/usr/share/doc/grub-0.97-r10/grub.conf.sample.bz2

~ # cd /lib/modules/
2.6.25-hardened-r13/ 2.6.28-hardened-r6/  2.6.28-hardened-r7/  2.6.28-hardened-r9/  3.3.8-gentoo/

~ # cd /usr/src/
.keep                     linux/                    linux-2.6.28-hardened-r7/ linux-2.6.28-hardened-r9/ linux-3.3.8-gentoo/


How to resolve this? Can I manually create a grub.conf file and add the kernel in it?


Last edited by midway on Wed Sep 19, 2012 12:44 pm; edited 3 times in total
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PostPosted: Tue Sep 18, 2012 10:35 am    Post subject: Reply with quote

More info on grub:

Code:

~ # emerge --oneshot -p grub
These are the packages that would be merged, in order:
Calculating dependencies... done!
[ebuild   R    ] sys-boot/grub-0.97-r10

~ # equery b grub
 * Searching for grub ...
sys-boot/grub-0.97-r10 (/sbin/grub)
sys-boot/grub-0.97-r10 (/lib/grub)
sys-boot/grub-0.97-r10 (/usr/share/grub)


Please note that this is a virtual machine (vmware).
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PostPosted: Tue Sep 18, 2012 11:31 am    Post subject: Reply with quote

Your running kernel is hidden from you because mounting /boot fails.
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PostPosted: Tue Sep 18, 2012 11:41 am    Post subject: Reply with quote

Probably. Or else grub was never installed to the boot partition. Can't really tell.

@nitish.anand, genkernel has an option called MOUNTBOOT that you will find in /etc/genkernel.conf that will take care of mounting the boot partition for you.

- John
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PostPosted: Tue Sep 18, 2012 11:48 am    Post subject: Reply with quote

John R. Graham wrote:

Probably. Or else grub was never installed to the boot partition. Can't really tell.
@nitish.anand, genkernel has an option called MOUNTBOOT that you will find in /etc/genkernel.conf that will take care of mounting the boot partition for you.
- John


mountboot is enabled:
http://pastebin.com/ApLLewzH

Code:

boot # cat /etc/fstab
/dev/sda1 /boot xfs defaults,noatime 1 2
/dev/sda2 swap swap sw 0 0
/dev/sda3 / xfs noatime 0 1
/dev/cdrom /mnt/cdrom auto defaults,noauto 0 0
none /proc proc defaults 0 0
none /dev/shm tmpfs nodev,nosuid,noexec,rw 0 0


Last edited by midway on Tue Sep 18, 2012 11:57 am; edited 1 time in total
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PostPosted: Tue Sep 18, 2012 11:56 am    Post subject: Reply with quote

I understand this was a kernel upgrade, so there is something that boots the system, probably Grub.
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PostPosted: Tue Sep 18, 2012 12:00 pm    Post subject: Reply with quote

Ah. Arg, you're right.

@nitish.anand, one possibility is that your new kernel doesn't include filesystem support for the filesystem used on the boot partition. Normally a genkernel-generated kernel will include support for most common filesystems, though. Have you been modifying the configuration heavily with the genkernel --menuconfig option? If so, you should do so again and check that you have support for the boot partition filesystem.

Wait, is XFS really your boot partition filesystem? Probably not as I don't believe grub supports XFS. An incorrect /etc/fstab could be why /boot isn't mounting.

- John
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PostPosted: Tue Sep 18, 2012 12:09 pm    Post subject: Reply with quote

John R. Graham wrote:
Ah. Arg, you're right.

@nitish.anand, one possibility is that your new kernel doesn't include filesystem support for the filesystem used on the boot partition. Normally a genkernel-generated kernel will include support for most common filesystems, though. Have you been modifying the configuration heavily with the genkernel --menuconfig option? If so, you should do so again and check that you have support for the boot partition filesystem.

- John


thx John and jaglover for your prompt responses. Yes this was a kernel upgrade from 2.6.36 hardened -r9 to 3.3.8
after emerging the gentoo-sources, I ran genkernel --menuconfig --bootloader=grub all.

In the menuconfig, the only thing I changed was Virtualization (changed from M to *). Thinking * will include the support for vmware.

Quote:
--- Virtualization │ │
│ │ <*> Kernel-based Virtual Machine (KVM) support │ │
│ │ <*> KVM for Intel processors support │ │
│ │ <*> KVM for AMD processors support │ │
│ │ [ ] Audit KVM MMU │ │
│ │ < > Host kernel accelerator for virtio net (EXPERIMENTAL) │ │
│ │ < > Linux hypervisor example code
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PostPosted: Tue Sep 18, 2012 12:31 pm    Post subject: Reply with quote

I edited my last response after noticing your posted /etc/fstab. Is XFS really your boot partition filesystem? Probably not as I don't believe grub supports XFS. An incorrect /etc/fstab could be why /boot isn't mounting.

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PostPosted: Tue Sep 18, 2012 12:34 pm    Post subject: Reply with quote

This is from log, why your current kernel can't see the boot device I do not know.
Code:
* Linux Kernel 3.3.8-gentoo for x86...
mount: special device /dev/sda1 does not exist
* WARNING: Failed to mount /boot!

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PostPosted: Tue Sep 18, 2012 1:07 pm    Post subject: Reply with quote

John R. Graham wrote:
I edited my last response after noticing your posted /etc/fstab. Is XFS really your boot partition filesystem? Probably not as I don't believe grub supports XFS. An incorrect /etc/fstab could be why /boot isn't mounting.

- John

This has reportedly since been fixed, and the 0.97 version (at least) of GRUB is apparently stable.
http://xfs.org/index.php/XFS_FAQ#Q:_Does_GRUB_work_with_XFS.3F

@Jaglover - no idea why my current kernel (linux-2.6.28-hardened-r9) cant find boot. I have not rebooted into the new kernel after upgrading to 3.3.8, could this be the cause? I am not sure of reboot as it might fail after.
Code:

boot # eselect kernel list
Available kernel symlink targets:
  [1]   linux-2.6.28-hardened-r7
  [2]   linux-2.6.28-hardened-r9
  [3]   linux-3.3.8-gentoo *

boot # nano /etc/make.conf
USE="symlink nptl nptlonly mysql curl gd imap jpeg png snmp tiff truetype xml2 spell apache2"

~ # nano /boot/
System.map-genkernel-x86-3.3.8-gentoo  initramfs-genkernel-x86-3.3.8-gentoo   kernel-genkernel-x86-3.3.8-gentoo


Last edited by midway on Tue Sep 18, 2012 1:14 pm; edited 2 times in total
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PostPosted: Tue Sep 18, 2012 1:11 pm    Post subject: Reply with quote

You cannot boot the new kernel, Grub won't find it. When you reboot you will be running your old kernel. What is the output of
Code:
fdisk -l

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PostPosted: Tue Sep 18, 2012 1:24 pm    Post subject: Reply with quote

More info:

Code:


dev # fdisk -l
dev #

dev # cat /proc/mounts
rootfs / rootfs rw 0 0
/dev/sda3 / xfs rw,noatime,attr2,noquota 0 0
none /proc proc rw 0 0
tmpfs /run tmpfs rw,nosuid,nodev,mode=755 0 0
rc-svcdir /lib/rc/init.d tmpfs rw,nosuid,nodev,noexec,size=1024k,mode=755 0 0
sysfs /sys sysfs rw,nosuid,nodev,noexec 0 0
securityfs /sys/kernel/security securityfs rw,nosuid,nodev,noexec 0 0
debugfs /sys/kernel/debug debugfs rw,nosuid,nodev,noexec 0 0
configfs /sys/kernel/config configfs rw,nosuid,nodev,noexec 0 0
udev /dev tmpfs rw,nosuid,size=10240k,mode=755 0 0
fusectl /sys/fs/fuse/connections fusectl rw 0 0
devpts /dev/pts devpts rw,nosuid,noexec,gid=5,mode=620 0 0
none /dev/shm tmpfs rw,nosuid,nodev,noexec 0 0
usbfs /proc/bus/usb usbfs rw,nosuid,noexec,devgid=85,devmode=664 0 0
rpc_pipefs /var/lib/nfs/rpc_pipefs rpc_pipefs rw 0 0
nfsd /proc/fs/nfsd nfsd rw,nosuid,nodev,noexec 0 0


dev # lspci -n
00:00.0 0600: 8086:7190 (rev 01)
00:01.0 0604: 8086:7191 (rev 01)
00:07.0 0601: 8086:7110 (rev 08)
00:07.1 0101: 8086:7111 (rev 01)
00:07.3 0680: 8086:7113 (rev 08)
00:0f.0 0300: 15ad:0405
00:10.0 0100: 1000:0030 (rev 01)
00:11.0 0200: 1022:2000 (rev 10)


dev # lspci
00:00.0 Host bridge: Intel Corporation 440BX/ZX/DX - 82443BX/ZX/DX Host bridge (rev 01)
00:01.0 PCI bridge: Intel Corporation 440BX/ZX/DX - 82443BX/ZX/DX AGP bridge (rev 01)
00:07.0 ISA bridge: Intel Corporation 82371AB/EB/MB PIIX4 ISA (rev 08)
00:07.1 IDE interface: Intel Corporation 82371AB/EB/MB PIIX4 IDE (rev 01)
00:07.3 Bridge: Intel Corporation 82371AB/EB/MB PIIX4 ACPI (rev 08)
00:0f.0 VGA compatible controller: VMware SVGA II Adapter
00:10.0 SCSI storage controller: LSI Logic / Symbios Logic 53c1030 PCI-X Fusion-MPT Dual Ultra320 SCSI (rev 01)
00:11.0 Ethernet controller: Advanced Micro Devices [AMD] 79c970 [PCnet32 LANCE] (rev 10)

dev # mount /dev/s
sg0       shm/      snapshot  stderr    stdin     stdout

dev # cat /proc/diskstats
   1       0 ram0 0 0 0 0 0 0 0 0 0 0 0
   1       1 ram1 0 0 0 0 0 0 0 0 0 0 0
   1       2 ram2 0 0 0 0 0 0 0 0 0 0 0
   1       3 ram3 0 0 0 0 0 0 0 0 0 0 0
   1       4 ram4 0 0 0 0 0 0 0 0 0 0 0
   1       5 ram5 0 0 0 0 0 0 0 0 0 0 0
   1       6 ram6 0 0 0 0 0 0 0 0 0 0 0
   1       7 ram7 0 0 0 0 0 0 0 0 0 0 0
   1       8 ram8 0 0 0 0 0 0 0 0 0 0 0
   1       9 ram9 0 0 0 0 0 0 0 0 0 0 0
   1      10 ram10 0 0 0 0 0 0 0 0 0 0 0
   1      11 ram11 0 0 0 0 0 0 0 0 0 0 0
   1      12 ram12 0 0 0 0 0 0 0 0 0 0 0
   1      13 ram13 0 0 0 0 0 0 0 0 0 0 0
   1      14 ram14 0 0 0 0 0 0 0 0 0 0 0
   1      15 ram15 0 0 0 0 0 0 0 0 0 0 0
   7       0 loop0 0 0 0 0 0 0 0 0 0 0 0
   7       1 loop1 0 0 0 0 0 0 0 0 0 0 0
   7       2 loop2 0 0 0 0 0 0 0 0 0 0 0
   7       3 loop3 0 0 0 0 0 0 0 0 0 0 0
   7       4 loop4 0 0 0 0 0 0 0 0 0 0 0
   7       5 loop5 0 0 0 0 0 0 0 0 0 0 0
   7       6 loop6 0 0 0 0 0 0 0 0 0 0 0
   7       7 loop7 0 0 0 0 0 0 0 0 0 0 0
   3       0 hda 0 0 0 0 0 0 0 0 0 0 0
   8       0 sda 276098 12771 21138983 5764960 4595941 477341 178894431 105089180 0 20876940 110838210
   8       1 sda1 0 0 0 0 0 0 0 0 0 0 0
   8       2 sda2 0 0 0 0 0 0 0 0 0 0 0
   8       3 sda3 276096 12771 21138967 5764900 4595941 477341 178894431 105089180 0 20876880 110838150

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PostPosted: Tue Sep 18, 2012 1:57 pm    Post subject: Reply with quote

You mentioned this is inside of a virtual machine. The lspci output you posted, is it run inside VM?
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PostPosted: Tue Sep 18, 2012 2:05 pm    Post subject: Reply with quote

Jaglover wrote:
You mentioned this is inside of a virtual machine. The lspci output you posted, is it run inside VM?

Yes I am running all these commands inside a vm (and this vm is running on a host which is running vmware esx3.5).
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PostPosted: Tue Sep 18, 2012 2:10 pm    Post subject: Reply with quote

Output of
Code:
ls /dev/sd*
might also be helpful.

- John
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PostPosted: Tue Sep 18, 2012 2:12 pm    Post subject: Reply with quote

Well, obviously your kernel has no support for [virtual] HDD controller. I've no experience with vmware nor genkernel, hopefully someone else can help you here.
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PostPosted: Tue Sep 18, 2012 2:13 pm    Post subject: Reply with quote

John R. Graham wrote:
Output of
Code:
ls /dev/sd*
might also be helpful.
- John


Already mentioned above.
Code:

dev # mount /dev/s
sg0       shm/      snapshot  stderr    stdin     stdout

dev # ls /dev/s
sg0       shm/      snapshot  stderr    stdin     stdout

dev # ls /dev/sd*
ls: cannot access /dev/sd*: No such file or directory


dmesg output (src, dest and mac altered):
http://pastebin.com/n5GA2bcd
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PostPosted: Tue Sep 18, 2012 2:39 pm    Post subject: Reply with quote

Fibbing doesn't help. Unless your system is seriously nonstandard, none of the commands you show above except the one I recommended produces the output you posted. Are you running in a chroot right now?

- John
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PostPosted: Tue Sep 18, 2012 2:54 pm    Post subject: Reply with quote

John R. Graham wrote:
Fibbing doesn't help.
- John


sorry John, didn't get you. I am just giving you what i see on my system. could this be because i am running gentoo under vmware?
inode is not 2 (correct me if i m wrong).
Code:

~ # pwd
/root
~ # ls -id /
128 /
~ # ls -ld
drwxr-xr-x 8 root root 4096 Sep 18 15:25 .
~ # ls -ld /proc/1/root
lrwxrwxrwx 1 root root 0 Sep 18 16:00 /proc/1/root -> /
~ # stat /
  File: `/'
  Size: 4096            Blocks: 8          IO Block: 4096   directory
Device: 803h/2051d      Inode: 128         Links: 18
Access: (0755/drwxr-xr-x)  Uid: (    0/    root)   Gid: (    0/    root)
Access: 2010-04-06 13:05:45.735183132 +0100
Modify: 2012-07-03 15:31:36.215719930 +0100
Change: 2012-07-03 15:31:36.215719930 +0100
 Birth: -
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PostPosted: Tue Sep 18, 2012 3:19 pm    Post subject: Reply with quote

Sorry; that's beyond my area of expertise. What do you think that tells you?

Looking at your "lspci -n" output, the driver for the virtual hard drive controller is a standard (although somewhat old) Intel ICH IDE controller. The device driver that handles it is
Code:
 -> Device Drivers
   -> Serial ATA and Parallel ATA drivers (ATA [=y])
     -> ATA SFF support (ATA_SFF [=y])
       -> ATA BMDMA support (ATA_BMDMA [=y])
        -> Intel ESB, ICH, PIIX3, PIIX4 PATA/SATA support
however I believe that the out of the box genkernel configuration should have support for that. You could reboot your virtual machine into the install CD (that is how you installed this, right?) enter the chroot, and then run
Code:
genkernel --menuconfig all
to see whether or not it's enabled (probably as a module). Note that you must properly set up grub to lave the initramfs available to properly boot a genkernel kernel image.

However, that all said, I've never see a system act like yours it: booted up but with the device nodes not existing the for root filesystem device. Perhaps someone with more virtualization experience will chime in.

- John
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PostPosted: Tue Sep 18, 2012 3:26 pm    Post subject: Reply with quote

Well, lspci also shows LSI Logic / Symbios Logic 53c1030 PCI-X Fusion-MPT Dual Ultra320 SCSI, maybe this one is in use, don't think genkernel supports it out of the box.
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PostPosted: Tue Sep 18, 2012 3:30 pm    Post subject: Reply with quote

John, I believe it booted up using legacy IDE drivers, udev will not create nodes for hd* but the way rootfs is mounted at boot still gives access to the root filesystem.

@nitish.anand
You should disable IDE support in kernel and enable PATA driver as John suggested.
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PostPosted: Tue Sep 18, 2012 4:55 pm    Post subject: Reply with quote

Interesting. Would've though that the legacy drivers would've been long gone from the genkernel-supplied kernel config files. Definitely worth checking, though.

- John
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PostPosted: Wed Sep 19, 2012 9:24 am    Post subject: Reply with quote

Quote:
You could reboot your virtual machine into the install CD (that is how you installed this, right?)

thx John and jaglover, this server was hosted on a separate hardware before and was imported into virtual environment (converted as vm) in 2010 (by my predecessor).

I tried rebooting my server last night with lots of problems (boot not found obviously and then modprobe.conf issues). So I have reverted back to earlier snapshot and gone back to kernel 2.6.28 (where sync + system + world + revdep works and the server reboots fine) - it is a bodge fix until I retry upgrading the kernel to 3.3.8. But I thought to first solve this 'boot not seen by kernel' issue before upgrading.
Code:

~ # uname -a
Linux 2.6.28-hardened-r9 #1 SMP Mon Apr 12 17:02:47 BST 2010 i686 Intel(R) Xeon(R) CPU X5450 @ 3.00GHz GenuineIntel GNU/Linux

~ # eselect kernel list
Available kernel symlink targets:
  [1]   linux-2.6.28-hardened-r7
  [2]   linux-2.6.28-hardened-r9 *

Code:

~ # cat /etc/fstab
/dev/sda1 /boot xfs defaults,noatime 1 2
/dev/sda2 swap swap sw 0 0
/dev/sda3 / xfs noatime 0 1
/dev/cdrom /mnt/cdrom auto defaults,noauto 0 0
none /proc proc defaults 0 0
none /dev/shm tmpfs nodev,nosuid,noexec,rw 0 0

~ # lspci
00:00.0 Host bridge: Intel Corporation 440BX/ZX/DX - 82443BX/ZX/DX Host bridge (rev 01)
00:01.0 PCI bridge: Intel Corporation 440BX/ZX/DX - 82443BX/ZX/DX AGP bridge (rev 01)
00:07.0 ISA bridge: Intel Corporation 82371AB/EB/MB PIIX4 ISA (rev 08)
00:07.1 IDE interface: Intel Corporation 82371AB/EB/MB PIIX4 IDE (rev 01)
00:07.3 Bridge: Intel Corporation 82371AB/EB/MB PIIX4 ACPI (rev 08)
00:0f.0 VGA compatible controller: VMware SVGA II Adapter
00:10.0 SCSI storage controller: LSI Logic / Symbios Logic 53c1030 PCI-X Fusion-MPT Dual Ultra320 SCSI (rev 01)
00:11.0 Ethernet controller: Advanced Micro Devices [AMD] 79c970 [PCnet32 LANCE] (rev 10)

~ # fdisk -l
~ #
~ # ls /dev/s
sg0       shm/      snapshot  stderr    stdin     stdout

~ # equery b genkernel
 * Searching for genkernel ...
sys-kernel/genkernel-3.4.24_p2 (/usr/share/bash-completion/genkernel)
sys-kernel/genkernel-3.4.24_p2 (/var/cache/genkernel)
sys-kernel/genkernel-3.4.24_p2 (/usr/share/genkernel)
sys-kernel/genkernel-3.4.24_p2 (/usr/bin/genkernel)


on vmware side, this is what i have tried (to check if I could mount to my /dev/cdrom - but this doesn't exist either):

In VMware > Select the Gentoo Vm > Edit Settings > CD /DVD Drive 1 > Then I have tried both:
1. Passthrough IDE and
2. Emulate IDE

again many thx for your time.
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