LVM2 - problem after update from 9 to 10

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LVM2 - problem after update from 9 to 10

Postby Chryses » 2019-07-29 20:30

Hi, I'm in the middle of a problem!
I recently find that the current stable is now buster, so I decided to upgrade from oldstable stretch. I update the source list and then I ran the apt update upgrade.
Till here no problem!

But I had some problem during upgrade:
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[...]
Installing new version of config file /etc/lvm/lvm.conf ...
update-initramfs: deferring update (trigger activated)
Removing obsolete conffile /etc/init.d/lvm2-lvmetad ...
Created symlink /etc/systemd/system/sysinit.target.wants/blk-availability.service → /lib/systemd/system/blk-availability.service.
Setting up grub-efi-amd64 (2.02+dfsg1-20) ...
Installing for x86_64-efi platform.
File descriptor 3 (pipe:[2873411]) leaked on vgs invocation. Parent PID 2340: grub-install
File descriptor 5 (/dev/sdd1) leaked on vgs invocation. Parent PID 2340: grub-install
File descriptor 12 (/dev/pts/1) leaked on vgs invocation. Parent PID 2340: grub-install
File descriptor 13 (/dev/pts/1) leaked on vgs invocation. Parent PID 2340: grub-install
File descriptor 3 (pipe:[2873411]) leaked on vgs invocation. Parent PID 2340: grub-install
File descriptor 5 (/dev/sdd1) leaked on vgs invocation. Parent PID 2340: grub-install
File descriptor 12 (/dev/pts/1) leaked on vgs invocation. Parent PID 2340: grub-install
File descriptor 13 (/dev/pts/1) leaked on vgs invocation. Parent PID 2340: grub-install
grub-install: warning: Cannot set EFI variable Boot0012.
grub-install: warning: efivarfs_set_variable: writing to fd 7 failed: No space left on device.
grub-install: warning: _efi_set_variable_mode: ops->set_variable() failed: No space left on device.
grub-install: error: failed to register the EFI boot entry: No space left on device.
Failed: grub-install --target=x86_64-efi
WARNING: Bootloader is not properly installed, system may not be bootable
Generating grub configuration file ...
File descriptor 12 (/dev/pts/1) leaked on vgs invocation. Parent PID 2612: /usr/sbin/grub-probe
File descriptor 13 (/dev/pts/1) leaked on vgs invocation. Parent PID 2612: /usr/sbin/grub-probe
File descriptor 12 (/dev/pts/1) leaked on vgs invocation. Parent PID 2612: /usr/sbin/grub-probe
File descriptor 13 (/dev/pts/1) leaked on vgs invocation. Parent PID 2612: /usr/sbin/grub-probe
[...]

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[...]
Processing triggers for initramfs-tools (0.133) ...
update-initramfs: Generating /boot/initrd.img-4.9.0-8-amd64
Processing triggers for libc-bin (2.28-10) ...
Processing triggers for libgdk-pixbuf2.0-0:amd64 (2.38.1+dfsg-1) ...
Processing triggers for systemd (241-5) ...
Errors were encountered while processing:
 shim-signed-common
 shim-signed:amd64
E: Sub-process /usr/bin/dpkg returned an error code (1)
[...]

I searched a bit but I can't find a solution. Seems that there's some problem with efivars but the only I can say is that debian is installed on a raid1 system and the boot is out of the lvm
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$ lsblk -f
NAME          FSTYPE            LABEL  UUID                                   FSAVAIL FSUSE% MOUNTPOINT
sda
└─sda1        ntfs              Magia  3624EB3324EAF531                        938.1G    50% /data/Magia
sdb
└─sdb1        linux_raid_member Qnap:0 8b168708-bb2d-aa44-0f05-17449ac9f15f
  └─md0       LVM2_member              087bEN-15VR-FQAI-4vf5-szpB-l61Z-I9LZJL
    ├─vg0-lv0 swap                     e999a470-b372-4146-9b1e-76a16dc99e96                  [SWAP]
    ├─vg0-lv1 ext4              root   4aea0113-a39c-4111-b710-0f894c453383    460.2M    90% /
    ├─vg0-lv2 ext4              home   20911b87-68c8-4f9d-aab8-6bfba2adcda8     25.2G     3% /home
    └─vg0-lv3 ext4              data   e7940358-4281-4cfc-b265-662811b4cab5    463.6G    82% /data
sdc
└─sdc1        linux_raid_member Qnap:0 8b168708-bb2d-aa44-0f05-17449ac9f15f
  └─md0       LVM2_member              087bEN-15VR-FQAI-4vf5-szpB-l61Z-I9LZJL
    ├─vg0-lv0 swap                     e999a470-b372-4146-9b1e-76a16dc99e96                  [SWAP]
    ├─vg0-lv1 ext4              root   4aea0113-a39c-4111-b710-0f894c453383    460.2M    90% /
    ├─vg0-lv2 ext4              home   20911b87-68c8-4f9d-aab8-6bfba2adcda8     25.2G     3% /home
    └─vg0-lv3 ext4              data   e7940358-4281-4cfc-b265-662811b4cab5    463.6G    82% /data
sdd
└─sdd1        vfat                     45D0-9CB5                                 477M     2% /boot/efi
sde
└─sde1        ntfs              Travel F00473F20473BA64                        868.3G     7% /data/Travel

I have not yet rebooted the device because I'm little worry about the fact it won't boot anymore!
Like you can see I'm not so expert so maybe the solution is pretty simple.

Do you have any idea or advice in order to resolve the problem?
Last edited by Chryses on 2019-07-30 20:47, edited 1 time in total.
Chryses
 
Posts: 21
Joined: 2019-02-22 11:06

Re: Grub problem during upgrade

Postby Head_on_a_Stick » 2019-07-30 14:36

Chryses wrote:
Code: Select all
grub-install: warning: Cannot set EFI variable Boot0012.
grub-install: warning: efivarfs_set_variable: writing to fd 7 failed: No space left on device.
grub-install: warning: _efi_set_variable_mode: ops->set_variable() failed: No space left on device.
grub-install: error: failed to register the EFI boot entry: No space left on device.

You can try using the efibootmgr command to erase unwanted boot entries. Run efibootmgr (without any arguments) to list all the boot entries and then use this to delete some of them:
Code: Select all
# efibootmgr -b xxxx -B # replace xxxx with the boot number
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Re: Grub problem during upgrade

Postby Chryses » 2019-07-30 14:49

Hi
This's the actual configuration:
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efibootmgr -v
BootCurrent: 0003
Timeout: 0 seconds
BootOrder: 0003,0004,0005,0006,0008,0009,000A,000B,000C,000D,000E,000F
Boot0000  Setup FvFile(721c8b66-426c-4e86-8e99-3457c46ab0b9)
Boot0001  Boot Menu     FvFile(86488440-41bb-42c7-93ac-450fbf7766bf)
Boot0002  Diagnostic Splash     FvFile(a7d8d9a6-6ab0-4aeb-ad9d-163e59a7a380)
Boot0003* USB HDD:      VenMsg(bc7838d2-0f82-4d60-8316-c068ee79d25b,33e821aaaf33bc4789bd419f88c50803)
Boot0004* USB CD:       VenMsg(bc7838d2-0f82-4d60-8316-c068ee79d25b,86701296aa5a7848b66cd49dd3ba6a55)
Boot0005* USB FDD:      VenMsg(bc7838d2-0f82-4d60-8316-c068ee79d25b,6ff015a28830b543a8b8641009461e49)
Boot0006* ATAPI CD:     VenMsg(bc7838d2-0f82-4d60-8316-c068ee79d25b,aea2090adfde214e8b3a5e471856a354)
Boot0007* CD-ROM:       VenMsg(bc7838d2-0f82-4d60-8316-c068ee79d25b,be9d0102e211f3489efa0b983c96839b)
Boot0008* ATA HDD0:     VenMsg(bc7838d2-0f82-4d60-8316-c068ee79d25b,91af625956449f41a7b91f4f892ab0f600)
Boot0009* ATA HDD1:     VenMsg(bc7838d2-0f82-4d60-8316-c068ee79d25b,91af625956449f41a7b91f4f892ab0f601)
Boot000A* ATA HDD2:     VenMsg(bc7838d2-0f82-4d60-8316-c068ee79d25b,91af625956449f41a7b91f4f892ab0f602)
Boot000B* ATA HDD3:     VenMsg(bc7838d2-0f82-4d60-8316-c068ee79d25b,91af625956449f41a7b91f4f892ab0f603)
Boot000C* ATA HDD4:     VenMsg(bc7838d2-0f82-4d60-8316-c068ee79d25b,91af625956449f41a7b91f4f892ab0f604)
Boot000D* ATA HDD5:     VenMsg(bc7838d2-0f82-4d60-8316-c068ee79d25b,91af625956449f41a7b91f4f892ab0f605)
Boot000E* Other HDD:    VenMsg(bc7838d2-0f82-4d60-8316-c068ee79d25b,91af625956449f41a7b91f4f892ab0f609)
Boot000F* Internal Shell        FvFile(c57ad6b7-0515-40a8-9d21-551652854e37)
Boot0010* ATA HDD       VenMsg(bc7838d2-0f82-4d60-8316-c068ee79d25b,91af625956449f41a7b91f4f892ab0f6)
Boot0011* Boot Next Boot Option VenMsg(bc7838d2-0f82-4d60-8316-c068ee79d25b,a7ca6d35b2c2684783721826a7404894)

If I follow the boot order I can remove some, but I don't know if is a good idea.

In meantime, I removed the shim-signed-common package, I don't have a secure boot enabled in bios (this's an old Atom Qnap with debian on it) and now the update run till the end but I noticed that I've one service with not-found
Code: Select all
lvm2-lvmetad.socket

I don't know if is relevant or not, but I'm on RAID1. What do you think?
See here:
Code: Select all
[37273.497121] perf: interrupt took too long (7772 > 7766), lowering kernel.perf_event_max_sample_rate to 25500
[273766.347035] systemd: 39 output lines suppressed due to ratelimiting
[273766.377371] systemd[1]: systemd 241 running in system mode. (+PAM +AUDIT +SELINUX +IMA +APPARMOR +SMACK +SYSVINIT +UTMP +LIBCRYPTSETUP +GCRYPT +GNUTLS +ACL +XZ +LZ4 +SECCOMP +BLKID +ELFUTILS +KMOD -IDN2 +IDN -PCRE2 default-hierarchy=hybrid)
[273766.378353] systemd[1]: Detected architecture x86-64.
[273766.590876] systemd[1]: File /lib/systemd/system/systemd-journald.service:12 configures an IP firewall (IPAddressDeny=any), but the local system does not support BPF/cgroup based firewalling.
[273766.591161] systemd[1]: Proceeding WITHOUT firewalling in effect! (This warning is only shown for the first loaded unit using IP firewalling.)
[273766.816861] systemd[1]: /lib/systemd/system/netdata.service:10: PIDFile= references path below legacy directory /var/run/, updating /var/run/netdata/netdata.pid → /run/netdata/netdata.pid; please update the unit file accordingly.
[273766.825717] systemd[1]: /lib/systemd/system/nmbd.service:9: PIDFile= references path below legacy directory /var/run/, updating /var/run/samba/nmbd.pid → /run/samba/nmbd.pid; please update the unit file accordingly.
[273766.847185] systemd[1]: /lib/systemd/system/smbd.service:8: PIDFile= references path below legacy directory /var/run/, updating /var/run/samba/smbd.pid → /run/samba/smbd.pid; please update the unit file accordingly.
[273766.852084] systemd[1]: /lib/systemd/system/minissdpd.service:10: PIDFile= references path below legacy directory /var/run/, updating /var/run/minissdpd.pid → /run/minissdpd.pid; please update the unit file accordingly.
[273767.323144] systemd[1]: Stopping Journal Service...
[273767.324147] systemd-journald[317]: Received SIGTERM from PID 1 (systemd).
[273767.355021] systemd[1]: systemd-journald.service: Succeeded.
[297132.744394] lvm2-activation-generator: lvmconfig failed
[297132.744539] lvm2-activation-generator: Activation generator failed.
[297133.428545] lvm2-activation-generator: lvmconfig failed
[297133.428685] lvm2-activation-generator: Activation generator failed.
[297134.149168] lvm2-activation-generator: lvmconfig failed
[297134.155041] lvm2-activation-generator: Activation generator failed.
[297139.335260] lvm2-activation-generator: lvmconfig failed
[...]
[354167.018343] efibootmgr[13960]: segfault at 561e0036c20c ip 00007f4487d65206 sp 00007ffc5344f2d8 error 4 in libc-2.28.so[7f4487cef000+148000]

This's from the update, lvmconfig give error and efibootmgr give error too.

What I can do to try to understand if at the very next boot the system really boot-up?
Chryses
 
Posts: 21
Joined: 2019-02-22 11:06

Re: Grub problem during upgrade

Postby Head_on_a_Stick » 2019-07-30 14:57

Chryses wrote:I don't know if is relevant or not, but I'm on RAID1. What do you think?

I have no idea, sorry, I don't use RAID or LVM. Perhaps if you add a bit more detail to the thread title then you can attract the attention of somebody who does.

In respect of your boot entry problem you can try the --removable option for the grub-install command, the system should then be bootable even in the absence of NVRAM entries (if your firmware is well-behaved).
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Re: Grub problem during upgrade

Postby Chryses » 2019-07-30 20:15

You right!
I update the title

Thanks
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