Re: How to repair/reinstall guix on foreign distro
Thorsten Wilms writes: > Hi! It seems every few weeks i’m thrown into a initramfs prompt, as > root got mounted read-only. The way out is always running fsck, which > reports errors and offers fixes that I either can’t map to anything, or > that refer to paths that belong to guix. Usually only below /gnu/store, > but this time also var/guix. > > Now `guix pull` fails with: > ``` > ;;; WARNING: loading compiled > file > /gnu/store/8bsnz1fk330qbn1p8k18i0j11vld4jxd-guix-module-union/lib/guile/3.0/site-ccache/guix/build-system/gnu.go > failed: ;;; In procedure load-thunk-from-memory: not an ELF file > Updating channel 'guix' from Git repository at > 'https://git.savannah.gnu.org/git/guix.git'... guix pull: error: Git > error: invalid data in index - incorrect header signature > ``` > > At first, I focused on the warning (sorry, leoprikler) ... the same git > error happens when using an older guix. > > Now a fix for that would be great, but independent of that, I have to > wonder how one should go about reinstalling guix on a foreign distro. I > cannot umount or remount and remove /gnu/store! > > Even after `sudo systemctl stop gnu-store.mount`, /gnu/store is busy. > `fuser -kim /gnu/store/` will throw me out of the session, even though > I would think everything that belongs to it is part of the host (Ubuntu > Unity 20.10). No sudo umount or remount or rm -rf allowed, /gnu/store > remains ro and busy. Short of booting another system (say an USB > stick), is there a way to clear /gnu/store? Or to safely replace its > content? Hi, Thorsten I was install guix on a ubuntu server and work right, can you reproduce you guix installation process? maybe the fault happen in install guix process. -- Best reguards, c4droid
Re: How to repair/reinstall guix on foreign distro
On Tue, 18 May 2021 11:20:41 +0200 Ricardo Wurmus wrote: > > I would still like to have a minimal invasive way to get beyond: > > ``` > > guix pull: error: Git error: invalid data in index - incorrect > > header > > signature > > ``` > > Try erasing the git cache at ~/.cache/guix/checkouts first. Thank you, that did the trick! -- Thorsten Wilms
Re: How to repair/reinstall guix on foreign distro
Thorsten Wilms writes: It does however claim that all except one power cylce has been an unsafe shutdown, even though I had only a few hard resets and usually shutdown by issuing `poweroff`. That’s worrying. “unsafe shutdown” leads to file system corruption, and Guix doesn’t like that at all. I would still like to have a minimal invasive way to get beyond: ``` guix pull: error: Git error: invalid data in index - incorrect header signature ``` Try erasing the git cache at ~/.cache/guix/checkouts first. -- Ricardo
Re: How to repair/reinstall guix on foreign distro
Thorsten Wilms writes: > On Mon, 17 May 2021 22:23:03 -0400 > Joshua Branson wrote: > >> Is ubuntu causing this issue? Why are you seeing an initramfs prompt >> every few weeks? If you are running guix on ubuntu...that seems like >> it's ubuntu's fault. Though I'm probably way wrong. > > If there are filesystem errors on boot, you get a initramfs shell that > allows running fsck on root for repairs. Sometimes, some files can’t be > fixed. > > The system resides on a Transcend 256GB MTE110S SSD. Now one would > probably assume that SSD is faulty. What’s curious is that so far, any > and all noticeable corruption has been limited to guix-related files! > smartctl repports "overall-health self-assessment test result: PASSED" > and has "No Errors Logged". Full output attached at the end. > > It does however claim that all except one power cylce has been an unsafe > shutdown, even though I had only a few hard resets and usually shutdown > by issuing `poweroff`. Searching the web for this issue led me to > turning off fast boot in the BIOS, but that didn’t help. > > I would still like to have a minimal invasive way to get beyond: > ``` > guix pull: error: Git error: invalid data in index - incorrect header > signature > ``` > Or a way to to remove/replace /gnu/store from the running system. If you are convinced on using guix on a foreign distro...then you could create a separate partition for /gnu/store and /var/guix. Then mount those at boot time. That way at least, you could not have to manually run fsck at an initramfs. You could do it when you've logged into ubuntu's gnome (or whatever it is that you use.) I wish I could be more helpful. -- Joshua Branson (joshuaBPMan in #guix) Sent from Emacs and Gnus https://gnucode.me https://video.hardlimit.com/accounts/joshua_branson/video-channels https://propernaming.org "You can have whatever you want, as long as you help enough other people get what they want." - Zig Ziglar
Re: How to repair/reinstall guix on foreign distro
On Tue, 18 May 2021 10:30:03 +0800 c4droid wrote: > I was install guix on a ubuntu server and work right, can you > reproduce you guix installation process? maybe the fault happen in > install guix process. Thanks, but this has been a working guix installation, so I very much doubt something went wrong during setup. -- Thorsten Wilms
Re: How to repair/reinstall guix on foreign distro
On Mon, 17 May 2021 22:23:03 -0400 Joshua Branson wrote: > Is ubuntu causing this issue? Why are you seeing an initramfs prompt > every few weeks? If you are running guix on ubuntu...that seems like > it's ubuntu's fault. Though I'm probably way wrong. If there are filesystem errors on boot, you get a initramfs shell that allows running fsck on root for repairs. Sometimes, some files can’t be fixed. The system resides on a Transcend 256GB MTE110S SSD. Now one would probably assume that SSD is faulty. What’s curious is that so far, any and all noticeable corruption has been limited to guix-related files! smartctl repports "overall-health self-assessment test result: PASSED" and has "No Errors Logged". Full output attached at the end. It does however claim that all except one power cylce has been an unsafe shutdown, even though I had only a few hard resets and usually shutdown by issuing `poweroff`. Searching the web for this issue led me to turning off fast boot in the BIOS, but that didn’t help. I would still like to have a minimal invasive way to get beyond: ``` guix pull: error: Git error: invalid data in index - incorrect header signature ``` Or a way to to remove/replace /gnu/store from the running system. ``` ~: sudo smartctl -x /dev/nvme0n1p2 [sudo] password for thorwil: smartctl 7.1 2019-12-30 r5022 [x86_64-linux-5.8.0-53-generic] (local build) Copyright (C) 2002-19, Bruce Allen, Christian Franke, www.smartmontools.org === START OF INFORMATION SECTION === Model Number: TS256GMTE110S Serial Number: G286710001 Firmware Version: S0905C3 PCI Vendor/Subsystem ID:0x126f IEEE OUI Identifier:0x00 Controller ID: 1 Number of Namespaces: 1 Namespace 1 Size/Capacity: 256.060.514.304 [256 GB] Namespace 1 Formatted LBA Size: 512 Local Time is: Tue May 18 09:23:26 2021 CEST Firmware Updates (0x12):1 Slot, no Reset required Optional Admin Commands (0x0007): Security Format Frmw_DL Optional NVM Commands (0x001f): Comp Wr_Unc DS_Mngmt Wr_Zero Sav/Sel_Feat Maximum Data Transfer Size: 64 Pages Warning Comp. Temp. Threshold: 83 Celsius Critical Comp. Temp. Threshold: 90 Celsius Supported Power States St Op Max Active Idle RL RT WL WT Ent_Lat Ex_Lat 0 + 9.00W --0 0 0 00 0 Supported LBA Sizes (NSID 0x1) Id Fmt Data Metadt Rel_Perf 0 + 512 0 0 === START OF SMART DATA SECTION === SMART overall-health self-assessment test result: PASSED SMART/Health Information (NVMe Log 0x02) Critical Warning: 0x00 Temperature:48 Celsius Available Spare:88% Available Spare Threshold: 10% Percentage Used:0% Data Units Read:1.136.204 [581 GB] Data Units Written: 1.901.390 [973 GB] Host Read Commands: 15.204.795 Host Write Commands:18.097.210 Controller Busy Time: 1.386 Power Cycles: 276 Power On Hours: 1.214 Unsafe Shutdowns: 275 Media and Data Integrity Errors:0 Error Information Log Entries: 0 Warning Comp. Temperature Time:0 Critical Comp. Temperature Time:0 Error Information (NVMe Log 0x01, max 64 entries) No Errors Logged ``` -- Thorsten Wilms
Re: How to repair/reinstall guix on foreign distro
Thorsten Wilms writes: > Hi! It seems every few weeks i’m thrown into a initramfs prompt, as > root got mounted read-only. The way out is always running fsck, which > reports errors and offers fixes that I either can’t map to anything, or > that refer to paths that belong to guix. Usually only below /gnu/store, > but this time also var/guix. Is ubuntu causing this issue? Why are you seeing an initramfs prompt every few weeks? If you are running guix on ubuntu...that seems like it's ubuntu's fault. Though I'm probably way wrong. > > Now `guix pull` fails with: > ``` > ;;; WARNING: loading compiled > file > /gnu/store/8bsnz1fk330qbn1p8k18i0j11vld4jxd-guix-module-union/lib/guile/3.0/site-ccache/guix/build-system/gnu.go > failed: ;;; In procedure load-thunk-from-memory: not an ELF file > Updating channel 'guix' from Git repository at > 'https://git.savannah.gnu.org/git/guix.git'... guix pull: error: Git > error: invalid data in index - incorrect header signature > ``` Man...I've no idea. I'm honestly responding just so you get a response. Why do you suppose you are getting into an initramfs...As in you always have to run fsck? What hardware are you using? > At first, I focused on the warning (sorry, leoprikler) ... the same git > error happens when using an older guix. > > Now a fix for that would be great, but independent of that, I have to > wonder how one should go about reinstalling guix on a foreign distro. I > cannot umount or remount and remove /gnu/store! > > Even after `sudo systemctl stop gnu-store.mount`, /gnu/store is busy. > `fuser -kim /gnu/store/` will throw me out of the session, even though > I would think everything that belongs to it is part of the host (Ubuntu > Unity 20.10). No sudo umount or remount or rm -rf allowed, /gnu/store > remains ro and busy. Short of booting another system (say an USB > stick), is there a way to clear /gnu/store? Or to safely replace its > content? -- Joshua Branson (joshuaBPMan in #guix) Sent from Emacs and Gnus https://gnucode.me https://video.hardlimit.com/accounts/joshua_branson/video-channels https://propernaming.org "You can have whatever you want, as long as you help enough other people get what they want." - Zig Ziglar
How to repair/reinstall guix on foreign distro
Hi! It seems every few weeks i’m thrown into a initramfs prompt, as root got mounted read-only. The way out is always running fsck, which reports errors and offers fixes that I either can’t map to anything, or that refer to paths that belong to guix. Usually only below /gnu/store, but this time also var/guix. Now `guix pull` fails with: ``` ;;; WARNING: loading compiled file /gnu/store/8bsnz1fk330qbn1p8k18i0j11vld4jxd-guix-module-union/lib/guile/3.0/site-ccache/guix/build-system/gnu.go failed: ;;; In procedure load-thunk-from-memory: not an ELF file Updating channel 'guix' from Git repository at 'https://git.savannah.gnu.org/git/guix.git'... guix pull: error: Git error: invalid data in index - incorrect header signature ``` At first, I focused on the warning (sorry, leoprikler) ... the same git error happens when using an older guix. Now a fix for that would be great, but independent of that, I have to wonder how one should go about reinstalling guix on a foreign distro. I cannot umount or remount and remove /gnu/store! Even after `sudo systemctl stop gnu-store.mount`, /gnu/store is busy. `fuser -kim /gnu/store/` will throw me out of the session, even though I would think everything that belongs to it is part of the host (Ubuntu Unity 20.10). No sudo umount or remount or rm -rf allowed, /gnu/store remains ro and busy. Short of booting another system (say an USB stick), is there a way to clear /gnu/store? Or to safely replace its content? -- Thorsten Wilms
