A new version of the RcppAPT package interfacing from R to the C++ library behind the awesome apt, apt-get, apt-cache, commands and their cache powering Debian, Ubuntu and the like arrived on CRAN yesterday. This comes a good year after the previous maintenance update for release 0.0.6. RcppAPT allows you to query the (Debian or Ubuntu) package dependency graph at will, with build-dependencies (if you have deb-src entries), reverse dependencies, and all other goodies. See the vignette and examples for illustrations. The maintenance release responds to call for updates from CRAN desiring that make all implicit dependencies on packages markdown and rmarkdown explicit via a Suggests: entry. Two of the many packages I maintain were part of the (large !!) list in the CRAN email, and this is one of them. While making the update, we refreshed two other packaging details.

Changes in version 0.0.7 (2021-04-16)

Add rmarkdown to Suggests: as an implicit conditional dependency

Switch vignette to minidown and its water framework, add minidown to Suggests as well

Update two URLs in the README.md file

Courtesy of my CRANberries, there is also a diffstat report for this release. A bit more information about the package is available here as well as as the GitHub repo. If you like this or other open-source work I do, you can now sponsor me at GitHub.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

I released version 2.6 of ledger2beancount, a ledger to beancount converter. Here are the changes in 2.6:

Round calculated total if needed for price==cost comparison
Add narration_tag config variable to set narration from metadata
Retain unconsummated payee/payer metadata
Ensure UTF-8 output and assume UTF-8 input
Document UTF-8 issue on Windows systems
Add option to move posting-level tags to the transaction itself
Add support for the alias sub-directive of account declarations
Add support for the payee sub-directive of account declarations
Support configuration file called .ledger2beancount.yaml
Fix uninitialised value warning in hledger mode
Print warning if account in assertion has sub-accounts
Set commodity for commodity-less balance assertion
Expand path name of beancount_header config variable
Document handling of buckets
Document pre- and post-processing examples
Add Dockerfile to create Docker image

Thanks to Alexander Baier, Daniele Nicolodi, and GitHub users bratekarate, faaafo and mefromthepast for various bug reports and other input. Thanks to Dennis Lee for adding a Dockerfile and to Vinod Kurup for fixing a bug. Thanks to Stefano Zacchiroli for testing. You can get ledger2beancount from GitHub.

Firstly a disclaimer, I m not an expert on this and I m not trying to instruct anyone who is aiming to become an expert. The aim of this blog post is to help someone who has a single kernel issue they want to debug as part of doing something that s mostly not kernel coding. I welcome comments about the second step to kernel debugging for the benefit of people who need more than this (which might include me next week). Also suggestions for people who can t use a kvm/qemu debugger would be good. Below is a command to run qemu with GDB. It should be run from the Linux kernel source directory. You can add other qemu options for a blog device and virtual networking if necessary, but the bug I encountered gave an oops from the initrd so I didn t need to go further. The nokaslr is to avoid address space randomisation which deliberately makes debugging tasks harder (from a certain perspective debugging a kernel and compromising a kernel are fairly similar). Loading the bzImage is fine, gdb can map that to the different file it looks at later on.

qemu-system-x86_64 -kernel arch/x86/boot/bzImage -initrd ../initrd-$KERN_VER -curses -m 2000 -append "root=/dev/vda ro nokaslr" -gdb tcp::1200

The command to run GDB is gdb vmlinux , when at the GDB prompt you can run the command target remote localhost:1200 to connect to the GDB server port 1200. Note that there is nothing special about port 1200, it was given in an example I saw and is as good as any other port. It is important that you run GDB against the vmlinux file in the main directory not any of the several stripped and packaged files, GDB can t handle a bzImage file but that s OK, it ends up much the same in RAM. When the target remote command is processed the kernel will be suspended by the debugger, if you are looking for a bug early in the boot you may need to be quick about this. Using qemu-system-x86_64 instead of kvm slows things down and can help in that regard. The bug I was hunting happened 1.6 seconds after kernel load with KVM and 7.8 seconds after kernel load with qemu. I am not aware of all the implications of the kvm vs qemu decision on debugging. If your bug is a race condition then trying both would be a good strategy. After the target remote command you can debug the kernel just like any other program. If you put a breakpoint on print_modules() that will catch the operation of printing an Oops which can be handy.

Supported Data Sources It will extract information from a wide variety of sources, including:

Python package metadata (PKG-INFO, setup.py, setup.cfg, pyproject.toml)
package.json
composer.json
package.xml
Perl package metadata (dist.ini, META.json, META.yml, Makefile.PL)
Perl POD files
GNU configure files
R DESCRIPTION files
Rust Cargo.toml
maven pom.xml
metainfo.xml
.git/config
SECURITY.md
DOAP
Haskell cabal files
Ruby gemspec files
go.mod
README ,.rst,.md files
Debian packaging metadata (debian/watch, debian/control, debian/rules, debian/get-orig-source.sh, debian/copyright, debian/patches)

Supported Fields Fields that it currently provides include:

Homepage: homepage URL
Name: name of the upstream project
Contact: contact address of some sort of the upstream (e-mail, mailing list URL)
Repository: VCS URL
Repository-Browse: Web URL for viewing the VCS
Bug-Database: Bug database URL (for web viewing, generally)
Bug-Submit: URL to use to submit new bugs (either on the web or an e-mail address)
Screenshots: List of URLs with screenshots
Archive: Archive used - e.g. SourceForge
Security-Contact: e-mail or URL with instructions for reporting security issues
Documentation: Link to documentation on the web:
Wiki: Wiki URL
Summary: one-line description of the project
Description: longer description of the project
License: Single line license description (e.g. GPL 2.0 ) as declared in the metadata[1]
Copyright: List of copyright holders
Version: Current upstream version
Security-MD: URL to markdown file with security policy

All data fields have a certainty associated with them ( certain , confident , likely or possible ), which gets set depending on how the data was derived or where it was found. If multiple possible values were found for a specific field, then the value with the highest certainty is taken.

Interface The ontologist provides a high-level Python API as well as two command-line tools that can write output in two different formats:

guess-upstream-metadata writes DEP-12-like YAML output
autodoap writes DOAP files

For example, running guess-upstream-metadata on dulwich:

 % guess-upstream-metadata
 <string>:2: (INFO/1) Duplicate implicit target name: "contributing".
 Name: dulwich
 Repository: https://www.dulwich.io/code/
 X-Security-MD: https://github.com/dulwich/dulwich/tree/HEAD/SECURITY.md
 X-Version: 0.20.21
 Bug-Database: https://github.com/dulwich/dulwich/issues
 X-Summary: Python Git Library
 X-Description:  
   This is the Dulwich project.
   It aims to provide an interface to git repos (both local and remote) that
   doesn't call out to git directly but instead uses pure Python.
 X-License: Apache License, version 2 or GNU General Public License, version 2 or later.
 Bug-Submit: https://github.com/dulwich/dulwich/issues/new

Lintian-Brush lintian-brush can update DEP-12-style debian/upstream/metadata files that hold information about the upstream project that is packaged as well as the Homepage in the debian/control file based on information provided by the upstream ontologist. By default, it only imports data with the highest certainty - you can override this by specifying the uncertain command-line flag.

[1]	Obviously this won t be able to describe the full licensing situation for many projects. Projects like scancode-toolkit are more appropriate for that.

Following on from 2020 in Fiction: In 2020 I read a couple of collections of short fiction from some of my favourite authors. I started the year with Christopher Priest's Episodes. The stories within are collected from throughout his long career, and vary in style and tone. Priest wrote new little prologues and epilogues for each of the stories, explaining the context in which they were written. I really enjoyed this additional view into their construction.

By contrast, Adam Robert's Adam Robots presents the stories on their own terms. Each of the stories is written in a different mode: one as golden-age SF, another as a kind of Cyberpunk, for example, although they all blend or confound sub-genres to some degree. I'm not clever enough to have decoded all their secrets on a first read, and I would have appreciated some "Cliff's Notes on any deeper meaning or intent.

Ted Chiang's Exhalation was up to the fantastic standard of his earlier collection and had some extremely thoughtful explorations of philosophical ideas. All the stories are strong but one stuck in my mind the longest: Omphalos) With my daughter I finished three of Terry Pratchett's short story collections aimed at children: Dragon at Crumbling Castle; The Witch's Vacuum Cleaner and The Time-Travelling Caveman. If you are a Pratchett fan and you've overlooked these because they're aimed at children, take another look. The quality varies, but there are some true gems in these. Several stories take place in common settings, either the town of Blackbury, in Gritshire (and the adjacent Even Moor), or the Welsh border-town of Llandanffwnfafegettupagogo. The sad thing was knowing that once I'd finished them (and the fourth, Father Christmas's Fake Beard) that was it: there will be no more.

8/31 of the "books" I read in 2020 were issues of Interzone. Counting them as "books" for my annual reading goal has encouraged me to read full issues, whereas before I would likely have only read a couple of stories from each issue. Reading full issues has rekindled the enjoyment I got out of it when I first discovered the magazine at the turn of the Century. I am starting to recognise stories by authors that have written stories in other issues, as well as common themes from the current era weaving their way into the work (Trump, Brexit, etc.) No doubt the Pandemic will leave its mark on 2021's stories.

It all started with the big bang! We nearly lost 33 of 36 disks on a Proxmox/Ceph Cluster; this is the story of how we recovered them. At the end of 2020, we eventually had a long outstanding maintenance window for taking care of system upgrades at a customer. During this maintenance window, which involved reboots of server systems, the involved Ceph cluster unexpectedly went into a critical state. What was planned to be a few hours of checklist work in the early evening turned out to be an emergency case; let s call it a nightmare (not only because it included a big part of the night). Since we have learned a few things from our post mortem and RCA, it s worth sharing those with others. But first things first, let s step back and clarify what we had to deal with. The system and its upgrade One part of the upgrade included 3 Debian servers (we re calling them server1, server2 and server3 here), running on Proxmox v5 + Debian/stretch with 12 Ceph OSDs each (65.45TB in total), a so-called Proxmox Hyper-Converged Ceph Cluster.

First, we went for upgrading the Proxmox v5/stretch system to Proxmox v6/buster, before updating Ceph Luminous v12.2.13 to the latest v14.2 release, supported by Proxmox v6/buster. The Proxmox upgrade included updating corosync from v2 to v3. As part of this upgrade, we had to apply some configuration changes, like adjust ring0 + ring1 address settings and add a mon_host configuration to the Ceph configuration. During the first two servers reboots, we noticed configuration glitches. After fixing those, we went for a reboot of the third server as well. Then we noticed that several Ceph OSDs were unexpectedly down. The NTP service wasn t working as expected after the upgrade. The underlying issue is a race condition of ntp with systemd-timesyncd (see #889290). As a result, we had clock skew problems with Ceph, indicating that the Ceph monitors clocks aren t running in sync (which is essential for proper Ceph operation). We initially assumed that our Ceph OSD failure derived from this clock skew problem, so we took care of it. After yet another round of reboots, to ensure the systems are running all with identical and sane configurations and services, we noticed lots of failing OSDs. This time all but three OSDs (19, 21 and 22) were down:

% sudo ceph osd tree
ID CLASS WEIGHT   TYPE NAME      STATUS REWEIGHT PRI-AFF
-1       65.44138 root default
-2       21.81310     host server1
 0   hdd  1.08989         osd.0    down  1.00000 1.00000
 1   hdd  1.08989         osd.1    down  1.00000 1.00000
 2   hdd  1.63539         osd.2    down  1.00000 1.00000
 3   hdd  1.63539         osd.3    down  1.00000 1.00000
 4   hdd  1.63539         osd.4    down  1.00000 1.00000
 5   hdd  1.63539         osd.5    down  1.00000 1.00000
18   hdd  2.18279         osd.18   down  1.00000 1.00000
20   hdd  2.18179         osd.20   down  1.00000 1.00000
28   hdd  2.18179         osd.28   down  1.00000 1.00000
29   hdd  2.18179         osd.29   down  1.00000 1.00000
30   hdd  2.18179         osd.30   down  1.00000 1.00000
31   hdd  2.18179         osd.31   down  1.00000 1.00000
-4       21.81409     host server2
 6   hdd  1.08989         osd.6    down  1.00000 1.00000
 7   hdd  1.08989         osd.7    down  1.00000 1.00000
 8   hdd  1.63539         osd.8    down  1.00000 1.00000
 9   hdd  1.63539         osd.9    down  1.00000 1.00000
10   hdd  1.63539         osd.10   down  1.00000 1.00000
11   hdd  1.63539         osd.11   down  1.00000 1.00000
19   hdd  2.18179         osd.19     up  1.00000 1.00000
21   hdd  2.18279         osd.21     up  1.00000 1.00000
22   hdd  2.18279         osd.22     up  1.00000 1.00000
32   hdd  2.18179         osd.32   down  1.00000 1.00000
33   hdd  2.18179         osd.33   down  1.00000 1.00000
34   hdd  2.18179         osd.34   down  1.00000 1.00000
-3       21.81419     host server3
12   hdd  1.08989         osd.12   down  1.00000 1.00000
13   hdd  1.08989         osd.13   down  1.00000 1.00000
14   hdd  1.63539         osd.14   down  1.00000 1.00000
15   hdd  1.63539         osd.15   down  1.00000 1.00000
16   hdd  1.63539         osd.16   down  1.00000 1.00000
17   hdd  1.63539         osd.17   down  1.00000 1.00000
23   hdd  2.18190         osd.23   down  1.00000 1.00000
24   hdd  2.18279         osd.24   down  1.00000 1.00000
25   hdd  2.18279         osd.25   down  1.00000 1.00000
35   hdd  2.18179         osd.35   down  1.00000 1.00000
36   hdd  2.18179         osd.36   down  1.00000 1.00000
37   hdd  2.18179         osd.37   down  1.00000 1.00000

Our blood pressure increased slightly! Did we just lose all of our cluster? What happened, and how can we get all the other OSDs back? We stumbled upon this beauty in our logs:

kernel: [   73.697957] XFS (sdl1): SB stripe unit sanity check failed
kernel: [   73.698002] XFS (sdl1): Metadata corruption detected at xfs_sb_read_verify+0x10e/0x180 [xfs], xfs_sb block 0xffffffffffffffff
kernel: [   73.698799] XFS (sdl1): Unmount and run xfs_repair
kernel: [   73.699199] XFS (sdl1): First 128 bytes of corrupted metadata buffer:
kernel: [   73.699677] 00000000: 58 46 53 42 00 00 10 00 00 00 00 00 00 00 62 00  XFSB..........b.
kernel: [   73.700205] 00000010: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00  ................
kernel: [   73.700836] 00000020: 62 44 2b c0 e6 22 40 d7 84 3d e1 cc 65 88 e9 d8  bD+.."@..=..e...
kernel: [   73.701347] 00000030: 00 00 00 00 00 00 40 08 00 00 00 00 00 00 01 00  ......@.........
kernel: [   73.701770] 00000040: 00 00 00 00 00 00 01 01 00 00 00 00 00 00 01 02  ................
ceph-disk[4240]: mount: /var/lib/ceph/tmp/mnt.jw367Y: mount(2) system call failed: Structure needs cleaning.
ceph-disk[4240]: ceph-disk: Mounting filesystem failed: Command '['/bin/mount', '-t', u'xfs', '-o', 'noatime,inode64', '--', '/dev/disk/by-parttypeuuid/4fbd7e29-9d25-41b8-afd0-062c0ceff05d.cdda39ed-5
ceph/tmp/mnt.jw367Y']' returned non-zero exit status 32
kernel: [   73.702162] 00000050: 00 00 00 01 00 00 18 80 00 00 00 04 00 00 00 00  ................
kernel: [   73.702550] 00000060: 00 00 06 48 bd a5 10 00 08 00 00 02 00 00 00 00  ...H............
kernel: [   73.702975] 00000070: 00 00 00 00 00 00 00 00 0c 0c 0b 01 0d 00 00 19  ................
kernel: [   73.703373] XFS (sdl1): SB validate failed with error -117.

The same issue was present for the other failing OSDs. We hoped, that the data itself was still there, and only the mounting of the XFS partitions failed. The Ceph cluster was initially installed in 2017 with Ceph jewel/10.2 with the OSDs on filestore (nowadays being a legacy approach to storing objects in Ceph). However, we migrated the disks to bluestore since then (with ceph-disk and not yet via ceph-volume what s being used nowadays). Using ceph-disk introduces these 100MB XFS partitions containing basic metadata for the OSD. Given that we had three working OSDs left, we decided to investigate how to rebuild the failing ones. Some folks on #ceph (thanks T1, ormandj + peetaur!) were kind enough to share how working XFS partitions looked like for them. After creating a backup (via dd), we tried to re-create such an XFS partition on server1. We noticed that even mounting a freshly created XFS partition failed:

synpromika@server1 ~ % sudo mkfs.xfs -f -i size=2048 -m uuid="4568c300-ad83-4288-963e-badcd99bf54f" /dev/sdc1
meta-data=/dev/sdc1              isize=2048   agcount=4, agsize=6272 blks
         =                       sectsz=4096  attr=2, projid32bit=1
         =                       crc=1        finobt=1, sparse=1, rmapbt=0
         =                       reflink=0
data     =                       bsize=4096   blocks=25088, imaxpct=25
         =                       sunit=128    swidth=64 blks
naming   =version 2              bsize=4096   ascii-ci=0, ftype=1
log      =internal log           bsize=4096   blocks=1608, version=2
         =                       sectsz=4096  sunit=1 blks, lazy-count=1
realtime =none                   extsz=4096   blocks=0, rtextents=0
synpromika@server1 ~ % sudo mount /dev/sdc1 /mnt/ceph-recovery
SB stripe unit sanity check failed
Metadata corruption detected at 0x433840, xfs_sb block 0x0/0x1000
libxfs_writebufr: write verifer failed on xfs_sb bno 0x0/0x1000
cache_node_purge: refcount was 1, not zero (node=0x1d3c400)
SB stripe unit sanity check failed
Metadata corruption detected at 0x433840, xfs_sb block 0x18800/0x1000
libxfs_writebufr: write verifer failed on xfs_sb bno 0x18800/0x1000
SB stripe unit sanity check failed
Metadata corruption detected at 0x433840, xfs_sb block 0x0/0x1000
libxfs_writebufr: write verifer failed on xfs_sb bno 0x0/0x1000
SB stripe unit sanity check failed
Metadata corruption detected at 0x433840, xfs_sb block 0x24c00/0x1000
libxfs_writebufr: write verifer failed on xfs_sb bno 0x24c00/0x1000
SB stripe unit sanity check failed
Metadata corruption detected at 0x433840, xfs_sb block 0xc400/0x1000
libxfs_writebufr: write verifer failed on xfs_sb bno 0xc400/0x1000
releasing dirty buffer (bulk) to free list!releasing dirty buffer (bulk) to free list!releasing dirty buffer (bulk) to free list!releasing dirty buffer (bulk) to free list!found dirty buffer (bulk) on free list!bad magic number
bad magic number
Metadata corruption detected at 0x433840, xfs_sb block 0x0/0x1000
libxfs_writebufr: write verifer failed on xfs_sb bno 0x0/0x1000
releasing dirty buffer (bulk) to free list!mount: /mnt/ceph-recovery: wrong fs type, bad option, bad superblock on /dev/sdc1, missing codepage or helper program, or other error.

Ouch. This very much looked related to the actual issue we re seeing. So we tried to execute mkfs.xfs with a bunch of different sunit/swidth settings. Using -d sunit=512 -d swidth=512 at least worked then, so we decided to force its usage in the creation of our OSD XFS partition. This brought us a working XFS partition. Please note, sunit must not be larger than swidth (more on that later!). Then we reconstructed how to restore all the metadata for the OSD (

activate.monmap, active, block_uuid, bluefs, ceph_fsid, fsid, keyring, kv_backend, magic, mkfs_done, ready, require_osd_release, systemd, type, whoami

). To identify the UUID, we can read the data from ceph --format json osd dump , like this for all our OSDs (Zsh syntax ftw!):

synpromika@server1 ~ % for f in  0..37  ; printf "osd-$f: %s\n" "$(sudo ceph --format json osd dump   jq -r ".osds[]   select(.osd==$f)   .uuid")"
osd-0: 4568c300-ad83-4288-963e-badcd99bf54f
osd-1: e573a17a-ccde-4719-bdf8-eef66903ca4f
osd-2: 0e1b2626-f248-4e7d-9950-f1a46644754e
osd-3: 1ac6a0a2-20ee-4ed8-9f76-d24e900c800c
[...]

Identifying the corresponding raw device for each OSD UUID is possible via:

synpromika@server1 ~ % UUID="4568c300-ad83-4288-963e-badcd99bf54f"
synpromika@server1 ~ % readlink -f /dev/disk/by-partuuid/"$ UUID "
/dev/sdc1

The OSD s key ID can be retrieved via:

synpromika@server1 ~ % OSD_ID=0
synpromika@server1 ~ % sudo ceph auth get osd."$ OSD_ID " -f json 2>/dev/null   jq -r '.[]   .key'
AQCKFpZdm0We[...]

Now we also need to identify the underlying block device:

synpromika@server1 ~ % OSD_ID=0
synpromika@server1 ~ % sudo ceph osd metadata osd."$ OSD_ID " -f json   jq -r '.bluestore_bdev_partition_path'    
/dev/sdc2

With all of this, we reconstructed the keyring, fsid, whoami, block + block_uuid files. All the other files inside the XFS metadata partition are identical on each OSD. So after placing and adjusting the corresponding metadata on the XFS partition for Ceph usage, we got a working OSD hurray! Since we had to fix yet another 32 OSDs, we decided to automate this XFS partitioning and metadata recovery procedure. We had a network share available on /srv/backup for storing backups of existing partition data. On each server, we tested the procedure with one single OSD before iterating over the list of remaining failing OSDs. We started with a shell script on server1, then adjusted the script for server2 and server3. This is the script, as we executed it on the 3rd server. Thanks to this, we managed to get the Ceph cluster up and running again. We didn t want to continue with the Ceph upgrade itself during the night though, as we wanted to know exactly what was going on and why the system behaved like that. Time for RCA! Root Cause Analysis So all but three OSDs on server2 failed, and the problem seems to be related to XFS. Therefore, our starting point for the RCA was, to identify what was different on server2, as compared to server1 + server3. My initial assumption was that this was related to some firmware issues with the involved controller (and as it turned out later, I was right!). The disks were attached as JBOD devices to a ServeRAID M5210 controller (with a stripe size of 512). Firmware state:

synpromika@server1 ~ % sudo storcli64 /c0 show all   grep '^Firmware'
Firmware Package Build = 24.16.0-0092
Firmware Version = 4.660.00-8156
synpromika@server2 ~ % sudo storcli64 /c0 show all   grep '^Firmware'
Firmware Package Build = 24.21.0-0112
Firmware Version = 4.680.00-8489
synpromika@server3 ~ % sudo storcli64 /c0 show all   grep '^Firmware'
Firmware Package Build = 24.16.0-0092
Firmware Version = 4.660.00-8156

This looked very promising, as server2 indeed runs with a different firmware version on the controller. But how so? Well, the motherboard of server2 got replaced by a Lenovo/IBM technician in January 2020, as we had a failing memory slot during a memory upgrade. As part of this procedure, the Lenovo/IBM technician installed the latest firmware versions. According to our documentation, some OSDs were rebuilt (due to the filestore->bluestore migration) in March and April 2020. It turned out that precisely those OSDs were the ones that survived the upgrade. So the surviving drives were created with a different firmware version running on the involved controller. All the other OSDs were created with an older controller firmware. But what difference does this make? Now let s check firmware changelogs. For the 24.21.0-0097 release we found this:

- Cannot create or mount xfs filesystem using xfsprogs 4.19.x kernel 4.20(SCGCQ02027889)
- xfs_info command run on an XFS file system created on a VD of strip size 1M shows sunit and swidth as 0(SCGCQ02056038)

Our XFS problem certainly was related to the controller s firmware. We also recalled that our monitoring system reported different sunit settings for the OSDs that were rebuilt in March and April. For example, OSD 21 was recreated and got different sunit settings:

WARN  server2.example.org  Mount options of /var/lib/ceph/osd/ceph-21      WARN - Missing: sunit=1024, Exceeding: sunit=512

We compared the new OSD 21 with an existing one (OSD 25 on server3):

synpromika@server2 ~ % systemctl show var-lib-ceph-osd-ceph\\x2d21.mount   grep sunit
Options=rw,noatime,attr2,inode64,sunit=512,swidth=512,noquota
synpromika@server3 ~ % systemctl show var-lib-ceph-osd-ceph\\x2d25.mount   grep sunit
Options=rw,noatime,attr2,inode64,sunit=1024,swidth=512,noquota

Thanks to our documentation, we could compare execution logs of their creation:

% diff -u ceph-disk-osd-25.log ceph-disk-osd-21.log
-synpromika@server2 ~ % sudo ceph-disk -v prepare --bluestore /dev/sdj --osd-id 25
+synpromika@server3 ~ % sudo ceph-disk -v prepare --bluestore /dev/sdi --osd-id 21
[...]
-command_check_call: Running command: /sbin/mkfs -t xfs -f -i size=2048 -- /dev/sdj1
-meta-data=/dev/sdj1              isize=2048   agcount=4, agsize=6272 blks
[...]
+command_check_call: Running command: /sbin/mkfs -t xfs -f -i size=2048 -- /dev/sdi1
+meta-data=/dev/sdi1              isize=2048   agcount=4, agsize=6336 blks
          =                       sectsz=4096  attr=2, projid32bit=1
          =                       crc=1        finobt=1, sparse=0, rmapbt=0, reflink=0
-data     =                       bsize=4096   blocks=25088, imaxpct=25
-         =                       sunit=128    swidth=64 blks
+data     =                       bsize=4096   blocks=25344, imaxpct=25
+         =                       sunit=64     swidth=64 blks
 naming   =version 2              bsize=4096   ascii-ci=0 ftype=1
 log      =internal log           bsize=4096   blocks=1608, version=2
          =                       sectsz=4096  sunit=1 blks, lazy-count=1
 realtime =none                   extsz=4096   blocks=0, rtextents=0
[...]

So back then, we even tried to track this down but couldn t make sense of it yet. But now this sounds very much like it is related to the problem we saw with this Ceph/XFS failure. We follow Occam s razor, assuming the simplest explanation is usually the right one, so let s check the disk properties and see what differs:

synpromika@server1 ~ % sudo blockdev --getsz --getsize64 --getss --getpbsz --getiomin --getioopt /dev/sdk
4685545472
2398999281664
512
4096
524288
262144
synpromika@server2 ~ % sudo blockdev --getsz --getsize64 --getss --getpbsz --getiomin --getioopt /dev/sdk
4685545472
2398999281664
512
4096
262144
262144

See the difference between server1 and server2 for identical disks? The getiomin option now reports something different for them:

synpromika@server1 ~ % sudo blockdev --getiomin /dev/sdk            
524288
synpromika@server1 ~ % cat /sys/block/sdk/queue/minimum_io_size
524288
synpromika@server2 ~ % sudo blockdev --getiomin /dev/sdk 
262144
synpromika@server2 ~ % cat /sys/block/sdk/queue/minimum_io_size
262144

It doesn t make sense that the minimum I/O size (iomin, AKA BLKIOMIN) is bigger than the optimal I/O size (ioopt, AKA BLKIOOPT). This leads us to Bug 202127 cannot mount or create xfs on a 597T device, which matches our findings here. But why did this XFS partition work in the past and fails now with the newer kernel version? The XFS behaviour change Now given that we have backups of all the XFS partition, we wanted to track down, a) when this XFS behaviour was introduced, and b) whether, and if so how it would be possible to reuse the XFS partition without having to rebuild it from scratch (e.g. if you would have no working Ceph OSD or backups left). Let s look at such a failing XFS partition with the Grml live system:

root@grml ~ # grml-version
grml64-full 2020.06 Release Codename Ausgehfuahangl [2020-06-24]
root@grml ~ # uname -a
Linux grml 5.6.0-2-amd64 #1 SMP Debian 5.6.14-2 (2020-06-09) x86_64 GNU/Linux
root@grml ~ # grml-hostname grml-2020-06
Setting hostname to grml-2020-06: done
root@grml ~ # exec zsh
root@grml-2020-06 ~ # dpkg -l xfsprogs util-linux
Desired=Unknown/Install/Remove/Purge/Hold
  Status=Not/Inst/Conf-files/Unpacked/halF-conf/Half-inst/trig-aWait/Trig-pend
 / Err?=(none)/Reinst-required (Status,Err: uppercase=bad)
 / Name           Version      Architecture Description
+++-==============-============-============-=========================================
ii  util-linux     2.35.2-4     amd64        miscellaneous system utilities
ii  xfsprogs       5.6.0-1+b2   amd64        Utilities for managing the XFS filesystem

There it s failing, no matter which mount option we try:

root@grml-2020-06 ~ # mount ./sdd1.dd /mnt
mount: /mnt: mount(2) system call failed: Structure needs cleaning.
root@grml-2020-06 ~ # dmesg   tail -30
[...]
[   64.788640] XFS (loop1): SB stripe unit sanity check failed
[   64.788671] XFS (loop1): Metadata corruption detected at xfs_sb_read_verify+0x102/0x170 [xfs], xfs_sb block 0xffffffffffffffff
[   64.788671] XFS (loop1): Unmount and run xfs_repair
[   64.788672] XFS (loop1): First 128 bytes of corrupted metadata buffer:
[   64.788673] 00000000: 58 46 53 42 00 00 10 00 00 00 00 00 00 00 62 00  XFSB..........b.
[   64.788674] 00000010: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00  ................
[   64.788675] 00000020: 32 b6 dc 35 53 b7 44 96 9d 63 30 ab b3 2b 68 36  2..5S.D..c0..+h6
[   64.788675] 00000030: 00 00 00 00 00 00 40 08 00 00 00 00 00 00 01 00  ......@.........
[   64.788675] 00000040: 00 00 00 00 00 00 01 01 00 00 00 00 00 00 01 02  ................
[   64.788676] 00000050: 00 00 00 01 00 00 18 80 00 00 00 04 00 00 00 00  ................
[   64.788677] 00000060: 00 00 06 48 bd a5 10 00 08 00 00 02 00 00 00 00  ...H............
[   64.788677] 00000070: 00 00 00 00 00 00 00 00 0c 0c 0b 01 0d 00 00 19  ................
[   64.788679] XFS (loop1): SB validate failed with error -117.
root@grml-2020-06 ~ # mount -t xfs -o rw,relatime,attr2,inode64,sunit=1024,swidth=512,noquota ./sdd1.dd /mnt/
mount: /mnt: wrong fs type, bad option, bad superblock on /dev/loop1, missing codepage or helper program, or other error.
32 root@grml-2020-06 ~ # dmesg   tail -1
[   66.342976] XFS (loop1): stripe width (512) must be a multiple of the stripe unit (1024)
root@grml-2020-06 ~ # mount -t xfs -o rw,relatime,attr2,inode64,sunit=512,swidth=512,noquota ./sdd1.dd /mnt/
mount: /mnt: mount(2) system call failed: Structure needs cleaning.
32 root@grml-2020-06 ~ # dmesg   tail -14
[   66.342976] XFS (loop1): stripe width (512) must be a multiple of the stripe unit (1024)
[   80.751277] XFS (loop1): SB stripe unit sanity check failed
[   80.751323] XFS (loop1): Metadata corruption detected at xfs_sb_read_verify+0x102/0x170 [xfs], xfs_sb block 0xffffffffffffffff 
[   80.751324] XFS (loop1): Unmount and run xfs_repair
[   80.751325] XFS (loop1): First 128 bytes of corrupted metadata buffer:
[   80.751327] 00000000: 58 46 53 42 00 00 10 00 00 00 00 00 00 00 62 00  XFSB..........b.
[   80.751328] 00000010: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00  ................
[   80.751330] 00000020: 32 b6 dc 35 53 b7 44 96 9d 63 30 ab b3 2b 68 36  2..5S.D..c0..+h6
[   80.751331] 00000030: 00 00 00 00 00 00 40 08 00 00 00 00 00 00 01 00  ......@.........
[   80.751331] 00000040: 00 00 00 00 00 00 01 01 00 00 00 00 00 00 01 02  ................
[   80.751332] 00000050: 00 00 00 01 00 00 18 80 00 00 00 04 00 00 00 00  ................
[   80.751333] 00000060: 00 00 06 48 bd a5 10 00 08 00 00 02 00 00 00 00  ...H............
[   80.751334] 00000070: 00 00 00 00 00 00 00 00 0c 0c 0b 01 0d 00 00 19  ................
[   80.751338] XFS (loop1): SB validate failed with error -117.

Also xfs_repair doesn t help either:

root@grml-2020-06 ~ # xfs_info ./sdd1.dd
meta-data=./sdd1.dd              isize=2048   agcount=4, agsize=6272 blks
         =                       sectsz=4096  attr=2, projid32bit=1
         =                       crc=1        finobt=1, sparse=0, rmapbt=0
         =                       reflink=0
data     =                       bsize=4096   blocks=25088, imaxpct=25
         =                       sunit=128    swidth=64 blks
naming   =version 2              bsize=4096   ascii-ci=0, ftype=1
log      =internal log           bsize=4096   blocks=1608, version=2
         =                       sectsz=4096  sunit=1 blks, lazy-count=1
realtime =none                   extsz=4096   blocks=0, rtextents=0
root@grml-2020-06 ~ # xfs_repair ./sdd1.dd
Phase 1 - find and verify superblock...
bad primary superblock - bad stripe width in superblock !!!
attempting to find secondary superblock...
..............................................................................................Sorry, could not find valid secondary superblock
Exiting now.

With the SB stripe unit sanity check failed message, we could easily track this down to the following commit fa4ca9c:

% git show fa4ca9c5574605d1e48b7e617705230a0640b6da   cat
commit fa4ca9c5574605d1e48b7e617705230a0640b6da
Author: Dave Chinner <dchinner@redhat.com>
Date:   Tue Jun 5 10:06:16 2018 -0700
    
    xfs: catch bad stripe alignment configurations
    
    When stripe alignments are invalid, data alignment algorithms in the
    allocator may not work correctly. Ensure we catch superblocks with
    invalid stripe alignment setups at mount time. These data alignment
    mismatches are now detected at mount time like this:
    
    XFS (loop0): SB stripe unit sanity check failed
    XFS (loop0): Metadata corruption detected at xfs_sb_read_verify+0xab/0x110, xfs_sb block 0xffffffffffffffff
    XFS (loop0): Unmount and run xfs_repair
    XFS (loop0): First 128 bytes of corrupted metadata buffer:
    0000000091c2de02: 58 46 53 42 00 00 10 00 00 00 00 00 00 00 10 00  XFSB............
    0000000023bff869: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00  ................
    00000000cdd8c893: 17 32 37 15 ff ca 46 3d 9a 17 d3 33 04 b5 f1 a2  .27...F=...3....
    000000009fd2844f: 00 00 00 00 00 00 00 04 00 00 00 00 00 00 06 d0  ................
    0000000088e9b0bb: 00 00 00 00 00 00 06 d1 00 00 00 00 00 00 06 d2  ................
    00000000ff233a20: 00 00 00 01 00 00 10 00 00 00 00 01 00 00 00 00  ................
    000000009db0ac8b: 00 00 03 60 e1 34 02 00 08 00 00 02 00 00 00 00  ... .4..........
    00000000f7022460: 00 00 00 00 00 00 00 00 0c 09 0b 01 0c 00 00 19  ................
    XFS (loop0): SB validate failed with error -117.
    
    And the mount fails.
    
    Signed-off-by: Dave Chinner <dchinner@redhat.com>
    Reviewed-by: Carlos Maiolino <cmaiolino@redhat.com>
    Reviewed-by: Darrick J. Wong <darrick.wong@oracle.com>
    Signed-off-by: Darrick J. Wong <darrick.wong@oracle.com>
diff --git fs/xfs/libxfs/xfs_sb.c fs/xfs/libxfs/xfs_sb.c
index b5dca3c8c84d..c06b6fc92966 100644
--- fs/xfs/libxfs/xfs_sb.c
+++ fs/xfs/libxfs/xfs_sb.c
@@ -278,6 +278,22 @@ xfs_mount_validate_sb(
                return -EFSCORRUPTED;
         
        
+       if (sbp->sb_unit)  
+               if (!xfs_sb_version_hasdalign(sbp)  
+                   sbp->sb_unit > sbp->sb_width  
+                   (sbp->sb_width % sbp->sb_unit) != 0)  
+                       xfs_notice(mp, "SB stripe unit sanity check failed");
+                       return -EFSCORRUPTED;
+                 
+         else if (xfs_sb_version_hasdalign(sbp))   
+               xfs_notice(mp, "SB stripe alignment sanity check failed");
+               return -EFSCORRUPTED;
+         else if (sbp->sb_width)  
+               xfs_notice(mp, "SB stripe width sanity check failed");
+               return -EFSCORRUPTED;
+        
+
+       
        if (xfs_sb_version_hascrc(&mp->m_sb) &&
            sbp->sb_blocksize < XFS_MIN_CRC_BLOCKSIZE)  
                xfs_notice(mp, "v5 SB sanity check failed");

This change is included in kernel versions 4.18-rc1 and newer:

% git describe --contains fa4ca9c5574605d1e48
v4.18-rc1~37^2~14

Now let s try with an older kernel version (4.9.0), using old Grml 2017.05 release:

root@grml ~ # grml-version
grml64-small 2017.05 Release Codename Freedatensuppe [2017-05-31]
root@grml ~ # uname -a
Linux grml 4.9.0-1-grml-amd64 #1 SMP Debian 4.9.29-1+grml.1 (2017-05-24) x86_64 GNU/Linux
root@grml ~ # lsb_release -a
No LSB modules are available.
Distributor ID: Debian
Description:    Debian GNU/Linux 9.0 (stretch)
Release:        9.0
Codename:       stretch
root@grml ~ # grml-hostname grml-2017-05
Setting hostname to grml-2017-05: done
root@grml ~ # exec zsh
root@grml-2017-05 ~ #
root@grml-2017-05 ~ # xfs_info ./sdd1.dd
xfs_info: ./sdd1.dd is not a mounted XFS filesystem
1 root@grml-2017-05 ~ # xfs_repair ./sdd1.dd
Phase 1 - find and verify superblock...
bad primary superblock - bad stripe width in superblock !!!
attempting to find secondary superblock...
..............................................................................................Sorry, could not find valid secondary superblock
Exiting now.
1 root@grml-2017-05 ~ # mount ./sdd1.dd /mnt
root@grml-2017-05 ~ # mount -t xfs
/root/sdd1.dd on /mnt type xfs (rw,relatime,attr2,inode64,sunit=1024,swidth=512,noquota)
root@grml-2017-05 ~ # ls /mnt
activate.monmap  active  block  block_uuid  bluefs  ceph_fsid  fsid  keyring  kv_backend  magic  mkfs_done  ready  require_osd_release  systemd  type  whoami
root@grml-2017-05 ~ # xfs_info /mnt
meta-data=/dev/loop1             isize=2048   agcount=4, agsize=6272 blks
         =                       sectsz=4096  attr=2, projid32bit=1
         =                       crc=1        finobt=1 spinodes=0 rmapbt=0
         =                       reflink=0
data     =                       bsize=4096   blocks=25088, imaxpct=25
         =                       sunit=128    swidth=64 blks
naming   =version 2              bsize=4096   ascii-ci=0 ftype=1
log      =internal               bsize=4096   blocks=1608, version=2
         =                       sectsz=4096  sunit=1 blks, lazy-count=1
realtime =none                   extsz=4096   blocks=0, rtextents=0

Mounting there indeed works! Now, if we mount the filesystem with new and proper sunit/swidth settings using the older kernel, it should rewrite them on disk:

root@grml-2017-05 ~ # mount -t xfs -o sunit=512,swidth=512 ./sdd1.dd /mnt/
root@grml-2017-05 ~ # umount /mnt/

And indeed, mounting this rewritten filesystem then also works with newer kernels:

root@grml-2020-06 ~ # mount ./sdd1.rewritten /mnt/
root@grml-2020-06 ~ # xfs_info /root/sdd1.rewritten
meta-data=/dev/loop1             isize=2048   agcount=4, agsize=6272 blks
         =                       sectsz=4096  attr=2, projid32bit=1
         =                       crc=1        finobt=1, sparse=0, rmapbt=0
         =                       reflink=0
data     =                       bsize=4096   blocks=25088, imaxpct=25
         =                       sunit=64    swidth=64 blks
naming   =version 2              bsize=4096   ascii-ci=0, ftype=1
log      =internal log           bsize=4096   blocks=1608, version=2
         =                       sectsz=4096  sunit=1 blks, lazy-count=1
realtime =none                   extsz=4096   blocks=0, rtextents=0
root@grml-2020-06 ~ # mount -t xfs                
/root/sdd1.rewritten on /mnt type xfs (rw,relatime,attr2,inode64,logbufs=8,logbsize=32k,sunit=512,swidth=512,noquota)

FTR: The sunit=512,swidth=512 from the xfs mount option is identical to xfs_info s output sunit=64,swidth=64 (because mount.xfs s sunit value is given in 512-byte block units, see man 5 xfs, and the xfs_info output reported here is in blocks with a block size (bsize) of 4096, so sunit = 512*512 := 64*4096 ). mkfs uses minimum and optimal sizes for stripe unit and stripe width; you can check this e.g. via (note that server2 with fixed firmware version reports proper values, whereas server3 with broken controller firmware reports non-sense):

synpromika@server2 ~ % for i in /sys/block/sd*/queue/ ; do printf "%s: %s %s\n" "$i" "$(cat "$i"/minimum_io_size)" "$(cat "$i"/optimal_io_size)" ; done
[...]
/sys/block/sdc/queue/: 262144 262144
/sys/block/sdd/queue/: 262144 262144
/sys/block/sde/queue/: 262144 262144
/sys/block/sdf/queue/: 262144 262144
/sys/block/sdg/queue/: 262144 262144
/sys/block/sdh/queue/: 262144 262144
/sys/block/sdi/queue/: 262144 262144
/sys/block/sdj/queue/: 262144 262144
/sys/block/sdk/queue/: 262144 262144
/sys/block/sdl/queue/: 262144 262144
/sys/block/sdm/queue/: 262144 262144
/sys/block/sdn/queue/: 262144 262144
[...]
synpromika@server3 ~ % for i in /sys/block/sd*/queue/ ; do printf "%s: %s %s\n" "$i" "$(cat "$i"/minimum_io_size)" "$(cat "$i"/optimal_io_size)" ; done
[...]
/sys/block/sdc/queue/: 524288 262144
/sys/block/sdd/queue/: 524288 262144
/sys/block/sde/queue/: 524288 262144
/sys/block/sdf/queue/: 524288 262144
/sys/block/sdg/queue/: 524288 262144
/sys/block/sdh/queue/: 524288 262144
/sys/block/sdi/queue/: 524288 262144
/sys/block/sdj/queue/: 524288 262144
/sys/block/sdk/queue/: 524288 262144
/sys/block/sdl/queue/: 524288 262144
/sys/block/sdm/queue/: 524288 262144
/sys/block/sdn/queue/: 524288 262144
[...]

This is the underlying reason why the initially created XFS partitions were created with incorrect sunit/swidth settings. The broken firmware of server1 and server3 was the cause of the incorrect settings they were ignored by old(er) xfs/kernel versions, but treated as an error by new ones. Make sure to also read the XFS FAQ regarding How to calculate the correct sunit,swidth values for optimal performance . We also stumbled upon two interesting reads in RedHat s knowledge base: 5075561 + 2150101 (requires an active subscription, though) and #1835947. Am I affected? How to work around it? To check whether your XFS mount points are affected by this issue, the following command line should be useful:

awk '$3 == "xfs" print $2 ' /proc/self/mounts   while read mount ; do echo -n "$mount " ; xfs_info $mount   awk '$0 ~ "swidth" gsub(/.*=/,"",$2); gsub(/.*=/,"",$3); print $2,$3 '   awk '  if ($1 > $2) print "impacted"; else print "OK" ' ; done

If you run into the above situation, the only known solution to get your original XFS partition working again, is to boot into an older kernel version again (4.17 or older), mount the XFS partition with correct sunit/swidth settings and then boot back into your new system (kernel version wise). Lessons learned

document everything and ensure to have all relevant information available (including actual times of changes, used kernel/package/firmware/ versions. The thorough documentation was our most significant asset in this case, because we had all the data and information we needed during the emergency handling as well as for the post mortem/RCA)
if something changes unexpectedly, dig deeper
know who to ask, a network of experts pays off
including timestamps in your shell makes reconstruction easier (the more people and documentation involved, the harder it gets to wade through it)
keep an eye on changelogs/release notes
apply regular updates and don t forget invisible layers (e.g. BIOS, controller/disk firmware, IPMI/OOB (ILO/RAC/IMM/ ) firmware)
apply regular reboots, to avoid a possible delta becoming bigger (which makes debugging harder)

Thanks: Darshaka Pathirana, Chris Hofstaedtler and Michael Hanscho. Looking for help with your IT infrastructure? Let us know!

One of my goals for Consfigurator is to make it capable of installing Debian to my laptop, so that I can stop booting to GRML and manually partitioning and debootstrapping a basic system, only to then turn to configuration management to set everything else up. My configuration management should be able to handle the partitioning and debootstrapping, too. The first stage was to make Consfigurator capable of debootstrapping a basic system, chrooting into it, and applying other arbitrary configuration, such as installing packages. That s been in place for some weeks now. It s sophisticated enough to avoid starting up newly installed services, but I still need to add some bind mounting. Another significant piece is teaching Consfigurator how to partition block devices. That s quite tricky to do in a sufficiently general way I want to cleanly support various combinations of LUKS, LVM and regular partitions, including populating /etc/crypttab and /etc/fstab. I have some ideas about how to do it, but it ll probably take a few tries to get the abstractions right. Let s imagine that code is all in place, such that Consfigurator can be pointed at a block device and it will install a bootable Debian system to it. Then to install Debian to my laptop I d just need to take my laptop s disk drive out and plug it into another system, and run Consfigurator on that system, as root, pointed at the block device representing my laptop s disk drive. For virtual machines, it would be easy to write code which loop-mounts an empty disk image, and then Consfigurator could be pointed at the loop-mounted block device, thereby making the disk image file bootable. This is adequate for virtual machines, or small single-board computers with tiny storage devices (not that I actually use any of those, but I want Consfigurator to be able to make disk images for them!). But it s not much good for my laptop. I casually referred to taking out my laptop s disk drive and connecting it to another computer, but this would void my laptop s warranty. And Consfigurator would not be able to update my laptop s NVRAM, as is needed on UEFI systems. What s wanted here is a live system which can run Consfigurator directly on the laptop, pointed at the block device representing its physical disk drive. Ideally this live system comes with a chroot with the root filesystem for the new Debian install already built, so that network access is not required, and all Consfigurator has to do is partition the drive and copy in the contents of the chroot. The live system could be set up to automatically start doing that upon boot, but another option is to just make Consfigurator itself available to be used interactively. The user boots the live system, starts up Emacs, starts up Lisp, and executes a Consfigurator deployment, supplying the block device representing the laptop s disk drive as an argument to the deployment. Consfigurator goes off and partitions that drive, copies in the contents of the chroot, and executes grub-install to make the laptop bootable. This is also much easier to debug than a live system which tries to start partitioning upon boot. It would look something like this:

    ;; melete.silentflame.com is a Consfigurator host object representing the
    ;; laptop, including information about the partitions it should have
    (deploy-these :local ...
      (chroot:partitioned-and-installed
        melete.silentflame.com "/srv/chroot/melete" "/dev/nvme0n1"))

Now, building live systems is a fair bit more involved than installing Debian to a disk drive and making it bootable, it turns out. While I want Consfigurator to be able to completely replace the Debian Installer, I decided that it is not worth trying to reimplement the relevant parts of the Debian Live tool suite, because I do not need to make arbitrary customisations to any live systems. I just need to have some packages installed and some files in place. Nevertheless, it is worth teaching Consfigurator how to invoke Debian Live, so that the customisation of the chroot which isn t just a matter of passing options to lb_config(1) can be done with Consfigurator. This is what I ve ended up with in Consfigurator s source code:

(defpropspec image-built :lisp (config dir properties)
  "Build an image under DIR using live-build(7), where the resulting live
system has PROPERTIES, which should contain, at a minimum, a property from
CONSFIGURATOR.PROPERTY.OS setting the Debian suite and architecture.  CONFIG
is a list of arguments to pass to lb_config(1), not including the '-a' and
'-d' options, which Consfigurator will supply based on PROPERTIES.
This property runs the lb_config(1), lb_bootstrap(1), lb_chroot(1) and
lb_binary(1) commands to build or rebuild the image.  Rebuilding occurs only
when changes to CONFIG or PROPERTIES mean that the image is potentially
out-of-date; e.g. if you just add some new items to PROPERTIES then in most
cases only lb_chroot(1) and lb_binary(1) will be re-run.
Note that lb_chroot(1) and lb_binary(1) both run after applying PROPERTIES,
and might undo some of their effects.  For example, to configure
/etc/apt/sources.list, you will need to use CONFIG not PROPERTIES."
  (:desc (declare (ignore config properties))
         #?"Debian Live image built in $ dir ")
  (let* (...)
    ;; ...
     (eseqprops
      ;; ...
      (on-change
          (eseqprops
           (on-change
               (file:has-content ,auto/config ,(auto/config config) :mode #o755)
             (file:does-not-exist ,@clean)
             (%lbconfig ,dir)
             (%lbbootstrap t ,dir))
           (%lbbootstrap nil ,dir)
           (deploys ((:chroot :into ,chroot)) ,host))
        (%lbchroot ,dir)
        (%lbbinary ,dir)))))

Here, %lbconfig is a property running lb_config(1), %lbbootstrap one which runs lb_bootstrap(1), etc. Those properties all just change directory to the right place and run the command, essentially, with a little extra code to handle failed debootstraps and the like. The ON-CHANGE and ESEQPROPS combinators work together to sequence the interaction of the Debian Live suite and Consfigurator.

In the innermost ON-CHANGE expression: create the file auto/config and populate it with the call to lb_config(1) that we need to make, as described in the Debian Live manual, chapter 6.
- If doing so resulted in a change to the auto/config file e.g. the user added some more options ensure that lb_config(1) and lb_bootstrap(1) both get rerun.
Now in the inner ESEQPROPS expression, use DEPLOYS to configure the chroot, essentially by forking into the chroot and recursively reinvoking Consfigurator.
Finally, if any of the above resulted in a change being made, call lb_chroot(1) and lb_binary(1).

This way, we only rebuild the chroot if the configuration changed, and we only rebuild the image if the chroot changed. Now over in my personal consfig:

(try-register-data-source
 :git-snapshot :name "consfig" :repo #P"src/cl/consfig/" ...)
(defproplist hybrid-live-iso-built :lisp ()
  "Build a Debian Live system in /srv/live/spw.
Typically this property is not applied in a DEFHOST form, but rather run as
needed at the REPL.  The reason for this is that otherwise the whole image will
get rebuilt each time a commit is made to my dotfiles repo or to my consfig."
  (:desc "Sean's Debian Live system image built")
  (live-build:image-built.
      '("--archive-areas" "main contrib non-free" ...)
      "/srv/live/spw"
    (os:debian-stable "buster" :amd64)
    (basic-props)
    (apt:installed "whatever" "you" "want")
    (git:snapshot-extracted "/etc/skel/src" "dotfiles")
    (file:is-copy-of "/etc/skel/.bashrc" "/etc/skel/src/dotfiles/.bashrc")
    (git:snapshot-extracted "/root/src/cl" "consfig")))

The first argument to LIVE-BUILD:IMAGE-BUILT. is additional arguments to lb_config(1). The third argument onwards are the properties for the live system. The cool thing is GIT:SNAPSHOT-EXTRACTED the calls to this ensure that a copy of my Emacs configuration and my consfig end up in the live image, ready to be used interactively to install Debian, as described above. I ll need to add something like

(chroot:host-chroot-bootstrapped
melete.silentflame.com "/srv/chroot/melete")

too. As with everything Consfigurator-related, Joey Hess s Propellor is the giant upon whose shoulders I m standing.

The Debian Janitor is an automated system that commits fixes for (minor) issues in Debian packages that can be fixed by software. It gradually started proposing merges in early December. The first set of changes sent out ran lintian-brush on sid packages maintained in Git. This post is part of a series about the progress of the Janitor. In my last blogpost, I introduced the buildlog consultant - a tool that can identify many reasons why a Debian build failed. For example, here s a fragment of a build log where the Build-Depends lack python3-setuptools:
849 850 851 852 853 854 855 856 857 858
dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --with python3,sphinxdoc --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:232: python3.9 setup.py clean Traceback (most recent call last): File "/<<PKGBUILDDIR>>/setup.py", line 2, in <module> from setuptools import setup ModuleNotFoundError: No module named 'setuptools' E: pybuild pybuild:353: clean: plugin distutils failed with: exit code=1: python3.9 setup.py clean

The buildlog consultant can identify the line in bold as being key, and interprets it:

 % analyse-sbuild-log --json ~/build.log
  
    "stage": "build",
    "section": "Build",
    "lineno": 857,
    "kind": "missing-python-module",
    "details":  "module": "setuptools", "python_version": 3, "minimum_version": null

Automatically acting on buildlog problems A common reason why Debian builds fail is missing dependencies or incorrect versions of dependencies declared in the package build depends. Based on the output of the buildlog consultant, it is possible in many cases to determine what dependency needs to be added to Build-Depends. In the example given above, we can use apt-file to look for the package that contains the path /usr/lib/python3/dist-packages/setuptools/__init__.py - and voila, we find python3-setuptools:

 % apt-file search /usr/lib/python3/dist-packages/setuptools/__init__.py
 python3-setuptools: /usr/lib/python3/dist-packages/setuptools/__init__.py

The deb-fix-build command automates these steps:

It builds the package using sbuild; if the package successfully builds then it just exits successfully
It tries to identify the problem by looking through the build log; if it can t or if it s a problem it has seen before (but apparently failed to resolve), then it exits with a non-zero exit code
It tries to find a dependency that can address the problem
It updates Build-Depends in debian/control or Depends in debian/tests/control
Go to step 1

This takes away the tedious manual process of building a package, discovering that a dependency is missing, updating Build-Depends and trying again. For example, when I ran deb-fix-build while packaging saneyaml, the output looks something like this:

 % deb-fix-build
 Using output directory /tmp/tmpyz0nkgqq
 Using sbuild chroot unstable-amd64-sbuild
 Using fixers:  
 Building debian packages, running 'sbuild --no-clean-source -A -s -v'.
 Attempting to use fixer upstream requirement fixer(apt) to address MissingPythonDistribution('setuptools_scm', python_version=3, minimum_version='4')
 Using apt-file to search apt contents
 Adding build dependency: python3-setuptools-scm (>= 4)
 Building debian packages, running 'sbuild --no-clean-source -A -s -v'.
 Attempting to use fixer upstream requirement fixer(apt) to address MissingPythonDistribution('toml', python_version=3, minimum_version=None)
 Adding build dependency: python3-toml
 Building debian packages, running 'sbuild --no-clean-source -A -s -v'.
 Built 0.5.2-1- changes files at [ saneyaml_0.5.2-1_amd64.changes ].

And in our Git repository, we see these changes as well:

% git log -p
 commit 5a1715f4c7273b042818fc75702f2284034c7277 (HEAD -> master)
 Author: Jelmer Vernoo  <jelmer@jelmer.uk>
 Date:   Sun Apr 4 02:35:56 2021 +0100
     Add missing build dependency on python3-toml.
 diff --git a/debian/control b/debian/control
 index 5b854dc..3b27b73 100644
 --- a/debian/control
 +++ b/debian/control
 @@ -1,6 +1,6 @@
  Rules-Requires-Root: no
  Standards-Version: 4.5.1
 -Build-Depends: debhelper-compat (= 12), dh-sequence-python3, python3-all, python3-setuptools (>= 50), python3-wheel, python3-setuptools-scm (>= 4)
 +Build-Depends: debhelper-compat (= 12), dh-sequence-python3, python3-all, python3-setuptools (>= 50), python3-wheel, python3-setuptools-scm (>= 4), python3-toml
  Testsuite: autopkgtest-pkg-python
  Source: python-saneyaml
  Priority: optional
 commit f03047da80fcd8468ee231fbc4cf8488d7a0acd1
 Author: Jelmer Vernoo  <jelmer@jelmer.uk>
 Date:   Sun Apr 4 02:35:34 2021 +0100
     Add missing build dependency on python3-setuptools-scm (>= 4).
 diff --git a/debian/control b/debian/control
 index a476cc2..5b854dc 100644
 --- a/debian/control
 +++ b/debian/control
 @@ -1,6 +1,6 @@
  Rules-Requires-Root: no
  Standards-Version: 4.5.1
 -Build-Depends: debhelper-compat (= 12), dh-sequence-python3, python3-all, python3-setuptools (>= 50), python3-wheel
 +Build-Depends: debhelper-compat (= 12), dh-sequence-python3, python3-all, python3-setuptools (>= 50), python3-wheel, python3-setuptools-scm (>= 4)
  Testsuite: autopkgtest-pkg-python
  Source: python-saneyaml
  Priority: optional

Using deb-fix-build You can run deb-fix-build by installing the ognibuild package from unstable. The only requirements for using it are that:

The package is maintained in Git
A sbuild schroot is available for use

Caveats deb-fix-build is fairly easy to understand, and if it doesn t work then you re no worse off than you were without it - you ll have to add your own Build-Depends. That said, there are a couple of things to keep in mind:

At the moment, it doesn t distinguish between general, Arch or Indep Build-Depends.
It can only add dependencies for things that are actually in the archive
Sometimes there are multiple packages that can provide a file, command or python package - it tries to find the right one with heuristics but doesn t always get it right

Reading build logs Build logs for Debian packages can be quite long and difficult for a human to read. Anybody who has looked at these logs trying to figure out why a build failed will have spent time scrolling through them and skimming for certain phrases (lines starting with error: for example). In many cases, you can spot the problem in the last 10 or 20 lines of output but it s also quite common that the error is somewhere at the beginning of many pages of error output.

The buildlog consultant The buildlog consultant project attempts to aid in this process by parsing sbuild and non-Debian (e.g. the output of make ) build logs and trying to identify the key line that explains why a build failed. It can then either display this specific line, or a fragment of the log around surrounding the key line.

Classification In addition to finding the key line explaining the failure, it can also classify and parse the error in many cases and return a result code and some metadata. For example, in a failed build of gnss-sdr that has produced 2119 lines of output, the reason for the failure is that log4cpp is missing which is on line 641:

 -- Required GNU Radio Component: ANALOG missing!
 -- Could NOT find GNURADIO (missing: GNURADIO_RUNTIME_FOUND)
 -- Could NOT find PkgConfig (missing: PKG_CONFIG_EXECUTABLE)
 -- Could NOT find LOG4CPP (missing: LOG4CPP_INCLUDE_DIRS
 LOG4CPP_LIBRARIES)
 CMake Error at CMakeLists.txt:593 (message):
   *** Log4cpp is required to build gnss-sdr
 -- Configuring incomplete, errors occurred!
 See also "/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles/
 CMakeOutput.log".
 See also "/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles/
 CMakeError.log".

In this case, the buildlog consultant can both figure out line was problematic and what the problem was:

 % analyse-sbuild-log build.log
 Failed stage: build
 Section: build
 Failed line: 641:
   *** Log4cpp is required to build gnss-sdr
 Error: Missing dependency: Log4cpp

Or, if you'd like to do something else with the output, use JSON output:

 % analyse-sbuild-log --json build.log
  "stage": "build", "section": "Build", "lineno": 641, "kind": "missing-dependency", "details":  "name": "Log4cpp""

How it works The consultant does some structured parsing (most notably it can parse the sections from a sbuild log), but otherwise is a large set of carefully crafted regular expressions and heuristics. It doesn t always find the problem, but has proven to be fairly accurate. It is constantly improved as part of the Debian Janitor project, and that exposes it to a wide variety of different errors. You can see the classification and error detection in action on the result codes page of the Janitor.

Using the buildlog consultant You can get the buildlog consultant from either pip or Debian unstable (package: python3-buildlog-consultant ). The buildlog consultant comes with two scripts analyse-build-log and analyse-sbuild-log, for analysing build logs and sbuild logs respectively.

Note: This is the continuation of part 1 and part 2. Going forward: growing Freexian Part 2: Extending the team By all accounts, Freexian is still a small company which relies largely on me in many aspects. The growth of its business is however providing enough financial margin to allow looking into ways to recruit external help, be it through direct hiring (for French residents) or via long term contracting (for people based in other countries). If you believe you could be the right person for one of the roles listed below, or if you know someone that we should contact, please reach out to raphael@freexian.com. Project manager I m looking for someone that cares about Debian and that has the following skills:

knows how to manage developers and software projects
- bonus points for any experience in environments mixing volunteers and paid contributors
is fluent and experienced enough in Python to be able to do software design and code reviews
- bonus points for experience with: Django, Test Driven Development

That person would handle (some of) the following tasks:

lead the Debian project funding initiative to a success
- find useful projects to fund, for example by
  - discussing with various Debian teams / contributors (including the DPL)
  - running a survey among Debian developers
  - doing your own analysis
- help with drafting and specifying the various projects
- help to find someone to implement and review the projects
- coordinate with those persons during execution
manage other free software projects that Freexian would like to pursue
- debusine: a software factory tailored for Debian packages
  - participate in design discussions, set milestones and goals
    - start with the short term needs of Freexian
    - but take into account the needs of Debian so that it can replace some aging infrastructure within Debian
  - coordinate with contractors, possibly implement some parts
- infrastructure to run the various Freexian services and automate most of the administrative work (see Part2: From Debian LTS to Debian for the Enterprise )
maybe coordinate the team of paid LTS/ELTS contributors

Debian/Python Developer While the current priority is on the above role, there could also be room for a developer role with the following tasks:

Creation and maintenance of Debian packages
Technical support
Software development in Python (debusine, internal infrastructure)
Security support (contributor to Debian LTS)

Sales manager / sales representative Up until now, the growth of Freexian has mostly been organic, through word of mouth and increased awareness of Debian LTS within the Debian community. We never spent a single euro on advertising, except for one promotional video and for Debconf sponsorship (with a flyer and stickers). But if we can manage to make a positive impact on Debian through the funding that Freexian brings, then I m interested to grow the company so that we can pay more people to work on Debian. That growth likely would have to go through some more active sales work. At the same time, it is an opportunity for me to delegate (some of) the administrative work that lies solely on my shoulders (invoicing, day to day customer relationship, etc.). I assume it will be hard to find a member of the Debian community that has an interest in those areas, but who knows This article is to be continued in an upcoming post. Stay tuned!

Google Pixel phones support what they call Motion Photo which is essentially a photo with a short video clip attached to it. They are quite nice since they bring the moment alive, especially as the capturing of the video starts a small moment before the shutter button is pressed. For most viewing programs they simply show as static JPEG photos, but there is more to the files.

I d really love proper Shotwell support for these file formats, so I posted a longish explanation with many of the details in this blog post to a ticket there too. Examples of the newer format are linked there too.

There are actually two different formats, an old one that is already obsolete, and a newer current format. The older ones are those that your Pixel phone recorded as MVIMG_[datetime].jpg", and they have the following meta-data:

Xmp.GCamera.MicroVideo                       XmpText     1  1
Xmp.GCamera.MicroVideoVersion                XmpText     1  1
Xmp.GCamera.MicroVideoOffset                 XmpText     7  4022143
Xmp.GCamera.MicroVideoPresentationTimestampUs XmpText     7  1331607

The offset is actually from the end of the file, so one needs to calculate accordingly. But it is exact otherwise, so one simply extract a file with that meta-data information:

#!/bin/bash
#
# Extracts the microvideo from a MVIMG_*.jpg file

# The offset is from the ending of the file, so calculate accordingly
offset=$(exiv2 -p X "$1"   grep MicroVideoOffset   sed 's/.*\"\(.*\)"/\1/')
filesize=$(du --apparent-size --block=1 "$1"   sed 's/^\([0-9]*\).*/\1/')
extractposition=$(expr $filesize - $offset)
echo offset: $offset
echo filesize: $filesize
echo extractposition=$extractposition
dd if="$1" skip=1 bs=$extractposition of="$(basename -s .jpg $1).mp4"

The newer format is recorded in filenames called PXL_[datetime].MP.jpg , and they have a _lot_ of additional metadata:

Xmp.GCamera.MotionPhoto                      XmpText     1  1
Xmp.GCamera.MotionPhotoVersion               XmpText     1  1
Xmp.GCamera.MotionPhotoPresentationTimestampUs XmpText     6  233320
Xmp.xmpNote.HasExtendedXMP                   XmpText    32  E1F7505D2DD64EA6948D2047449F0FFA
Xmp.Container.Directory                      XmpText     0  type="Seq"
Xmp.Container.Directory[1]                   XmpText     0  type="Struct"
Xmp.Container.Directory[1]/Container:Item    XmpText     0  type="Struct"
Xmp.Container.Directory[1]/Container:Item/Item:Mime XmpText    10  image/jpeg
Xmp.Container.Directory[1]/Container:Item/Item:Semantic XmpText     7  Primary
Xmp.Container.Directory[1]/Container:Item/Item:Length XmpText     1  0
Xmp.Container.Directory[1]/Container:Item/Item:Padding XmpText     1  0
Xmp.Container.Directory[2]                   XmpText     0  type="Struct"
Xmp.Container.Directory[2]/Container:Item    XmpText     0  type="Struct"
Xmp.Container.Directory[2]/Container:Item/Item:Mime XmpText     9  video/mp4
Xmp.Container.Directory[2]/Container:Item/Item:Semantic XmpText    11  MotionPhoto
Xmp.Container.Directory[2]/Container:Item/Item:Length XmpText     7  1679555
Xmp.Container.Directory[2]/Container:Item/Item:Padding XmpText     1  0

Sounds like fun and lots of information. However I didn t see why the length in first item is 0 and I didn t see how to use the latter Length info. But I can use the mp4 headers to extract it:

#!/bin/bash
#
# Extracts the motion part of a MotionPhoto file PXL_*.MP.mp4

extractposition=$(grep --binary --byte-offset --only-matching --text \
-P "\x00\x00\x00\x18\x66\x74\x79\x70\x6d\x70\x34\x32" $1   sed 's/^\([0-9]*\).*/\1/')

dd if="$1" skip=1 bs=$extractposition of="$(basename -s .jpg $1).mp4"

UPDATE: I wrote most of this blog post earlier. When now actually getting to publishing it a week later, I see the obvious ie the Length is again simply the offset from the end of the file so one could do the same less brute force approach as for MVIMG. I ll leave the above as is however for the of binary grepping.(cross-posted to my other blog)

A new release 1.1.39-3 of x13binary, of the X-13ARIMA-SEATS program by the US Census Bureau (with upstream release 1.1.39) is now on CRAN. The x13binary package takes the pain out of installing X-13ARIMA-SEATS by making it a fully resolved CRAN dependency. For example, when installing the excellent seasonal package by Christoph, then X-13ARIMA-SEATS will get pulled in via the x13binary package and things just work. Just depend on x13binary and on all major OSs supported by R you should have an X-13ARIMA-SEATS binary installed which will be called seamlessly by the higher-level packages such as seasonal or gunsales. With this the full power of the what is likely the world s most sophisticated deseasonalization and forecasting package is now at your fingertips and the R prompt, just like any other of the 17350+ CRAN packages. You can read more about this (and the seasonal package) in the Journal of Statistical Software paper by Christoph and myself. This release was needed because the recent M1mac build was reporting leftover detritus in the temporary directory, which we addressed with an explicit removal at end. We also addressed another CRAN Policy change since the last release, namely a conversion of the configure script from bash to sh. Now, sadly, that second aspect blew up on Solaris, and the detritus issue appears to be persist. By now Christoph and a colleague have installed R(-devel) on such an M1 machine, but still cannot reproduce. We will reach out to CRAN to learn more. A follow-up release 1.1.39-4 is likely. The good news is that the standard macOS binary works on M1 as do other binaries thanks to the translation layer. We do however lack a genuine binary for Solaris so if any of the esteemed readers of this post happens to have access to R on Solaris along with a basic Fortran compiler, we would love to hear from you. Building X-13ARIMA-SEATS from source on Solaris should be straightforward, it is on the other OSs. Courtesy of my CRANberries, there is also a diffstat report for this release showing changes to the previous release. If you like this or other open-source work I do, you can sponsor me at GitHub.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

Kubernetes is moving aways from docker to alternative container engines presenting a smaller core having just the functionality needed. The two most populars alternatives are:

containerd, a subset of docker, used for instance in Google Kubernetes Engine
cri-o, a new implementation of a container engine, used for instance in Red Hat's Kubernetes offering (OpenShift)

These alternatives are meant to be used programatically via a unix domain socket, and therefore have a limited command line interface.Let's play around in a VM.Install a throwaway VM with Vagrant

apt install vagrant vagrant-libvirt
vagrant init debian/testing64

Start the VM, install dependencies

vagrant up
vagrant ssh

sudo apt update
sudo apt install --yes curl gnupg jq

Install cri-o the container engine

sudo bash
export OS=Debian_Testing VERSION=1.20

echo "deb https://download.opensuse.org/repositories/devel:/kubic:/libcontainers:/stable/$OS/ /" > /etc/apt/sources.list.d/libcontainers.list
echo "deb https://download.opensuse.org/repositories/devel:/kubic:/libcontainers:/stable:/cri-o:/$VERSION/$OS/ /" > /etc/apt/sources.list.d/cri-o:$VERSION.list
curl -L https://download.opensuse.org/repositories/devel:kubic:libcontainers:stable:cri-o:$VERSION/$OS/Release.key   apt-key add -
curl -L https://download.opensuse.org/repositories/devel:/kubic:/libcontainers:/stable/$OS/Release.key   apt-key add -
apt install cri-o cri-o-runc containernetworking-plugins conntrack

Verify it is running properly

systemctl restart cri-o
systemctl status cri-o
...
Started Container Runtime Interface for OCI (CRI-O).

Say hello to cri-o via its unix domain socket

curl --silent  --unix-socket /var/run/crio/crio.sock http://localhost/info   jq 
 
  "storage_driver": "overlay",
  "storage_root": "/var/lib/containers/storage",
  "cgroup_driver": "systemd",
  "default_id_mappings":  
    "uids": [
       
        "container_id": 0,
        "host_id": 0,
        "size": 4294967295
       
    ],
    "gids": [
       
        "container_id": 0,
        "host_id": 0,
        "size": 4294967295
       
    ]

Install crictl, a Kubernetes debugging tool for containers

wget --directory-prefix=/tmp https://github.com/kubernetes-sigs/cri-tools/releases/download/v1.20.0/crictl-v1.20.0-linux-amd64.tar.gz
tar -xaf /tmp/crictl-v1.20.0-linux-amd64.tar.gz -C /usr/local/sbin/
chmod +x /usr/local/sbin/crictl

crictl info
 
  "status":  
    "conditions": [
       
        "type": "RuntimeReady",
        "status": true,
        "reason": "",
        "message": ""
       ,
       
        "type": "NetworkReady",
        "status": true,
        "reason": "",
        "message": ""
       
    ]

From there on you can create a container following the examples in https://github.com/kubernetes-sigs/cri-tools/blob/master/docs/crictl.md

How can you help free software? Aside from donating to the excellent free software nonprofits out there, and contributing to a project by building software or other resources, there are things you can do to help the free software cause. The two biggest things I think are providing mentorship and gently normalizing free software.

Providing Mentorship Allison Randal introduced me to the idea that mentorship doesn t have to be an ongoing process. This is to say, you don t have to sign up to be someone s best friend and advisor for life (though you certainly can). Providing short term, project or skill based, or one off mentorship is useful for building community because it makes people feel welcome and cared for and helps build skills that benefit free software. I do a lot of proofreading and editing of people s writing especially people with minimal writing experience and/or non-native English speakers who are writing important documents in English. If the person is interested, I try to talk to them about their writing and why I m making these particular suggestions. I hope this helps them with their writing in the future. Other examples are working on a particular project or skill, this can be helping them develop a particular skill (e.g. git outside of the command line), or giving advice on a project with a level of specificity and detail you re both comfortable with. These can, again, be one off things or things that require minimal effort/occasional conversation. I have some friends who I consider my Debian mentors who just answer functional questions whenever I have trouble doing something. I also love love love talking with people about their free software trajectories, their goals and desires and dreams for their involvement in free software, whether that s finding a place in a community, developing a skill set, or other things about their future (like job hopes, schooling, etc). These conversations have been so helpful for me personally, and I like to think they help others.

Gently Normalizing Free Software I think normalizing free software is very important to its success and adoption. It s not helpful to insist someone who has never done so before to create a Debian boot disk and install it. It is helpful to suggest using Big Blue Button or jitsi. If a friend wants help finding audio editing software, suggest they try audacity. I d go as far as to suggest doing this without explaining that it s free software, and instead focus on why it ll work and that it s available at no cost. If they like it, then it s a great time to talk about rights and freedoms. Of course if they already care about these sorts of things, if you re discussing privacy software, if anti-surveillance is an issue, or any number of other things, software freedom is a great thing to bring up!

Above all, just be nice. Be nice. It s basically the best thing you can do for free software.

Review: JavaScript: The Definitive Guide, by David Flanagan

Publisher:	O'Reilly
Copyright:	May 2020
ISBN:	1-4919-5202-4
Format:	Trade paperback
Pages:	665

JavaScript: The Definitive Guide has been frequently revised for new versions of JavaScript and therefore has multiple editions. This review is of the seventh edition, first published in May of 2020. Reviews of programming language books are challenging since people learn languages in different ways. A short calibration for my preferences may therefore be useful. I'm both an experienced programmer in multiple languages (C, Perl, Python, and some Java and Ruby professionally; Rust, some PHP, and a few minor languages as a hobby) and I specialized in software theory in college. I therefore like to learn languages comparatively and am comfortable with a lot of up-front syntax and discussion of the unique properties of the language. Introductory programs and practical exercises doesn't matter as much to me; I'm happy to hold the syntax in my head until enough of the language has been introduced to write simple programs. For me, this book is excellent. It's one of the best language manuals that I've read, and that requires some work because JavaScript is a sprawling mess with odd corners, deprecated features, and alternate implementations of core constructs. Flanagan takes the syntax-first, comprehensive approach that I prefer, working methodically through the language (defining your own functions aren't introduced until chapter eight) and discussing all of the quirks as he goes. I felt like I thoroughly understood each portion of the language before moving on. And this book is tight. Some comprehensive language introductions sprawl, but the benefit of seven editions of iteration is a book that has been honed to the most direct and effective explanation of each concept. The section on type conversions with operators, for example, was so good that I was able to immediately understand the unintuitive result of [1] + 2 (the string '12'), despite this being one of the most confusing parts of the language. The sections on JavaScript's prototype-based object type system and its three concurrency models (callbacks, promises, and async/await) were equally good. I came away feeling like I not only understood promises and callback chains but had a feel for how the same code would look when written in the different systems. The drawback in this approach is that if you instead want a language reference that only tells you the parts of the language that you should use and leaves out the legacy weirdness and obscure corners for later (or never), this may not be the book for you. Flanagan labels the obsolete constructs, but he's meticulous about explaining the entire language, including such things as new Boolean or var variables that no one should use. This is what I wanted; I prefer to have a thorough grounding in language primitives so that it doesn't surprise me. But it can be a lot to juggle and prune in your head. JavaScript is a language used in some very different domains. The approach Flanagan takes to that is to spend as long as possible on the core language that's usable both in the browser and on the server (while marking the pieces, such as the module system, that are markedly different between Node and browsers). He then puts two monster chapters at the back of the book that cover JavaScript in web browsers and JavaScript as implemented by Node. Both are more of overviews than orientations, since a comprehensive manual for either is probably as long again as this book, but they were more than adequate for my purposes. (I bogged down a bit in the web browser chapter, in part because I didn't have an immediate use for most of the material.) Flanagan wisely defers to MDN as the reference manual for the JavaScript APIs available in web browsers. I thought Flanagan also hit the right balance of explanation to examples, and did a good job controlling the length of the examples. Most of the code excerpts are short and to the point. The longer ones have a high level of explanatory power per line, since Flanagan uses them to pull together multiple concepts and show how they interact. I was particularly impressed with the example that closes the chapter on web browsers, which uses <canvas>, ImageData, generators, promises, web workers, and other areas of the language Flanagan previously explained to implement a Mandelbrot set explorer in eleven pages of code. I think that's the longest example in the book, and it's well worth it. This sort of introduction will always have limitations. Flanagan provides a brief orientation to the ecosystem surrounding JavaScript in the last chapter, but most JavaScript programmers will be working with packaging tools and frameworks that could themselves be the topic of another book and that he doesn't have room to cover. JavaScript, even more than most languages, is commonly used via a heavy layer of supporting libraries and abstractions, so you will probably not be able to tackle a practical JavaScript project using solely the material in this book. But if you're the sort of programmer who wants to start with a solid syntactical and conceptual understanding of the language core before starting on more applied topics, I've rarely seen it done better than this book. If you want a quick-start guide that will get you writing code quickly and is opinionated about what parts of the language you should learn, this may not be the book for you. But if you're comfortable with comprehensive detail in your language guides, this was exactly what I was looking for. Recommended. Rating: 9 out of 10

Too much has been written, a war of support letters is going on, Debian is heading head first like Lemmings into the same war. And then, there is this by the first female President of the American Civil Liberties Union (ACLU): Civil Rights Activist Nadine Strossen s Response To #CancelStallman:

I find it so odd that the strong zeal for revenge and punishment if someone says anything that is perceived to be sexist or racist or discriminatory comes from liberals and progressives. There are so many violations [in cases like Stallman s] of such fundamental principles to which progressives and liberals cling in general as to what is justice, what is fairness, what is due process.
One is proportionality: that the punishment should be proportional to the offense. Another one is restorative justice: that rather than retribution and punishment, we should seek to have the person constructively come to understand, repent, and make amends for an infraction. Liberals generally believe society to be too punitive, too harsh, not forgiving enough. They are certainly against the death penalty and other harsh punishments even for the most violent, the mass murderers. Progressives are right now advocating for the release of criminals, even murderers. To then have exactly the opposite attitude towards something that certainly is not committing physical violence against somebody, I don t understand the double standard!
Another cardinal principle is we shouldn t have any guilt by association. [To hold culpable] these board members who were affiliated with him and ostensibly didn t do enough to punish him for things that he said which by the way were completely separate from the Free Software Foundation is multiplying the problems of unwarranted punishment. It extends the punishment where the argument for responsibility and culpability becomes thinner and thinner to the vanishing point. That is also going to have an enormous adverse impact on the freedom of association, which is an important right protected in the U.S. by the First Amendment.
The Supreme Court has upheld freedom of association in cases involving organizations that were at the time highly controversial. It started with NAACP (National Association for the Advancement of Colored People) during the civil rights movement in the 1950s and 60s, but we have a case that s going to the Supreme Court right now regarding Black Lives Matter. The Supreme Court says even if one member of the group does commit a crime in both of those cases physical violence and assault that is not a justification for punishing other members of the group unless they specifically intended to participate in the particular punishable conduct.
Now, let s assume for the sake of argument, Stallman had an attitude that was objectively described as discriminatory on the basis on race and gender (and by the way I have seen nothing to indicate that), that he s an unrepentant misogynist, who really believes women are inferior. We are not going to correct those ideas, to enlighten him towards rejecting them and deciding to treat women as equals through a punitive approach! The only approach that could possibly work is an educational one! Engaging in speech, dialogue, discussion and leading him to re-examine his own ideas.
Even if I strongly disagree with a position or an idea, an expression of an idea, advocacy of an idea, and even if the vast majority of the public disagrees with the idea and finds it offensive, that is not a justification for suppressing the idea. And it s not a justification for taking away the equal rights of the person who espouses that idea including the right to continue holding a tenured position or other prominent position for which that person is qualified.
But a number of the ideas for which Richard Stallman has been attacked and punished are ideas that I as a feminist advocate of human rights find completely correct and positive from the perspective of women s equality and dignity! So for example, when he talks about the misuse and over use and flawed use of the term sexual assault, I completely agree with that critique! People are indiscriminantly using that term or synonyms to describe everything from the most appaulling violent abuse of helpless vulnerable victims (such as a rape of a minor) to any conduct or expression in the realm of gender or sexuality that they find unpleasant or disagreeable.
So we see the term sexual assault and sexual harrassment used for example, when a guy asks a woman out on a date and she doesn t find that an appealing invitation. Maybe he used poor judgement in asking her out, maybe he didn t, but in any case that is NOT sexual assault or harassment. To call it that is to really demean the huge horror and violence and predation that does exist when you are talking about violent sexual assault. People use the term sexual assault/ sexual harassment to refer to any comment about gender or sexuality issues that they disagree with or a joke that might not be in the best taste, again is that to be commended? No! But to condemn it and equate it with a violent sexual assault again is really denying and demeaning the actual suffering that people who are victims of sexual assault endure. It trivializes the serious infractions that are committed by people like Jeffrey Epstein and Harvey Weinstein. So that is one point that he made that I think is very important that I strongly agree with.
Secondly and relatedly, [Richard Stallman] never said that he endorse child pornography, which by definition the United States Supreme Court has defined it multiple times is the sexual exploitation of an actual minor. Coerced, forced, sexual activity by that minor, with that minor that happens to be filmed or photographed. That is the definition of child pornography. He never defends that! What the point he makes, a very important one, which the U.S. Supreme Court has also made, is mainly that we overuse and distort the term child pornography to refer to any depiction of any minor in any context that is even vaguely sexual.
So some people have not only denounced as child pornography but prosecuted and jailed loving devoted parents who committed the crime of taking a nude or semi-nude picture of their own child in a bathtub or their own child in a bathing suit. Again it is the hysteria that has totally refused to draw an absolutely critical distinction between actual violence and abuse, which is criminal and should be criminal, to any potentially sexual depiction of a minor. And I say potentially because I think if you look at a picture a parent has taken of a child in a bathtub and you see that as sexual, then I d say there s something in your perspective that might be questioned or challenged! But don t foist that upon the parent who is lovingly documenting their beloved child s life and activities without seeing anything sexual in that image.
This is a decision that involves line drawing. We tend to have this hysteria where once we hear terms like pedophilia of course you are going to condemn anything that could possibly have that label. Of course you would. But societies around the world throughout history various cultures and various religions and moral positions have disagreed about at what age do you respect the autonomy and individuality and freedom of choice of a young person around sexuality. And the U.S. Supreme Court held that in a case involving minors right to choose to have an abortion.
By the way, [contraception and abortion] is a realm of sexuality where liberals and progressives and feminists have been saying, Yes! If you re old enough to have sex. You should have the right to contraception and access to it. You should have the right to have an abortion. You shouldn t have to consult with your parents and have their permission or a judge s permission because you re sufficiently mature. And the Supreme Court sided in accord of that position. The U.S. Supreme Court said constitutional rights do not magically mature and spring into being only when someone happens to attain the state defined age of majority.
In other words the constitution doesn t prevent anyone from exercising rights, including Rights and sexual freedoms, freedom of choice and autonomy at a certain age! And so you can t have it both ways. You can t say well we re strongly in favor of minors having the right to decide what to do with their own bodies, to have an abortion what is in some people s minds murder but we re not going to trust them to decide to have sex with somewhat older than they are.
And I say somewhat older than they are because that s something where the law has also been subject to change. On all issues of when you obtain the age of majority, states differ on that widely and they choose different ages for different activities. When you re old enough to drive, to have sex with someone around your age, to have sex with someone much older than you. There is no magic objective answer to these questions. I think people need to take seriously the importance of sexual freedom and autonomy and that certainly includes women, feminists. They have to take seriously the question of respecting a young person s autonomy in that area.
There have been famous cases of 18 year olds who have gone to prison because they had consensual sex with their girlfriends who were a couple of years younger. A lot of people would not consider that pedophilia and yet under some strict laws and some absolute definitions it is. Romeo and Juliet laws make an exception to pedophilia laws when there is only a relatively small age difference. But what is relatively small? So to me, especially when he says he is re-examining his position, Stallman is just thinking through the very serious debate of how to be protective and respectful of young people. He is not being disrespectful, much less wishing harm upon young people, which seems to be what his detractors think he s doing.

Unfortunately, I don t think the Anti-Harassment Team of Debian and others of the usual group of warriors will ever read less understand what is written there. So sad.

The Debian CI platform is comprised of 30+ (virtual) machines. Maintaining this many machines, and being able to add new ones with some degree of reliability requires one to use some sort of configuration management. Until about a week ago, we were using Chef for our configuration management. I was, for several years, the main maintainer of Chef in Debian, so using it was natural to me, as I had used it before for personal and work projects. But last year I decided to request the removal of Chef from Debian, so that it won't be shipped with Debian 11 (bullseye). After evaluating a few options, I believed that the path of least resistance was to migrate to itamae. itamae was inspired by chef, and uses a DSL that is very similar to the Chef one. Even though the itamae team claim it's not compatible with Chef, the changes that I needed to do were relatively limited. The necessary code changes might look like a lot, but a large part of them could be automated or done in bulk, like doing simple search and replace operations, and moving entire directories around. In the rest of this post, I will describe the migration process, starting with the infrastructure changes, the types of changes I needed to make to the configuration management code, and my conclusions about the process. Infrastructure changes The first step was to add support for itamae to chake, a configuration management wrapper tool that I wrote. chake was originally written as a serverless remote executor for Chef, so this involved a bit of a redesign. I thought it was worth it to do, because at that point chake had gained several interesting managements features that we no directly tied to Chef. This work was done a bit slowly over the course of the several months, starting almost exactly one year ago, and was completed 3 months ago. I wasn't in a hurry and knew I had time before Debian 11 is released and I had to upgrade the platform. After this was done, I started the work of migrating the then Chef cookbooks to itamae, and the next sections present the main types of changes that were necessary. During the entire process, I sent a few patches out:

itamae #317 - Make output unbuffered
itamae #325 - file: add support for sensitive files
itamae #327 - file: improve diff output
itamae #337 - package: add :upgrade action. This is work in progress at the moment, and wasn't merged yet.
serverspec #727 - debian: add support for Debian testing and unstable

Code changes These are the main types of changes that were necessary in the configuration code to accomplish the migration to itamae. Replace cookbook_file with remote_file. The resource known as cookbook_file in Chef is called remote_file in itamae. Fixing this is just a matter of search and replace, e.g.:

-cookbook_file '/etc/apt/apt.conf.d/00updates' do
+remote_file '/etc/apt/apt.conf.d/00updates' do

Changed file locations The file structure assumed by itamae is a lot simpler than the one in Chef. The needed changes were:

static files and templates moved from cookbooks/$ cookbook / files,templates /default to cookbooks/$ cookbook / files,templates
recipes moved from cookbooks/$ cookbook /recipes/*.rb to cookbooks/$ cookbook /*.rb
host-specific files and templates are not supported directly, but can be implemented just by using an explicit source statement, like this:
```
remote_file "/etc/foo.conf" do
  source "files/host-# node['fqdn'] /foo.conf"
end
```

Explicit file ownership and mode Chef is usually design to run as root on the nodes, and files created are owned by root and have move 0644 by default. With itamae, files are by default owned by the user that was used to SSH into the machine. Because of this, I had to review all file creation resources and add owner, group and mode explicitly:

-cookbook_file '/etc/apt/apt.conf.d/00updates' do
-  source 'apt.conf'
+remote_file '/etc/apt/apt.conf.d/00updates' do
+  source 'files/apt.conf'
+  owner   'root'
+  group   'root'
+  mode    "0644"
 end

In the end, I guess being explicit make the configuration code more understandable, so I take that as a win. Different execution context One of the major differences between Chef itamae comes down the execution context of the recipes. In both Chef and itamae, the configuration is written in DSL embedded in Ruby. This means that the recipes are just Ruby code, and difference here has to do with where that code is executed. With Chef, the recipes are always execute on the machine you are configuring, while with itamae the recipe is executed on the workstation where you run itamae, and that gets translated to commands that need to be executed on the machine being configured. For example, if you need to configure a service based on how much RAM the machine has, with Chef you could do something like this:

total_ram = File.readlines("/proc/meminfo").find do  l 
  l.split.first == "MemTotal:"
end.split[1]
file "/etc/service.conf" do
  # use 20% of the total RAM
  content "cache_size = # ram / 5 KB"
end

With itamae, all that Ruby code will run on the client, so total_ram will contain the wrong number. In the Debian CI case, I worked around that by explicitly declaring the amount of RAM in the static host configuration, and the above construct ended up as something like this:

file "/etc/service.conf" do
  # use 20% of the total RAM
  content "cache_size = # node['total_ram'] / 5 KB"
end

Lessons learned This migration is now complete, and there are a few points that I take away from it:

The migration is definitely viable, and I'm glad I picked itamae after all.
Of course, itamae is way simpler than Chef, and has less features. On the other hand, this means that it a simple package to maintain, with less dependencies and keeping it up to date is a lot easier.
itamae is considerably slower than Chef. On my local tests, a noop execution (e.g. re-applying the configuration a second time) against local VMs with itamae takes 3x the time it takes with Chef.

All in all, the system is working just fine, and I consider this to have been a successful migration. I'm happy it worked out.

With Debian packages now widely being maintained in Git repositories, there has been an uptick in the number of bulk changes made to Debian packages. Several maintainers are running commands over many packages (e.g. all packages owned by a specific team) to fix common issues in packages. Examples of changes being made include:

Updating the Vcs-Git and Vcs-Browser URLs after migrating from alioth to salsa

Stripping trailing whitespace in various control files

Updating e.g. homepage URLs to use https rather than http

Most of these can be fixed with simple sed or perl one-liners. Some of these scripts are publically available, for example:

The R packaging team's routine-update,

Ond ej Nov 's onovy-mass repository.

Lintian-Brush Lintian-Brush is both a simple wrapper around a set of these kinds of scripts and a repository for these scripts, with the goal of making it easy for any Debian maintainer to run them. The lintian-brush command-line tool is a simple wrapper that runs a set of "fixer scripts", and for each:

Reverts the changes made by the script if it failed with an error

Commits the changes to the VCS with an appropriate commit message

Adds a changelog entry (if desired)

The tool also provides some basic infrastructure for testing that these scripts do what they should, and e.g. don't have unintended side-effects. The idea is that it should be safe, quick and unobtrusive to run lintian-brush, and get it to opportunistically fix lintian issues and to leave the source tree alone when it can't.

Example For example, running lintian-brush on the package talloc fixes two minor lintian issues:

 % debcheckout talloc
 declared git repository at https://salsa.debian.org/samba-team/talloc.git
 git clone https://salsa.debian.org/samba-team/talloc.git talloc ...
 Cloning into 'talloc'...
 remote: Enumerating objects: 2702, done.
 remote: Counting objects: 100% (2702/2702), done.
 remote: Compressing objects: 100% (996/996), done.
 remote: Total 2702 (delta 1627), reused 2601 (delta 1550)
 Receiving objects: 100% (2702/2702), 1.70 MiB   565.00 KiB/s, done.
 Resolving deltas: 100% (1627/1627), done.
 % cd talloc
 talloc% lintian-brush
 Lintian tags fixed:  'insecure-copyright-format-uri', 'public-upstream-key-not-minimal' 
 % git log
 commit 0ea35f4bb76f6bca3132a9506189ef7531e5c680 (HEAD -> master)
 Author: Jelmer Vernoo  <jelmer@debian.org>
 Date:   Tue Dec 4 16:42:35 2018 +0000
     Re-export upstream signing key without extra signatures.
     Fixes lintian: public-upstream-key-not-minimal
     See https://lintian.debian.org/tags/public-upstream-key-not-minimal.html for more details.
  debian/changelog                    1 +
  debian/upstream/signing-key.asc   102 +++++++++++++++---------------------------------------------------------------------------------------
  2 files changed, 16 insertions(+), 87 deletions(-)
 commit feebce3147df561aa51a385c53d8759b4520c67f
 Author: Jelmer Vernoo  <jelmer@debian.org>
 Date:   Tue Dec 4 16:42:28 2018 +0000
     Use secure copyright file specification URI.
     Fixes lintian: insecure-copyright-format-uri
     See https://lintian.debian.org/tags/insecure-copyright-format-uri.html for more details.
  debian/changelog   3 +++
  debian/copyright   2 +-
  2 files changed, 4 insertions(+), 1 deletion(-)

Script Interface A fixer script is run in the root directory of a package, where it can make changes it deems necessary, and write a summary of what it's done for the changelog (and commit message) to standard out. If a fixer can not provide any improvements, it can simply leave the working tree untouched - lintian-brush will not create any commits for it or update the changelog. If it exits with a non-zero exit code, then it is assumed that it failed to run and it will be listed as such and its changes reset rather than committed. In addition, tests can be added for fixers by providing various before and after source package trees, to verify that a fixer script makes the expected changes. For more details, see the documentation on writing new fixers.

Availability lintian-brush is currently available in unstable and testing. See man lintian-brush(1) for an explanation of the command-line options. Fixer scripts are included that can fix (some of the instances of) 34 lintian tags. Feedback would be great if you try lintian-brush - please file bugs in the BTS, or propose pull requests with new fixers on salsa.

TL:DR; lost half my mail (150,000 messages, ~6GB) last night. Cause uncertain, but possibly a combination of a dead CMOS battery, systemd OnCalendar=daily, a (locking?) bug in syncmaildir, and generally, a system too exotic and complicated.

The crash So I somehow lost half my mail:

anarcat@angela:~(main)$ du -sh Maildir/
7,9G    Maildir/
anarcat@curie:~(main)$ du -sh Maildir
14G     Maildir
anarcat@marcos:~$ du -sh Maildir
8,0G    Maildir

Those are three different machines:

angela: my laptop, not always on
curie: my workstation, mostly always on
marcos: my mail server, always on

Those mails are synchronized using a rather exotic system based on SSH, syncmaildir and rsendmail. The anomaly started on curie:

-- Reboot --
mar 22 16:13:00 curie systemd[3199]: Starting pull emails with syncmaildir...
mar 22 16:13:00 curie smd-pull[4801]: rm: impossible de supprimer '/home/anarcat/.smd/workarea/Maildir': Le dossier n'est pas vide
mar 22 16:13:00 curie systemd[3199]: smd-pull.service: Main process exited, code=exited, status=1/FAILURE
mar 22 16:13:00 curie systemd[3199]: smd-pull.service: Failed with result 'exit-code'.
mar 22 16:13:00 curie systemd[3199]: Failed to start pull emails with syncmaildir.
mar 22 16:14:00 curie systemd[3199]: Starting pull emails with syncmaildir...
mar 22 16:14:00 curie smd-pull[7025]:  4091 ?        00:00:00 smd-push
mar 22 16:14:00 curie smd-pull[7025]: Already running.
mar 22 16:14:00 curie smd-pull[7025]: If this is not the case, remove /home/anarcat/.smd/lock by hand.
mar 22 16:14:00 curie smd-pull[7025]: any: smd-pushpull@localhost: TAGS: error::context(locking) probable-cause(another-instance-is-running) human-intervention(necessary) suggested-actions(run(kill 4091) run(rm /home/anarcat/.smd/lock))
mar 22 16:14:00 curie systemd[3199]: smd-pull.service: Main process exited, code=exited, status=1/FAILURE
mar 22 16:14:00 curie systemd[3199]: smd-pull.service: Failed with result 'exit-code'.
mar 22 16:14:00 curie systemd[3199]: Failed to start pull emails with syncmaildir.

Then it seems like smd-push (from curie) started destroying the universe for some reason:

mar 22 16:20:00 curie systemd[3199]: Starting pull emails with syncmaildir...
mar 22 16:20:00 curie smd-pull[9319]:  4091 ?        00:00:00 smd-push
mar 22 16:20:00 curie smd-pull[9319]: Already running.
mar 22 16:20:00 curie smd-pull[9319]: If this is not the case, remove /home/anarcat/.smd/lock by hand.
mar 22 16:20:00 curie smd-pull[9319]: any: smd-pushpull@localhost: TAGS: error::context(locking) probable-cause(another-instance-is-running) human-intervention(necessary) suggested-actions(ru
mar 22 16:20:00 curie systemd[3199]: smd-pull.service: Main process exited, code=exited, status=1/FAILURE
mar 22 16:20:00 curie systemd[3199]: smd-pull.service: Failed with result 'exit-code'.
mar 22 16:20:00 curie systemd[3199]: Failed to start pull emails with syncmaildir.
mar 22 16:21:34 curie smd-push[4091]: default: smd-client@smd-server-anarcat: TAGS: stats::new-mails(0), del-mails(293920), bytes-received(0), xdelta-received(26995)
mar 22 16:21:35 curie smd-push[9374]: register: smd-client@smd-server-register: TAGS: stats::new-mails(0), del-mails(0), bytes-received(0), xdelta-received(215)
mar 22 16:21:35 curie systemd[3199]: smd-push.service: Succeeded.

Notice the del-mails(293920) there: it is actively trying to destroy basically every email in my mail spool. Then somehow push and pull started both at once:

mar 22 16:21:35 curie systemd[3199]: Started push emails with syncmaildir.
mar 22 16:21:35 curie systemd[3199]: Starting push emails with syncmaildir...
mar 22 16:22:00 curie systemd[3199]: Starting pull emails with syncmaildir...
mar 22 16:22:00 curie smd-pull[10333]:  9455 ?        00:00:00 smd-push
mar 22 16:22:00 curie smd-pull[10333]: Already running.
mar 22 16:22:00 curie smd-pull[10333]: If this is not the case, remove /home/anarcat/.smd/lock by hand.
mar 22 16:22:00 curie smd-pull[10333]: any: smd-pushpull@localhost: TAGS: error::context(locking) probable-cause(another-instance-is-running) human-intervention(necessary) suggested-actions(r
mar 22 16:22:00 curie systemd[3199]: smd-pull.service: Main process exited, code=exited, status=1/FAILURE
mar 22 16:22:00 curie systemd[3199]: smd-pull.service: Failed with result 'exit-code'.
mar 22 16:22:00 curie systemd[3199]: Failed to start pull emails with syncmaildir.
mar 22 16:22:00 curie smd-push[9455]: smd-client: ERROR: Data transmission failed.
mar 22 16:22:00 curie smd-push[9455]: smd-client: ERROR: This problem is transient, please retry.
mar 22 16:22:00 curie smd-push[9455]: smd-client: ERROR: server sent ABORT or connection died
mar 22 16:22:00 curie smd-push[9455]: smd-server: ERROR: Unable to open Maildir/.kobo/cur/1498563708.M122624P22121.marcos,S=32234,W=32792:2,S: Maildir/.kobo/cur/1498563708.M122624P22121.marco
mar 22 16:22:00 curie smd-push[9455]: smd-server: ERROR: The problem should be transient, please retry.
mar 22 16:22:00 curie smd-push[9455]: smd-server: ERROR: Unable to open requested file.
mar 22 16:22:00 curie smd-push[9455]: default: smd-client@smd-server-anarcat: TAGS: stats::new-mails(0), del-mails(293920), bytes-received(0), xdelta-received(26995)
mar 22 16:22:00 curie smd-push[9455]: default: smd-client@smd-server-anarcat: TAGS: error::context(receive) probable-cause(network) human-intervention(avoidable) suggested-actions(retry)
mar 22 16:22:00 curie smd-push[9455]: default: smd-server@localhost: TAGS: error::context(transmit) probable-cause(simultaneous-mailbox-edit) human-intervention(avoidable) suggested-actions(r
mar 22 16:22:00 curie systemd[3199]: smd-push.service: Main process exited, code=exited, status=1/FAILURE
mar 22 16:22:00 curie systemd[3199]: smd-push.service: Failed with result 'exit-code'.
mar 22 16:22:00 curie systemd[3199]: Failed to start push emails with syncmaildir.

There it seems push tried to destroy the universe again: del-mails(293920). Interestingly, the push started again in parallel with the pull, right that minute:

mar 22 16:22:00 curie systemd[3199]: Starting push emails with syncmaildir...

... but didn't complete for a while, here's pull trying to start again:

mar 22 16:24:00 curie systemd[3199]: Starting pull emails with syncmaildir...
mar 22 16:24:00 curie smd-pull[12051]: 10466 ?        00:00:00 smd-push
mar 22 16:24:00 curie smd-pull[12051]: Already running.
mar 22 16:24:00 curie smd-pull[12051]: If this is not the case, remove /home/anarcat/.smd/lock by hand.
mar 22 16:24:00 curie smd-pull[12051]: any: smd-pushpull@localhost: TAGS: error::context(locking) probable-cause(another-instance-is-running) human-intervention(necessary) suggested-actions(run(kill 10466) run(rm /home/anarcat/.smd/lock))
mar 22 16:24:00 curie systemd[3199]: smd-pull.service: Main process exited, code=exited, status=1/FAILURE
mar 22 16:24:00 curie systemd[3199]: smd-pull.service: Failed with result 'exit-code'.
mar 22 16:24:00 curie systemd[3199]: Failed to start pull emails with syncmaildir.

... and the long push finally resolving:

mar 22 16:24:00 curie smd-push[10466]: smd-client: ERROR: Data transmission failed.
mar 22 16:24:00 curie smd-push[10466]: smd-client: ERROR: This problem is transient, please retry.
mar 22 16:24:00 curie smd-push[10466]: smd-client: ERROR: server sent ABORT or connection died
mar 22 16:24:00 curie smd-push[10466]: smd-client: ERROR: Data transmission failed.
mar 22 16:24:00 curie smd-push[10466]: smd-client: ERROR: This problem is transient, please retry.
mar 22 16:24:00 curie smd-push[10466]: smd-client: ERROR: server sent ABORT or connection died
mar 22 16:24:00 curie smd-push[10466]: smd-server: ERROR: Unable to open Maildir/.kobo/cur/1498563708.M122624P22121.marcos,S=32234,W=32792:2,S: Maildir/.kobo/cur/1498563708.M122624P22121.marcos,S=32234,W=32792:2,S: No such file or directory
mar 22 16:24:00 curie smd-push[10466]: smd-server: ERROR: The problem should be transient, please retry.
mar 22 16:24:00 curie smd-push[10466]: smd-server: ERROR: Unable to open requested file.
mar 22 16:24:00 curie smd-push[10466]: default: smd-client@smd-server-anarcat: TAGS: stats::new-mails(0), del-mails(293920), bytes-received(0), xdelta-received(26995)
mar 22 16:24:00 curie smd-push[10466]: default: smd-client@smd-server-anarcat: TAGS: error::context(receive) probable-cause(network) human-intervention(avoidable) suggested-actions(retry)
mar 22 16:24:00 curie smd-push[10466]: default: smd-server@localhost: TAGS: error::context(transmit) probable-cause(simultaneous-mailbox-edit) human-intervention(avoidable) suggested-actions(retry)
mar 22 16:24:00 curie systemd[3199]: smd-push.service: Main process exited, code=exited, status=1/FAILURE
mar 22 16:24:00 curie systemd[3199]: smd-push.service: Failed with result 'exit-code'.
mar 22 16:24:00 curie systemd[3199]: Failed to start push emails with syncmaildir.
mar 22 16:24:00 curie systemd[3199]: Starting push emails with syncmaildir...

This pattern repeats until 16:35, when that locking issue silently recovered somehow:

mar 22 16:35:03 curie systemd[3199]: Starting pull emails with syncmaildir...
mar 22 16:35:41 curie smd-pull[20788]: default: smd-client@localhost: TAGS: stats::new-mails(5), del-mails(1), bytes-received(21885), xdelta-received(6863398)
mar 22 16:35:42 curie smd-pull[21373]: register: smd-client@localhost: TAGS: stats::new-mails(0), del-mails(0), bytes-received(0), xdelta-received(215)
mar 22 16:35:42 curie systemd[3199]: smd-pull.service: Succeeded.
mar 22 16:35:42 curie systemd[3199]: Started pull emails with syncmaildir.
mar 22 16:36:35 curie systemd[3199]: Starting pull emails with syncmaildir...
mar 22 16:36:36 curie smd-pull[21738]: default: smd-client@localhost: TAGS: stats::new-mails(0), del-mails(0), bytes-received(0), xdelta-received(214)
mar 22 16:36:37 curie smd-pull[21816]: register: smd-client@localhost: TAGS: stats::new-mails(0), del-mails(0), bytes-received(0), xdelta-received(215)
mar 22 16:36:37 curie systemd[3199]: smd-pull.service: Succeeded.
mar 22 16:36:37 curie systemd[3199]: Started pull emails with syncmaildir.

... notice that huge xdelta-received there, that's 7GB right there. Mysteriously, the curie mail spool survived this, possibly because smd-pull started failing again:

mar 22 16:38:00 curie systemd[3199]: Starting pull emails with syncmaildir...
mar 22 16:38:00 curie smd-pull[23556]: 21887 ?        00:00:00 smd-push
mar 22 16:38:00 curie smd-pull[23556]: Already running.
mar 22 16:38:00 curie smd-pull[23556]: If this is not the case, remove /home/anarcat/.smd/lock by hand.
mar 22 16:38:00 curie smd-pull[23556]: any: smd-pushpull@localhost: TAGS: error::context(locking) probable-cause(another-instance-is-running) human-intervention(necessary) suggested-actions(run(kill 21887) run(rm /home/anarcat/.smd/lock))
mar 22 16:38:00 curie systemd[3199]: smd-pull.service: Main process exited, code=exited, status=1/FAILURE
mar 22 16:38:00 curie systemd[3199]: smd-pull.service: Failed with result 'exit-code'.
mar 22 16:38:00 curie systemd[3199]: Failed to start pull emails with syncmaildir.

That could have been when i got on angela to check my mail, and it was busy doing the nasty removal stuff... although the times don't match. Here is when angela came back online:

anarcat@angela:~(main)$ last
anarcat  :0           :0               Mon Mar 22 19:57   still logged in
reboot   system boot  5.10.0-0.bpo.3-a Mon Mar 22 19:57   still running
anarcat  :0           :0               Mon Mar 22 17:43 - 18:47  (01:03)
reboot   system boot  5.10.0-0.bpo.3-a Mon Mar 22 17:39   still running

Then finally the sync on curie started failing with:

mar 22 16:46:35 curie systemd[3199]: Starting pull emails with syncmaildir...
mar 22 16:46:42 curie smd-pull[27455]: smd-server: ERROR: Client aborted, removing /home/anarcat/.smd/curie-anarcat__Maildir.db.txt.new and /home/anarcat/.smd/curie-anarcat__Maildir.db.txt.mtime.new
mar 22 16:46:42 curie smd-pull[27455]: smd-client: ERROR: Failed to copy Maildir/.debian/cur/1613401668.M901837P27073.marcos,S=3740,W=3815:2,S to Maildir/.koumbit/cur/1613401640.M415457P27063.marcos,S=3790,W=3865:2,S
mar 22 16:46:42 curie smd-pull[27455]: smd-client: ERROR: The destination already exists but its content differs.
mar 22 16:46:42 curie smd-pull[27455]: smd-client: ERROR: To fix this problem you have two options:
mar 22 16:46:42 curie smd-pull[27455]: smd-client: ERROR: - rename Maildir/.koumbit/cur/1613401640.M415457P27063.marcos,S=3790,W=3865:2,S by hand so that Maildir/.debian/cur/1613401668.M901837P27073.marcos,S=3740,W=3815:2,S
mar 22 16:46:42 curie smd-pull[27455]: smd-client: ERROR:   can be copied without replacing it.
mar 22 16:46:42 curie smd-pull[27455]: smd-client: ERROR:   Executing  cd; mv -n "Maildir/.koumbit/cur/1613401640.M415457P27063.marcos,S=3790,W=3865:2,S" "Maildir/.koumbit/cur/1616446002.1.localhost"  should work.
mar 22 16:46:42 curie smd-pull[27455]: smd-client: ERROR: - run smd-push so that your changes to Maildir/.koumbit/cur/1613401640.M415457P27063.marcos,S=3790,W=3865:2,S
mar 22 16:46:42 curie smd-pull[27455]: smd-client: ERROR:   are propagated to the other mailbox
mar 22 16:46:42 curie smd-pull[27455]: default: smd-client@localhost: TAGS: error::context(copy-message) probable-cause(concurrent-mailbox-edit) human-intervention(necessary) suggested-actions(run(mv -n "/home/anarcat/.smd/workarea/Maildir/.koumbit/cur/1613401640.M415457P27063.marcos,S=3790,W=3865:2,S" "/home/anarcat/.smd/workarea/Maildir/.koumbit/tmp/1613401640.M415457P27063.marcos,S=3790,W=3865:2,S") run(smd-push default))
mar 22 16:46:42 curie systemd[3199]: smd-pull.service: Main process exited, code=exited, status=1/FAILURE
mar 22 16:46:42 curie systemd[3199]: smd-pull.service: Failed with result 'exit-code'.
mar 22 16:46:42 curie systemd[3199]: Failed to start pull emails with syncmaildir.

It went on like this until I found the problem. This is, presumably, a good thing because those emails were not being destroyed. On angela, things looked like this:

-- Reboot --
mar 22 17:39:29 angela systemd[1677]: Started run notmuch new at least once a day.
mar 22 17:39:29 angela systemd[1677]: Started run smd-pull regularly.
mar 22 17:40:46 angela systemd[1677]: Starting pull emails with syncmaildir...
mar 22 17:43:18 angela smd-pull[3916]: smd-server: ERROR: Unable to open Maildir/.tor/new/1616446842.M285912P26118.marcos,S=8860,W=8996: Maildir/.tor/new/1616446842.M285912P26118.marcos,S=886
0,W=8996: No such file or directory
mar 22 17:43:18 angela smd-pull[3916]: smd-server: ERROR: The problem should be transient, please retry.
mar 22 17:43:18 angela smd-pull[3916]: smd-server: ERROR: Unable to open requested file.
mar 22 17:43:18 angela smd-pull[3916]: smd-client: ERROR: Data transmission failed.
mar 22 17:43:18 angela smd-pull[3916]: smd-client: ERROR: This problem is transient, please retry.
mar 22 17:43:18 angela smd-pull[3916]: smd-client: ERROR: server sent ABORT or connection died
mar 22 17:43:18 angela smd-pull[3916]: default: smd-server@smd-server-anarcat: TAGS: error::context(transmit) probable-cause(simultaneous-mailbox-edit) human-intervention(avoidable) suggested
-actions(retry)
mar 22 17:43:18 angela smd-pull[3916]: default: smd-client@localhost: TAGS: error::context(receive) probable-cause(network) human-intervention(avoidable) suggested-actions(retry)
mar 22 17:43:18 angela systemd[1677]: smd-pull.service: Main process exited, code=exited, status=1/FAILURE
mar 22 17:43:18 angela systemd[1677]: smd-pull.service: Failed with result 'exit-code'.
mar 22 17:43:18 angela systemd[1677]: Failed to start pull emails with syncmaildir.
mar 22 17:43:18 angela systemd[1677]: Starting pull emails with syncmaildir...
mar 22 17:43:29 angela smd-pull[4847]: default: smd-client@localhost: TAGS: stats::new-mails(29), del-mails(0), bytes-received(401519), xdelta-received(38914)
mar 22 17:43:29 angela smd-pull[5600]: register: smd-client@localhost: TAGS: stats::new-mails(2), del-mails(0), bytes-received(92150), xdelta-received(471)
mar 22 17:43:29 angela systemd[1677]: smd-pull.service: Succeeded.
mar 22 17:43:29 angela systemd[1677]: Started pull emails with syncmaildir.
mar 22 17:43:29 angela systemd[1677]: Starting push emails with syncmaildir...
mar 22 17:43:32 angela smd-push[5693]: default: smd-client@smd-server-anarcat: TAGS: stats::new-mails(0), del-mails(0), bytes-received(0), xdelta-received(217)
mar 22 17:43:33 angela smd-push[6575]: register: smd-client@smd-server-register: TAGS: stats::new-mails(0), del-mails(0), bytes-received(0), xdelta-received(219)
mar 22 17:43:33 angela systemd[1677]: smd-push.service: Succeeded.
mar 22 17:43:33 angela systemd[1677]: Started push emails with syncmaildir.

Notice how long it took to get the first error, in that first failure: it failed after 3 minutes! Presumably that's when it started deleting all that mail. And this is during pull, not push, so the error didn't come from angela.

Affected data It seems 2GB of mail from my main INBOX was destroyed. Another 2.4GB of spam (kept for training purposes) was also destroyed, along with 700MB of Sent mail. The rest is hard to figure out, because the folders are actually still there, just smaller. So I relied on ncdu to figure out the size changes. (Note that I don't really archive (or delete much of) my mail since I use notmuch, which is why the INBOX is so large...) Concretely, according to the notmuch-new.service which still runs periodically on marcos, here are the changes that happened on the server:

mar 22 16:17:12 marcos notmuch[10729]: Added 7 new messages to the database. Removed 57985 messages. Detected 1372 file renames.
mar 22 16:22:43 marcos notmuch[12826]: No new mail. Removed 143842 messages. Detected 6072 file renames.
mar 22 16:27:02 marcos notmuch[13969]: No new mail. Removed 82071 messages. Detected 1783 file renames.
mar 22 16:29:45 marcos notmuch[15079]: Added 22743 new messages to the database. Detected 1 file rename.
mar 22 16:31:48 marcos notmuch[16196]: Added 22779 new messages to the database. Removed 5 messages.
mar 22 16:33:11 marcos notmuch[17192]: Added 3711 new messages to the database.
mar 22 16:40:41 marcos notmuch[19122]: Added 74558 new messages to the database. Detected 1 file rename.
mar 22 16:43:21 marcos notmuch[20325]: Added 9061 new messages to the database. Detected 4 file renames.
mar 22 17:43:08 marcos notmuch[7420]: Added 1793 new messages to the database. Detected 6 file renames.

That is basically the entire mail spool destroyed at first (283 898 messages), and then bits and pieces of it progressively re-added (134 645 messages), somehow, so 149 253 mails were lost, presumably.

Recovery I disabled the services all over the place:

systemctl --user --now disable smd-pull.service smd-pull.timer smd-push.service smd-push.timer notmuch-new.service notmuch-new.timer

(Well, technically, I did that only on angela, as I thought the problem was there. Luckily, curie kept going but it seems like it was harmless.) I made a backup of the mail spool on curie:

tar cf - Maildir/   pv -s 14G   gzip -c > Maildir.tgz

Then I crossed my fingers and ran smd-push -v -s, as that was suggested by smd error codes themselves. That thankfully started restoring mail. It failed a few times on weird cases of files being duplicates, but I resolved this by following the instructions. Or mostly: I actually deleted the files instead of moving them, which made smd even unhappier (if there ever was such a thing). I had to recreate some of those files, so, lesson learned: do follow the advice smd gives you, even if it seems useless or strange. But then smd-push was humming along, uploading tens of thousands of messages, saturating the upload in the office, refilling the mail spool on the server... yaay!... ? Except... well, of course that didn't quite work: the mail spool in the office eventually started to grow beyond the size of the mail spool on the workstation. That is what smd-push eventually settled on:

default: smd-client@smd-server-anarcat: TAGS: error::context(receive) probable-cause(network) human-intervention(avoidable) suggested-actions(retry)
default: smd-client@smd-server-anarcat: TAGS: error::context(receive) probable-cause(network) human-intervention(avoidable) suggested-actions(retry)
default: smd-client@smd-server-anarcat: TAGS: stats::new-mails(151697), del-mails(0), bytes-received(7539147811), xdelta-received(10881198)

It recreated 151 697 emails, adding about 2000 emails to the pool, kind of from nowhere at all. On marcos, before:

ncdu 1.13 ~ Use the arrow keys to navigate, press ? for help
--- /home/anarcat/Maildir ------------------------------------
    4,0 GiB [##########] /.notmuch
  717,3 MiB [#         ] /.Archives.2014
  498,2 MiB [#         ] /.feeds.debian-planet
  453,1 MiB [#         ] /.Archives.2012
  414,5 MiB [#         ] /.debian
  408,2 MiB [#         ] /.quoifaire
  389,8 MiB [          ] /.rapports
  356,6 MiB [          ] /.tor
  182,6 MiB [          ] /.koumbit
  179,8 MiB [          ] /tmp
   56,8 MiB [          ] /.nn
   43,0 MiB [          ] /.act-mtl
   32,6 MiB [          ] /.feeds.sysadvent
   31,7 MiB [          ] /.feeds.releases
   31,4 MiB [          ] /.Sent.2005
   26,3 MiB [          ] /.sage
   25,5 MiB [          ] /.freedombox
   24,0 MiB [          ] /.feeds.git-annex
   21,1 MiB [          ] /.Archives.2011
   19,1 MiB [          ] /.Sent.2003
   16,7 MiB [          ] /.bugtraq
   16,2 MiB [          ] /.mlug
 Total disk usage:   8,0 GiB  Apparent size:   7,6 GiB  Items: 184426

After:

ncdu 1.13 ~ Use the arrow keys to navigate, press ? for help
--- /home/anarcat/Maildir ------------------------------------
    4,7 GiB [##########] /.notmuch
    2,7 GiB [#####     ] /.junk
    1,9 GiB [###       ] /cur
  717,3 MiB [#         ] /.Archives.2014
  659,3 MiB [#         ] /.Sent
  513,9 MiB [#         ] /.Archives.2012
  498,2 MiB [#         ] /.feeds.debian-planet
  449,6 MiB [          ] /.Archives.2015
  414,5 MiB [          ] /.debian
  408,2 MiB [          ] /.quoifaire
  389,8 MiB [          ] /.rapports
  380,8 MiB [          ] /.Archives.2013
  356,6 MiB [          ] /.tor
  261,1 MiB [          ] /.Archives.2011
  240,9 MiB [          ] /.koumbit
  183,6 MiB [          ] /.Archives.2010
  179,8 MiB [          ] /tmp
  128,4 MiB [          ] /.lists
  106,1 MiB [          ] /.inso-interne
  103,0 MiB [          ] /.github
   75,0 MiB [          ] /.nanog
   69,8 MiB [          ] /.full-disclosure
 Total disk usage:  16,2 GiB  Apparent size:  15,5 GiB  Items: 341143

That is 156 717 files more. On curie:

ncdu 1.13 ~ Use the arrow keys to navigate, press ? for help
--- /home/anarcat/Maildir ------------------------------------------------------------------
    2,7 GiB [##########] /.junk
    2,3 GiB [########  ] /.notmuch
    1,9 GiB [######    ] /cur
  661,2 MiB [##        ] /.Archives.2014
  655,3 MiB [##        ] /.Sent
  512,0 MiB [#         ] /.Archives.2012
  447,3 MiB [#         ] /.Archives.2015
  438,5 MiB [#         ] /.feeds.debian-planet
  406,5 MiB [#         ] /.quoifaire
  383,6 MiB [#         ] /.debian
  378,6 MiB [#         ] /.Archives.2013
  303,3 MiB [#         ] /.tor
  296,0 MiB [#         ] /.rapports
  237,6 MiB [          ] /.koumbit
  233,2 MiB [          ] /.Archives.2011
  182,1 MiB [          ] /.Archives.2010
  127,0 MiB [          ] /.lists
  104,8 MiB [          ] /.inso-interne
  102,7 MiB [          ] /.register
   89,6 MiB [          ] /.github
   67,1 MiB [          ] /.full-disclosure
   66,5 MiB [          ] /.nanog
 Total disk usage:  13,3 GiB  Apparent size:  12,6 GiB  Items: 342465

Interestingly, there are more files, but less disk usage. It's possible the notmuch database there is more efficient. So maybe there's nothing to worry about. Last night's marcos backup has:

root@marcos:/home/anarcat# find /mnt/home/anarcat/Maildir   pv -l   wc -l
 341k 0:00:16 [20,4k/s] [                             <=>                                                                                                                                     ]
341040

... 341040 files, which seems about right, considering some mail was delivered during the day. An audit can be performed with hashdeep:

borg mount /media/sdb2/borg/::marcos-auto-2021-03-22 /mnt
hashdeep -c sha256 -r /mnt/home/anarcat/Maildir   pv -l -s 341k > Maildir-backup-manifest.txt

And then compared with:

hashdeep -c sha256 -k Maildir-backup-manifest.txt Maildir/

Some extra files should show up in the Maildir, and very few should actually be missing, because I shouldn't have deleted mail from the previous day the next day, or at least very few. The actual summary hashdeep gave me was:

hashdeep: Audit failed
   Input files examined: 0
  Known files expecting: 0
          Files matched: 339080
Files partially matched: 0
            Files moved: 782
        New files found: 107
  Known files not found: 106

So 106 files added, 107 deleted. Seems good enough for me... Postfix was stopped at Mar 22 21:12:59 to try and stop external events from confusing things even further. I reviewed the delivery log to see if mail that came in during the problem window disappeared:

grep 'dovecot:.*stored mail into mailbox' /var/log/mail.log  
  tail -20  
  sed 's/.*msgid=<//;s/>.*//'   
  while read msgid; do 
    notmuch count --exclude=false id:$msgid  
      grep 0 && echo $msgid missing;
  done

And things looked okay. Now of course if we go further back, we find mail I actually deleted (because I do do that sometimes), so it's hard to use this log as an audit trail. We can only hope that the curie spool is sufficiently coherent to be relied on. Worst case, we'll have to restore from last night's backup, but that's getting far away now: I get hundreds of mails a day in that mail spool, and reseting back to last night does not seem like a good idea. A dry run of smd-pull on angela seems to agree that it's missing some files:

default: smd-client@localhost: TAGS: stats::new-mails(154914), del-mails(0), bytes-received(0), xdelta-received(0)

... a number of mails somewhere in between the other two, go figure. A "wet" run of this was started, without deletion (-n), which gave us:

default: smd-client@localhost: TAGS: stats::new-mails(154911), del-mails(0), bytes-received(7658160107), xdelta-received(10837609)

Strange that it sync'd three less emails, but that's still better than nothing, and we have a mail spool on angela again:

anarcat@angela:~(main)$ notmuch new
purging with prefix '.': spam moved (0), ham moved (0), deleted (0), done
Note: Ignoring non-mail file: /home/anarcat/Maildir//.uidvalidity
Processed 1779 total files in 26s (66 files/sec.).
Added 1190 new messages to the database. Removed 3 messages. Detected 593 file renames.
tagging with prefix '.': spam, sent, feeds, koumbit, tor, lists, rapports, folders, done.

Notice how only 1190 messages were re-added, that is because I killed notmuch before it had time to remove all those mails from its database.

Possible causes I am totally at a loss as to why `smd` started destroying everything like it did. But a few things come to mind:

I rewired my office on that day.

This meant unplugging `curie`, the workstation.

It has a bad CMOS battery (known problem), so it jumped around the time continuum a few times, sometimes by years.

The `smd` services are ran from a systemd unit with `OnCalendar=*:0/2`. I have heard that it's possible that major time jumps "pile up" execution of jobs, and it seems this happened in this case.

It's possible that locking in `smd` is not as great as it could be, and that it corrupted its internal data structures on `curie`, which led it to command a destruction of the remote mail spool.

It's also possible that there was a disk failure on the server, `marcos`. But since it's running on a (software) RAID-1 array, and no errors have been found (according to `dmesg`), I don't think that's a plausible hypothesis.

Lessons learned

follow what `smd` says, even if it seems useless or strange.

trust but verify: just backup everything before you do anything, especially the largest data set.

daily backups are not great for email, unless you're ready to lose a day of email (which I'm not).

hashdeep is great. I keep finding new use cases for it. Last time it was to audit my camera SD card to make sure I didn't forget anything, and now this. it's fast and powerful.

borg is great too. the FUSE mount was especially useful, and it was pretty fast to explore the backup, even through that overhead: checksumming 15GB of mail took about 35 minutes, which gives a respectable 8MB/s, probably bottlenecked by the crap external USB drive I use for backups (!).

I really need to finish my backup system so that I have automated offsite backups, although in this case that would actually have been much slower (certainly not 8MB/s!).

Workarounds and solutions I setup fake-hwclock on curie, so that the next power failure will not upset my clock that badly. I am thinking of switching to ZFS or BTRFS for most of my filesystems, so that I can use filesystem snapshots (including remotely!) as a backup strategy. This seems so much more powerful than crawling the filesystem for changes, and allows for truly offsite backups protected from an attacker (hopefully). But it's a long way there. I'm also thinking of rebuilding my mail setup without `smd`. It's not the first time something like this happens with `smd`. It's the first time I am more confident it's the root cause of the problem, however, and it makes me really nervous for the future. I have used offlineimap in the past and it seems it was finally ported to Python 3 so that could be an option again. isync/mbsync is another option, which I tried before but do not remember why I didn't switch. A complete redesign with something like getmail and/or nncp could also be an option. But alas, I lack the time to go crazy with those experiments. Somehow, doing like everyone else and just going with Google still doesn't seem to be an option for me. Screw big tech. But I am afraid they will win, eventually. In any case, I'm just happy I got mail again, strangely.

At the Wikimedia Foundation they configure basically all servers with IPv4/IPv6 dual stack, at least in the control plane interface (those used for SSH management, etc). IPv6 is not supported yet on the Cloud Services dataplane (openstack), but it will in the near future. An elegant solution for this IPv4/IPv6 dual stack configuration in the control plane is to embed the IPv4 address into the IPv6 address, something like this:

IPv4: 208.80.154.23
IPv6: 2620:0:861:1:208:80:154:23
                   ^^^^^^^^^^^^^

The gateways send prefix advertisements and by default IPv6 autoconfiguration uses such routers prefixes plus the interface MAC address to build the final address. This behavior can be somewhat changed, you can explicitly set some data instead of the MAC address for the kernel to use when building the final IPv6 address. The trick is to use the ip token command, and further context and reasoning for this can be seen in the puppet manifest that the SRE team uses to configure this:

The token command explicitly configures the lower 64 bits that will be used with any autoconf
address, as opposed to one derived from the macaddr. This aligns the autoconf-assigned address with
the fixed one set above, and can do so as a pre-up command to avoid ever having another address
even temporarily, when this is all set up before boot.

For example:

user@debian:~$ sudo ip token list
token ::208:80:154:23 dev eno1
token :: dev eno2
token :: dev eno3
token :: dev eno4
user@debian:~$ sudo ip token set dev eno2 ::beef
user@debian:~$ ip token get dev eno2
token ::beef dev eno2
user@debian:~$ ip token list
token ::208:80:154:23 dev eno1
token ::beef dev eno2
token :: dev eno3
token :: dev eno4

I was installing a new server the other day and the networking service (ifupdown) was failing to bring the interface up. The issue was the ip token command failing:

root@cloudgw2002-dev:~# ip token set ::10:192:20:18 dev eno1
RTNETLINK answers: Invalid argument

RTNETLINK error reporting is awful. What could be wrong about that command? Well, I had to dig into the kernel source code to try figuring out where was that EINVAL being generated. The routine can be seen in the function inet6_set_iftoken() (source):

static int inet6_set_iftoken(struct inet6_dev *idev, struct in6_addr *token)
 
	struct inet6_ifaddr *ifp;
	struct net_device *dev = idev->dev;
	bool clear_token, update_rs = false;
	struct in6_addr ll_addr;
	ASSERT_RTNL();
	if (!token)
		return -EINVAL;
	if (dev->flags & (IFF_LOOPBACK   IFF_NOARP))
		return -EINVAL;
	if (!ipv6_accept_ra(idev))
		return -EINVAL;
	if (idev->cnf.rtr_solicits == 0)
		return -EINVAL;
[..]

I couldn t identify the reason at first glance, apparently I pass every check in there:

the token is being set, obviously
the interface is not loopback
the interface has the sysctl net.ipv6.conf.eno1.accept_ra = 1 (enabled)
the interface has the sysctl net.ipv6.conf.eno1.router_solicitations = -1 (disabled)

Something was wrong here. Upon deeper checks, I finally read the ipv6_accept_ra() function (source):

static inline bool ipv6_accept_ra(struct inet6_dev *idev)
 
	/* If forwarding is enabled, RA are not accepted unless the special
	 * hybrid mode (accept_ra=2) is enabled.
	 */
	return idev->cnf.forwarding ? idev->cnf.accept_ra == 2 :
	    idev->cnf.accept_ra;
 

That was it! Forwarding was enabled on the interface, and it shouldn t. I fixed my configuration with a simple patch for the sysctl configuration. Original issue on the Wikimedia Foundation ticketing system: Phabricator T277287

Search Results: "xam"

17 April 2021

Dirk Eddelbuettel: RcppAPT 0.0.7: Micro Update

Changes in version 0.0.7 (2021-04-16)

Add rmarkdown to Suggests: as an implicit conditional dependency

Switch vignette to minidown and its water framework, add minidown to Suggests as well

Update two URLs in the README.md file

15 April 2021

Martin Michlmayr: ledger2beancount 2.6 released

14 April 2021

Russell Coker: Basics of Linux Kernel Debugging

11 April 2021

Jelmer Vernooij: The upstream ontologist

Jonathan Dowland: 2020 in short fiction

9 April 2021

Michael Prokop: A Ceph war story

8 April 2021

Sean Whitton: consfigurator-live-build

6 April 2021

Jelmer Vernooij: Automatic Fixing of Debian Build Dependencies

5 April 2021

Jelmer Vernooij: The Buildlog Consultant

1 April 2021

Raphaël Hertzog: Challenging times for Freexian (3/4)

31 March 2021

Timo Jyrinki: MotionPhoto / MicroVideo File Formats on Pixel Phones

30 March 2021

Dirk Eddelbuettel: x13binary 1.1.39-3 on CRAN: (Imperfect) Package Updates

Emmanuel Kasper: Playing with cri-o, a container runtime built for Kubernetes

Molly de Blanc: Helping

Above all, just be nice. Be nice. It s basically the best thing you can do for free software.

29 March 2021

Russ Allbery: Review: JavaScript: The Definitive Guide

28 March 2021

Norbert Preining: RMS, Debian, and the world

27 March 2021

Antonio Terceiro: Migrating from Chef to itamae

25 March 2021

Jelmer Vernooij: The Buildlog Consultant

23 March 2021

Antoine Beaupr : Major email crash with syncmaildir

18 March 2021

Arturo Borrero Gonz lez: Debugging ip token set RTNETLINK error

Search Results: "xam"

17 April 2021

Changes in version 0.0.7 (2021-04-16) Add rmarkdown to Suggests: as an implicit conditional dependency Switch vignette to minidown and its water framework, add minidown to Suggests as well Update two URLs in the README.md file

15 April 2021

14 April 2021

11 April 2021

9 April 2021

8 April 2021

6 April 2021

5 April 2021

1 April 2021

31 March 2021

30 March 2021

Above all, just be nice. Be nice. It s basically the best thing you can do for free software.

29 March 2021

28 March 2021

27 March 2021

25 March 2021

23 March 2021

18 March 2021

Changes in version 0.0.7 (2021-04-16)

Add rmarkdown to Suggests: as an implicit conditional dependency

Switch vignette to minidown and its water framework, add minidown to Suggests as well

Update two URLs in the README.md file