Search Results: "marco"

9 July 2022

Dirk Eddelbuettel: Rcpp 1.0.9 on CRAN: Regular Updates

rcpp logo The Rcpp team is please to announce the newest release 1.0.9 of Rcpp which hit CRAN late yesterday, and has been uploaded to Debian as well. Windows and macOS builds should appear at CRAN in the next few days, as will builds in different Linux distribution and of course at r2u. The release was prepared om July 2, but it took a few days to clear a handful of spurious errors as false positives with CRAN this can when the set of reverse dependencies is so large, and the CRAN team remains busy. This release continues with the six-months cycle started with release 1.0.5 in July 2020. (This time, CRAN had asked for an interim release to silence a C++ warning; we then needed a quick follow-up to tweak tests.) As a reminder, interim dev or rc releases should generally be available in the Rcpp drat repo. These rolling release tend to work just as well, and are also fully tested against all reverse-dependencies. Rcpp has become the most popular way of enhancing R with C or C++ code. Right now, around 2559 packages on CRAN depend on Rcpp for making analytical code go faster and further, along with 252 in BioConductor. On CRAN, 13.9% of all packages depend (directly) on CRAN, and 58.5% of all compiled packages do. From the cloud mirror of CRAN (which is but a subset of all CRAN downloads), Rcpp has been downloaded 61.5 million times. This release is incremental and extends Rcpp with a number of small improvements all detailed in the NEWS file as well as below. We want to highlight the external contributions: a precious list tag is cleared on removal, and a move constructor and assignment for strings has been added (thanks to Dean Scarff), and (thanks to Bill Denney and Marco Colombo) two minor errors are corrected in the vignette documentation. A big Thank You! to everybody who contributed pull request, opened or answered issues, or questions at StackOverflow or on the mailing list. The full list of details follows.

Changes in Rcpp hotfix release version 1.0.9 (2022-07-02)
  • Changes in Rcpp API:
    • Accomodate C++98 compilation by adjusting attributes.cpp (Dirk in #1193 fixing #1192)
    • Accomodate newest compilers replacing deprecated std::unary_function and std::binary_function with std::function (Dirk in #1202 fixing #1201 and CRAN request)
    • Upon removal from precious list, the tag is set to null (I aki in #1205 fixing #1203)
    • Move constructor and assignment for strings have been added (Dean Scarff in #1219).
  • Changes in Rcpp Documentation:
    • Adjust one overflowing column (Bill Denney in #1196 fixing #1195)
    • Correct a typo in the FAQ (Marco Colombo in #1217)
  • Changes in Rcpp Deployment:
    • Accomodate four digit version numbers in unit test (Dirk)
    • Do not run complete test suite to limit test time to CRAN preference (Dirk in #1206)
    • Small updates to the CI test containers have been made
    • Some of changes also applied to an interim release 1.0.8.3 made for CRAN on 2022-03-14.

Thanks to my CRANberries, you can also look at a diff to the previous release. Questions, comments etc should go to the rcpp-devel mailing list off the R-Forge page. Bugs reports are welcome at the GitHub issue tracker as well (where one can also search among open or closed issues); questions are also welcome under rcpp tag at StackOverflow which also allows searching among the (currently) 2886 previous questions. 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.

23 January 2022

Antoine Beaupr : Switching from OpenNTPd to Chrony

A friend recently reminded me of the existence of chrony, a "versatile implementation of the Network Time Protocol (NTP)". The excellent introduction is worth quoting in full:
It can synchronise the system clock with NTP servers, reference clocks (e.g. GPS receiver), and manual input using wristwatch and keyboard. It can also operate as an NTPv4 (RFC 5905) server and peer to provide a time service to other computers in the network. It is designed to perform well in a wide range of conditions, including intermittent network connections, heavily congested networks, changing temperatures (ordinary computer clocks are sensitive to temperature), and systems that do not run continuosly, or run on a virtual machine. Typical accuracy between two machines synchronised over the Internet is within a few milliseconds; on a LAN, accuracy is typically in tens of microseconds. With hardware timestamping, or a hardware reference clock, sub-microsecond accuracy may be possible.
Now that's already great documentation right there. What it is, why it's good, and what to expect from it. I want more. They have a very handy comparison table between chrony, ntp and openntpd.

My problem with OpenNTPd Following concerns surrounding the security (and complexity) of the venerable ntp program, I have, a long time ago, switched to using openntpd on all my computers. I hadn't thought about it until I recently noticed a lot of noise on one of my servers:
jan 18 10:09:49 curie ntpd[1069]: adjusting local clock by -1.604366s
jan 18 10:08:18 curie ntpd[1069]: adjusting local clock by -1.577608s
jan 18 10:05:02 curie ntpd[1069]: adjusting local clock by -1.574683s
jan 18 10:04:00 curie ntpd[1069]: adjusting local clock by -1.573240s
jan 18 10:02:26 curie ntpd[1069]: adjusting local clock by -1.569592s
You read that right, openntpd was constantly rewinding the clock, sometimes in less than two minutes. The above log was taken while doing diagnostics, looking at the last 30 minutes of logs. So, on average, one 1.5 seconds rewind per 6 minutes! That might be due to a dying real time clock (RTC) or some other hardware problem. I know for a fact that the CMOS battery on that computer (curie) died and I wasn't able to replace it (!). So that's partly garbage-in, garbage-out here. But still, I was curious to see how chrony would behave... (Spoiler: much better.) But I also had trouble on another workstation, that one a much more recent machine (angela). First, it seems OpenNTPd would just fail at boot time:
anarcat@angela:~(main)$ sudo systemctl status openntpd
  openntpd.service - OpenNTPd Network Time Protocol
     Loaded: loaded (/lib/systemd/system/openntpd.service; enabled; vendor pres>
     Active: inactive (dead) since Sun 2022-01-23 09:54:03 EST; 6h ago
       Docs: man:openntpd(8)
    Process: 3291 ExecStartPre=/usr/sbin/ntpd -n $DAEMON_OPTS (code=exited, sta>
    Process: 3294 ExecStart=/usr/sbin/ntpd $DAEMON_OPTS (code=exited, status=0/>
   Main PID: 3298 (code=exited, status=0/SUCCESS)
        CPU: 34ms
jan 23 09:54:03 angela systemd[1]: Starting OpenNTPd Network Time Protocol...
jan 23 09:54:03 angela ntpd[3291]: configuration OK
jan 23 09:54:03 angela ntpd[3297]: ntp engine ready
jan 23 09:54:03 angela ntpd[3297]: ntp: recvfrom: Permission denied
jan 23 09:54:03 angela ntpd[3294]: Terminating
jan 23 09:54:03 angela systemd[1]: Started OpenNTPd Network Time Protocol.
jan 23 09:54:03 angela systemd[1]: openntpd.service: Succeeded.
After a restart, somehow it worked, but it took a long time to sync the clock. At first, it would just not consider any peer at all:
anarcat@angela:~(main)$ sudo ntpctl -s all
0/20 peers valid, clock unsynced
peer
   wt tl st  next  poll          offset       delay      jitter
159.203.8.72 from pool 0.debian.pool.ntp.org
    1  5  2    6s    6s             ---- peer not valid ----
138.197.135.239 from pool 0.debian.pool.ntp.org
    1  5  2    6s    7s             ---- peer not valid ----
216.197.156.83 from pool 0.debian.pool.ntp.org
    1  4  1    2s    9s             ---- peer not valid ----
142.114.187.107 from pool 0.debian.pool.ntp.org
    1  5  2    5s    6s             ---- peer not valid ----
216.6.2.70 from pool 1.debian.pool.ntp.org
    1  4  2    2s    8s             ---- peer not valid ----
207.34.49.172 from pool 1.debian.pool.ntp.org
    1  4  2    0s    5s             ---- peer not valid ----
198.27.76.102 from pool 1.debian.pool.ntp.org
    1  5  2    5s    5s             ---- peer not valid ----
158.69.254.196 from pool 1.debian.pool.ntp.org
    1  4  3    1s    6s             ---- peer not valid ----
149.56.121.16 from pool 2.debian.pool.ntp.org
    1  4  2    5s    9s             ---- peer not valid ----
162.159.200.123 from pool 2.debian.pool.ntp.org
    1  4  3    1s    6s             ---- peer not valid ----
206.108.0.131 from pool 2.debian.pool.ntp.org
    1  4  1    6s    9s             ---- peer not valid ----
205.206.70.40 from pool 2.debian.pool.ntp.org
    1  5  2    8s    9s             ---- peer not valid ----
2001:678:8::123 from pool 2.debian.pool.ntp.org
    1  4  2    5s    9s             ---- peer not valid ----
2606:4700:f1::1 from pool 2.debian.pool.ntp.org
    1  4  3    2s    6s             ---- peer not valid ----
2607:5300:205:200::1991 from pool 2.debian.pool.ntp.org
    1  4  2    5s    9s             ---- peer not valid ----
2607:5300:201:3100::345c from pool 2.debian.pool.ntp.org
    1  4  4    1s    6s             ---- peer not valid ----
209.115.181.110 from pool 3.debian.pool.ntp.org
    1  5  2    5s    6s             ---- peer not valid ----
205.206.70.42 from pool 3.debian.pool.ntp.org
    1  4  2    0s    6s             ---- peer not valid ----
68.69.221.61 from pool 3.debian.pool.ntp.org
    1  4  1    2s    9s             ---- peer not valid ----
162.159.200.1 from pool 3.debian.pool.ntp.org
    1  4  3    4s    7s             ---- peer not valid ----
Then it would accept them, but still wouldn't sync the clock:
anarcat@angela:~(main)$ sudo ntpctl -s all
20/20 peers valid, clock unsynced
peer
   wt tl st  next  poll          offset       delay      jitter
159.203.8.72 from pool 0.debian.pool.ntp.org
    1  8  2    5s    6s         0.672ms    13.507ms     0.442ms
138.197.135.239 from pool 0.debian.pool.ntp.org
    1  7  2    4s    8s         1.260ms    13.388ms     0.494ms
216.197.156.83 from pool 0.debian.pool.ntp.org
    1  7  1    3s    5s        -0.390ms    47.641ms     1.537ms
142.114.187.107 from pool 0.debian.pool.ntp.org
    1  7  2    1s    6s        -0.573ms    15.012ms     1.845ms
216.6.2.70 from pool 1.debian.pool.ntp.org
    1  7  2    3s    8s        -0.178ms    21.691ms     1.807ms
207.34.49.172 from pool 1.debian.pool.ntp.org
    1  7  2    4s    8s        -5.742ms    70.040ms     1.656ms
198.27.76.102 from pool 1.debian.pool.ntp.org
    1  7  2    0s    7s         0.170ms    21.035ms     1.914ms
158.69.254.196 from pool 1.debian.pool.ntp.org
    1  7  3    5s    8s        -2.626ms    20.862ms     2.032ms
149.56.121.16 from pool 2.debian.pool.ntp.org
    1  7  2    6s    8s         0.123ms    20.758ms     2.248ms
162.159.200.123 from pool 2.debian.pool.ntp.org
    1  8  3    4s    5s         2.043ms    14.138ms     1.675ms
206.108.0.131 from pool 2.debian.pool.ntp.org
    1  6  1    0s    7s        -0.027ms    14.189ms     2.206ms
205.206.70.40 from pool 2.debian.pool.ntp.org
    1  7  2    1s    5s        -1.777ms    53.459ms     1.865ms
2001:678:8::123 from pool 2.debian.pool.ntp.org
    1  6  2    1s    8s         0.195ms    14.572ms     2.624ms
2606:4700:f1::1 from pool 2.debian.pool.ntp.org
    1  7  3    6s    9s         2.068ms    14.102ms     1.767ms
2607:5300:205:200::1991 from pool 2.debian.pool.ntp.org
    1  6  2    4s    9s         0.254ms    21.471ms     2.120ms
2607:5300:201:3100::345c from pool 2.debian.pool.ntp.org
    1  7  4    5s    9s        -1.706ms    21.030ms     1.849ms
209.115.181.110 from pool 3.debian.pool.ntp.org
    1  7  2    0s    7s         8.907ms    75.070ms     2.095ms
205.206.70.42 from pool 3.debian.pool.ntp.org
    1  7  2    6s    9s        -1.729ms    53.823ms     2.193ms
68.69.221.61 from pool 3.debian.pool.ntp.org
    1  7  1    1s    7s        -1.265ms    46.355ms     4.171ms
162.159.200.1 from pool 3.debian.pool.ntp.org
    1  7  3    4s    8s         1.732ms    35.792ms     2.228ms
It took a solid five minutes to sync the clock, even though the peers were considered valid within a few seconds:
jan 23 15:58:41 angela systemd[1]: Started OpenNTPd Network Time Protocol.
jan 23 15:58:58 angela ntpd[84086]: peer 142.114.187.107 now valid
jan 23 15:58:58 angela ntpd[84086]: peer 198.27.76.102 now valid
jan 23 15:58:58 angela ntpd[84086]: peer 207.34.49.172 now valid
jan 23 15:58:58 angela ntpd[84086]: peer 209.115.181.110 now valid
jan 23 15:58:59 angela ntpd[84086]: peer 159.203.8.72 now valid
jan 23 15:58:59 angela ntpd[84086]: peer 138.197.135.239 now valid
jan 23 15:58:59 angela ntpd[84086]: peer 162.159.200.123 now valid
jan 23 15:58:59 angela ntpd[84086]: peer 2607:5300:201:3100::345c now valid
jan 23 15:59:00 angela ntpd[84086]: peer 2606:4700:f1::1 now valid
jan 23 15:59:00 angela ntpd[84086]: peer 158.69.254.196 now valid
jan 23 15:59:01 angela ntpd[84086]: peer 216.6.2.70 now valid
jan 23 15:59:01 angela ntpd[84086]: peer 68.69.221.61 now valid
jan 23 15:59:01 angela ntpd[84086]: peer 205.206.70.40 now valid
jan 23 15:59:01 angela ntpd[84086]: peer 205.206.70.42 now valid
jan 23 15:59:02 angela ntpd[84086]: peer 162.159.200.1 now valid
jan 23 15:59:04 angela ntpd[84086]: peer 216.197.156.83 now valid
jan 23 15:59:05 angela ntpd[84086]: peer 206.108.0.131 now valid
jan 23 15:59:05 angela ntpd[84086]: peer 2001:678:8::123 now valid
jan 23 15:59:05 angela ntpd[84086]: peer 149.56.121.16 now valid
jan 23 15:59:07 angela ntpd[84086]: peer 2607:5300:205:200::1991 now valid
jan 23 16:03:47 angela ntpd[84086]: clock is now synced
That seems kind of odd. It was also frustrating to have very little information from ntpctl about the state of the daemon. I understand it's designed to be minimal, but it could inform me on his known offset, for example. It does tell me about the offset with the different peers, but not as clearly as one would expect. It's also unclear how it disciplines the RTC at all.

Compared to chrony Now compare with chrony:
jan 23 16:07:16 angela systemd[1]: Starting chrony, an NTP client/server...
jan 23 16:07:16 angela chronyd[87765]: chronyd version 4.0 starting (+CMDMON +NTP +REFCLOCK +RTC +PRIVDROP +SCFILTER +SIGND +ASYNCDNS +NTS +SECHASH +IPV6 -DEBUG)
jan 23 16:07:16 angela chronyd[87765]: Initial frequency 3.814 ppm
jan 23 16:07:16 angela chronyd[87765]: Using right/UTC timezone to obtain leap second data
jan 23 16:07:16 angela chronyd[87765]: Loaded seccomp filter
jan 23 16:07:16 angela systemd[1]: Started chrony, an NTP client/server.
jan 23 16:07:21 angela chronyd[87765]: Selected source 206.108.0.131 (2.debian.pool.ntp.org)
jan 23 16:07:21 angela chronyd[87765]: System clock TAI offset set to 37 seconds
First, you'll notice there's none of that "clock synced" nonsense, it picks a source, and then... it's just done. Because the clock on this computer is not drifting that much, and openntpd had (presumably) just sync'd it anyways. And indeed, if we look at detailed stats from the powerful chronyc client:
anarcat@angela:~(main)$ sudo chronyc tracking
Reference ID    : CE6C0083 (ntp1.torix.ca)
Stratum         : 2
Ref time (UTC)  : Sun Jan 23 21:07:21 2022
System time     : 0.000000311 seconds slow of NTP time
Last offset     : +0.000807989 seconds
RMS offset      : 0.000807989 seconds
Frequency       : 3.814 ppm fast
Residual freq   : -24.434 ppm
Skew            : 1000000.000 ppm
Root delay      : 0.013200894 seconds
Root dispersion : 65.357254028 seconds
Update interval : 1.4 seconds
Leap status     : Normal
We see that we are nanoseconds away from NTP time. That was ran very quickly after starting the server (literally in the same second as chrony picked a source), so stats are a bit weird (e.g. the Skew is huge). After a minute or two, it looks more reasonable:
Reference ID    : CE6C0083 (ntp1.torix.ca)
Stratum         : 2
Ref time (UTC)  : Sun Jan 23 21:09:32 2022
System time     : 0.000487002 seconds slow of NTP time
Last offset     : -0.000332960 seconds
RMS offset      : 0.000751204 seconds
Frequency       : 3.536 ppm fast
Residual freq   : +0.016 ppm
Skew            : 3.707 ppm
Root delay      : 0.013363549 seconds
Root dispersion : 0.000324015 seconds
Update interval : 65.0 seconds
Leap status     : Normal
Now it's learning how good or bad the RTC clock is ("Frequency"), and is smoothly adjusting the System time to follow the average offset (RMS offset, more or less). You'll also notice the Update interval has risen, and will keep expanding as chrony learns more about the internal clock, so it doesn't need to constantly poll the NTP servers to sync the clock. In the above, we're 487 micro seconds (less than a milisecond!) away from NTP time. (People interested in the explanation of every single one of those fields can read the excellent chronyc manpage. That thing made me want to nerd out on NTP again!) On the machine with the bad clock, chrony also did a 1.5 second adjustment, but just once, at startup:
jan 18 11:54:33 curie chronyd[2148399]: Selected source 206.108.0.133 (2.debian.pool.ntp.org) 
jan 18 11:54:33 curie chronyd[2148399]: System clock wrong by -1.606546 seconds 
jan 18 11:54:31 curie chronyd[2148399]: System clock was stepped by -1.606546 seconds 
jan 18 11:54:31 curie chronyd[2148399]: System clock TAI offset set to 37 seconds 
Then it would still struggle to keep the clock in sync, but not as badly as openntpd. Here's the offset a few minutes after that above startup:
System time     : 0.000375352 seconds slow of NTP time
And again a few seconds later:
System time     : 0.001793046 seconds slow of NTP time
I don't currently have access to that machine, and will update this post with the latest status, but so far I've had a very good experience with chrony on that machine, which is a testament to its resilience, and it also just works on my other machines as well.

Extras On top of "just working" (as demonstrated above), I feel that chrony's feature set is so much superior... Here's an excerpt of the extras in chrony, taken from the comparison table:
  • source frequency tracking
  • source state restore from file
  • temperature compensation
  • ready for next NTP era (year 2036)
  • replace unreachable / falseticker servers
  • aware of jitter
  • RTC drift tracking
  • RTC trimming
  • Restore time from file w/o RTC
  • leap seconds correction, in slew mode
  • drops root privileges
I even understand some of that stuff. I think. So kudos to the chrony folks, I'm switching.

Caveats One thing to keep in mind in the above, however is that it's quite possible chrony does as bad of a job as openntpd on that old machine, and just doesn't tell me about it. For example, here's another log sample from another server (marcos):
jan 23 11:13:25 marcos ntpd[1976694]: adjusting clock frequency by 0.451035 to -16.420273ppm
I get those basically every day, which seems to show that it's at least trying to keep track of the hardware clock. In other words, it's quite possible I have no idea what I'm talking about and you definitely need to take this article with a grain of salt. I'm not an NTP expert. Update: I should also mentioned that I haven't evaluated systemd-timesyncd, for a few reasons:
  1. I have enough things running under systemd
  2. I wasn't aware of it when I started writing this
  3. I couldn't find good documentation on it... later I found the above manpage and of course the Arch Wiki but that is very minimal
  4. therefore I can't tell how it compares with chrony or (open)ntpd, so I don't see an enticing reason to switch
It has a few things going for it though:
  • it's likely shipped with your distribution already
  • it drops privileges (possibly like chrony, unclear if it also has seccomp filters)
  • it's minimalist: it only does SNTP so not the server side
  • the status command is good enough that you can tell the clock frequency, precision, and so on (especially when compared to openntpd's ntpctl)
So I'm reserving judgement over it, but I'd certainly note that I'm always a little weary in trusting systemd daemons with the network, and would prefer to keep that attack surface to a minimum. Diversity is a good thing, in general, so I'll keep chrony for now. It would certainly nice to see it added to chrony's comparison table.

Switching to chrony Because the default configuration in chrony (at least as shipped in Debian) is sane (good default peers, no open network by default), installing it is as simple as:
apt install chrony
And because it somehow conflicts with openntpd, that also takes care of removing that cruft as well.

Update: Debian defaults So it seems like I managed to write this entire blog post without putting it in relation with the original reason I had to think about this in the first place, which is odd and should be corrected. This conversation came about on an IRC channel that mentioned that the ntp package (and upstream) is in bad shape in Debian. In that discussion, chrony and ntpsec were discussed as possible replacements, but when we had the discussion on chat, I mentioned I was using openntpd, and promptly realized I was actually unhappy with it. A friend suggested chrony, I tried it, and it worked amazingly, I switched, wrote this blog post, end of story. Except today (2022-02-07, two weeks later), I actually read that thread and realized that something happened in Debian I wasn't actually aware of. In bookworm, systemd-timesyncd was not only shipped, but it was installed by default, as it was marked as a hard dependency of systemd. That was "fixed" in systemd-247.9-2 (see bug 986651), but only by making the dependency a Recommends and marking it as Priority: important. So in effect, systemd-timesyncd became the default NTP daemon in Debian in bookworm, which I find somewhat surprising. timesyncd has many things going for it (as mentioned above), but I do find it a bit annoying that systemd is replacing all those utilities in such a way. I also wonder what is going to happen on upgrades. This is all a little frustrating too because there is no good comparison between the other NTP daemons and timesyncd anywhere. The chrony comparison table doesn't mention it, and an audit by the Core Infrastructure Initiative from 2017 doesn't mention it either, even though timesyncd was announced in 2014. (Same with this blog post from Facebook.)

21 November 2021

Antoine Beaupr : mbsync vs OfflineIMAP

After recovering from my latest email crash (previously, previously), I had to figure out which tool I should be using. I had many options but I figured I would start with a popular one (mbsync). But I also evaluated OfflineIMAP which was resurrected from the Python 2 apocalypse, and because I had used it before, for a long time. Read on for the details.

Benchmark setup All programs were tested against a Dovecot 1:2.3.13+dfsg1-2 server, running Debian bullseye. The client is a Purism 13v4 laptop with a Samsung SSD 970 EVO 1TB NVMe drive. The server is a custom build with a AMD Ryzen 5 2600 CPU, and a RAID-1 array made of two NVMe drives (Intel SSDPEKNW010T8 and WDC WDS100T2B0C). The mail spool I am testing against has almost 400k messages and takes 13GB of disk space:
$ notmuch count --exclude=false
372758
$ du -sh --exclude xapian Maildir
13G Maildir
The baseline we are comparing against is SMD (syncmaildir) which performs the sync in about 7-8 seconds locally (3.5 seconds for each push/pull command) and about 10-12 seconds remotely. Anything close to that or better is good enough. I do not have recent numbers for a SMD full sync baseline, but the setup documentation mentions 20 minutes for a full sync. That was a few years ago, and the spool has obviously grown since then, so that is not a reliable baseline. A baseline for a full sync might be also set with rsync, which copies files at nearly 40MB/s, or 317Mb/s!
anarcat@angela:tmp(main)$ time rsync -a --info=progress2 --exclude xapian  shell.anarc.at:Maildir/ Maildir/
 12,647,814,731 100%   37.85MB/s    0:05:18 (xfr#394981, to-chk=0/395815)    
72.38user 106.10system 5:19.59elapsed 55%CPU (0avgtext+0avgdata 15988maxresident)k
8816inputs+26305112outputs (0major+50953minor)pagefaults 0swaps
That is 5 minutes to transfer the entire spool. Incremental syncs are obviously pretty fast too:
anarcat@angela:tmp(main)$ time rsync -a --info=progress2 --exclude xapian  shell.anarc.at:Maildir/ Maildir/
              0   0%    0.00kB/s    0:00:00 (xfr#0, to-chk=0/395815)    
1.42user 0.81system 0:03.31elapsed 67%CPU (0avgtext+0avgdata 14100maxresident)k
120inputs+0outputs (3major+12709minor)pagefaults 0swaps
As an extra curiosity, here's the performance with tar, pretty similar with rsync, minus incremental which I cannot be bothered to figure out right now:
anarcat@angela:tmp(main)$ time ssh shell.anarc.at tar --exclude xapian -cf - Maildir/   pv -s 13G   tar xf - 
56.68user 58.86system 5:17.08elapsed 36%CPU (0avgtext+0avgdata 8764maxresident)k
0inputs+0outputs (0major+7266minor)pagefaults 0swaps
12,1GiO 0:05:17 [39,0MiB/s] [===================================================================> ] 92%
Interesting that rsync manages to almost beat a plain tar on file transfer, I'm actually surprised by how well it performs here, considering there are many little files to transfer. (But then again, this maybe is exactly where rsync shines: while tar needs to glue all those little files together, rsync can just directly talk to the other side and tell it to do live changes. Something to look at in another article maybe?) Since both ends are NVMe drives, those should easily saturate a gigabit link. And in fact, a backup of the server mail spool achieves much faster transfer rate on disks:
anarcat@marcos:~$ tar fc - Maildir   pv -s 13G > Maildir.tar
15,0GiO 0:01:57 [ 131MiB/s] [===================================] 115%
That's 131Mibyyte per second, vastly faster than the gigabit link. The client has similar performance:
anarcat@angela:~(main)$ tar fc - Maildir   pv -s 17G > Maildir.tar
16,2GiO 0:02:22 [ 116MiB/s] [==================================] 95%
So those disks should be able to saturate a gigabit link, and they are not the bottleneck on fast links. Which begs the question of what is blocking performance of a similar transfer over the gigabit link, but that's another question altogether, because no sync program ever reaches the above performance anyways. Finally, note that when I migrated to SMD, I wrote a small performance comparison that could be interesting here. It show SMD to be faster than OfflineIMAP, but not as much as we see here. In fact, it looks like OfflineIMAP slowed down significantly since then (May 2018), but this could be due to my larger mail spool as well.

mbsync The isync (AKA mbsync) project is written in C and supports syncing Maildir and IMAP folders, with possibly multiple replicas. I haven't tested this but I suspect it might be possible to sync between two IMAP servers as well. It supports partial mirorrs, message flags, full folder support, and "trash" functionality.

Complex configuration file I started with this .mbsyncrc configuration file:
SyncState *
Sync New ReNew Flags
IMAPAccount anarcat
Host imap.anarc.at
User anarcat
PassCmd "pass imap.anarc.at"
SSLType IMAPS
CertificateFile /etc/ssl/certs/ca-certificates.crt
IMAPStore anarcat-remote
Account anarcat
MaildirStore anarcat-local
# Maildir/top/sub/sub
#SubFolders Verbatim
# Maildir/.top.sub.sub
SubFolders Maildir++
# Maildir/top/.sub/.sub
# SubFolders legacy
# The trailing "/" is important
#Path ~/Maildir-mbsync/
Inbox ~/Maildir-mbsync/
Channel anarcat
# AKA Far, convert when all clients are 1.4+
Master :anarcat-remote:
# AKA Near
Slave :anarcat-local:
# Exclude everything under the internal [Gmail] folder, except the interesting folders
#Patterns * ![Gmail]* "[Gmail]/Sent Mail" "[Gmail]/Starred" "[Gmail]/All Mail"
# Or include everything
Patterns *
# Automatically create missing mailboxes, both locally and on the server
#Create Both
Create slave
# Sync the movement of messages between folders and deletions, add after making sure the sync works
#Expunge Both
Long gone are the days where I would spend a long time reading a manual page to figure out the meaning of every option. If that's your thing, you might like this one. But I'm more of a "EXAMPLES section" kind of person now, and I somehow couldn't find a sample file on the website. I started from the Arch wiki one but it's actually not great because it's made for Gmail (which is not a usual Dovecot server). So a sample config file in the manpage would be a great addition. Thankfully, the Debian packages ships one in /usr/share/doc/isync/examples/mbsyncrc.sample but I only found that after I wrote my configuration. It was still useful and I recommend people take a look if they want to understand the syntax. Also, that syntax is a little overly complicated. For example, Far needs colons, like:
Far :anarcat-remote:
Why? That seems just too complicated. I also found that sections are not clearly identified: IMAPAccount and Channel mark section beginnings, for example, which is not at all obvious until you learn about mbsync's internals. There are also weird ordering issues: the SyncState option needs to be before IMAPAccount, presumably because it's global. Using a more standard format like .INI or TOML could improve that situation.

Stellar performance A transfer of the entire mail spool takes 56 minutes and 6 seconds, which is impressive. It's not quite "line rate": the resulting mail spool was 12GB (which is a problem, see below), which turns out to be about 29Mbit/s and therefore not maxing the gigabit link, and an order of magnitude slower than rsync. The incremental runs are roughly 2 seconds, which is even more impressive, as that's actually faster than rsync:
===> multitime results
1: mbsync -a
            Mean        Std.Dev.    Min         Median      Max
real        2.015       0.052       1.930       2.029       2.105       
user        0.660       0.040       0.592       0.661       0.722       
sys         0.338       0.033       0.268       0.341       0.387    
Those tests were performed with isync 1.3.0-2.2 on Debian bullseye. Tests with a newer isync release originally failed because of a corrupted message that triggered bug 999804 (see below). Running 1.4.3 under valgrind works around the bug, but adds a 50% performance cost, the full sync running in 1h35m. Once the upstream patch is applied, performance with 1.4.3 is fairly similar, considering that the new sync included the register folder with 4000 messages:
120.74user 213.19system 59:47.69elapsed 9%CPU (0avgtext+0avgdata 105420maxresident)k
29128inputs+28284376outputs (0major+45711minor)pagefaults 0swaps
That is ~13GB in ~60 minutes, which gives us 28.3Mbps. Incrementals are also pretty similar to 1.3.x, again considering the double-connect cost:
===> multitime results
1: mbsync -a
            Mean        Std.Dev.    Min         Median      Max
real        2.500       0.087       2.340       2.491       2.629       
user        0.718       0.037       0.679       0.711       0.793       
sys         0.322       0.024       0.284       0.320       0.365
Those tests were all done on a Gigabit link, but what happens on a slower link? My server uplink is slow: 25 Mbps down, 6 Mbps up. There mbsync is worse than the SMD baseline:
===> multitime results
1: mbsync -a
Mean        Std.Dev.    Min         Median      Max
real        31.531      0.724       30.764      31.271      33.100      
user        1.858       0.125       1.721       1.818       2.131       
sys         0.610       0.063       0.506       0.600       0.695       
That's 30 seconds for a sync, which is an order of magnitude slower than SMD.

Great user interface Compared to OfflineIMAP and (ahem) SMD, the mbsync UI is kind of neat:
anarcat@angela:~(main)$ mbsync -a
Notice: Master/Slave are deprecated; use Far/Near instead.
C: 1/2  B: 204/205  F: +0/0 *0/0 #0/0  N: +1/200 *0/0 #0/0
(Note that nice switch away from slavery-related terms too.) The display is minimal, and yet informative. It's not obvious what does mean at first glance, but the manpage is useful at least for clarifying that:
This represents the cumulative progress over channels, boxes, and messages affected on the far and near side, respectively. The message counts represent added messages, messages with updated flags, and trashed messages, respectively. No attempt is made to calculate the totals in advance, so they grow over time as more information is gathered. (Emphasis mine).
In other words:
  • C 2/2: channels done/total (2 done out of 2)
  • B 204/205: mailboxes done/total (204 out of 205)
  • F: changes on the far side
  • N: +10/200 *0/0 #0/0: changes on the "near" side:
    • +10/200: 10 out of 200 messages downloaded
    • *0/0: no flag changed
    • #0/0: no message deleted
You get used to it, in a good way. It does not, unfortunately, show up when you run it in systemd, which is a bit annoying as I like to see a summary mail traffic in the logs.

Interoperability issue In my notmuch setup, I have bound key S to "mark spam", which basically assigns the tag spam to the message and removes a bunch of others. Then I have a notmuch-purge script which moves that message to the spam folder, for training purposes. It basically does this:
notmuch search --output=files --format=text0 "$search_spam" \
      xargs -r -0 mv -t "$HOME/Maildir/$ PREFIX junk/cur/"
This method, which worked fine in SMD (and also OfflineIMAP) created this error on sync:
Maildir error: duplicate UID 37578.
And indeed, there are now two messages with that UID in the mailbox:
anarcat@angela:~(main)$ find Maildir/.junk/ -name '*U=37578*'
Maildir/.junk/cur/1637427889.134334_2.angela,U=37578:2,S
Maildir/.junk/cur/1637348602.2492889_221804.angela,U=37578:2,S
This is actually a known limitation or, as mbsync(1) calls it, a "RECOMMENDATION":
When using the more efficient default UID mapping scheme, it is important that the MUA renames files when moving them between Maildir fold ers. Mutt always does that, while mu4e needs to be configured to do it:
(setq mu4e-change-filenames-when-moving t)
So it seems I would need to fix my script. It's unclear how the paths should be renamed, which is unfortunate, because I would need to change my script to adapt to mbsync, but I can't tell how just from reading the above. (A manual fix is actually to rename the file to remove the U= field: mbsync will generate a new one and then sync correctly.) Fortunately, someone else already fixed that issue: afew, a notmuch tagging script (much puns, such hurt), has a move mode that can rename files correctly, specifically designed to deal with mbsync. I had already been told about afew, but it's one more reason to standardize my notmuch hooks on that project, it looks like. Update: I have tried to use afew and found it has significant performance issues. It also has a completely different paradigm to what I am used to: it assumes all incoming mail has a new and lays its own tags on top of that (inbox, sent, etc). It can only move files from one folder at a time (see this bug) which breaks my spam training workflow. In general, I sync my tags into folders (e.g. ham, spam, sent) and message flags (e.g. inbox is F, unread is "not S", etc), and afew is not well suited for this (although there are hacks that try to fix this). I have worked hard to make my tagging scripts idempotent, and it's something afew doesn't currently have. Still, it would be better to have that code in Python than bash, so maybe I should consider my options here.

Stability issues The newer release in Debian bookworm (currently at 1.4.3) has stability issues on full sync. I filed bug 999804 in Debian about this, which lead to a thread on the upstream mailing list. I have found at least three distinct crashes that could be double-free bugs "which might be exploitable in the worst case", not a reassuring prospect. The thing is: mbsync is really fast, but the downside of that is that it's written in C, and with that comes a whole set of security issues. The Debian security tracker has only three CVEs on isync, but the above issues show there could be many more. Reading the source code certainly did not make me very comfortable with trusting it with untrusted data. I considered sandboxing it with systemd (below) but having systemd run as a --user process makes that difficult. I also considered using an apparmor profile but that is not trivial because we need to allow SSH and only some parts of it... Thankfully, upstream has been diligent at addressing the issues I have found. They provided a patch within a few days which did fix the sync issues. Update: upstream actually took the issue very seriously. They not only got CVE-2021-44143 assigned for my bug report, they also audited the code and found several more issues collectively identified as CVE-2021-3657, which actually also affect 1.3 (ie. Debian 11/bullseye/stable). Somehow my corpus doesn't trigger that issue, but it was still considered serious enough to warrant a CVE. So one the one hand: excellent response from upstream; but on the other hand: how many more of those could there be in there?

Automation with systemd The Arch wiki has instructions on how to setup mbsync as a systemd service. It suggests using the --verbose (-V) flag which is a little intense here, as it outputs 1444 lines of messages. I have used the following .service file:
[Unit]
Description=Mailbox synchronization service
ConditionHost=!marcos
Wants=network-online.target
After=network-online.target
Before=notmuch-new.service
[Service]
Type=oneshot
ExecStart=/usr/bin/mbsync -a
Nice=10
IOSchedulingClass=idle
NoNewPrivileges=true
[Install]
WantedBy=default.target
And the following .timer:
[Unit]
Description=Mailbox synchronization timer
ConditionHost=!marcos
[Timer]
OnBootSec=2m
OnUnitActiveSec=5m
Unit=mbsync.service
[Install]
WantedBy=timers.target
Note that we trigger notmuch through systemd, with the Before and also by adding mbsync.service to the notmuch-new.service file:
[Unit]
Description=notmuch new
After=mbsync.service
[Service]
Type=oneshot
Nice=10
ExecStart=/usr/bin/notmuch new
[Install]
WantedBy=mbsync.service
An improvement over polling repeatedly with a .timer would be to wake up only on IMAP notify, but neither imapnotify nor goimapnotify seem to be packaged in Debian. It would also not cover for the "sent folder" use case, where we need to wake up on local changes.

Password-less setup The sample file suggests this should work:
IMAPStore remote
Tunnel "ssh -q host.remote.com /usr/sbin/imapd"
Add BatchMode, restrict to IdentitiesOnly, provide a password-less key just for this, add compression (-C), find the Dovecot imap binary, and you get this:
IMAPAccount anarcat-tunnel
Tunnel "ssh -o BatchMode=yes -o IdentitiesOnly=yes -i ~/.ssh/id_ed25519_mbsync -o HostKeyAlias=shell.anarc.at -C anarcat@imap.anarc.at /usr/lib/dovecot/imap"
And it actually seems to work:
$ mbsync -a
Notice: Master/Slave are deprecated; use Far/Near instead.
C: 0/2  B: 0/1  F: +0/0 *0/0 #0/0  N: +0/0 *0/0 #0/0imap(anarcat): Error: net_connect_unix(/run/dovecot/stats-writer) failed: Permission denied
C: 2/2  B: 205/205  F: +0/0 *0/0 #0/0  N: +1/1 *3/3 #0/0imap(anarcat)<1611280><90uUOuyElmEQlhgAFjQyWQ>: Info: Logged out in=10808 out=15396642 deleted=0 expunged=0 trashed=0 hdr_count=0 hdr_bytes=0 body_count=1 body_bytes=8087
It's a bit noisy, however. dovecot/imap doesn't have a "usage" to speak of, but even the source code doesn't hint at a way to disable that Error message, so that's unfortunate. That socket is owned by root:dovecot so presumably Dovecot runs the imap process as $user:dovecot, which we can't do here. Oh well? Interestingly, the SSH setup is not faster than IMAP. With IMAP:
===> multitime results
1: mbsync -a
            Mean        Std.Dev.    Min         Median      Max
real        2.367       0.065       2.220       2.376       2.458       
user        0.793       0.047       0.731       0.776       0.871       
sys         0.426       0.040       0.364       0.434       0.476
With SSH:
===> multitime results
1: mbsync -a
            Mean        Std.Dev.    Min         Median      Max
real        2.515       0.088       2.274       2.532       2.594       
user        0.753       0.043       0.645       0.766       0.804       
sys         0.328       0.045       0.212       0.340       0.393
Basically: 200ms slower. Tolerable.

Migrating from SMD The above was how I migrated to mbsync on my first workstation. The work on the second one was more streamlined, especially since the corruption on mailboxes was fixed:
  1. install isync, with the patch:
    dpkg -i isync_1.4.3-1.1~_amd64.deb
    
  2. copy all files over from previous workstation to avoid a full resync (optional):
    rsync -a --info=progress2 angela:Maildir/ Maildir-mbsync/
    
  3. rename all files to match new hostname (optional):
    find Maildir-mbsync/ -type f -name '*.angela,*' -print0    rename -0 's/\.angela,/\.curie,/'
    
  4. trash the notmuch database (optional):
    rm -rf Maildir-mbsync/.notmuch/xapian/
    
  5. disable all smd and notmuch services:
    systemctl --user --now disable smd-pull.service smd-pull.timer smd-push.service smd-push.timer notmuch-new.service notmuch-new.timer
    
  6. do one last sync with smd:
    smd-pull --show-tags ; smd-push --show-tags ; notmuch new ; notmuch-sync-flagged -v
    
  7. backup notmuch on the client and server:
    notmuch dump   pv > notmuch.dump
    
  8. backup the maildir on the client and server:
    cp -al Maildir Maildir-bak
    
  9. create the SSH key:
    ssh-keygen -t ed25519 -f .ssh/id_ed25519_mbsync
    cat .ssh/id_ed25519_mbsync.pub
    
  10. add to .ssh/authorized_keys on the server, like this: command="/usr/lib/dovecot/imap",restrict ssh-ed25519 AAAAC...
  11. move old files aside, if present:
    mv Maildir Maildir-smd
    
  12. move new files in place (CRITICAL SECTION BEGINS!):
    mv Maildir-mbsync Maildir
    
  13. run a test sync, only pulling changes: mbsync --create-near --remove-none --expunge-none --noop anarcat-register
  14. if that works well, try with all mailboxes: mbsync --create-near --remove-none --expunge-none --noop -a
  15. if that works well, try again with a full sync: mbsync register mbsync -a
  16. reindex and restore the notmuch database, this should take ~25 minutes:
    notmuch new
    pv notmuch.dump   notmuch restore
    
  17. enable the systemd services and retire the smd-* services: systemctl --user enable mbsync.timer notmuch-new.service systemctl --user start mbsync.timer rm ~/.config/systemd/user/smd* systemctl daemon-reload
During the migration, notmuch helpfully told me the full list of those lost messages:
[...]
Warning: cannot apply tags to missing message: CAN6gO7_QgCaiDFvpG3AXHi6fW12qaN286+2a7ERQ2CQtzjSEPw@mail.gmail.com
Warning: cannot apply tags to missing message: CAPTU9Wmp0yAmaxO+qo8CegzRQZhCP853TWQ_Ne-YF94MDUZ+Dw@mail.gmail.com
Warning: cannot apply tags to missing message: F5086003-2917-4659-B7D2-66C62FCD4128@gmail.com
[...]
Warning: cannot apply tags to missing message: mailman.2.1316793601.53477.sage-members@mailman.sage.org
Warning: cannot apply tags to missing message: mailman.7.1317646801.26891.outages-discussion@outages.org
Warning: cannot apply tags to missing message: notmuch-sha1-000458df6e48d4857187a000d643ac971deeef47
Warning: cannot apply tags to missing message: notmuch-sha1-0079d8e0c3340e6f88c66f4c49fca758ea71d06d
Warning: cannot apply tags to missing message: notmuch-sha1-0194baa4cfb6d39bc9e4d8c049adaccaa777467d
Warning: cannot apply tags to missing message: notmuch-sha1-02aede494fc3f9e9f060cfd7c044d6d724ad287c
Warning: cannot apply tags to missing message: notmuch-sha1-06606c625d3b3445420e737afd9a245ae66e5562
Warning: cannot apply tags to missing message: notmuch-sha1-0747b020f7551415b9bf5059c58e0a637ba53b13
[...]
As detailed in the crash report, all of those were actually innocuous and could be ignored. Also note that we completely trash the notmuch database because it's actually faster to reindex from scratch than let notmuch slowly figure out that all mails are new and all the old mails are gone. The fresh indexing took:
nov 19 15:08:54 angela notmuch[2521117]: Processed 384679 total files in 23m 41s (270 files/sec.).
nov 19 15:08:54 angela notmuch[2521117]: Added 372610 new messages to the database.
While a reindexing on top of an existing database was going twice as slow, at about 120 files/sec.

Current config file Putting it all together, I ended up with the following configuration file:
SyncState *
Sync All
# IMAP side, AKA "Far"
IMAPAccount anarcat-imap
Host imap.anarc.at
User anarcat
PassCmd "pass imap.anarc.at"
SSLType IMAPS
CertificateFile /etc/ssl/certs/ca-certificates.crt
IMAPAccount anarcat-tunnel
Tunnel "ssh -o BatchMode=yes -o IdentitiesOnly=yes -i ~/.ssh/id_ed25519_mbsync -o HostKeyAlias=shell.anarc.at -C anarcat@imap.anarc.at /usr/lib/dovecot/imap"
IMAPStore anarcat-remote
Account anarcat-tunnel
# Maildir side, AKA "Near"
MaildirStore anarcat-local
# Maildir/top/sub/sub
#SubFolders Verbatim
# Maildir/.top.sub.sub
SubFolders Maildir++
# Maildir/top/.sub/.sub
# SubFolders legacy
# The trailing "/" is important
#Path ~/Maildir-mbsync/
Inbox ~/Maildir/
# what binds Maildir and IMAP
Channel anarcat
Far :anarcat-remote:
Near :anarcat-local:
# Exclude everything under the internal [Gmail] folder, except the interesting folders
#Patterns * ![Gmail]* "[Gmail]/Sent Mail" "[Gmail]/Starred" "[Gmail]/All Mail"
# Or include everything
#Patterns *
Patterns * !register  !.register
# Automatically create missing mailboxes, both locally and on the server
Create Both
#Create Near
# Sync the movement of messages between folders and deletions, add after making sure the sync works
Expunge Both
# Propagate mailbox deletion
Remove both
IMAPAccount anarcat-register-imap
Host imap.anarc.at
User register
PassCmd "pass imap.anarc.at-register"
SSLType IMAPS
CertificateFile /etc/ssl/certs/ca-certificates.crt
IMAPAccount anarcat-register-tunnel
Tunnel "ssh -o BatchMode=yes -o IdentitiesOnly=yes -i ~/.ssh/id_ed25519_mbsync -o HostKeyAlias=shell.anarc.at -C register@imap.anarc.at /usr/lib/dovecot/imap"
IMAPStore anarcat-register-remote
Account anarcat-register-tunnel
MaildirStore anarcat-register-local
SubFolders Maildir++
Inbox ~/Maildir/.register/
Channel anarcat-register
Far :anarcat-register-remote:
Near :anarcat-register-local:
Create Both
Expunge Both
Remove both
Note that it may be out of sync with my live (and private) configuration file, as I do not publish my "dotfiles" repository publicly for security reasons.

OfflineIMAP I've used OfflineIMAP for a long time before switching to SMD. I don't exactly remember why or when I started using it, but I do remember it became painfully slow as I started using notmuch, and would sometimes crash mysteriously. It's been a while, so my memory is hazy on that. It also kind of died in a fire when Python 2 stop being maintained. The main author moved on to a different project, imapfw which could serve as a framework to build IMAP clients, but never seemed to implement all of the OfflineIMAP features and certainly not configuration file compatibility. Thankfully, a new team of volunteers ported OfflineIMAP to Python 3 and we can now test that new version to see if it is an improvement over mbsync.

Crash on full sync The first thing that happened on a full sync is this crash:
Copy message from RemoteAnarcat:junk:
 ERROR: Copying message 30624 [acc: Anarcat]
  decoding with 'X-EUC-TW' codec failed (AttributeError: 'memoryview' object has no attribute 'decode')
Thread 'Copy message from RemoteAnarcat:junk' terminated with exception:
Traceback (most recent call last):
  File "/usr/share/offlineimap3/offlineimap/imaputil.py", line 406, in utf7m_decode
    for c in binary.decode():
AttributeError: 'memoryview' object has no attribute 'decode'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
  File "/usr/share/offlineimap3/offlineimap/threadutil.py", line 146, in run
    Thread.run(self)
  File "/usr/lib/python3.9/threading.py", line 892, in run
    self._target(*self._args, **self._kwargs)
  File "/usr/share/offlineimap3/offlineimap/folder/Base.py", line 802, in copymessageto
    message = self.getmessage(uid)
  File "/usr/share/offlineimap3/offlineimap/folder/IMAP.py", line 342, in getmessage
    data = self._fetch_from_imap(str(uid), self.retrycount)
  File "/usr/share/offlineimap3/offlineimap/folder/IMAP.py", line 908, in _fetch_from_imap
    ndata1 = self.parser['8bit-RFC'].parsebytes(data[0][1])
  File "/usr/lib/python3.9/email/parser.py", line 123, in parsebytes
    return self.parser.parsestr(text, headersonly)
  File "/usr/lib/python3.9/email/parser.py", line 67, in parsestr
    return self.parse(StringIO(text), headersonly=headersonly)
  File "/usr/lib/python3.9/email/parser.py", line 56, in parse
    feedparser.feed(data)
  File "/usr/lib/python3.9/email/feedparser.py", line 176, in feed
    self._call_parse()
  File "/usr/lib/python3.9/email/feedparser.py", line 180, in _call_parse
    self._parse()
  File "/usr/lib/python3.9/email/feedparser.py", line 385, in _parsegen
    for retval in self._parsegen():
  File "/usr/lib/python3.9/email/feedparser.py", line 298, in _parsegen
    for retval in self._parsegen():
  File "/usr/lib/python3.9/email/feedparser.py", line 385, in _parsegen
    for retval in self._parsegen():
  File "/usr/lib/python3.9/email/feedparser.py", line 256, in _parsegen
    if self._cur.get_content_type() == 'message/delivery-status':
  File "/usr/lib/python3.9/email/message.py", line 578, in get_content_type
    value = self.get('content-type', missing)
  File "/usr/lib/python3.9/email/message.py", line 471, in get
    return self.policy.header_fetch_parse(k, v)
  File "/usr/lib/python3.9/email/policy.py", line 163, in header_fetch_parse
    return self.header_factory(name, value)
  File "/usr/lib/python3.9/email/headerregistry.py", line 601, in __call__
    return self[name](name, value)
  File "/usr/lib/python3.9/email/headerregistry.py", line 196, in __new__
    cls.parse(value, kwds)
  File "/usr/lib/python3.9/email/headerregistry.py", line 445, in parse
    kwds['parse_tree'] = parse_tree = cls.value_parser(value)
  File "/usr/lib/python3.9/email/_header_value_parser.py", line 2675, in parse_content_type_header
    ctype.append(parse_mime_parameters(value[1:]))
  File "/usr/lib/python3.9/email/_header_value_parser.py", line 2569, in parse_mime_parameters
    token, value = get_parameter(value)
  File "/usr/lib/python3.9/email/_header_value_parser.py", line 2492, in get_parameter
    token, value = get_value(value)
  File "/usr/lib/python3.9/email/_header_value_parser.py", line 2403, in get_value
    token, value = get_quoted_string(value)
  File "/usr/lib/python3.9/email/_header_value_parser.py", line 1294, in get_quoted_string
    token, value = get_bare_quoted_string(value)
  File "/usr/lib/python3.9/email/_header_value_parser.py", line 1223, in get_bare_quoted_string
    token, value = get_encoded_word(value)
  File "/usr/lib/python3.9/email/_header_value_parser.py", line 1064, in get_encoded_word
    text, charset, lang, defects = _ew.decode('=?' + tok + '?=')
  File "/usr/lib/python3.9/email/_encoded_words.py", line 181, in decode
    string = bstring.decode(charset)
AttributeError: decoding with 'X-EUC-TW' codec failed (AttributeError: 'memoryview' object has no attribute 'decode')
Last 1 debug messages logged for Copy message from RemoteAnarcat:junk prior to exception:
thread: Register new thread 'Copy message from RemoteAnarcat:junk' (account 'Anarcat')
ERROR: Exceptions occurred during the run!
ERROR: Copying message 30624 [acc: Anarcat]
  decoding with 'X-EUC-TW' codec failed (AttributeError: 'memoryview' object has no attribute 'decode')
Traceback:
  File "/usr/share/offlineimap3/offlineimap/folder/Base.py", line 802, in copymessageto
    message = self.getmessage(uid)
  File "/usr/share/offlineimap3/offlineimap/folder/IMAP.py", line 342, in getmessage
    data = self._fetch_from_imap(str(uid), self.retrycount)
  File "/usr/share/offlineimap3/offlineimap/folder/IMAP.py", line 908, in _fetch_from_imap
    ndata1 = self.parser['8bit-RFC'].parsebytes(data[0][1])
  File "/usr/lib/python3.9/email/parser.py", line 123, in parsebytes
    return self.parser.parsestr(text, headersonly)
  File "/usr/lib/python3.9/email/parser.py", line 67, in parsestr
    return self.parse(StringIO(text), headersonly=headersonly)
  File "/usr/lib/python3.9/email/parser.py", line 56, in parse
    feedparser.feed(data)
  File "/usr/lib/python3.9/email/feedparser.py", line 176, in feed
    self._call_parse()
  File "/usr/lib/python3.9/email/feedparser.py", line 180, in _call_parse
    self._parse()
  File "/usr/lib/python3.9/email/feedparser.py", line 385, in _parsegen
    for retval in self._parsegen():
  File "/usr/lib/python3.9/email/feedparser.py", line 298, in _parsegen
    for retval in self._parsegen():
  File "/usr/lib/python3.9/email/feedparser.py", line 385, in _parsegen
    for retval in self._parsegen():
  File "/usr/lib/python3.9/email/feedparser.py", line 256, in _parsegen
    if self._cur.get_content_type() == 'message/delivery-status':
  File "/usr/lib/python3.9/email/message.py", line 578, in get_content_type
    value = self.get('content-type', missing)
  File "/usr/lib/python3.9/email/message.py", line 471, in get
    return self.policy.header_fetch_parse(k, v)
  File "/usr/lib/python3.9/email/policy.py", line 163, in header_fetch_parse
    return self.header_factory(name, value)
  File "/usr/lib/python3.9/email/headerregistry.py", line 601, in __call__
    return self[name](name, value)
  File "/usr/lib/python3.9/email/headerregistry.py", line 196, in __new__
    cls.parse(value, kwds)
  File "/usr/lib/python3.9/email/headerregistry.py", line 445, in parse
    kwds['parse_tree'] = parse_tree = cls.value_parser(value)
  File "/usr/lib/python3.9/email/_header_value_parser.py", line 2675, in parse_content_type_header
    ctype.append(parse_mime_parameters(value[1:]))
  File "/usr/lib/python3.9/email/_header_value_parser.py", line 2569, in parse_mime_parameters
    token, value = get_parameter(value)
  File "/usr/lib/python3.9/email/_header_value_parser.py", line 2492, in get_parameter
    token, value = get_value(value)
  File "/usr/lib/python3.9/email/_header_value_parser.py", line 2403, in get_value
    token, value = get_quoted_string(value)
  File "/usr/lib/python3.9/email/_header_value_parser.py", line 1294, in get_quoted_string
    token, value = get_bare_quoted_string(value)
  File "/usr/lib/python3.9/email/_header_value_parser.py", line 1223, in get_bare_quoted_string
    token, value = get_encoded_word(value)
  File "/usr/lib/python3.9/email/_header_value_parser.py", line 1064, in get_encoded_word
    text, charset, lang, defects = _ew.decode('=?' + tok + '?=')
  File "/usr/lib/python3.9/email/_encoded_words.py", line 181, in decode
    string = bstring.decode(charset)
Folder junk [acc: Anarcat]:
 Copy message UID 30626 (29008/49310) RemoteAnarcat:junk -> LocalAnarcat:junk
Command exited with non-zero status 100
5252.91user 535.86system 3:21:00elapsed 47%CPU (0avgtext+0avgdata 846304maxresident)k
96344inputs+26563792outputs (1189major+2155815minor)pagefaults 0swaps
That only transferred about 8GB of mail, which gives us a transfer rate of 5.3Mbit/s, more than 5 times slower than mbsync. This bug is possibly limited to the bullseye version of offlineimap3 (the lovely 0.0~git20210225.1e7ef9e+dfsg-4), while the current sid version (the equally gorgeous 0.0~git20211018.e64c254+dfsg-1) seems unaffected.

Tolerable performance The new release still crashes, except it does so at the very end, which is an improvement, since the mails do get transferred:
 *** Finished account 'Anarcat' in 511:12
ERROR: Exceptions occurred during the run!
ERROR: Exception parsing message with ID (<20190619152034.BFB8810E07A@marcos.anarc.at>) from imaplib (response type: bytes).
 AttributeError: decoding with 'X-EUC-TW' codec failed (AttributeError: 'memoryview' object has no attribute 'decode')
Traceback:
  File "/usr/share/offlineimap3/offlineimap/folder/Base.py", line 810, in copymessageto
    message = self.getmessage(uid)
  File "/usr/share/offlineimap3/offlineimap/folder/IMAP.py", line 343, in getmessage
    data = self._fetch_from_imap(str(uid), self.retrycount)
  File "/usr/share/offlineimap3/offlineimap/folder/IMAP.py", line 910, in _fetch_from_imap
    raise OfflineImapError(
ERROR: Exception parsing message with ID (<40A270DB.9090609@alternatives.ca>) from imaplib (response type: bytes).
 AttributeError: decoding with 'x-mac-roman' codec failed (AttributeError: 'memoryview' object has no attribute 'decode')
Traceback:
  File "/usr/share/offlineimap3/offlineimap/folder/Base.py", line 810, in copymessageto
    message = self.getmessage(uid)
  File "/usr/share/offlineimap3/offlineimap/folder/IMAP.py", line 343, in getmessage
    data = self._fetch_from_imap(str(uid), self.retrycount)
  File "/usr/share/offlineimap3/offlineimap/folder/IMAP.py", line 910, in _fetch_from_imap
    raise OfflineImapError(
ERROR: IMAP server 'RemoteAnarcat' does not have a message with UID '32686'
Traceback:
  File "/usr/share/offlineimap3/offlineimap/folder/Base.py", line 810, in copymessageto
    message = self.getmessage(uid)
  File "/usr/share/offlineimap3/offlineimap/folder/IMAP.py", line 343, in getmessage
    data = self._fetch_from_imap(str(uid), self.retrycount)
  File "/usr/share/offlineimap3/offlineimap/folder/IMAP.py", line 889, in _fetch_from_imap
    raise OfflineImapError(reason, severity)
Command exited with non-zero status 1
8273.52user 983.80system 8:31:12elapsed 30%CPU (0avgtext+0avgdata 841936maxresident)k
56376inputs+43247608outputs (811major+4972914minor)pagefaults 0swaps
"offlineimap  -o " took 8 hours 31 mins 15 secs
This is 8h31m for transferring 12G, which is around 3.1Mbit/s. That is nine times slower than mbsync, almost an order of magnitude! Now that we have a full sync, we can test incremental synchronization. That is also much slower:
===> multitime results
1: sh -c "offlineimap -o   true"
            Mean        Std.Dev.    Min         Median      Max
real        24.639      0.513       23.946      24.526      25.708      
user        23.912      0.473       23.404      23.795      24.947      
sys         1.743       0.105       1.607       1.729       2.002
That is also an order of magnitude slower than mbsync, and significantly slower than what you'd expect from a sync process. ~30 seconds is long enough to make me impatient and distracted; 3 seconds, less so: I can wait and see the results almost immediately.

Integrity check That said: this is still on a gigabit link. It's technically possible that OfflineIMAP performs better than mbsync over a slow link, but I Haven't tested that theory. The OfflineIMAP mail spool is missing quite a few messages as well:
anarcat@angela:~(main)$ find Maildir-offlineimap -type f -type f -a \! -name '.*'   wc -l 
381463
anarcat@angela:~(main)$ find Maildir -type f -type f -a \! -name '.*'   wc -l 
385247
... although that's probably all either new messages or the register folder, so OfflineIMAP might actually be in a better position there. But digging in more, it seems like the actual per-folder diff is fairly similar to mbsync: a few messages missing here and there. Considering OfflineIMAP's instability and poor performance, I have not looked any deeper in those discrepancies.

Other projects to evaluate Those are all the options I have considered, in alphabetical order
  • doveadm-sync: requires dovecot on both ends, can tunnel over SSH, may have performance issues in incremental sync, written in C
  • fdm: fetchmail replacement, IMAP/POP3/stdin/Maildir/mbox,NNTP support, SOCKS support (for Tor), complex rules for delivering to specific mailboxes, adding headers, piping to commands, etc. discarded because no (real) support for keeping mail on the server, and written in C
  • getmail: fetchmail replacement, IMAP/POP3 support, supports incremental runs, classification rules, Python
  • interimap: syncs two IMAP servers, apparently faster than doveadm and offlineimap, but requires running an IMAP server locally, Perl
  • isync/mbsync: TLS client certs and SSH tunnels, fast, incremental, IMAP/POP/Maildir support, multiple mailbox, trash and recursion support, and generally has good words from multiple Debian and notmuch people (Arch tutorial), written in C, review above
  • mail-sync: notify support, happens over any piped transport (e.g. ssh), diff/patch system, requires binary on both ends, mentions UUCP in the manpage, mentions rsmtp which is a nice name for rsendmail. not evaluated because it seems awfully complex to setup, Haskell
  • nncp: treat the local spool as another mail server, not really compatible with my "multiple clients" setup, Golang
  • offlineimap3: requires IMAP, used the py2 version in the past, might just still work, first sync painful (IIRC), ways to tunnel over SSH, review above, Python
Most projects were not evaluated due to lack of time.

Conclusion I'm now using mbsync to sync my mail. I'm a little disappointed by the synchronisation times over the slow link, but I guess that's on par for the course if we use IMAP. We are bound by the network speed much more than with custom protocols. I'm also worried about the C implementation and the crashes I have witnessed, but I am encouraged by the fast upstream response. Time will tell if I will stick with that setup. I'm certainly curious about the promises of interimap and mail-sync, but I have ran out of time on this project.

Antoine Beaupr : The last syncmaildir crash

My syncmaildir (SMD) setup failed me one too many times (previously, previously). In an attempt to migrate to an alternative mail synchronization tool, I looked into using my IMAP server again, and found out my mail spool was in a pretty bad shape. I'm comparing mbsync and offlineimap in the next post but this post talks about how I recovered the mail spool so that tools like those could correctly synchronise the mail spool again.

The latest crash On Monday, SMD just started failing with this error:
nov 15 16:12:19 angela systemd[2305]: Starting pull emails with syncmaildir...
nov 15 16:12:22 angela systemd[2305]: smd-pull.service: Succeeded.
nov 15 16:12:22 angela systemd[2305]: Finished pull emails with syncmaildir.
nov 15 16:14:08 angela systemd[2305]: Starting pull emails with syncmaildir...
nov 15 16:14:11 angela systemd[2305]: smd-pull.service: Main process exited, code=exited, status=1/FAILURE
nov 15 16:14:11 angela systemd[2305]: smd-pull.service: Failed with result 'exit-code'.
nov 15 16:14:11 angela systemd[2305]: Failed to start pull emails with syncmaildir.
nov 15 16:16:14 angela systemd[2305]: Starting pull emails with syncmaildir...
nov 15 16:16:17 angela smd-pull[27178]: smd-client: ERROR: Network error.
nov 15 16:16:17 angela smd-pull[27178]: smd-client: ERROR: Unable to get any data from the other endpoint.
nov 15 16:16:17 angela smd-pull[27178]: smd-client: ERROR: This problem may be transient, please retry.
nov 15 16:16:17 angela smd-pull[27178]: smd-client: ERROR: Hint: did you correctly setup the SERVERNAME variable
nov 15 16:16:17 angela smd-pull[27178]: smd-client: ERROR: on your client? Did you add an entry for it in your ssh
nov 15 16:16:17 angela smd-pull[27178]: smd-client: ERROR: configuration file?
nov 15 16:16:17 angela smd-pull[27178]: smd-client: ERROR: Network error
nov 15 16:16:17 angela smd-pull[27188]: register: smd-client@localhost: TAGS: error::context(handshake) probable-cause(network) human-intervention(avoidable) suggested-actions(retry)
nov 15 16:16:17 angela systemd[2305]: smd-pull.service: Main process exited, code=exited, status=1/FAILURE
nov 15 16:16:17 angela systemd[2305]: smd-pull.service: Failed with result 'exit-code'.
nov 15 16:16:17 angela systemd[2305]: Failed to start pull emails with syncmaildir.
What is frustrating is that there's actually no network error here. Running the command by hand I did see a different message, but now I have lost it in my backlog. It had something to do with a filename being too long, and I gave up debugging after a while. This happened suddenly too, which added to the confusion. In a fit of rage I started this blog post and experimenting with alternatives, which led me down a lot of rabbit holes. Reviewing my previous mail crash documentation, it seems most solutions involve talking to an IMAP server, so I figured I would just do that. Wanting to try something new, i gave isync (AKA mbsync) a try. Oh dear, I did not expect how much trouble just talking to my IMAP server would be, which wasn't not isync's fault, for what that's worth. It was the primary tool I used to debug things, and served me well in that regard.

Mailbox corruption The first thing I found out is that certain messages in the IMAP spool were corrupted. mbsync would stop on a FETCH command and Dovecot would give me those errors on the server side.

"wrong W value"
nov 16 15:31:27 marcos dovecot[3621800]: imap(anarcat)<3630489><wAmSzO3QZtfAqAB1>: Error: Mailbox junk: Maildir filename has wrong W value, renamed the file from /home/anarcat/Maildir/.junk/cur/1454623938.M101164P22216.marcos,S=2495,W=2578:2,S to /home/anarcat/Maildir/.junk/cur/1454623938.M101164P22216.marcos,S=2495:2,S
nov 16 15:31:27 marcos dovecot[3621800]: imap(anarcat)<3630489><wAmSzO3QZtfAqAB1>: Error: Mailbox junk: Deleting corrupted cache record uid=1582: UID 1582: Broken virtual size in mailbox junk: read(/home/anarcat/Maildir/.junk/cur/1454623938.M101164P22216.marcos,S=2495,W=2578:2,S): FETCH BODY[] got too little data: 2540 vs 2578
At least this first error was automatically healed by Dovecot (by renaming the file without the W= flag). The problem is that the FETCH command fails and mbsync exits noisily. So you need to constantly restart mbsync with a silly command like:
while ! mbsync -a; do sleep 1; done

"cached message size larger than expected"
nov 16 13:53:08 marcos dovecot[3520770]: imap(anarcat)<3594402><M5JHb+zQ3NLAqAB1>: Error: Mailbox Sent: UID=19288: read(/home/anarcat/Maildir/.Sent/cur/1224790447.M898726P9811V000000000000FE06I00794FB1_0.marvin,S=2588:2,S) failed: Cached message size larger than expected (2588 > 2482, box=Sent, UID=19288) (read reason=mail stream)
nov 16 13:53:08 marcos dovecot[3520770]: imap(anarcat)<3594402><M5JHb+zQ3NLAqAB1>: Error: Mailbox Sent: Deleting corrupted cache record uid=19288: UID 19288: Broken physical size in mailbox Sent: read(/home/anarcat/Maildir/.Sent/cur/1224790447.M898726P9811V000000000000FE06I00794FB1_0.marvin,S=2588:2,S) failed: Cached message size larger than expected (2588 > 2482, box=Sent, UID=19288)
nov 16 13:53:08 marcos dovecot[3520770]: imap(anarcat)<3594402><M5JHb+zQ3NLAqAB1>: Error: Mailbox Sent: UID=19288: read(/home/anarcat/Maildir/.Sent/cur/1224790447.M898726P9811V000000000000FE06I00794FB1_0.marvin,S=2588:2,S) failed: Cached message size larger than expected (2588 > 2482, box=Sent, UID=19288) (read reason=)
nov 16 13:53:08 marcos dovecot[3520770]: imap-login: Panic: epoll_ctl(del, 7) failed: Bad file descriptor
This second problem is much harder to fix, because dovecot does not recover automatically. This is Dovecot complaining that the cached size (the S= field, but also present in Dovecot's metadata files) doesn't match the file size. I wonder if at least some of those messages were corrupted in the OfflineIMAP to syncmaildir migration because part of that procedure is to run the strip_header script to remove content from the emails. That could easily have broken things since the files do not also get renamed.

Workaround So I read a lot of the Dovecot documentation on the maildir format, and wrote an extensive fix script for those two errors. The script worked and mbsync was able to sync the entire mail spool. And no, rebuilding the index files didn't work. Also tried doveadm force-resync -u anarcat which didn't do anything. In the end I also had to do this, because the wrong cache values were also stored elsewhere.
service dovecot stop ; find -name 'dovecot*' -delete; service dovecot start
This would have totally broken any existing clients, but thankfully I'm starting from scratch (except maybe webmail, but I'm hoping it will self-heal as well, assuming it only has a cache and not a full replica of the mail spool).

Incoherence between Maildir and IMAP Unfortunately, the first mbsync was incomplete as it was missing about 15,000 mails:
anarcat@angela:~(main)$ find Maildir -type f -type f -a \! -name '.*'   wc -l 
384836
anarcat@angela:~(main)$ find Maildir-mbsync/ -type f -a \! -name '.*'   wc -l 
369221
As it turns out, mbsync was not at fault here either: this was yet more mail spool corruption. It's actually 26 folders (out of 205) with inconsistent sizes, which can be found with:
for folder in * .[^.]* ; do 
  printf "%s\t%d\n" $folder $(find "$folder" -type f -a \! -name '.*'   wc -l );
done
The special \! -name '.*' bit is to ignore the mbsync metadata, which creates .uidvalidity and .mbsyncstate in every folder. That ignores about 200 files but since they are spread around all folders, which was making it impossible to review where the problem was. Here is what the diff looks like:
--- Maildir-list    2021-11-17 20:42:36.504246752 -0500
+++ Maildir-mbsync-list 2021-11-17 20:18:07.731806601 -0500
@@ -6,16 +6,15 @@
[...]
 .Archives  1
 .Archives.2010 3553
-.Archives.2011 3583
-.Archives.2012 12593
+.Archives.2011 3582
+.Archives.2012 620
 .Archives.2013 8576
 .Archives.2014 11057
-.Archives.2015 8173
+.Archives.2015 8165
 .Archives.2016 54
 .band  34
 .bitbuck   1
@@ -38,13 +37,12 @@
 .couchsurfers  2
-cur    11285
+cur    11280
 .current   130
 .cv    2
 .debbug    262
-.debian    37544
-drafts 1
-.Drafts    4
+.debian    37533
+.Drafts    2
 .drone 241
 .drupal    188
 .drupal-devel  303
[...]

Misfiled messages It's a bit all over the place, but we can already notice some huge differences between mailboxes, for example in the Archives folders. As it turns out, at least 12,000 of those missing mails were actually misfiled: instead of being in the Maildir/.Archives.2012/cur/ folder, they were directly in Maildir/.Archives.2012/. This is something that doesn't matter for SMD (and possibly for notmuch? it does matter, notmuch suddenly found 12,000 new mails) but that definitely matters to Dovecot and therefore mbsync... After moving those files around, we still have 4,000 message missing:
anarcat@angela:~(main)$ find Maildir-mbsync/  -type f -a \! -name '.*'   wc -l 
381196
anarcat@angela:~(main)$ find Maildir/  -type f -a \! -name '.*'   wc -l 
385053
The problem is that those 4,000 missing mails are harder to track. Take, for example, .Archives.2011, which has a single message missing, out of 3,582. And the files are not identical: the checksums don't match after going through the IMAP transport, so we can't use a tool like hashdeep to compare the trees and find why any single file is missing.

"register" folder One big chunk of the 4,000, however, is a special folder called register in my spool, which I am syncing separately (see Securing registration email for details on that setup). That actually covers 3,700 of those messages, so I actually have a more modest 300 messages to figure out, after (easily!) configuring mbsync to sync that folder separately:
 @@ -30,9 +33,29 @@ Slave :anarcat-local:
  # Exclude everything under the internal [Gmail] folder, except the interesting folders
  #Patterns * ![Gmail]* "[Gmail]/Sent Mail" "[Gmail]/Starred" "[Gmail]/All Mail"
  # Or include everything
 -Patterns *
 +#Patterns *
 +Patterns * !register  !.register
  # Automatically create missing mailboxes, both locally and on the server
  #Create Both
  Create slave
  # Sync the movement of messages between folders and deletions, add after making sure the sync works
  #Expunge Both
 +
 +IMAPAccount anarcat-register
 +Host imap.anarc.at
 +User register
 +PassCmd "pass imap.anarc.at-register"
 +SSLType IMAPS
 +CertificateFile /etc/ssl/certs/ca-certificates.crt
 +
 +IMAPStore anarcat-register-remote
 +Account anarcat-register
 +
 +MaildirStore anarcat-register-local
 +SubFolders Maildir++
 +Inbox ~/Maildir-mbsync/.register/
 +
 +Channel anarcat-register
 +Master :anarcat-register-remote:
 +Slave :anarcat-register-local:
 +Create slave

"tmp" folders and empty messages After syncing the "register" messages, I end up with the measly little 160 emails out of sync:
anarcat@angela:~(main)$ find Maildir-mbsync/  -type f -a \! -name '.*'   wc -l 
384900
anarcat@angela:~(main)$ find Maildir/  -type f -a \! -name '.*'   wc -l 
385059
Argh. After more digging, I have found 131 mails in the tmp/ directories of the client's mail spool. Mysterious! On the server side, it's even more files, and not the same ones. Possible that those were mails that were left there during a failed delivery of some sort, during a power failure or some sort of crash? Who knows. It could be another race condition in SMD if it runs while mail is being delivered in tmp/... The first thing to do with those is to cleanup a bunch of empty files (21 on angela):
find .[^.]*/tmp -type f -empty -delete
As it turns out, they are all duplicates, in the sense that notmuch can easily find a copy of files with the same message ID in its database. In other words, this hairy command returns nothing
find .[^.]*/tmp -type f   while read path; do
  msgid=$(grep -m 1  -i ^message-id "$path"   sed 's/Message-ID: //i;s/[<>]//g');
  if notmuch count --exclude=false  "id:$msgid"   grep -q 0; then
    echo "$path <$msgid> not in notmuch" ;
  fi;
done
... which is good. Or, to put it another way, this is safe:
find .[^.]*/tmp -type f -delete
Poof! 314 mails cleaned on the server side. Interestingly, SMD doesn't pick up on those changes at all and still sees files in tmp/ directories on the client side, so we need to operate the same twisted logic there.

notmuch to the rescue again After cleaning that on the client, we get:
anarcat@angela:~(main)$ find Maildir/  -type f -a \! -name '.*'   wc -l 
384928
anarcat@angela:~(main)$ find Maildir-mbsync/  -type f -a \! -name '.*'   wc -l 
384901
Ha! 27 mails difference. Those are the really sticky, unclear ones. I was hoping a full sync might clear that up, but after deleting the entire directory and starting from scratch, I end up with:
anarcat@angela:~(main)$ find Maildir -type f -type f -a \! -name '.*'   wc -l 
385034
anarcat@angela:~(main)$ find Maildir-mbsync -type f -type f -a \! -name '.*'   wc -l 
384993
That is: even more messages missing (now 37). Sigh. Thankfully, this is something notmuch can help with: it can index all files by Message-ID (which I learned is case-insensitive, yay) and tell us which messages don't make it through. Considering the corruption I found in the mail spool, I wouldn't be the least surprised those messages are just skipped by the IMAP server. Unfortunately, there's nothing on the Dovecot server logs that would explain the discrepancy. Here again, notmuch comes to the rescue. We can list all message IDs to figure out that discrepancy:
notmuch search --exclude=false --output=messages '*'   pv -s 18M   sort > Maildir-msgids
notmuch --config=.notmuch-config-mbsync search --exclude=false --output=messages '*'   pv -s 18M   sort > Maildir-mbsync-msgids
And then we can see how many messages notmuch thinks are missing:
$ wc -l *msgids
372723 Maildir-mbsync-msgids
372752 Maildir-msgids
That's 29 messages. Oddly, it doesn't exactly match the find output:
anarcat@angela:~(main)$ find Maildir-mbsync -type f -type f -a \! -name '.*'   wc -l 
385204
anarcat@angela:~(main)$ find Maildir -type f -type f -a \! -name '.*'   wc -l 
385241
That is 10 more messages. Ugh. But actually, I know what those are: more misfiled messages (in a .folder/draft/ directory, bizarrely, so the totals actually match. In the notmuch output, there's a lot of stuff like this:
id:notmuch-sha1-fb880d673e24f5dae71b6b4d825d4a0d5d01cde4
Those are messages without a valid Message-ID. Notmuch (presumably) constructs one based on the file's checksum. Because the files differ between the IMAP server and the local mail spool (which is unfortunate, but possibly inevitable), those do not match. There are exactly the same number of those on both sides, so I'll go ahead and assume those are all accounted for. What remains is:
anarcat@angela:~(main)$ diff -u Maildir-mbsync-msgids Maildir-msgids    grep '^\-[^-]'   grep -v sha1   wc -l 
2
anarcat@angela:~(main)$ diff -u Maildir-mbsync-msgids Maildir-msgids    grep '^\+[^+]'   grep -v sha1   wc -l 
21
anarcat@angela:~(main)$ 
ie. 21 missing from mbsync, and, surprisingly, 2 missing from the original mail spool. Further inspection also showed they were all messages with some sort of "corruption": no body and only headers. I am not sure that is a legal email format in the first place. Since they were mostly spam or administrative emails ("You have been unsubscribed from mailing list..."), it seems fairly harmless to ignore those.

Conclusion As we'll see in the next article, SMD has stellar performance. But that comes at a huge cost: it accesses the mail storage directly. This can (and has) created significant problems on the mail server. It's unclear exactly why those things happen, but Dovecot expects a particular storage format on its file, and it seems unwise to bypass that. In the future, I'll try to remember to avoid that, especially since mechanisms like SMD require special server access (SSH) which, in the long term, I am not sure I want to maintain or expect. In other words, just talking with an IMAP server opens up a lot more possibilities of hosting than setting up a custom synchronisation protocol over SSH. It's also safer and more reliable, as we have seen. Thankfully, I've been able to recover from all the errors I could find, but it could have gone differently and it would have been possible for SMD to permanently corrupt significant part of my mail archives. In the end, however, the last drop was just another weird bug which, ironically, SMD mysteriously recovered from on its own while I was writing this documentation and migrating away from it. In any case, I recommend SMD users start looking for alternatives. The project has been archived upstream, and the Debian package has been orphaned. I have seen significant mail box corruption, including entire mail spool destruction, mostly due to incorrect locking code. I have filed a release-critical bug in Debian to make sure it doesn't ship with Debian bookworm. Alternatives like mbsync provide fast and reliable transport, including over SSH. See the next article for further discussion of the alternatives.

6 November 2021

Reproducible Builds: Reproducible Builds in October 2021

Welcome to the October 2021 report from the Reproducible Builds project!
This month Samanta Navarro posted to the oss-security security mailing on a novel category of exploit in the .tar archive format, where a single .tar file contains different contents depending on the tar utility being used. Naturally, this has consequences for reproducible builds as Samanta goes onto reply:

Arch Linux uses libarchive (bsdtar) in its build environment. The default tar program installed is GNU tar. It is possible to create a source distribution which leads to different files seen by the build environment than compared to a careful reviewer and other Linux distributions.
Samanta notes that addressing the tar utilities themselves will not be a sufficient fix:
I have submitted bug reports and patches to some projects but eventually I had to conclude that the problem itself cannot be fixed by these implementations alone. The best choice for these tools would be to only allow archives which are fully compatible to standards but this in turn would render a lot of archives broken.
Reproducible builds, with its twin ideas of reaching consensus on the build outputs as well as precisely recording and describing the build environment, would help address this problem at a higher level.
Codethink announced that they had achieved ISO-26262 ASIL D Tool Certification, a way of determining specific safety standards for software. Codethink used open source tooling to achieve this, but they also leverage:
Reproducibility, repeatability and traceability of builds, drawing heavily on best-practices championed by the Reproducible Builds project.

Elsewhere on the internet, according to a comment on Hacker News, Microsoft are now comparing NPM Javascript packages with their original source repositories:
I got a PR in my repository a few days ago leading back to a team trying to make it easier for packages to be reproducible from source.

Lastly, Martin Monperrus started an interesting thread on our mailing list about Github, specifically that their autogenerated release tarballs are not deterministic . The thread generated a significant number of replies that are worth reading.

Events and presentations

Community news On our mailing list this month:
There were quite a few changes to the Reproducible Builds website and documentation this month as well, including Feng Chai updating some links on our publications page [ ] and marco updated our project metadata around the Bitcoin Core building guide [ ].
Lastly, we ran another productive meeting on IRC during October. A full set of notes from the meeting is available to view.

Distribution work Qubes was heavily featured in the latest edition of Linux Weekly News, and a significant section was dedicated to discussing reproducibility. For example, it was mentioned that the Qubes project has been working on incorporating reproducible builds into its continuous integration (CI) infrastructure . But the LWN article goes on to describe that:
The current goal is to be able to build the Qubes OS Debian templates solely from packages that can be built reproducibly. Templates in Qubes OS are VM images that can be used to start an application qube quickly based on the template. The qube will have read-only access to the root filesystem of the template, so that the same root filesystem can be shared with multiple application qubes. There are official templates for several variants of both Fedora and Debian, as well as community maintained templates for several other distributions.
You can view the whole article on LWN, and Fr d ric also published a lengthy summary about their work on reproducible builds in Qubes as well for those wishing to learn more.
In Debian this month, 133 reviews of Debian packages were added, 81 were updated and 24 were removed this month, adding to Debian s ever-growing knowledge about identified issues. A number of issues were categorised and added by Chris Lamb and Vagrant Cascadian too [ ][ ][ ]. In addition, work on alternative snapshot service has made progress by Fr d ric Pierret and Holger Levsen this month, including moving from the existing host (snapshot.notset.fr) to snapshot.reproducible-builds.org (more info) thanks to OSUOSL for the machine and hosting and Debian for the disks.
Finally, Bernhard M. Wiedemann posted his monthly reproducible builds status report.

diffoscope diffoscope is our in-depth and content-aware diff utility. Not only can it locate and diagnose reproducibility issues, it can provide human-readable diffs from many kinds of binary formats. This month, Chris Lamb made the following changes, including preparing and uploading versions 186, 187, 188 and 189 to Debian
  • New features:
    • Add support for Python Sphinx inventory files (usually named objects.inv on-disk). [ ]
    • Add support for comparing .pyc files. Thanks to Sergei Trofimovich for the inspiration. [ ]
    • Try some alternative suffixes (e.g. .py) to support distributions that strip or retain them. [ ][ ]
  • Bug fixes:
    • Fix Python decompilation tests under Python 3.10+ [ ] and for Python 3.7 [ ].
    • Don t raise a traceback if we cannot unmarshal Python bytecode. This is in order to support Python 3.7 failing to load .pyc files generated with newer versions of Python. [ ]
    • Skip Python bytecode testing where we do not have an expected diff. [ ]
  • Codebase improvements:
    • Use our file_version_is_lt utility instead of accepting both versions of uImage expected diff. [ ]
    • Split out a custom call to assert_diff for a .startswith equivalent. [ ]
    • Use skipif instead of manual conditionals in some tests. [ ]
In addition, Jelle van der Waa added external tool references for Arch Linux for ocamlobjinfo, openssl and ffmpeg [ ][ ][ ] and added Arch Linux as a Continuous Integration (CI) test target. [ ] and Vagrant Cascadian updated the testsuite to skip Python bytecode comparisons when file(1) is older than 5.39. [ ] as well as added external tool references for the Guix distribution for dumppdf and ppudump. [ ][ ]. Vagrant Cascadian also updated the diffoscope package in GNU Guix [ ][ ]. Lastly, Guangyuan Yang updated the FreeBSD package name on the website [ ], Mattia Rizzolo made a change to override a new Lintian warning due to the new test files [ ], Roland Clobus added support to detect and log if the GNU_BUILD_ID field in an ELF binary been modified [ ], Sandro J ckel updated a number of helpful links on the website [ ] and Sergei Trofimovich made the uImage test output support file() version 5.41 [ ].

reprotest reprotest is the Reproducible Build s project end-user tool to build same source code twice in widely differing environments, checking the binaries produced by the builds for any differences. This month, reprotest version 0.7.18 was uploaded to Debian unstable by Holger Levsen, which also included a change by Holger to clarify that Python 3.9 is used nowadays [ ], but it also included two changes by Vasyl Gello to implement realistic CPU architecture shuffling [ ] and to log the selected variations when the verbosity is configured at a sufficiently high level [ ]. Finally, Vagrant Cascadian updated reprotest to version 0.7.18 in GNU Guix.

Upstream patches The Reproducible Builds project detects, dissects and attempts to fix unreproducible packages. We try to send all of our patches upstream where appropriate. We authored a large number of such patches this month, including:

Testing framework The Reproducible Builds project runs a testing framework at tests.reproducible-builds.org, to check packages and other artifacts for reproducibility. This month, the following changes were made:
  • Holger Levsen:
    • Debian-related changes:
      • Incorporate a fix from bremner into builtin-pho related to binary-NMUs. [ ]
      • Keep bullseye environments around longer, in an attempt to fix a Jenkins issue. [ ]
      • Improve the documentation of buildinfos.debian.net. [ ]
      • Improve documentation for the builtin-pho setup. [ ][ ]
    • OpenWrt-related changes:
      • Also use -j1 for better debugging. [ ]
      • Document that that Python 3.x is now used. [ ]
      • Enable further debugging for the toolchain build. [ ]
    • New snapshot.reproducible-builds.org service:
      • Actually add new node. [ ][ ]
      • Install xfsprogs on snapshot.reproducible-builds.org. [ ]
      • Create account for fpierret on new node. [ ]
      • Run node_health_check job on new node too. [ ]
  • Mattia Rizzolo:
    • Debian-related changes:
      • Handle schroot errors when invoking diffoscope instead of masking them. [ ][ ]
      • Declare and define some variables separately to avoid masking the subshell return code. [ ]
      • Fix variable name. [ ]
      • Improve log reporting. [ ]
      • Execute apt-get update with the -q argument to get more decent logs. [ ]
      • Set the Debian HTTP mirror and proxy for snapshot.reproducible-builds.org. [ ]
      • Install the libarchive-tools package (instead of bsdtar) when updating Jenkins nodes. [ ]
    • Be stricter about errors when starting the node agent [ ] and don t overwrite NODE_NAME so that we can expect Jenkins to properly set for us [ ].
    • Explicitly warn if the NODE_NAME is not a fully-qualified domain name (FQDN). [ ]
    • Document whether a node runs in the future. [ ]
    • Disable postgresql_autodoc as it not available in bullseye. [ ]
    • Don t be so eager when deleting schroot internals, call to schroot -e to terminate the schroots instead. [ ]
    • Only consider schroot underlays for deletion that are over a month old. [ ][ ]
    • Only try to unmount /proc if it s actually mounted. [ ]
    • Move the db_backup task to its own Jenkins job. [ ]
Lastly, Vasyl Gello added usage information to the reproducible_build.sh script [ ].

Contributing If you are interested in contributing to the Reproducible Builds project, please visit our Contribute page on our website. However, you can get in touch with us via:

13 September 2021

Bits from Debian: New Debian Developers and Maintainers (July and August 2021)

The following contributors got their Debian Developer accounts in the last two months: The following contributors were added as Debian Maintainers in the last two months: Congratulations!

25 July 2021

Marco d'Itri: Run an Ansible playbook in a chroot

Running a playbook in a remote chroot or container is not supported by Ansible, but I have invented a good workaround to do it anyway. The first step is to install Mitogen for Ansible (ansible-mitogen in Debian) and then configure ansible.cfg to use it:
[defaults]
strategy = mitogen_linear
But everybody should use Mitogen anyway, because it makes Ansible much faster. The trick to have Ansible operate in a chroot is to make it call a wrapper script instead of Python. The wrapper can be created manually or by another playbook, e.g.:
  vars:
  - fsroot: /mnt
  tasks:
  - name: Create the chroot wrapper
    copy:
      dest: "/usr/local/sbin/chroot_ inventory_hostname_short "
      mode: 0755
      content:  
        #!/bin/sh -e
        exec chroot  fsroot  /usr/bin/python3 "$@"
  - name: Continue with stage 2 inside the chroot
    debug:
      msg:
        - "Please run:"
        - "ansible-playbook therealplaybook.yaml -l  inventory_hostname  -e ansible_python_interpreter=/usr/local/sbin/chroot_ inventory_hostname_short "
This works thanks to Mitogen, which funnels all remote tasks inside that single call to Python. It would not work with standard Ansible, because it copies files to the remote system with SFTP and would do it outside of the chroot. The same principle can also be applied to containers by changing wrapper script, e.g:
#!/bin/sh -e
exec systemd-run --quiet --pipe --machine= container_name  --service-type=exec /usr/bin/python3 "$@"
After the wrapper will have been installed then you can run the real playbook by setting the ansible_python_interpreter variable, either on the command line, in the inventory or anywhere else that variables can be defined:
ansible-playbook therealplaybook.yaml -l  inventory_hostname  -e ansible_python_interpreter=/usr/local/sbin/chroot_ inventory_hostname_short 

29 June 2021

Antoine Beaupr : Another syncmaildir crash

So I had another major email crash with my syncmaildir setup. This time I was at least able to confirm the issue, and I still haven't lost mail thanks to backups and sheer luck (again).

The crash It is not really worth going over the crash in details, it's fairly similar to the last one: something bad happened and smd started destroying everything. The hint is that it takes a long time to do what usually takes seconds. It helps that I now have a second monitor showing logs. I still lost much more mail than the last time. I used to have "301 723 messages", according to notmuch. But then when I ran smd-pull by hand, it was telling me:
95K emails scanned
Oops. You can see notmuch happily noticing the destroyed files on the server:
jun 28 16:33:40 marcos notmuch[28532]: No new mail. Removed 65498 messages. Detected 1699 file renames.
jun 28 16:36:05 marcos notmuch[29746]: No new mail. Removed 68883 messages. Detected 2488 file renames.
jun 28 16:41:40 marcos notmuch[31972]: No new mail. Removed 118295 messages. Detected 3657 file renames.
The final count ended up being 81 042 messages, according to notmuch. A whopping 220 000 mails deleted. The interesting bit, this time around, is that I caught smd in the act of running two processes in parallel:
jun 28 16:30:09 curie systemd[2845]: Finished pull emails with syncmaildir. 
jun 28 16:30:09 curie systemd[2845]: Starting push emails with syncmaildir... 
jun 28 16:30:09 curie systemd[2845]: Starting pull emails with syncmaildir... 
So clearly that is the source of the bug.

Recovery Emergency stop on curie:
notmuch dump > notmuch.dump
systemctl --user --now disable smd-pull.service smd-pull.timer smd-push.service smd-push.timer notmuch-new.service notmuch-new.timer
On marcos (the server), guessed the number of messages delivered since the last backup to be 71, just looking at timestamps in the mail log. Made a list:
grep postfix/local /var/log/mail.log   tail -71 > lost-mail
Found postfix queue IDs:
sed 's/.*\]://;s/:.*//' lost-mail > qids
Turn those into message IDs, find those that are missing from the disk (had previously ran notmuch new just to be sure it's up to date):
while read qid ; do 
    grep "$qid: message-id" /var/log/mail.log
done < qids    sed 's/.*message-id=<//;s/>//'   while read msgid; do
    sudo -u anarcat notmuch count --exclude=false id:$msgid   grep -q 0 && echo $msgid
done
Copy this back on curie as missing-msgids and:
$ wc -l missing-msgids 
48 missing-msgids
$ while read msgid ; do notmuch count --exclude=false id:$msgid   grep -q 0 && echo $msgid ; done < missing-msgids
mailman.189.1624881611.23397.nodes-reseaulibre.ca@reseaulibre.ca
AnwMy7rdSpK-N-vt4AiOag@ismtpd0148p1mdw1.sendgrid.net
only two mails missing! whoohoo! Copy those back onto marcos as really-missing-msgids, and look at the full mail logs to see what they are:
~anarcat/src/koumbit-scripts/mail/postfix-trace --from-file really-missing-msgids2
I actually remembered deleting those, so no mail lost! Rebuild the list of msgids that were lost, on marcos:
while read qid ; do grep "$qid: message-id" /var/log/mail.log; done < qids    sed 's/.*message-id=<//;s/>//'
Copy that on curie as lost-mail-msgids, then copy the files over in a test dir:
while read msgid ; do
    notmuch search --output=files --exclude=false "id:$msgid"
done < lost-mail-msgids   sed 's#/home/anarcat/Maildir/##'   rsync -v  --files-from=- /home/anarcat/Maildir/ shell.anarc.at:restore/Maildir-angela/
If that looks about right, on marcos:
find restore/Maildir-angela/ -type f   wc -l
... should match the number of missing mails, roughly. Copy if in the real spool:
while read msgid ; do
    notmuch search --output=files --exclude=false "id:$msgid"
done < lost-mail-msgids   sed 's#/home/anarcat/Maildir/##'   rsync -v  --files-from=- /home/anarcat/Maildir/ shell.anarc.at:Maildir/
Then on the server, notmuch new should find the new emails, and we shouldn't have any lost mail anymore:
while read qid ; do grep "$qid: message-id" /var/log/mail.log; done < qids    sed 's/.*message-id=<//;s/>//'   while read msgid; do sudo -u anarcat notmuch count --exclude=false id:$msgid   grep -q 0 && echo $msgid ; done
Then, crucial moment, try to pull the new mails from the backups on curie:
anarcat@curie:~(main)$ smd-pull  -n  --show-tags -v
Found lockfile of a dead instance. Ignored.
Phase 0: handshake
Phase 1: changes detection
    5K emails scanned
   10K emails scanned
   15K emails scanned
   20K emails scanned
   25K emails scanned
   30K emails scanned
   35K emails scanned
   40K emails scanned
   45K emails scanned
   50K emails scanned
Phase 2: synchronization
Phase 3: agreement
default: smd-client@localhost: TAGS: stats::new-mails(49687), del-mails(0), bytes-received(215752279), xdelta-received(3703852)
"smd-pull  -n  --show-tags -v" took 3 mins 39 secs
This brought me back to the state after the backup plus the mails delivered during the day, which means I had to catchup with all my holiday's read emails (1440 mails!) but thankfully I made a dump of the notmuch database on curie at the start of the procedure, so this actually restored a sane state:
pv notmuch.dump   notmuch restore
Phew!

Workaround I have filed this as a bug in upstream issue 18. Considering I filed 11 issues and only 3 of those were closed, I'm not holding my breath. I nevertheless filed PR 19 in the hope that this will fix my particular issue, but I'm not even sure this is the right fix...

Fix At this point, I'm really ready to give up on SMD. It's really, really nice to be able to sync mail over SSH because I don't need to store my IMAP password on disk. But surely there are more reliable syncing mechanisms. I do not remember ever losing that much mail before. At worst, offlineimap would duplicate emails like mad, but never destroy my entire mail spool that way. As mentioned before, there are other programs that sync mail. I'm looking at:
  • offlineimap3: requires IMAP, used the py2 version in the past, might just still work, first sync painful (IIRC), ways to tunnel over SSH, see comment below
  • isync/mbsync: might be faster, I remember having trouble switching from offlineimap to this, has support for TLS client certs, running over SSH, and generally has good words from multiple Debian and notmuch people
  • getmail: just downloads email, might not be enough
  • nncp: treat the local spool as another mail server, might not be compatible with my "multiple clients" setup
  • doveadm-sync: requires dovecot on both ends, but supports using SSH to sync, will try this next, may have performance problems, see comment below
  • interimap: syncs two IMAP servers, apparently faster than doveadm and offlineimap
  • mail-sync: notify support, happens over any piped transport (e.g. ssh), diff/patch system, requires binary on both ends, mentions UUCP in the manpage, seems awfully complicated to setup, mentions rsmtp which is a nice name for rsendmail

1 June 2021

Paul Wise: FLOSS Activities May 2021

Focus This month I didn't have any particular focus. I just worked on issues in my info bubble.

Changes

Issues

Review

Administration
  • Debian wiki: unblock IP addresses, approve accounts

Communication
  • Joined the great IRC migration
  • Respond to queries from Debian users and contributors on the mailing lists and IRC

Sponsors The purple-discord, sptag and esprima-python work was sponsored by my employer. All other work was done on a volunteer basis.

19 May 2021

Marco d'Itri: My resignation from freenode

As it is now known, the freenode IRC network has been taken over by a Trumpian wannabe korean royalty bitcoins millionaire. To make a long story short, the former freenode head of staff secretly "sold" the network to this person even if it was not hers to sell, and our lawyers have advised us that there is not much that we can do about it without some of us risking financial ruin. Fuck you Christel, lilo's life work did not deserve this. What you knew as freenode after 12:00 UTC of May 19 will be managed by different people. As I have no desire to volunteer under the new regime, this marks the end of my involvement with freenode. It had started in 1999 when I encouraged the good parts of #linux-it to leave ircnet, and soon after I became senior staff. Even if I have not been very active recently, at this point I was the longest-serving freenode staff member and now I expect that I will hold this record forever. The people that I have met on IRC, on freenode and other networks, have been and still are a very important part of my life, second only to the ones that I have known thanks to Usenet. I am not fine, but I know that the communities which I have been a part of are not defined by a domain name and will regroup somewhere else. The current freenode staff members have resigned with me, these are some of their farewell messages:
  • amdj
  • edk
  • emilsp
  • Fuchs
  • jess
  • JonathanD
  • kline
  • niko
  • mniip
  • Swant
  • Together we have created Libera.Chat, a new IRC network based on the same principles of the old freenode.

    1 April 2021

    Paul Wise: FLOSS Activities March 2021

    Focus This month I didn't have any particular focus. I just worked on issues in my info bubble.

    Changes

    Issues

    Debugging

    Review

    Administration
    • Debian packages: migrate flower git repo from alioth-archive to salsa
    • Debian: restart bacula-director after PostgreSQL restart
    • Debian wiki: block spammer, clean up spam, approve accounts

    Communication

    Sponsors The librecaptcha/libpst/flower/marco work was sponsored by my employers. All other work was done on a volunteer basis.

    23 March 2021

    Antoine Beaupr : Major email crash with syncmaildir

    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:
    1. I rewired my office on that day.
    2. This meant unplugging curie, the workstation.
    3. It has a bad CMOS battery (known problem), so it jumped around the time continuum a few times, sometimes by years.
    4. 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.
    5. 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
    1. follow what smd says, even if it seems useless or strange.
    2. trust but verify: just backup everything before you do anything, especially the largest data set.
    3. daily backups are not great for email, unless you're ready to lose a day of email (which I'm not).
    4. 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.
    5. 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 (!).
    6. 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.

    9 February 2021

    Kees Cook: security things in Linux v5.8

    Previously: v5.7 Linux v5.8 was released in August, 2020. Here s my summary of various security things that caught my attention: arm64 Branch Target Identification
    Dave Martin added support for ARMv8.5 s Branch Target Instructions (BTI), which are enabled in userspace at execve() time, and all the time in the kernel (which required manually marking up a lot of non-C code, like assembly and JIT code). With this in place, Jump-Oriented Programming (JOP, where code gadgets are chained together with jumps and calls) is no longer available to the attacker. An attacker s code must make direct function calls. This basically reduces the usable code available to an attacker from every word in the kernel text to only function entries (or jump targets). This is a low granularity forward-edge Control Flow Integrity (CFI) feature, which is important (since it greatly reduces the potential targets that can be used in an attack) and cheap (implemented in hardware). It s a good first step to strong CFI, but (as we ve seen with things like CFG) it isn t usually strong enough to stop a motivated attacker. High granularity CFI (which uses a more specific branch-target characteristic, like function prototypes, to track expected call sites) is not yet a hardware supported feature, but the software version will be coming in the future by way of Clang s CFI implementation. arm64 Shadow Call Stack
    Sami Tolvanen landed the kernel implementation of Clang s Shadow Call Stack (SCS), which protects the kernel against Return-Oriented Programming (ROP) attacks (where code gadgets are chained together with returns). This backward-edge CFI protection is implemented by keeping a second dedicated stack pointer register (x18) and keeping a copy of the return addresses stored in a separate shadow stack . In this way, manipulating the regular stack s return addresses will have no effect. (And since a copy of the return address continues to live in the regular stack, no changes are needed for back trace dumps, etc.) It s worth noting that unlike BTI (which is hardware based), this is a software defense that relies on the location of the Shadow Stack (i.e. the value of x18) staying secret, since the memory could be written to directly. Intel s hardware ROP defense (CET) uses a hardware shadow stack that isn t directly writable. ARM s hardware defense against ROP is PAC (which is actually designed as an arbitrary CFI defense it can be used for forward-edge too), but that depends on having ARMv8.3 hardware. The expectation is that SCS will be used until PAC is available. Kernel Concurrency Sanitizer infrastructure added
    Marco Elver landed support for the Kernel Concurrency Sanitizer, which is a new debugging infrastructure to find data races in the kernel, via CONFIG_KCSAN. This immediately found real bugs, with some fixes having already landed too. For more details, see the KCSAN documentation. new capabilities
    Alexey Budankov added CAP_PERFMON, which is designed to allow access to perf(). The idea is that this capability gives a process access to only read aspects of the running kernel and system. No longer will access be needed through the much more powerful abilities of CAP_SYS_ADMIN, which has many ways to change kernel internals. This allows for a split between controls over the confidentiality (read access via CAP_PERFMON) of the kernel vs control over integrity (write access via CAP_SYS_ADMIN). Alexei Starovoitov added CAP_BPF, which is designed to separate BPF access from the all-powerful CAP_SYS_ADMIN. It is designed to be used in combination with CAP_PERFMON for tracing-like activities and CAP_NET_ADMIN for networking-related activities. For things that could change kernel integrity (i.e. write access), CAP_SYS_ADMIN is still required. network random number generator improvements
    Willy Tarreau made the network code s random number generator less predictable. This will further frustrate any attacker s attempts to recover the state of the RNG externally, which might lead to the ability to hijack network sessions (by correctly guessing packet states). fix various kernel address exposures to non-CAP_SYSLOG
    I fixed several situations where kernel addresses were still being exposed to unprivileged (i.e. non-CAP_SYSLOG) users, though usually only through odd corner cases. After refactoring how capabilities were being checked for files in /sys and /proc, the kernel modules sections, kprobes, and BPF exposures got fixed. (Though in doing so, I briefly made things much worse before getting it properly fixed. Yikes!) RISCV W^X detection
    Following up on his recent work to enable strict kernel memory protections on RISCV, Zong Li has now added support for CONFIG_DEBUG_WX as seen for other architectures. Any writable and executable memory regions in the kernel (which are lovely targets for attackers) will be loudly noted at boot so they can get corrected. execve() refactoring continues
    Eric W. Biederman continued working on execve() refactoring, including getting rid of the frequently problematic recursion used to locate binary handlers. I used the opportunity to dust off some old binfmt_script regression tests and get them into the kernel selftests. multiple /proc instances
    Alexey Gladkov modernized /proc internals and provided a way to have multiple /proc instances mounted in the same PID namespace. This allows for having multiple views of /proc, with different features enabled. (Including the newly added hidepid=4 and subset=pid mount options.) set_fs() removal continues
    Christoph Hellwig, with Eric W. Biederman, Arnd Bergmann, and others, have been diligently working to entirely remove the kernel s set_fs() interface, which has long been a source of security flaws due to weird confusions about which address space the kernel thought it should be accessing. Beyond things like the lower-level per-architecture signal handling code, this has needed to touch various parts of the ELF loader, and networking code too. READ_IMPLIES_EXEC is no more for native 64-bit
    The READ_IMPLIES_EXEC flag was a work-around for dealing with the addition of non-executable (NX) memory when x86_64 was introduced. It was designed as a way to mark a memory region as well, since we don t know if this memory region was expected to be executable, we must assume that if we need to read it, we need to be allowed to execute it too . It was designed mostly for stack memory (where trampoline code might live), but it would carry over into all mmap() allocations, which would mean sometimes exposing a large attack surface to an attacker looking to find executable memory. While normally this didn t cause problems on modern systems that correctly marked their ELF sections as NX, there were still some awkward corner-cases. I fixed this by splitting READ_IMPLIES_EXEC from the ELF PT_GNU_STACK marking on x86 and arm/arm64, and declaring that a native 64-bit process would never gain READ_IMPLIES_EXEC on x86_64 and arm64, which matches the behavior of other native 64-bit architectures that correctly didn t ever implement READ_IMPLIES_EXEC in the first place. array index bounds checking continues
    As part of the ongoing work to use modern flexible arrays in the kernel, Gustavo A. R. Silva added the flex_array_size() helper (as a cousin to struct_size()). The zero/one-member into flex array conversions continue with over a hundred commits as we slowly get closer to being able to build with -Warray-bounds. scnprintf() replacement continues
    Chen Zhou joined Takashi Iwai in continuing to replace potentially unsafe uses of sprintf() with scnprintf(). Fixing all of these will make sure the kernel avoids nasty buffer concatenation surprises. That s it for now! Let me know if there is anything else you think I should mention here. Next up: Linux v5.9.

    2021, Kees Cook. This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 License.
    CC BY-SA 4.0

    29 January 2021

    Russ Allbery: INN 2.6.4

    INN 2.6.4 has been released. This is a bug fix and minor feature release over INN 2.6.3, and the upgrade should be painless. You can download the new release from ftp.isc.org or my personal INN pages. The latter also has links to the full changelog and the other INN documentation. As always, thanks to Julien LIE for preparing this release and doing most of the maintenance work on INN! Changes in this release:

    16 November 2020

    Bits from Debian: New Debian Developers and Maintainers (September and October 2020)

    The following contributors got their Debian Developer accounts in the last two months: The following contributors were added as Debian Maintainers in the last two months: Congratulations!

    26 October 2020

    Marco d'Itri: RPKI validation with FORT Validator

    This article documents how to install FORT Validator (an RPKI relying party software which also implements the RPKI to Router protocol in a single daemon) on Debian 10 to provide RPKI validation to routers. If you are using testing or unstable then you can just skip the part about apt pinnings. The packages in bullseye (Debian testing) can be installed as is on Debian stable with no need to rebuild them, by configuring an appropriate pinning for apt:
    cat <<END > /etc/apt/sources.list.d/bullseye.list
    deb http://deb.debian.org/debian/ bullseye main
    END
    cat <<END > /etc/apt/preferences.d/pin-rpki
    # by default do not install anything from bullseye
    Package: *
    Pin: release bullseye
    Pin-Priority: 100
    Package: fort-validator rpki-trust-anchors
    Pin: release bullseye
    Pin-Priority: 990
    END
    apt update
    
    Before starting, make sure that curl (or wget) and the web PKI certificates are installed:
    apt install curl ca-certificates
    
    If you already know about the legal issues related to the ARIN TAL then you may instruct the package to automatically install it. If you skip this step then you will be asked at installation time about it, either way is fine.
    echo 'rpki-trust-anchors rpki-trust-anchors/get_arin_tal boolean true' \
        debconf-set-selections
    
    Install the package as usual:
    apt install fort-validator
    
    You may also install rpki-client and gortr on Debian 10, or maybe cfrpki and gortr. I have also tried packaging Routinator 3000 for Debian, but this effort is currently on hold because the Rust ecosystem is broken and hostile to the good packaging practices of Linux distributions.

    Marco d'Itri: RPKI validation with OpenBSD's rpki-client and Cloudflare's gortr

    This article documents how to install rpki-client (an RPKI relying party software, the actual validator) and gortr (which implements the RPKI to Router protocol) on Debian 10 to provide RPKI validation to routers. If you are using testing or unstable then you can just skip the part about apt pinnings. The packages in bullseye (Debian testing) can be installed as is on Debian stable with no need to rebuild them, by configuring an appropriate pinning for apt:
    cat <<END > /etc/apt/sources.list.d/bullseye.list
    deb http://deb.debian.org/debian/ bullseye main
    END
    cat <<END > /etc/apt/preferences.d/pin-rpki
    # by default do not install anything from bullseye
    Package: *
    Pin: release bullseye
    Pin-Priority: 100
    Package: gortr rpki-client rpki-trust-anchors
    Pin: release bullseye
    Pin-Priority: 990
    END
    apt update
    
    Before starting, make sure that curl (or wget) and the web PKI certificates are installed:
    apt install curl ca-certificates
    
    If you already know about the legal issues related to the ARIN TAL then you may instruct the package to automatically install it. If you skip this step then you will be asked at installation time about it, either way is fine.
    echo 'rpki-trust-anchors rpki-trust-anchors/get_arin_tal boolean true' \
        debconf-set-selections
    
    Install the packages as usual:
    apt install rpki-client gortr
    
    And then configure rpki-client to generate its output in the the JSON format needed by gortr:
    echo 'OPTIONS=-j' > /etc/default/rpki-client
    
    You may manually start the service unit to immediately generate the data instead of waiting for the next timer run:
    systemctl start rpki-client &
    
    gortr too needs to be configured to use the JSON data generated by rpki-client:
    echo 'GORTR_ARGS=-bind :323 -verify=false -checktime=false -cache /var/lib/rpki-client/json' > /etc/default/gortr
    
    And then it needs to be restarted to use the new configuration:
    systemctl restart gortr
    
    You may also install FORT Validator on Debian 10, or maybe cfrpki with gortr. I have also tried packaging Routinator 3000 for Debian, but this effort is currently on hold because the Rust ecosystem is broken and hostile to the packaging practices of Linux distributions.

    21 July 2020

    Bits from Debian: New Debian Developers and Maintainers (May and June 2020)

    The following contributors got their Debian Developer accounts in the last two months: The following contributors were added as Debian Maintainers in the last two months: Congratulations!

    15 April 2020

    Antoine Beaupr : OpenDKIM configuration to send debian.org email

    Debian.org added support for DKIM in 2020. To configure this on my side, I had to do the following, on top of my email configuration.
    1. add this line to /etc/opendkim/signing.table:
      *@debian.org marcos-debian.anarcat.user
      
    2. add this line to /etc/opendkim/key.table:
      marcos-debian.anarcat.user debian.org:marcos-debian.anarcat.user:/etc/opendkim/keys/marcos-debian.anarcat.user.private
      
      Yes, that's quite a mouthful! That magic selector is long in that way because it needs a special syntax (specifically the .anarcat.user suffix) for Debian to be happy. The -debian string is to tell me where the key is published. The marcos prefix is to remind me where the private is used.
    3. generate the key with:
      opendkim-genkey --directory=/etc/opendkim/keys/ --selector=marcos-debian.anarcat.user --domain=debian.org --verbose
      
      This creates the DNS record in /etc/opendkim/keys/marcos-debian.anarcat.user.txt (alongside the private key in .key).
    4. restart OpenDKIM:
      service opendkim restart
      
      The DNS record will look something like this:
      marcos-debian.anarcat.user._domainkey   IN  TXT ( "v=DKIM1; h=sha256; k=rsa; "
      "p=MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAtKzBK2f8vg5yV307WAOatOhypQt3ANQ95iDaewkVehmx42lZ6b4PzA1k5DkIarxjkk+7m6oSpx5H3egrUSLMirUiMGsIb5XVGBPFmKZhDVmC7F5G1SV7SRqqKZYrXTufRRSne1eEtA31xpMP0B32f6v6lkoIZwS07yQ7DDbwA9MHfyb6MkgAvDwNJ45H4cOcdlCt0AnTSVndcl"
      "pci5/2o/oKD05J9hxFTtlEblrhDXWRQR7pmthN8qg4WaNI4WszbB3Or4eBCxhUdvAt2NF9c9eYLQGf0jfRsbOcjSfeus0e2fpsKW7JMvFzX8+O5pWfSpRpdPatOt80yy0eqpm1uQIDAQAB" )  ; ----- DKIM key marcos-debian.anarcat.user for debian.org
      
    5. The "p=MIIB..." string needs to be joined together, without the quotes and the p=, and sent in a signed email to changes@db.debian.org:
      -----BEGIN PGP SIGNED MESSAGE-----
      dkimPubKey: marcos.anarcat.user MIIB[...]
      -----BEGIN PGP SIGNATURE-----
      [...]
      
    6. Wait a few minutes for DNS to propagate. You can check if they have with:
      host -t TXT marcos-debian.anarcat.user._domainkey.debian.org nsp.dnsnode.net
      
      (nsp.dnsnode.net being one of the NS records of the debian.org zone.)
    If all goes well, the tests should pass when sending from your server as anarcat@debian.org.

    Testing Test messages can be sent to dkimvalidator, mail-tester.com or check-auth@verifier.port25.com. Those tools will run Spamassassin on the received emails and report the results. What you are looking for is:
    • -0.1 DKIM_VALID: Message has at least one valid DKIM or DK signature
    • -0.1 DKIM_VALID_AU: Message has a valid DKIM or DK signature from author's domain
    • -0.1 DKIM_VALID_EF: Message has a valid DKIM or DK signature from envelope-from domain
    If one of those is missing, then you are doing something wrong and your "spamminess" score will be worse. The latter is especially tricky as it validates the "Envelope From", which is the MAIL FROM: header as sent by the originating MTA, which you see as from=<> in the postfix lost. The following will happen anyways, as soon as you have a signature, that's normal:
    • 0.1 DKIM_SIGNED: Message has a DKIM or DK signature, not necessarily valid
    And this might happen if you have a ADSP record but do not correctly sign the message with a domain field that matches the record:
    • 1.1 DKIM_ADSP_ALL No valid author signature, domain signs all mail
    That's bad and will affect your spam core badly. I fixed that issue by using a wildcard key in the key table:
    --- a/opendkim/key.table
    +++ b/opendkim/key.table
    @@ -1 +1 @@
    -marcos anarc.at:marcos:/etc/opendkim/keys/marcos.private
    +marcos %:marcos:/etc/opendkim/keys/marcos.private
    

    References This is a copy of a subset of my more complete email configuration.

    16 July 2017

    Jose M. Calhariz: Crossgrading a complex Desktop and Debian Developer machine running Debian 9

    This article is an experiment in progress, please recheck, while I am updating with the new information. I have a very old installation of Debian, possibly since v2, dot not remember, that I have upgraded since then both in software and hardware. Now the hardware is 64bits, runs a kernel of 64bits but the run-time is still 32bits. For 99% of tasks this is very good. Now that I have made many simulations I may have found a solution to do a crossgrade of my desktop. I write here the tentative procedure and I will update with more ideias on the problems that I may found. First you need to install a 64bits kernel and boot with it. See my previous post on how to do it. Second you need to do a bootstrap of crossgrading and the instalation of all the libs as amd64:
     apt-get update
     apt-get upgrade
     apt-get clean
     dpkg --list > original.dpkg
     apt-get --download-only install dpkg:amd64 tar:amd64 apt:amd64 bash:amd64 dash:amd64 init:amd64 mawk:amd64
     cd /var/cache/apt/archives/
     dpkg --install dpkg_*amd64.deb tar_*amd64.deb apt_*amd64.deb bash_*amd64.deb dash_*amd64.deb *.deb
     dpkg --configure --pending
     dpkg -i --skip-same-version dpkg_*_amd64.deb apt_*_amd64.deb bash_*_amd64.deb dash_*_amd64.deb mawk_*_amd64.deb *.deb
     
     for pack32 in $(grep i386 original.dpkg    egrep "^ii "   awk ' print $2 ' ) ; do 
       echo $pack32 ; 
       if dpkg --status $pack32   grep -q "Multi-Arch: same" ; then 
         apt-get --download-only install -y --allow-remove-essential $ pack32%:i386 :amd64 ; 
       fi ; 
     done
     dpkg --install /var/cache/apt/archives/*_amd64.deb
     dpkg --install /var/cache/apt/archives/*_amd64.deb
     dpkg --print-architecture
     dpkg --print-foreign-architectures
    
    But this procedure does not prevent the "apt-get install" to have broken dependencies. So trying to install the core packages and the libraries using "dpkg -i".
    apt-get update
    apt-get upgrade
    apt-get autoremove
    apt-get clean
    dpkg --list > original.dpkg
    apt-get --download-only install dpkg:amd64 tar:amd64 apt:amd64 bash:amd64 dash:amd64 init:amd64 mawk:amd64
    for pack32 in $(grep i386 original.dpkg   egrep "^ii "   awk ' print $2 ' ) ; do 
      echo $pack32 ; 
      if dpkg --status $pack32   grep -q "Multi-Arch: same" ; then 
        apt-get --download-only install -y --allow-remove-essential $ pack32%:i386 :amd64 ; 
      fi ; 
    done
    cd /var/cache/apt/archives/
    dpkg --install dpkg_*amd64.deb tar_*amd64.deb apt_*amd64.deb bash_*amd64.deb dash_*amd64.deb *.deb
    dpkg --configure --pending
    dpkg --install --skip-same-version dpkg_*_amd64.deb apt_*_amd64.deb bash_*_amd64.deb dash_*_amd64.deb mawk_*_amd64.deb *.deb
    dpkg --remove libcurl4-openssl-dev
    dpkg -i libcurl4-openssl-dev_*_amd64.deb
    
    Remove packages until all there is no brokens packages
    dpkg --print-architecture
    dpkg --print-foreign-architectures
    apt-get --fix-broken --allow-remove-essential install
    
    Still broken, because apt-get removed dpkg So instead of only installing the libs with dpkg -i, I am going to try to install all the packages with dpkg -i:
    apt-get update
    apt-get upgrade
    apt-get autoremove
    apt-get clean
    dpkg --list > original.dpkg
    apt-get --download-only install dpkg:amd64 tar:amd64 apt:amd64 bash:amd64 dash:amd64 init:amd64 mawk:amd64
    for pack32 in $(grep i386 original.dpkg   egrep "^ii "   awk ' print $2 ' ) ; do 
      echo $pack32 ; 
      apt-get --download-only install -y --allow-remove-essential $ pack32%:i386 :amd64 ; 
    done
    cd /var/cache/apt/archives/
    dpkg --install dpkg_*amd64.deb tar_*amd64.deb apt_*amd64.deb bash_*amd64.deb dash_*amd64.deb *.deb
    dpkg --configure --pending
    dpkg --install --skip-same-version dpkg_*_amd64.deb apt_*_amd64.deb bash_*_amd64.deb dash_*_amd64.deb mawk_*_amd64.deb *.deb
    dpkg --configure --pending
    
    Remove packages and reinstall selected packages until you fix all off them. Follow the trial for my machine:
    dpkg --remove rkhunter
    dpkg --remove libmarco-private1:i386 marco mate-control-center mate-desktop-environment-core mate-desktop-environment-core  mate-desktop-environment mate-desktop-environment-core mate-desktop-environment-extras
    dpkg --remove libmate-menu2:i386 libmate-window-settings1:i386 mate-panel mate-screensaver python-mate-menu libmate-slab0:i386 mozo mate-menus
    dpkg --remove libmate-menu2:i386 mate-panel python-mate-menu mate-applets mate-menus
    dpkg -i libmate-menu2_1.16.0-2_amd64.deb
    dpkg --remove  gir1.2-ibus-1.0:i386 gnome-shell gnome-shell-extensions gdm3 gnome-session
    dpkg --remove  gir1.2-ibus-1.0:i386
    dpkg --remove libmateweather1:i386
    dpkg -i libmateweather1_1.16.1-2_amd64.deb
    apt-get --fix-broken --download-only install
    dpkg --skip-same-version --install dpkg_*amd64.deb tar_*amd64.deb apt_*amd64.deb bash_*amd64.deb dash_*amd64.deb *.deb
    dpkg --configure --pending
    dpkg -i python_2.7.13-2_amd64.deb
    dpkg --configure --pending
    dpkg -i perl_5.24.1-3+deb9u1_amd64.deb perl-base_5.24.1-3+deb9u1_amd64.deb
    dpkg -i exim4-daemon-light_4.89-2+deb9u1_amd64.deb exim4-base_4.89-2+deb9u1_amd64.deb
    dpkg -i libuuid-perl_0.27-1_amd64.deb
    dpkg --configure --pending
    dpkg --install gstreamer1.0-plugins-bad_1.10.4-1_amd64.deb libmpeg2encpp-2.1-0_1%3a2.1.0+debian-5_amd64.deb libmplex2-2.1-0_1%3a2.1.0+debian-5_amd64.deb
    dpkg --configure --pending
    dpkg --audit
    
    Now fixing broken dependencies on apt-get. Found no other way than removing all the broken packages.
    dpkg --remove $(apt-get --fix-broken install   cut -f 2 -d ' ' )
    apt-get install $(grep -v ":i386" ~/original.dpkg   egrep "^ii"   grep -v "aiccu"   grep -v "acroread"   grep -v "flash-player-properties"   grep -v "flashplayer-mozilla"   egrep -v "tp-flash-marillat"   awk ' print $2 ')
    

    Next.