mbsync hanging when running inside emacs/mu4e

[Nico S. <ni...@sc...>]

Good morning,

I've recently switched to a new alpine installation with the following 
package versions:

[16:44] bridge:~% apk list -I | grep -e mu4e -e isync -e emacs
isync-doc-1.3.1-r1 x86_64 {isync} (GPL-3.0-or-later) [installed]
emacs-x11-26.3-r2 x86_64 {emacs} (GPL-3.0-or-later) [installed]
isync-1.3.1-r1 x86_64 {isync} (GPL-3.0-or-later) [installed]
mu4e-1.4.10-r0 x86_64 {mu} (GPL-3.0) [installed]
[16:44] bridge:~%

For some years I am using mu/mu4e with a simple shell script that opens 
up an ssh tunnel to the remote side, runs mbsync -a and then mu takes 
over for indexing.

Now, since this installation, mbsync hangs for minutes/hours when run 
from emacs like this:

nico     14121  0.2  0.3 206432 121644 ?       Ssl  Jul06   3:04 
/usr/bin/emacs --daemon
nico     19040  0.0  0.0   1572     4 pts/8    Ss+  14:11   0:00  \_ 
/bin/sh /home/nico/bin/hole_mails
nico     19108 61.8  1.2 416024 413588 pts/8   R+   14:11  90:05  |   \_ 
mbsync -a -q
nico      5705  0.0  0.1  58288 52068 ?        Ss   16:22   0:00  \_ 
/usr/bin/mu server


However when I run it manually from outside, it finishes within half a 
minute on a fast connection:

[14:25] bridge:~% date; mbsync -a ; mu index ; date
Tue Jul  7 15:17:52 CEST 2020
C: 0/2  B: 15/17  M: +0/0 *0/0 #0/0  S: +19/19 *0/0 #0/0
Error: channel 
:ungleich-remote:the-old-archive-:ungleich-local:the-old-archive is 
locked
C: 2/2  B: 22/22  M: +0/0 *0/0 #0/0  S: +20/20 *0/0 #0/0
database-path      : /home/nico/.cache/mu/xapian
messages in store  : 1492681
schema-version     : 451
created            : Thu Jul  2 13:58:45 2020
maildir            : /home/nico/Maildir
personal-addresses : <none>
- processing mail; processed: 1319925; updated/new: 37, cleaned-up: 0
mu: message seems invalid, ignoring 
(/home/nico/Maildir/ungleich/the-old-archive/new/1594069516.22865_3.bridge,U=2:2,)
/ processing mail; processed: 1414350; updated/new: 37, cleaned-up: 0
mu: message seems invalid, ignoring 
(/home/nico/Maildir/ungleich/the-old-archive/new/1594101384.6276_417010.bridge,U=649479:2,)
/ processing mail; processed: 1492650; updated/new: 37, cleaned-up: 0
cleaning up messages [/home/nico/.cache/mu/xapian]
| processing mail; processed: 1492719; updated/new: 0, cleaned-up: 0
elapsed: 4 second(s), ~ 373179 msg/s
/ processing mail; processed: 1492719; updated/new: 0, cleaned-up: 0
elapsed: 23 second(s), ~ 64900 msg/s
Tue Jul  7 15:18:20 CEST 2020
[15:18] bridge:~%

It also uses a huge amount of cpu, peaking at 100% of one core often.

Does anyone have a hint on what might be going wrong here?

Best regards,

Nico

p.s.: There are some error messages I started seeing only on this 
installation, like:

Notice: conflicting changes in (356090,1688)
Notice: conflicting changes in (356091,1689)
Notice: conflicting changes in (356104,1702)
Notice: conflicting changes in (356109,1707)