djcb / mu

maildir indexer/searcher + emacs mail client + guile bindings
http://www.djcbsoftware.nl/code/mu
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[mu4e bug] mu 1.6.1 emacs interface very slow #2089

Closed telmich closed 1 year ago

telmich commented 3 years ago

Describe the bug

As reported before, mu4e can be extremely slow. Right now with mu 1.6.1 there is however a huge difference between searching inside emacs and searching using mu find:

To Reproduce

Index ca. 1.5M messages, execute a simple search like:

find flag:flagged OR maildir:/ungleich/inbox OR maildir:/gmail/inbox OR maildir:/otherfish/inbox

Time with mu find: ca. 1s Time with mu4e: minutes (ca 2-3m)

If I repeat the same query, it always takes extremely long inside emacs and is always fast outside.

While in my previous report it was related to updating and did not always happen, the situation changed now:

(independent of whether update is running or not)

Environment

nb3:~# apk list -I mu mu4e emacs-x11
mu-1.6.1-r0 x86_64 {mu} (GPL-3.0) [installed]
mu4e-1.6.1-r0 x86_64 {mu} (GPL-3.0) [installed]
emacs-x11-27.2-r1 x86_64 {emacs} (GPL-3.0-or-later) [installed]

[17:18] nb3:~% du -sh Maildir/
35G Maildir/
[17:17] nb3:~% find Maildir/ -type f | wc -l
1510809

Checklist

djcb commented 3 years ago

What options did you use with the mu find vs mu4e (w.r.t. related messages / threads)? Does this happen with a singular query, i.e. just flag:flagged?

telmich commented 3 years ago

The problem also happens with only flag:flagged (still running in mu4e as of writing this). In terms of configuration, I am not sure which ones are affecting the related messages/threads, so I'll add my complete mu4e related settings without the contexts:

(require 'mu4e)
(setq mu4e-view-use-gnus nil)
(add-to-list 'mu4e-view-actions
             '("ViewInBrowser" . mu4e-action-view-in-browser) t)

;; needed for some emails in mu4e
(setq max-specpdl-size 5000)  ; default is 1000, reduce the backtrace level

(add-to-list 'mu4e-view-actions
             '("ViewInBrowser" . mu4e-action-view-in-browser) t)

(add-hook 'message-mode-hook 'turn-on-orgtbl)

(setq mu4e-compose-complete-only-after (format-time-string
                                        "%Y-%m-%d"
                                        (time-subtract (current-time) (days-to-time 600))))

(setq mu4e-headers-sort-direction 'descending)

(setq mu4e-headers-include-related nil)

(setq mu4e-attachment-dir  "~/Downloads")
(setq mu4e-drafts-folder "/ungleich/drafts")
(setq mu4e-sent-folder   "/ungleich/sent")
(setq mu4e-trash-folder  "/ungleich/trash")
(setq mu4e-refile-folder
      (lambda (msg) (concat "/ungleich/" (format-time-string "%Y"))))

;; mbsync workaround
;; https://stackoverflow.com/questions/39513469/mbsync-error-uid-is-beyond-highest-assigned-uid
(setq mu4e-change-filenames-when-moving t)
(setq mu4e-bookmarks '())

; allow all results
(setq mu4e-headers-full-search t)
(add-to-list 'mu4e-bookmarks
             '("maildir:/ungleich/archive" "archive" ?a))

(add-to-list 'mu4e-bookmarks
             '("maildir:/ungleich/drafts" "drafts" ?d))

(add-to-list 'mu4e-bookmarks
             '("maildir:/sent OR maildir:/outgoing OR maildir:/ungleich/sent" "sent" ?s))

(add-to-list 'mu4e-bookmarks
             '("(flag:flagged OR maildir:/ungleich/inbox OR maildir:/gmail/inbox) AND redmine" "redmine" ?r))

(add-to-list 'mu4e-bookmarks
             '("flag:flagged OR maildir:/ungleich/inbox OR maildir:/gmail/inbox OR maildir:/otherfish/inbox"
               "inbox" ?i))

(add-to-list 'mu4e-bookmarks
             '("maildir:/otherfish/inbox"       "otherfish" ?f))

(add-to-list 'mu4e-bookmarks
             '("maildir:/gmail/inbox"       "gmail" ?g))

(add-to-list 'mu4e-bookmarks
             '("maildir:/ungleich/inbox"       "ungleich" ?u))

(setq mu4e-hide-index-messages t           ;; Don't annoy the user
      mu4e-get-mail-command "hole_mails"   ;; custom script for security
      mu4e-attachment-dir "~")             ;; [Don't] fill up the home dir

(add-hook 'mu4e-view-mode-hook 'visual-line-mode)

;; Always sign
(add-hook 'message-setup-hook 'mml-secure-sign-pgpmime)

(setq message-kill-buffer-on-exit t)

(require 'org-mu4e)
(define-key mu4e-headers-mode-map (kbd "C-c c") 'mu4e-org-store-and-capture)
(define-key mu4e-view-mode-map    (kbd "C-c c") 'mu4e-org-store-and-capture)
(setq mu4e-headers-skip-duplicates nil)

(setq org-mu4e-link-query-in-headers-mode nil)
telmich commented 3 years ago

I just checked on another machine, using 1.4.15 queries with the same configuration are fast:

[21:14] line:~% find Maildir/ -type f  | wc -l
1509616
[21:14] line:~% dpkg -l | grep mu4e           
ii  mu4e                                     1.4.15-1                                     all          e-mail client for Emacs based on mu (maildir-utils)
haji-ali commented 3 years ago

I had a similar issue, not sure if yours is the same. In my case, the first search in mu4e after an mbsync update was always slow because it seems that mu4e indexes messages before searching; which is slow on a large database. Since I updated frequently, this meant that most searches were slow.

djcb commented 3 years ago

The command-line query needs to have the equivalent flags to allow for comparison, so

$ mu find  --threads flag:flagged

and perhaps, to isolate the server part from mu4e:

$ mu server --eval '(find :query "flag:flagged" :threads t)' 

How many results do you have for that query? If there are many, (setq mu4e-headers-full-search t) will make things slow.

telmich commented 3 years ago
mu find  --threads flag:flagged

runs in < 1s

[21:51] nb3:~% mu server --eval '(find :query "flag:flagged" :threads t)' 
[b](:erase t)
[b](:found 0)

runs in ca. 1s

I actually have zero results for that particular query. Using something slightly bigger takes 13s:

[22:17] nb3:~% date; mu server --eval '(find :query "maildir:/ungleich/2021" :threads t)'  >/dev/null; date
Sun Aug 15 22:17:44 CEST 2021
Sun Aug 15 22:17:57 CEST 2021

with mu find still being much faster:

[22:19] nb3:~% date; mu find --threads  "maildir:/ungleich/2021" > /dev/null; date 
Sun Aug 15 22:19:33 CEST 2021
Sun Aug 15 22:19:34 CEST 2021
djcb commented 3 years ago

You mentioned the problem happened in mu4e even with flag:flagged -- how long does it take there? (that's an interesting case since apparently it only takes one sec with mu server eval).

Some other things that would be interesting to check: what happens when you (setq mu4e-headers-full-search nil) (i.e. the default value)? And for various values of mu4e-headers-results-limit (like, 500, 1000, 5000)?

telmich commented 3 years ago

I just (setq mu4e-headers-full-search nil) and searching for the inbox (bookmark bi) takes about 2 minutes:

[12:18] nb3:~% date
Mon Aug 16 12:18:08 CEST 2021
[12:18] nb3:~% date
Mon Aug 16 12:20:11 CEST 2021

Searching for flag:flagged takes 4m

[12:20] nb3:~% date
Mon Aug 16 12:20:22 CEST 2021
[12:23] nb3:~% date
Mon Aug 16 12:24:38 CEST 2021

I noticed that during the mu4e search the SSD is 100% busy.

I cannot observe the same behaviour with mu find, as that one exists faster than I can see the disk stats.

Setting (setq mu4e-headers-result-limit 500) additional to (setq mu4e-headers-full-search nil) returned the result instantly.

I'll keep that setting on for the moment to see if it behaves consistent or not.

telmich commented 3 years ago

While the search result was fast, loading a message is still very slow. It took about 5m:

[12:27] nb3:~% date
Mon Aug 16 12:27:48 CEST 2021
[12:27] nb3:~% date
Mon Aug 16 12:28:56 CEST 2021
[12:29] nb3:~% date             
Mon Aug 16 12:33:39 CEST 2021

Besides the SSD usage spiking 100%, CPU usage also spikes 100% from the mu process - not in waiting state, but actually running. Over 10s (atop interval) I see the mu process reading around 500MB data for trying to display a message.

telmich commented 3 years ago

Another observation: for every query in mu4e, I see the mu process reading Gigabytes of data. The mu process itself barely exceeds 300MB RAM size.

Is it possible that there is a query / maximum memory size in the mu process and because the maildir is 35GB (xapian in the cache directory: 11GB) that for every query from mu4e the whole database is read over and over again?

There is another thought on how to improve the speed: my main queries are "give me mails in the following three maildirs", which would be a sub-second query given that the filesystem was queried directly.

I was wondering if there could be a flag telling mu/mu4e to directly query the fs, if the query only contains maildir:... expressions? I would not mind waiting for 3m once in a while, but for it is a bit excessive for every inbox query.

theophilusx commented 3 years ago

Note that you might find using the 'time' command more informative than date and more accurate.

telmich commented 3 years ago

Thanks for the emacs -q pointer in the other issue, @theophilusx. I have been using mu4e fast for about 20 minutes, until I started retrieving emails.

The index process after retrieving emails takes about 1-2 minutes and I had to set

(setq mu4e-update-interval nil)

to be able to use mu4e. By default I have

(setq mu4e-update-interval 240)

But given that the update process takes 120s+, half of the time mu is spending time in indexing. I am now continuing to test with it being set to nil, maybe 1.6.1 has just become much slower in indexing.

However it still does not explain why the CLI still replies with answers while mu4e hangs.

telmich commented 3 years ago

Coming back to this discussion / following up on the "xapian is not slow" comment from the other ticket: at the moment in a fresh, emacs -q minimal environment an update post mbsync retrieval is taking about 4 minutes inside mu4e or outside mu4e (just mu index) of time during which no queries can be answered.

Am I doing something specifically wrong or is there anything I can do to improve this situation?

I have recorded the index process on https://www.nico.schottelius.org/temp/mu-index-2021-08-23.mkv to show how it looks like for me.

djcb commented 3 years ago

This looks typical for the first-time indexing after init -- seems you're indexing all messages starting from zero; however, normally it should be much faster -- i.e., If you do another mu index after that first one.

telmich commented 3 years ago

Quick note, the following setup loads usually loads mails in less than 40s:

mu4e                                     1.4.15-1
libxapian30:amd64                        1.4.18-3  
emacs                                    1:27.1+1-3.1
telmich commented 3 years ago

I just ran another test, with mbsync disabled and only running mu index in a loop:

[10:57] nb3:~% while true; do echo -n "start: "; date; time mu index; echo -n "end: " ; date; sleep 10; done
start: Tue Aug 24 10:57:13 CEST 2021
indexing maildir /home/nico/Maildir -> store /home/nico/.cache/mu/xapian
- indexing messages; processed: 122084; updated/new: 122217; cleaned-up: 7
mu index  117.03s user 70.19s system 96% cpu 3:14.67 total
end: Tue Aug 24 11:00:28 CEST 2021
start: Tue Aug 24 11:00:38 CEST 2021
indexing maildir /home/nico/Maildir -> store /home/nico/.cache/mu/xapian
| indexing messages; processed: 122011; updated/new: 122141; cleaned-up: 0
mu index  120.86s user 70.42s system 95% cpu 3:19.95 total
end: Tue Aug 24 11:03:58 CEST 2021
start: Tue Aug 24 11:04:08 CEST 2021
indexing maildir /home/nico/Maildir -> store /home/nico/.cache/mu/xapian
| indexing messages; processed: 122049; updated/new: 122141; cleaned-up: 0
mu index  121.76s user 69.15s system 98% cpu 3:12.94 total
end: Tue Aug 24 11:07:21 CEST 2021
start: Tue Aug 24 11:07:31 CEST 2021
indexing maildir /home/nico/Maildir -> store /home/nico/.cache/mu/xapian
| indexing messages; processed: 122080; updated/new: 122141; cleaned-up: 0
mu index  121.95s user 66.02s system 101% cpu 3:04.95 total
end: Tue Aug 24 11:10:36 CEST 2021
start: Tue Aug 24 11:10:46 CEST 2021
indexing maildir /home/nico/Maildir -> store /home/nico/.cache/mu/xapian
\ indexing messages; processed: 122045; updated/new: 122141; cleaned-up: 0
mu index  125.05s user 68.13s system 101% cpu 3:09.70 total
end: Tue Aug 24 11:13:56 CEST 2021
start: Tue Aug 24 11:14:06 CEST 2021
indexing maildir /home/nico/Maildir -> store /home/nico/.cache/mu/xapian
\ indexing messages; processed: 122066; updated/new: 122141; cleaned-up: 0
mu index  122.90s user 66.12s system 101% cpu 3:05.70 total
end: Tue Aug 24 11:17:11 CEST 2021

So it seems that mu believes there are always around 120k new messages, which is certainly not the case, as there is no MUA running and no mbsync either. Can I ask mu index

I also see that mu index seems to use +/- exactly one core and wonder if that could be changed to support multi process/threading.

I am now running mu index --debug, but so far the output looks the same as if it was running without that flag

theophilusx commented 3 years ago

I think it look like the updated index information is not being written to the xapian database correctly. While an initial index will take a few minutes when you have 100K+ messages, subsequent runs should be almost instantaneous if there have been no changes.

Might be worthwhile posting output from mu info to check the schema version is correct.

I'm assuming when you updated to 1.6.3 you deleted the previous .cache/mu directory, re-ran mu init and then ran mu index?

telmich commented 3 years ago

I am actually on 1.6.1 (latest in Alpine Linux) and I did run mu init again after upgrading.

[11:25] nb3:~% mu info
maildir           : /home/nico/Maildir
database-path     : /home/nico/.cache/mu/xapian
schema-version    : 452
max-message-size  : 100000000
batch-size        : 250000
messages in store : 1509533
created           : Sat Aug 14 14:46:58 2021
personal-address  : <none>
[11:43] nb3:~% mu --version
mu (mail indexer/searcher) version 1.6.1
Copyright (C) 2008-2020 Dirk-Jan C. Binnema
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>.
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
[11:43] nb3:~% 
theophilusx commented 3 years ago

The fact every time you run mu index it re-indexes everything indicates something is wrong with your install. It is not 'normal' behaviour.

The schema version and other settings look correct, so either it is something wrong with the build provided by Alpine or something didn't work correctly with mu init.

I would clone the mu repository, build and install (after removing the alpine version). I'd then delete .cache/mu, re-run mu init and try mu index and see if that helps.

Out of interest, what file system are you running?

telmich commented 3 years ago

@theophilusx mu index does not re-index everythink - it only redoes 120k messages out of 1.5M.

Re filesystem: I am on ext4.

I have just compiled 1.6.4 and the issue still persists / mu re-indexes 120k messages every time:

[12:17] nb3:~% mu index        
indexing maildir /home/nico/Maildir -> store /home/nico/.cache/mu/xapian
/ indexing messages; processed: 122027; updated/new: 122141; cleaned-up: 0
[12:20] nb3:~% mu index
indexing maildir /home/nico/Maildir -> store /home/nico/.cache/mu/xapian
- indexing messages; processed: 122069; updated/new: 122141; cleaned-up: 0
[12:24] nb3:~% mu --version
mu (mail indexer/searcher) version 1.6.4
Copyright (C) 2008-2021 Dirk-Jan C. Binnema
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>.
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
[12:31] nb3:~% mu info
maildir           : /home/nico/Maildir
database-path     : /home/nico/.cache/mu/xapian
schema-version    : 452
max-message-size  : 100000000
batch-size        : 250000
messages in store : 1509533
created           : Sat Aug 14 14:46:58 2021
personal-address  : <none>
[12:31] nb3:~% 

I am now resetting ~/.cache/mu and re-indexing.

djcb commented 3 years ago

For the debug logs, check journal (if you use systemd) or the log file. Anyway, please check what those 120K messages are (logs should help) and what makes them different from the rest.

telmich commented 3 years ago

Just reran the loop with 1.6.4 and the 120k message re-index is still there:

[12:17] nb3:~% mu --version
mu (mail indexer/searcher) version 1.6.4
Copyright (C) 2008-2021 Dirk-Jan C. Binnema
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>.
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
[12:17] nb3:~% rm -rf .cache/mu/
[12:32] nb3:~% mu init 
maildir           : /home/nico/Maildir
database-path     : /home/nico/.cache/mu/xapian
schema-version    : 452
max-message-size  : 100000000
batch-size        : 250000
messages in store : 0
created           : Tue Aug 24 12:32:50 2021
personal-address  : <none>

store created; use the 'index' command to fill/update it.
[12:32] nb3:~% date; mu index; date; echo "1st done"; date; mu index; date
Tue Aug 24 12:33:12 CEST 2021
indexing maildir /home/nico/Maildir -> store /home/nico/.cache/mu/xapian
/ indexing messages; processed: 1509533; updated/new: 1509533; cleaned-up: 0
Tue Aug 24 13:25:32 CEST 2021
1st done
Tue Aug 24 13:25:32 CEST 2021
indexing maildir /home/nico/Maildir -> store /home/nico/.cache/mu/xapian
| indexing messages; processed: 122070; updated/new: 122141; cleaned-up: 0
Tue Aug 24 13:30:24 CEST 2021

Now running mu index --debug to see what is happening

telmich commented 3 years ago

I am taking a random message that is added again:

2021-08-24 13:36:33 ** (mu:13905): DEBUG: 13:36:33.241: created message from /home/nico/Maildir/ungleich/2005/cur/1617069045.29086_200746.nb3,U=43607:2,S in 294 μs
2021-08-24 13:36:33 ** (mu:13905): DEBUG: 13:36:33.242: added message @ /home/nico/Maildir/ungleich/2005/cur/1617069045.29086_200746.nb3,U=43607:2,S; docid = 672503

As it is a public message, I attached the mail to this thread. mail.txt

Running it a third time, this time grep'ing for 43607:

2021-08-24 13:42:28 ** (mu:14658): DEBUG: 13:42:28.336: created message from /home/nico/Maildir/ungleich/2005/cur/1617069045.29086_200746.nb3,U=43607:2,S in 162 μs
2021-08-24 13:42:28 ** (mu:14658): DEBUG: 13:42:28.337: added message @ /home/nico/Maildir/ungleich/2005/cur/1617069045.29086_200746.nb3,U=43607:2,S; docid = 672503
telmich commented 3 years ago

For reference: the aport in Alpine Linux changed from 1.4.15 (does not have this problem) to 1.6.1 and the compile parameters did not change on version change:

commit f55dcc04958b57e3c1e26b7269b3ae296106366f
Author: Justin Berthault <justin.berthault@zaclys.net>
Date:   Mon Aug 2 12:54:46 2021 +0200

    community/mu: upgrade to 1.6.1

diff --git a/community/mu/APKBUILD b/community/mu/APKBUILD
index 5c1689b53e..4135f4a667 100644
--- a/community/mu/APKBUILD
+++ b/community/mu/APKBUILD
@@ -4,7 +4,7 @@
 # Contributor: Nico Schottelius <nico.schottelius@ungleich.ch>
 # Maintainer: Justin Berthault <justin.berthault@zaclys.net>
 pkgname=mu
-pkgver=1.4.15
+pkgver=1.6.1
 pkgrel=0
 pkgdesc="A collection of utilities for indexing and searching Maildirs"
 # armv7 and x86 blocked by gmime
@@ -66,4 +66,6 @@ mu4e() {
        mv "$pkgdir"/usr/share "$subpkgdir"/usr
 }

-sha512sums="dd0426c1fb7fe2430b47fc1232e067d1c017b3c428bbd8012c542f6e1ffa7741bb145c6851f40cbc945403534dabb4aa99faf369166167d187f083dde1d30546  mu-1.4.15.tar.gz"
+sha512sums="
+6d18f417dd1de73d6c16d1a6ba11a6b7489026b1f551e24f41cfb6cd57eb789f48801da59cbdd603c846d2a6248fee7ee6fa6f6e5de648b54ad8a8e14946e0bf  mu-1.6.1.tar.gz
+"
djcb commented 3 years ago

Thanks for checking. It seems that mu considers those message(s) not to be up to date for some reason.

Nothing special about that message, suspect it's the metadata. Are these message that need re-indexing always the same messages? Same maildir? Is anything touching those messages (check the time stamps)?

And/or are the message actually indexed and written etc., ie. can you mu find them after indexing?

telmich commented 3 years ago

Regarding the metadata:

[13:44] nb3:~% ls -l /home/nico/Maildir/ungleich/2005/cur/1617069045.29086_200746.nb3,U=43607:2,S 
-rw------- 1 nico nico 5081 Mar 30 03:50 '/home/nico/Maildir/ungleich/2005/cur/1617069045.29086_200746.nb3,U=43607:2,S'
[17:45] nb3:~% stat /home/nico/Maildir/ungleich/2005/cur/1617069045.29086_200746.nb3,U=43607:2,S 
  File: /home/nico/Maildir/ungleich/2005/cur/1617069045.29086_200746.nb3,U=43607:2,S
  Size: 5081        Blocks: 16         IO Block: 4096   regular file
Device: fd00h/64768d    Inode: 29406777    Links: 1
Access: (0600/-rw-------)  Uid: ( 1000/    nico)   Gid: ( 1000/    nico)
Access: 2021-08-24 11:00:08.465251405 +0200
Modify: 2021-03-30 03:50:45.596691524 +0200
Change: 2021-03-30 03:50:45.596691524 +0200
 Birth: -

I checked and the mail in question seems to be 4 times in the index, however re-indexing does not add it a 5th time:

[17:48] nb3:~% mu find from:john.e.maher@gmail.com "subject:automating gnupg decryption" 
Fri Nov 11 23:20:04 2005 John Maher <john.e.maher@gmail.com> Re: automating gnupg decryption
Fri Nov 11 23:20:04 2005 John Maher <john.e.maher@gmail.com> Re: automating gnupg decryption
Fri Nov 11 23:20:04 2005 John Maher <john.e.maher@gmail.com> Re: automating gnupg decryption
Fri Nov 11 23:20:04 2005 John Maher <john.e.maher@gmail.com> Re: automating gnupg decryption
[17:48] nb3:~% mu index
indexing maildir /home/nico/Maildir -> store /home/nico/.cache/mu/xapian
\ indexing messages; processed: 122007; updated/new: 122141; cleaned-up: 0
[17:51] nb3:~% mu find from:john.e.maher@gmail.com "subject:automating gnupg decryption"
Fri Nov 11 23:20:04 2005 John Maher <john.e.maher@gmail.com> Re: automating gnupg decryption
Fri Nov 11 23:20:04 2005 John Maher <john.e.maher@gmail.com> Re: automating gnupg decryption
Fri Nov 11 23:20:04 2005 John Maher <john.e.maher@gmail.com> Re: automating gnupg decryption
Fri Nov 11 23:20:04 2005 John Maher <john.e.maher@gmail.com> Re: automating gnupg decryption
[17:58] nb3:~% 

The re-index seems to happen only in the ungleich/2005 maildir, essentially by checking using

tail -F mu.log | grep -v 2005
[18:02] nb3:~% ls -ltra Maildir/ungleich/2005/ 
total 19400
-rw-------  1 nico nico       18 Mar 29 19:14 .uidvalidity
drwx------  2 nico nico     4096 Mar 29 19:14 tmp
drwx------  2 nico nico 16302080 Mar 29 19:14 cur
-rw-------  1 nico nico  3541554 Mar 29 19:14 .mbsyncstate
drwxr-xr-x 36 nico nico     4096 Mar 29 22:12 ..
drwx------  2 nico nico     4096 Mar 30 03:49 new
drwx------  5 nico nico     4096 Aug 24 10:56 .

Is there a per maildir maximum limit somewhere? Because this maildir seems to be the biggest one:

[18:05] nb3:~% ls Maildir/ungleich/2005/cur/ | wc -l
234648

[18:05] nb3:ungleich% for i in *; do echo -n $i: ; find $i -type f | wc -l ; done 
1999:2
2000:34830
2001:25330
2002:226
2003:128
2004:96612
2005:234650
2006:158466
2007:195966
2008:181821
2009:131027
2010:155082
2011:25206
2012:23779
2013:34307
2014:58277
2015:27976
2016:15849
2017:15738
2018:8368
2019:15846
2020:21728
2021:20460
djcb commented 3 years ago

So you need to index the messages in the 2005 maildir, say, 4 times until the indexing won't try them again? And are the messages present (searchable) after, say, 1 times of indexing? In other words, is the problem that the messages don't make it to the store? And this is with 1.6.4?

But after that, is 2005 okay, or does the unwanted re-indexing return? (You might be able to avoid that with a .noupdate)

telmich commented 3 years ago

Sorry, above output might have been confusing. The situation is:

The weird thing is that mu4e 1.4.15 did work normal, since 1.6.1 something changed - it's still the same maildir.

telmich commented 3 years ago

I just downgraded to 1.4.15 and running mu index a second time takes about 30s:

[10:22] nb3:~% mu --version
mu (mail indexer/searcher) version 1.4.15
Copyright (C) 2008-2020 Dirk-Jan C. Binnema
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>.
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
[10:22] nb3:~% mu info     
database-path      : /home/nico/.cache/mu/xapian
messages in store  : 0
schema-version     : 451
created            : Wed Aug 25 10:22:42 2021
maildir            : /home/nico/Maildir
personal-addresses : <none>
[10:23] nb3:~% date; mu index; date
Wed Aug 25 10:23:09 CEST 2021
database-path      : /home/nico/.cache/mu/xapian
messages in store  : 0
schema-version     : 451
created            : Wed Aug 25 10:22:42 2021
maildir            : /home/nico/Maildir
personal-addresses : <none>
\ processing mail; processed: 1509000; updated/new: 1509000, cleaned-up: 0
cleaning up messages [/home/nico/.cache/mu/xapian]
| processing mail; processed: 1509031; updated/new: 0, cleaned-up: 0
elapsed: 14 second(s), ~ 107787 msg/s
/ processing mail; processed: 1509031; updated/new: 0, cleaned-up: 0
elapsed: 3351 second(s), ~ 450 msg/s
Wed Aug 25 11:19:01 CEST 2021
[11:19] nb3:~% date; mu index; date
Wed Aug 25 11:20:30 CEST 2021
database-path      : /home/nico/.cache/mu/xapian
messages in store  : 1509031
schema-version     : 451
created            : Wed Aug 25 10:22:42 2021
maildir            : /home/nico/Maildir
personal-addresses : <none>
\ processing mail; processed: 1509000; updated/new: 0, cleaned-up: 0
cleaning up messages [/home/nico/.cache/mu/xapian]
| processing mail; processed: 1509031; updated/new: 0, cleaned-up: 0
elapsed: 5 second(s), ~ 301806 msg/s
/ processing mail; processed: 1509031; updated/new: 0, cleaned-up: 0
elapsed: 29 second(s), ~ 52035 msg/s
Wed Aug 25 11:20:59 CEST 2021
[11:20] nb3:~% 
telmich commented 3 years ago

Independently of the 1.4.x vs 1.6.x speed issue: In the postgres ticket it was mentioned that searching during index should be possible. Is that correct? Because in both 1.4.15 and 1.6.1/1.6.4 the mu4e search is completely blocking during index update.

Or is it that mu can search & index, but mu4e can't due to emacs single process design?

djcb commented 3 years ago

Okay, so mu does index the message, but then for some reason thinks they're not up to date. But not always. Hmmm....

mu4e cannot do things with the mu server when it's busy (e.g. with indexing); but that's unrelated to emacs' design and command-line mu.

djcb commented 3 years ago

Anyway, don't really understand what's going on your system; as a temp measure, you can drop a .update in your 2005 dir (see mu index manpage), that should avoid the prob.

telmich commented 3 years ago

I quickly did a comparison with notmuch, which is basically using the same indexer. The initial index time is similar (1.5h), however there are quite some differences afterwards:

[9:45] nb3:~% notmuch search --output=messages '*' | wc -l        
728206
[9:47] nb3:~% date; notmuch new; date           
Sat Aug 28 09:47:20 CEST 2021
Processed 26 total files in almost no time.
No new mail.
Sat Aug 28 09:47:20 CEST 2021

@djcb I am not too deep into the mu internals, but seeing above timing I wonder if notmuch is taking the atime/mtime of a folder to decide on whether or not to skip indexing. Would that possible make sense for mu as well?

Update: I did above comparison to see whether or not musl / Alpine Linux can be the triggering issue here - however with notmuch being fast, the problem is probably not in the xapian core.

telmich commented 3 years ago

I might have discovered another very slow case / dead lock: I hit bi for the inbox query about 20 minutes ago at which time an index was running. At this point right now the inbox query did not yet finish and it is now running for 3m+ with the mu server being idle. Quitting mu4e inside emacs and then starting again fails with the mu server still running.

I few minutes later, mu server is still running

nico      5462  1.2  0.2  54200 45608 ?        Ss   Aug30  49:29 /usr/bin/mu server

This is now with mu 1.4.15. After 5 minutes of waiting, I killed mu server.

djcb commented 3 years ago

A backtrace or it didn't happen! And I don't think the 1.4 series will see much change...

Oh, note, there's a change in 1.7.x (87ac89b0), which should be cherry-pickable for 1.6, and helps for at least some cases of re-indexing the same messages again and again.

telmich commented 2 years ago

A short update from 1.6.1 use: I did fully disable indexing and a query for a maildir:/... search still takes minutes, while mu find returns within a second. I am using a separate emacs instance to exclude any emacs daemon/sharing related issues.

I'll try to compile mu 1.7.x these days for comparison and come back to this ticket.

telmich commented 2 years ago

I just compiled 1.6.5-46-g191f0f47 and the query

flag:flagged OR maildir:/a/inbox OR maildir:/b/inbox OR maildir:/c/inbox OR maildir:/c/inbox

has been running for 2 minutes. The last mail retrieval is 2 hours ago, but mu server is running with 90% cpu and SSDs are 100% busy. I am not sure whether the index from 2 hours ago is still running or the query caused the high load.

After 7 minutes, I just got the result of the query. The same query executed with mu find returns within 1~2 seconds (even in parallel). Reloading the query now works fast.

The re-index of existing messages seems to be solved in this version:

[14:52] nb3:~% date; time mu index; date 
Sat Sep 18 14:53:41 KST 2021
indexing maildir /home/nico/Maildir -> store /home/nico/.cache/mu/xapian
- indexing messages; processed: 0; updated/new: 0; cleaned-up: 0
mu index  7.78s user 18.47s system 85% cpu 30.659 total
Sat Sep 18 14:54:12 KST 2021
[14:54] nb3:~% 

Running mbsync -a outside of mu4e and then calling M-x mu4e-update-index blocks message loading for about 40s, which seems to be +/- in line with the indexing. However as noted above, this is not always the case with load times up to 7m.

I am running all tests now in an isolated emacs instance to avoid any possible interaction of other modes/modules.

I compared the run time with notmuch new that I did not run for some weeks and it ran in about 15s. I understand that this is the time xapian based solutions will need, but it would be great if there was any way to decouple indexing and loading messages / querying the index.

ArneBab commented 2 years ago

I see this in 1.6.6:

$ time mu index; time mu index
indexing maildir /home/arne/.local/share/mail -> store /home/arne/.cache/mu/xapian
/ indexing messages; processed: 65740; updated/new: 65743; cleaned-up: 0

real    3m59,968s
user    2m45,607s
sys 0m51,293s
indexing maildir /home/arne/.local/share/mail -> store /home/arne/.cache/mu/xapian
| indexing messages; processed: 65739; updated/new: 65743; cleaned-up: 0

real    3m19,634s
user    2m29,826s
sys 0m43,685s
djcb commented 2 years ago

Aha.... so it is indeed the same problem. For some reason, a subset of the messages is not recognized as being indexed already, and hence re-indexed each time.

ArneBab commented 2 years ago

How can I help track down which messages are not recognized?

djcb commented 2 years ago

You could try to run in --debug mode (from the command-line) or with (setq mu4e-mu-debug t) (in mu4e), and check what's in the log files.

I think it's about messages in specific directories, that somehow aren't recognized as "already seen" (when in lazy mode). It seems it's (re)indexing 65739 messages each time - are those all you have?

If you have time, you might want to give 1.7.3 a try, and see if/how that differs.

ArneBab commented 2 years ago

Sorry for the late answer; I was bogged down with other issues.

Those 65739 messages are not all. I have 420 094 messages in my maildir (verified with fd | wc -l).

Here’s an example message from a public mailing list that turned up in the log multiple times (parts of email addresses replaced by XXXXXXXXXXXXXXXX) and is located at ~/.local/share/mail/to.arne_bab/new/1593168968.5935_2.fluss:

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Hey!

I am architecting our final HTCondor configuration over here and I have =
an idea I am unsure about and I would like to ask some experienced users =
for their opinion.

Background, we have a small, relatively homogenous cluster (with no =
special universes) and less than 10 users. Since each user has their own =
workstation separate from our cluster I thought the following =
configuration would suit our needs, but I want to make sure there isn't =
a huge disadvantage I am missing:

1. Set the Central Manager to be highly available to the point of =
tolerating N cluster machine failures
2. Put a Submit on each of the users' workstations (I am a little =
worried about the resource usage of the condor_shadow and condor_schedd, =
my users are already running into RAM consumption issues over time as it =
is)
3. Place an Execute on each of the cluster machines, which would lead to =
the central manager being on a machine that is also executing jobs

Fortunately both my users' and cluster machines all have access to the =
same network storage, and we have centralized authentication so we can =
just use our users' credentials to authenticate everywhere.=20

Before I set this in dry mud, does anyone have any retrospective =
recommendations I could benefit hearing from, since I am still pretty =
new to the project?

Thank you!
-Wes

Wesley Taylor =E2=80=93 Cluster Manager
Numerica Corporation (www.numerica.us)
5042 Technology Parkway #100
Fort Collins, Colorado 80528
=E2=98=8E=EF=B8=8F (970) 207 2233
=F0=9F=93=A7 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX@numerica.us

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This is with mu (mail indexer/searcher) version 1.6.10

djcb commented 2 years ago

If you run mu with --debug and/or mu4e with mu4e-mu-debug set to non-nil, you should see a bit more output from the indexer (in the journal if you use systemd, or in the log file) and why it decides to visit / index certain directories or not.

ArneBab commented 2 years ago

I don’t see that — it just shows that it enters the directory: mu index --debug and tail -F ~/.cache/mu/mu.log:

2022-03-13 22:42:03 ** (mu:10906): DEBUG: 22:42:03.434: process ~/.local/share/mail/archiv/cur/tmp
2022-03-13 22:42:03 ** (mu:10906): DEBUG: 22:42:03.436: created message from ~/.local/share/mail/archiv/cur/1375740521.17978_27494.kaverne:2, in 1863 μs
2022-03-13 22:42:03 ** (mu:10906): DEBUG: 22:42:03.481: added message @ ~/.local/share/mail/archiv/cur/1375740521.17978_27494.kaverne:2,; docid = 16782
2022-03-13 22:42:03 ** (mu:10906): DEBUG: 22:42:03.482: started worker
2022-03-13 22:42:03 ** (mu:10906): DEBUG: 22:42:03.486: created message from ~/.local/share/mail/archiv/cur/1375740303.17978_23610.kaverne:2, in 4986 μs
2022-03-13 22:42:03 ** (mu:10906): DEBUG: 22:42:03.496: added message @ ~/.local/share/mail/archiv/cur/1375740303.17978_23610.kaverne:2,; docid = 16786

When I run this again, I see the same message with the same docid:

$ tail -F ~/.cache/mu/mu.log  | grep 1375740303.17978_23610
2022-03-13 22:49:44 ** (mu:15315): DEBUG: 22:49:44.493: created message from ~/.local/share/mail/archiv/cur/1375740303.17978_23610.kaverne:2, in 4105 μs
2022-03-13 22:49:44 ** (mu:15315): DEBUG: 22:49:44.501: added message @ ~/.local/share/mail/archiv/cur/1375740303.17978_23610.kaverne:2,; docid = 16786
ArneBab commented 2 years ago

Is there something else I can do to give you additional debugging information?

The only error I see is:

2022-03-13 22:56:06  ** (mu:9264): WARNING **: 22:56:06.437: error adding message @ ~/.local/share/mail/drafts/cur/1569906673.82520a3fc48e6b21.fluss:2,DS: failed to create message: message seems invalid, ignoring (~/.local/share/mail/drafts/cur/1569906673.82520a3fc48e6b21.fluss:2,DS)
ArneBab commented 2 years ago

Could you replicate the problem with this info?

djcb commented 2 years ago

Hmmm, it's hard to say. From these logs, there's nothing immediately suspicious....

Did you ever try the 1.7.x (git master) series? That one has a bunch of changes to indexing.

ArneBab commented 2 years ago

mu 1.7.x is not yet in guix — once it is, I’ll try right away.

If you copy the mail I quoted to your maildir, does parsing it fail, too?

djcb commented 2 years ago

No, it seems to work just fine. Does it not for you?

ArneBab commented 2 years ago

No, it gets indexed again and again on every run of mu index — as one of now 32393 files that get indexed and named as "updated/new" on every run.