[Akonadi] [Bug 340813] sometimes two copies of mysqld are running with Akonadi

[RJVB via KDE Bugzilla]

https://bugs.kde.org/show_bug.cgi?id=340813

RJVB  changed:

   What|Removed |Added

 CC||rjvber...@gmail.com

--- Comment #13 from RJVB  ---
So here's an additional observation, from 4.13.3/ akonadi 1.13.1 but maybe
still useful.
As I just reported in a duplicate (https://bugs.kde.org/show_bug.cgi?id=367638)
I get the 1452 error even when I don't have 2 mysql daemons running. Not
continuously at least.

Looking at it today I first thought that they were generated only after a full
sync (Ctrl-L) but then I noticed the error messages also appeared while I was
browsing an email and no sync activity was occurring.
I then made the link with the search folder I created yesterday, which was
designed to combine the entries from several folders in a virtual folder. For
that, I defined a search working on the folders of interest and returning all
items with a total size >= 0kb. I left the 2nd field empty.

When I deleted that search folder the error messages disappeared, but the
unread email in one of the target folders disappeared too. From kmail; Claws
shows they're still there, fortunately.

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[Akonadi] [Bug 340813] sometimes two copies of mysqld are running with Akonadi

[Daniel Vrátil via KDE Bugzilla]

https://bugs.kde.org/show_bug.cgi?id=340813

Daniel Vrátil  changed:

   What|Removed |Added

 CC||dvra...@kde.org

--- Comment #12 from Daniel Vrátil  ---
I am not 100% sure that this works flawlessly, so I don't feel like putting it
into to stable branch now without enough real-life testing. I don't want to
risk breaking starting of database on Akonadi startup.

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[Akonadi] [Bug 340813] sometimes two copies of mysqld are running with Akonadi

[Martin Steigerwald via KDE Bugzilla]

https://bugs.kde.org/show_bug.cgi?id=340813

--- Comment #11 from Martin Steigerwald  ---
Yay! Thank you, Dan! Would you backport this to 16.08 as well?

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[Akonadi] [Bug 340813] sometimes two copies of mysqld are running with Akonadi

[Daniel Vrátil via KDE Bugzilla]

https://bugs.kde.org/show_bug.cgi?id=340813

Daniel Vrátil  changed:

   What|Removed |Added

 Status|UNCONFIRMED |RESOLVED
 Resolution|--- |FIXED
   Version Fixed In||16.12.0
  Latest Commit||http://commits.kde.org/akon
   ||adi/2ef0fe95bd83643d0a1e69b
   ||0b59124fa76be5b2f

--- Comment #10 from Daniel Vrátil  ---
Git commit 2ef0fe95bd83643d0a1e69b0b59124fa76be5b2f by Daniel Vrátil.
Committed on 14/09/2016 at 13:19.
Pushed by dvratil into branch 'master'.

If the mysql server is already running, try to connect

Instead of starting another mysqld process on top of the same data,
try to reconnect to the running server.

Generally this situation should not really happen, but there are
some cases when the database cannot be properly shut down, like
when the server crashes.
FIXED-IN: 16.12.0

M  +57   -50   src/server/storage/dbconfigmysql.cpp

http://commits.kde.org/akonadi/2ef0fe95bd83643d0a1e69b0b59124fa76be5b2f

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[Akonadi] [Bug 340813] sometimes two copies of mysqld are running with Akonadi

[Christian Saemann via KDE Bugzilla]

https://bugs.kde.org/show_bug.cgi?id=340813

Christian Saemann  changed:

   What|Removed |Added

 CC||christian.saem...@gmx.de

--- Comment #9 from Christian Saemann  ---
I'm not sure if this helps, but I also run into situations where Akonadi seems
to initiate two mysqld processes. This is with the latest KDE packages (16.08)
from openSUSE Tumbleweed.

The first one is just after startup, I can often read and browse emails for 10
seconds or so, then  kmail says akonadi is not running properly. I then have to
killall mysqld and restart akonadi.

The second one, and this happens reliably each time, is when I initiate an
email search, having deleted all prior search folders. Kmail states that it
can't connect to akonadi-service, and stops working properly. After this, I
always have two mysqld processes running.

akonadiserver.error.old contains just one line:
Connecting to deprecated signal
QDBusConnectionInterface::serviceOwnerChanged(QString,QString,QString)

If there's any additional specific error logs or debug information you'd like
to see, just let me know.

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[Akonadi] [Bug 340813] sometimes two copies of mysqld are running with Akonadi

[Denis Kurz via KDE Bugzilla]

https://bugs.kde.org/show_bug.cgi?id=340813

Denis Kurz  changed:

   What|Removed |Added

 CC||i...@aschoettler.com

--- Comment #8 from Denis Kurz  ---
*** Bug 367638 has been marked as a duplicate of this bug. ***

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[Akonadi] [Bug 340813] sometimes two copies of mysqld are running with Akonadi

[via KDE Bugzilla]

https://bugs.kde.org/show_bug.cgi?id=340813

bjoe...@arcor.de changed:

   What|Removed |Added

 CC||bjoe...@arcor.de

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[Akonadi] [Bug 340813] sometimes two copies of mysqld are running with Akonadi

[Martin Steigerwald]

https://bugs.kde.org/show_bug.cgi?id=340813

--- Comment #7 from Martin Steigerwald m...@teamix.de ---
Okay, I think I got a hint today on why it might not finished MySQL properly.
Today I got connection losses with Exchange again (its seems quite easy to
trigger these, I am at the moment using archivemail to reduce amount of mails
on the server to see whether it may help). And to bring things back up I
stopped Akonadi with the intention to start it again. Yet on stopping I got:

ms@merkaba:~ tail -f ~/.xsession-errors
Executing search kmail2-1312955980-SearchSession 
Search done kmail2-1312955980-SearchSession (without remote search) 
Result: 0 matches 
posting retrieval request for item 1890571  there are  1  queues and  0  items
in mine 
request for item 1890571 still pending - waiting 
processing retrieval request for item 1890571  parts: (RFC822)  of resource:
akonadi_imap_resource_0 
QFileSystemWatcher: failed to add paths:
/home/ms/.kde/share/config/activitymanager-pluginsrc
konsole(3229) Konsole::Session::run: Attempted to re-run an already running
session. 
konsole(3229) Konsole::Session::run: Attempted to re-run an already running
session. 
akonadi_imap_resource_0(3221) ChangeItemsFlagsTask::onSelectDone: Select
failed:  Die Verbindung zum Server ist abgebrochen. 

This is up to the connection loss I think. Die Verbindung zum Server ist
abgebrochen means the connection to the server aborted

Then I stop akonadi with akonadictl stop and get:

X Error: BadWindow (invalid Window parameter) 3
  Major opcode: 2 (X_ChangeWindowAttributes)
  Resource id:  0x221afce
QFileSystemWatcher: failed to add paths:
/home/ms/.kde/share/config/activitymanager-pluginsrc
QFileSystemWatcher: failed to add paths:
/home/ms/.kde/share/config/activitymanager-pluginsrc
QFileSystemWatcher: failed to add paths:
/home/ms/.kde/share/config/activitymanager-pluginsrc
Lost connection to resource
org.freedesktop.Akonadi.Resource.akonadi_contacts_resource_0 , discarding
cached interface 
Lost connection to resource
org.freedesktop.Akonadi.Resource.akonadi_akonotes_resource_0 , discarding
cached interface 
Lost connection to resource
org.freedesktop.Akonadi.Resource.akonadi_akonotes_resource_1 , discarding
cached interface 
void Akonadi::Server::NotificationSource::serviceUnregistered(const QString)
Notification source AkonadiAgentServer_3218_fhsA1R now serving: () 
Lost connection to resource
org.freedesktop.Akonadi.Resource.akonadi_icaldir_resource_0 , discarding
cached interface 
void Akonadi::Server::NotificationSource::serviceUnregistered(const QString)
Notification source AkonadiAgentServer_3214_GN8Sxx now serving: () 
void Akonadi::Server::NotificationSource::serviceUnregistered(const QString)
Notification source akonadi_maildispatcher_agent_3225_ScB4Dq now serving: () 
void Akonadi::Server::NotificationSource::serviceUnregistered(const QString)
Notification source akonadi_maildispatcher_agent_3225_B0L8JT now serving: () 
void Akonadi::Server::NotificationSource::serviceUnregistered(const QString)
Notification source akonadi_maildispatcher_agent_3225_ietFlF now serving: () 
void Akonadi::Server::NotificationSource::serviceUnregistered(const QString)
Notification source akonadi_migration_agent_3227_ndcikE now serving: () 
void Akonadi::Server::NotificationSource::serviceUnregistered(const QString)
Notification source AkonadiAgentServer_3215_D1kzHt now serving: () 
void Akonadi::Server::NotificationSource::serviceUnregistered(const QString)
Notification source akonadi_icaldir_resource_0_3220_eX2EKU now serving: () 
void Akonadi::Server::NotificationSource::serviceUnregistered(const QString)
Notification source akonadi_followupreminder_agent_3219_2ncps7 now serving:
() 
void Akonadi::Server::NotificationSource::serviceUnregistered(const QString)
Notification source akonadi_notes_agent_3230_1JJLlc now serving: () 
void Akonadi::Server::NotificationSource::serviceUnregistered(const QString)
Notification source akonadi_notes_agent_3230_OLDXpN now serving: () 
Application '/usr/bin/akonadi_sendlater_agent' exited normally...
Application '/usr/local/bin/akonadi_agent_launcher' exited normally...
void Akonadi::Server::NotificationSource::serviceUnregistered(const QString)
Notification source akonadi_sendlater_agent_3231_VHVu4n now serving: () 
void Akonadi::Server::NotificationSource::serviceUnregistered(const QString)
Notification source AkonadiAgentServer_3223_mmVsO9 now serving: () 
Unregistering search instance akonadi_imap_resource_1 
Lost connection to resource
org.freedesktop.Akonadi.Resource.akonadi_maildir_resource_0 , discarding
cached interface 
Lost connection to resource
org.freedesktop.Akonadi.Resource.akonadi_imap_resource_1 , discarding cached
interface 
void Akonadi::Server::NotificationSource::serviceUnregistered(const QString)
Notification source akonadi_imap_resource_1_3222_X2bKII now serving: () 
void Akonadi::Server::NotificationSource::serviceUnregistered(const QString)
Notification source 

[Akonadi] [Bug 340813] sometimes two copies of mysqld are running with Akonadi

[Martin Steigerwald]

https://bugs.kde.org/show_bug.cgi?id=340813

--- Comment #4 from Martin Steigerwald m...@teamix.de ---
Created attachment 90734
  -- https://bugs.kde.org/attachment.cgi?id=90734action=edit
mysql.err.old with corruption that I think may have happened due to this bug

This is related to my last comment and it clearly shows that MySQL wasn´t too
happy about running twice on the same database. I did not shutdown any mysqld
process uncleanly, so that message may just be related to that another mysqld
process was still running at the time of the message in the log. I will now
start akonadi again and watch the error log. I didn´t kill the old instance of
mysqld here on purpose to show this bug again, I hope the database is still
sound and mysql is able to recover.

141029 13:49:02 [Note] Plugin 'FEDERATED' is disabled.
141029 13:49:02 InnoDB: The InnoDB memory heap is disabled
141029 13:49:02 InnoDB: Mutexes and rw_locks use GCC atomic builtins
141029 13:49:02 InnoDB: Compressed tables use zlib 1.2.8
141029 13:49:02 InnoDB: Using Linux native AIO
141029 13:49:02 InnoDB: Initializing buffer pool, size = 512.0M
141029 13:49:02 InnoDB: Completed initialization of buffer pool
141029 13:49:02 InnoDB: highest supported file format is Barracuda.
InnoDB: The log sequence number in ibdata files does not match
InnoDB: the log sequence number in the ib_logfiles!
141029 13:49:02  InnoDB: Database was not shut down normally!
InnoDB: Starting crash recovery.
InnoDB: Reading tablespace information from the .ibd files...
InnoDB: Restoring possible half-written data pages from the doublewrite
InnoDB: buffer...
141029 13:49:03  InnoDB: Waiting for the background threads to start
141029 13:49:04 InnoDB: 5.5.39 started; log sequence number 30133605273
141029 13:49:04 [Note] /usr/sbin/mysqld: ready for connections.
Version: '5.5.39-1'  socket: '/tmp/akonadi-ms.L69DqH/mysql.socket'  port: 0 
(Debian)

Status information:

Current dir: /home/ms/.local/share/akonadi/db_data/
Running threads: 34  Stack size: 262144
Current locks:
lock: 0x7f9bec1c9db0:

lock: 0x7f9bec1c2bd0:

lock: 0x7f9bec1c0630:

lock: 0x7f9bec1bde60:
[…]


141029 14:38:11 [Note] Plugin 'FEDERATED' is disabled.
141029 14:38:11 InnoDB: The InnoDB memory heap is disabled
141029 14:38:11 InnoDB: Mutexes and rw_locks use GCC atomic builtins
141029 14:38:11 InnoDB: Compressed tables use zlib 1.2.8
141029 14:38:11 InnoDB: Using Linux native AIO
141029 14:38:11 InnoDB: Initializing buffer pool, size = 512.0M
141029 14:38:11 InnoDB: Completed initialization of buffer pool
141029 14:38:11 InnoDB: highest supported file format is Barracuda.
InnoDB: The log sequence number in ibdata files does not match
InnoDB: the log sequence number in the ib_logfiles!
141029 14:38:11  InnoDB: Database was not shut down normally!
InnoDB: Starting crash recovery.
InnoDB: Reading tablespace information from the .ibd files...
InnoDB: Restoring possible half-written data pages from the doublewrite
InnoDB: buffer...
141029 14:38:12  InnoDB: Waiting for the background threads to start
141029 14:38:13 InnoDB: 5.5.39 started; log sequence number 30141310511
141029 14:38:13 [Note] /usr/sbin/mysqld: ready for connections.
Version: '5.5.39-1'  socket: '/tmp/akonadi-ms.ixkIX5/mysql.socket'  port: 0 
(Debian)
141029 15:10:51 [Note] /usr/sbin/mysqld: Normal shutdown

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[Akonadi] [Bug 340813] sometimes two copies of mysqld are running with Akonadi

[Martin Steigerwald]

https://bugs.kde.org/show_bug.cgi?id=340813

--- Comment #5 from Martin Steigerwald m...@teamix.de ---
I think I had luck:

150128 10:14:24 [Note] Plugin 'FEDERATED' is disabled.
150128 10:14:24 InnoDB: The InnoDB memory heap is disabled
150128 10:14:24 InnoDB: Mutexes and rw_locks use GCC atomic builtins
150128 10:14:24 InnoDB: Compressed tables use zlib 1.2.8
150128 10:14:24 InnoDB: Using Linux native AIO
150128 10:14:24 InnoDB: Initializing buffer pool, size = 512.0M
150128 10:14:24 InnoDB: Completed initialization of buffer pool
150128 10:14:24 InnoDB: highest supported file format is Barracuda.
150128 10:14:24  InnoDB: Waiting for the background threads to start
150128 10:14:25 InnoDB: 5.5.40 started; log sequence number 54593147801
150128 10:14:25 [Note] /usr/sbin/mysqld: ready for connections.
Version: '5.5.40-1'  socket: '/tmp/akonadi-ms.QEKpW0/mysql.socket'  port: 0 
(Debian)

Seems fine to far, I will now look into the mysql.err copy I made for as I lost
the database completely.

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[Akonadi] [Bug 340813] sometimes two copies of mysqld are running with Akonadi

[Martin Steigerwald]

https://bugs.kde.org/show_bug.cgi?id=340813

Martin Steigerwald m...@teamix.de changed:

   What|Removed |Added

   Severity|normal  |critical

--- Comment #3 from Martin Steigerwald m...@teamix.de ---
This does still happen (this is with Akonadi 1.13 master git branch with
database optimizations and KDEPIM + Runtime 4.14.2 as packages in Debian
unstable):

ms@merkaba:~ akonadictl stop  
Akonadi is not running. 
ms@merkaba:~#4 akonadictl status
Akonadi Control: stopped
Akonadi Server: stopped
search paths:  (/usr/local/lib/kde4, /home/ms/.kde/lib/kde4/plugins/,
/usr/lib/kde4/plugins/, /usr/local/lib/plugins/,
/usr/lib/x86_64-linux-gnu/qt4/plugins, /usr/local/bin,
/usr/lib/kde4/plugins, /usr/local/lib/plugins, /home/ms/.kde/lib/kde4/,
/usr/lib/kde4/) 
Akonadi Server Search Support: available (Remote Search, Akonadi Baloo Search
Plugin)
Available Agent Types: akonadi_akonotes_resource, akonadi_archivemail_agent,
akonadi_baloo_indexer, akonadi_birthdays_resource, akonadi_contacts_resource,
akonadi_davgroupware_resource, akonadi_folderarchive_agent,
akonadi_followupreminder_agent, akonadi_googlecalendar_resource,
akonadi_googlecontacts_resource, akonadi_ical_resource,
akonadi_icaldir_resource, akonadi_imap_resource, akonadi_invitations_agent,
akonadi_kabc_resource, akonadi_kalarm_dir_resource, akonadi_kalarm_resource,
akonadi_kcal_resource, akonadi_kdeaccounts_resource, akonadi_knut_resource,
akonadi_kolab_resource, akonadi_kolabproxy_resource,
akonadi_localbookmarks_resource, akonadi_maildir_resource,
akonadi_maildispatcher_agent, akonadi_mailfilter_agent,
akonadi_mailtransport_dummy_resource, akonadi_mbox_resource,
akonadi_migration_agent, akonadi_mixedmaildir_resource, akonadi_nepomuk_feeder,
akonadi_newmailnotifier_agent, akonadi_nntp_resource, akonadi_notes_agent,
akonadi_notes_resource, akonadi_openxchange_resource, akonadi_pop3_resource,
akonadi_sendlater_agent, akonadi_vcard_resource, akonadi_vcarddir_resource
ms@merkaba:~ ps aux | grep [m]ysql | grep ms
ms4006  0.4  3.8 2809592 631456 ?  Sl   Jan27   6:26
/usr/sbin/mysqld --defaults-file=/home/ms/.local/share/akonadi/mysql.conf
--datadir=/home/ms/.local/share/akonadi/db_data/
--socket=/tmp/akonadi-ms.QEKpW0/mysql.socket

After minutes after issuing akonadictl stop:

ms@merkaba:~ ps aux | grep [m]ysql | grep ms
ms4006  0.4  3.8 2809592 631456 ?  Sl   Jan27   6:27
/usr/sbin/mysqld --defaults-file=/home/ms/.local/share/akonadi/mysql.conf
--datadir=/home/ms/.local/share/akonadi/db_data/
--socket=/tmp/akonadi-ms.QEKpW0/mysql.socket

And look when I start it again:

ms@merkaba:~ ps aux | grep [m]ysql | grep ms
ms4006  0.4  3.8 2809592 632112 ?  Sl   Jan27   6:40
/usr/sbin/mysqld --defaults-file=/home/ms/.local/share/akonadi/mysql.conf
--datadir=/home/ms/.local/share/akonadi/db_data/
--socket=/tmp/akonadi-ms.QEKpW0/mysql.socket
ms   29368  1.0  0.5 787196 85964 ?Sl   09:54   0:00
/usr/sbin/mysqld --defaults-file=/home/ms/.local/share/akonadi/mysql.conf
--datadir=/home/ms/.local/share/akonadi/db_data/
--socket=/tmp/akonadi-ms.QEKpW0/mysql.socket


This is a *huge*, *big* *no-go*. At no point of time Akonadi should there
*ever* be *two* instances of MySQL running for the same user and the *same*
database.

As this bug is about the stopping of Akonadi I will file a new bug about having
two instances of MySQL running. From all I know this just is a very, very bad
idea.


And I think I lost my private Akonadi MySQL database due to this in combination
with some impatience of mine as I saw mysqld replaying from log file and
bursting writes of about 150-300 MiB/s sustained for *minutes*, totalling to
several times the size of the complete MySQL database. I stopped it with
SIGKILL to end the excessive writing.

As I think that this causes *real* data loss, loss of the complete Akonadi
MySQL database I am raising bug severity. I think I still have the MySQL error
log available.

Now even after writing all of this, the initial left over mysqld still did not
end:

ms@merkaba:~ ps aux | grep [m]ysql | grep ms
ms4006  0.4  3.9 2809592 632260 ?  Sl   Jan27   6:45
/usr/sbin/mysqld --defaults-file=/home/ms/.local/share/akonadi/mysql.conf
--datadir=/home/ms/.local/share/akonadi/db_data/
--socket=/tmp/akonadi-ms.QEKpW0/mysql.socket

Yet a friendly SIGTERM finishes it:

ms@merkaba:~ kill 4006
ms@merkaba:~ ps aux | grep [m]ysql | grep ms
ms@merkaba:~#1 

And I have this:

ms@merkaba:~/.local/share/akonadi/db_data cat mysql.err
150128  9:54:11 [Note] Plugin 'FEDERATED' is disabled.
150128  9:54:11 InnoDB: The InnoDB memory heap is disabled
150128  9:54:11 InnoDB: Mutexes and rw_locks use GCC atomic builtins
150128  9:54:11 InnoDB: Compressed tables use zlib 1.2.8
150128  9:54:11 InnoDB: Using Linux native AIO
150128  9:54:11 InnoDB: Initializing buffer 

[Akonadi] [Bug 340813] sometimes two copies of mysqld are running with Akonadi

[Martin Steigerwald]

https://bugs.kde.org/show_bug.cgi?id=340813

--- Comment #6 from Martin Steigerwald mar...@lichtvoll.de ---
Okay, I think I deleted the mysql.err log I had on my private KDEPIM / Akonadi
setup after restoring from scratch by letting it build a new database, cause I
was just too angry at all of this.

What happened there was: I had two instanced for mysqld running after stopping
and starting Akonadi after I put SizeTreshold=32768 running and I didn´t notice
that. Due to this bug I usually check whether a MySQL daemon is still around
and kill it manually with SIGTERM friendly if it still is around after some
time. At this time I forgot about this.

What happened on one of the next restarts was that mysqld was trying to recover
from log file and it wrote in bursts of 150 to 300 MiB per seconds onto the
Dual SSD BTRFS RAID 1 for minutes. Akonadi was almost totally blocked. The
MySQL easily wrote more than ten times or even more data than the whole size
the database had as this time (around 2 GiB).

At one time I lost my patience and also wanted to avoid needless excessive
writes to the SSD. So I went on to kill mysqld with SIGTERM. It didn´t respond.
I then after some time did SIGKILL.

On the next restart of Akonadi it started to write excessively again, while it
may be that the mysqld at some point would have been able to repair itself from
logfile, I cannot tell, as I lost my patience after a while and well, I even
tough SSD can take lots, I didn´t want to have mysqld to write onto it like
this for hours.

Thus I send redid my Akonadi setup from scratch.

Okay, since I cannot prove the data loss as it may have completed I am
downgrading the bug again a bit, but still I think its a grave issue that
Akonadi tolerates two mysqld processing running on the same database. At least
on akonadictl start if it finds an old MySQL process for the database still
around I think it is good if it prints a BIG FAT WARNING, and does not continue
with starting up Akonadi.

But I think for usability it may be good if after some timeout Akonadi also
sends the mysqld process a SIGTERM and also complains if it doesn´t respond to
it without some time.

For robustness sake, I think thats very important. I am pondering to use a
central MySQL or PostgreSQL server again for this reason. On any account two
mysqld process on the same database is a pretty bad idea.

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[Akonadi] [Bug 340813] sometimes two copies of mysqld are running with Akonadi

[Martin Steigerwald]

https://bugs.kde.org/show_bug.cgi?id=340813

Martin Steigerwald m...@teamix.de changed:

   What|Removed |Added

   Severity|critical|grave

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[Akonadi] [Bug 340813] sometimes two copies of mysqld are running with Akonadi

[Martin Steigerwald]

https://bugs.kde.org/show_bug.cgi?id=340813

Martin Steigerwald m...@teamix.de changed:

   What|Removed |Added

 CC||mar...@lichtvoll.de

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[Akonadi] [Bug 340813] sometimes two copies of mysqld are running with Akonadi

[Martin Steigerwald]

https://bugs.kde.org/show_bug.cgi?id=340813

--- Comment #1 from Martin Steigerwald m...@teamix.de ---
Created attachment 89518
  -- https://bugs.kde.org/attachment.cgi?id=89518action=edit
Old MySQL error log

This seems to be of the old mysqld process which actually got some shutdown
requests it seems to me.

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[Akonadi] [Bug 340813] sometimes two copies of mysqld are running with Akonadi

[Martin Steigerwald]

https://bugs.kde.org/show_bug.cgi?id=340813

--- Comment #2 from Martin Steigerwald m...@teamix.de ---
Created attachment 89519
  -- https://bugs.kde.org/attachment.cgi?id=89519action=edit
Old akonadiserver log

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