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  • Jan 29 00:12
    NicolasCARPi closed #4080
  • Jan 29 00:12
    NicolasCARPi commented #4080
  • Jan 28 16:08
    alexgu2008 opened #4080
  • Jan 27 21:27
    MarcelBolten synchronize #4077
  • Jan 27 21:27

    MarcelBolten on marcel-extended-search-visibility

    BASE_IMAGE_VERSION=SCRUTINIZER_… wait for mysql container (compare)

  • Jan 27 15:37
    NicolasCARPi reopened #4041
  • Jan 27 15:36
    NicolasCARPi commented #4041
  • Jan 27 15:09
    seignovert commented #4041
  • Jan 27 06:56
    MarcelBolten synchronize #4077
  • Jan 27 06:56

    MarcelBolten on marcel-extended-search-visibility

    2 space indentation, try to set… (compare)

  • Jan 26 17:05
    NicolasCARPi commented #4075
  • Jan 26 16:42
    InnovPlantProtect closed #4075
  • Jan 26 16:42
    InnovPlantProtect commented #4075
  • Jan 26 14:33
    NicolasCARPi commented #4075
  • Jan 26 14:29
    EgonHeuson commented #4078
  • Jan 26 14:29
    NicolasCARPi labeled #4075
  • Jan 26 14:29
    NicolasCARPi closed #4078
  • Jan 26 14:29
    NicolasCARPi commented #4078
  • Jan 26 13:12
    EgonHeuson commented #4078
  • Jan 26 13:12
    EgonHeuson commented #4078
alexander-haller
@alexander-haller
I would stop the mysql container, point the volume to another location on ext4 like /tmp/whatever and try to start
  • /tmp/elabftwmysql:/var/lib/mysql
besselfunct
@besselfunct
I've made a new directory in my ext4 volume. Is the docker command just docker start mysql -d /tmp/elabftwmysql:/var/lib/mysql
alexander-haller
@alexander-haller
I would replace the line in elabftw.conf (comment out the old one) and use elabctl start. just to be sure it is the same process
do your docker images also exist on a zfs volume? not sure if that matters tbh.
/var/lib/docker/ iirc
besselfunct
@besselfunct
I tried changing the location to /tmp/testing in both elabctl.conf and elabctl.yml
And I'm running into a similar error
/var/lib/ is on an ext4 volume
the only thing on datastore (which is my only ZFS volume) is the stuff that elabctl puts there when it reads the elabctl.conf
I tried elabctl uninstall followed by elabctl install with the default values, which point to an ext4 volume, and have the same error
I'm going to try removing zfsutils-linux and see if the issue persists
alexander-haller
@alexander-haller
what does "docker logs --details mysql" say now?
besselfunct
@besselfunct
 2022-07-12 19:13:51+02:00 [Note] [Entrypoint]: Entrypoint script for MySQL Server 8.0.29-1.el8 started.
 2022-07-12 19:13:51+02:00 [Note] [Entrypoint]: Switching to dedicated user 'mysql'
 2022-07-12 19:13:51+02:00 [Note] [Entrypoint]: Entrypoint script for MySQL Server 8.0.29-1.el8 started.
 2022-07-12 19:13:52+02:00 [Note] [Entrypoint]: Initializing database files
 2022-07-12T17:13:52.042553Z 0 [Warning] [MY-010918] [Server] 'default_authentication_plugin' is deprecated and will be removed in a future release. Please use au                thentication_policy instead.
 2022-07-12T17:13:52.042567Z 0 [System] [MY-013169] [Server] /usr/sbin/mysqld (mysqld 8.0.29) initializing of server in progress as process 42
 2022-07-12T17:13:52.054078Z 1 [System] [MY-013576] [InnoDB] InnoDB initialization has started.
 2022-07-12T17:13:53.238893Z 1 [System] [MY-013577] [InnoDB] InnoDB initialization has ended.
 2022-07-12T17:13:56.404692Z 6 [Warning] [MY-010453] [Server] root@localhost is created with an empty password ! Please consider switching off the --initialize-in                secure option.
 2022-07-12 19:14:02+02:00 [Note] [Entrypoint]: Database files initialized
 2022-07-12 19:14:02+02:00 [Note] [Entrypoint]: Starting temporary server
 2022-07-12T17:14:02.872144Z 0 [Warning] [MY-010918] [Server] 'default_authentication_plugin' is deprecated and will be removed in a future release. Please use au                thentication_policy instead.
 2022-07-12T17:14:02.872163Z 0 [System] [MY-010116] [Server] /usr/sbin/mysqld (mysqld 8.0.29) starting as process 91
 2022-07-12T17:14:02.890474Z 1 [System] [MY-013576] [InnoDB] InnoDB initialization has started.
 2022-07-12T17:14:03.087866Z 1 [System] [MY-013577] [InnoDB] InnoDB initialization has ended.
 2022-07-12T17:14:03.441798Z 0 [Warning] [MY-010068] [Server] CA certificate ca.pem is self signed.
 2022-07-12T17:14:03.441865Z 0 [System] [MY-013602] [Server] Channel mysql_main configured to support TLS. Encrypted connections are now supported for this channe                l.
 2022-07-12T17:14:03.480641Z 0 [System] [MY-011323] [Server] X Plugin ready for connections. Socket: /var/run/mysqld/mysqlx.sock
 2022-07-12T17:14:03.480764Z 0 [System] [MY-010931] [Server] /usr/sbin/mysqld: ready for connections. Version: '8.0.29'  socket: '/var/run/mysqld/mysqld.sock'  po                rt: 0  MySQL Community Server - GPL.
 2022-07-12 19:14:03+02:00 [Note] [Entrypoint]: Temporary server started.
 '/var/lib/mysql/mysql.sock' -> '/var/run/mysqld/mysqld.sock'
 Warning: Unable to load '/usr/share/zoneinfo/iso3166.tab' as time zone. Skipping it.
 Warning: Unable to load '/usr/share/zoneinfo/leapseconds' as time zone. Skipping it.
 Warning: Unable to load '/usr/share/zoneinfo/tzdata.zi' as time zone. Skipping it.
 Warning: Unable to load '/usr/share/zoneinfo/zone.tab' as time zone. Skipping it.
 Warning: Unable to load '/usr/share/zoneinfo/zone1970.tab' as time zone. Skipping it.
 2022-07-12 19:14:05+02:00 [Note] [Entrypoint]: Creating database elabftw
 2022-07-12 19:14:05+02:00 [Note] [Entrypoint]: Creating user elabftw
 2022-07-12 19:14:05+02:00 [Note] [Entrypoint]: Giving user elabftw access to schema elabftw

 2022-07-12 19:14:05+02:00 [Note] [Entrypoint]: Stopping temporary server
 2022-07-12T17:14:05.792537Z 13 [System] [MY-013172] [Server] Received SHUTDOWN from user root. Shutting down mysqld (Version: 8.0.29).
 2022-07-12T17:14:08.130313Z 0 [System] [MY-010910] [Server] /usr/sbin/mysqld: Shutdown complete (mysqld 8.0.29)  MySQL Community Server - GPL.
 2022-07-12 19:14:08+02:00 [Note] [Entrypoint]: Temporary server stopped

 2022-07-12 19:14:08+02:00 [Note] [Entrypoint]: MySQL init process done. Ready for start up.

 2022-07-12T17:14:09.053252Z 0 [Warning] [MY-010918] [Server] 'default_authentication_plugin' is deprecated and will be removed in a future release. Please use au                thentication_policy instead.
 2022-07-12T17:14:09.053270Z 0 [System] [MY-010116] [Server] /usr/sbin/mysqld (mysqld 8.0.29) starting as process 1
 2022-07-12T17:14:09.060015Z 1 [System] [MY-013576]
alexander-haller
@alexander-haller
and elabctl status
besselfunct
@besselfunct

      _          _     _____ _______        __
  ___| |    __ _| |__ |  ___|_   _\ \      / /
 / _ \ |   / _| | '_ \| |_    | |  \ \ /\ / /
|  __/ |__| (_| | |_) |  _|   | |   \ V  V /
 \___|_____\__,_|_.__/|_|     |_|    \_/\_/


Using elabctl configuration file: using default values (no config file found)
Using elabftw configuration file: /etc/elabftw.yml
---------------------------------------------
 Name                Command                  State                      Ports
----------------------------------------------------------------------------------------------
elabftw   /init                            Up (healthy)   0.0.0.0:443->443/tcp,:::443->443/tcp
mysql     docker-entrypoint.sh --def ...   Up             3306/tcp, 33060/tcp
alexander-haller
@alexander-haller
now try elabctl initialize ?
besselfunct
@besselfunct
elabctl initialize was successful this time, but I'm not sure if it's because I removed zfsutils-linux
I retried the installation with zfsutils-linux installed and it was successful again, using the default data locations
alexander-haller
@alexander-haller
the default data locations are on ext4 I assume?
besselfunct
@besselfunct
Yes
alexander-haller
@alexander-haller
well my guess is you hit the above bug with zfs - not 100% sure since I do have little experience with zfs myself
besselfunct
@besselfunct
Yeah, it looks like this is a ZFS issue.
I'm not certain how to proceed from here though. I like using ZFS because of the redundancy, and expanding a zpool is trivial
If I can't use ZFS, I'm going to have to figure out another file system, or hunt down a hardware raid solution
alexander-haller
@alexander-haller
there seems to be a bugfix:
because this is does affect mysql on zfs I would assume it will get pushed quickly for ubuntu
besselfunct
@besselfunct
Yeah, it looks like 2.1.5 will fix the issue and I'm running 2.1.4
alexander-haller
@alexander-haller
I'm off for today - if you have more infos note them here. It's always good for the community to have this feedback
besselfunct
@besselfunct
@alexander-haller Many many thanks for helping me nail down this issue. I'm familiar with *NIX systems, but docker and containerization technologies are a complete black box to me. I just need to get this working so I can finish my PhD thesis
Nicolas CARPi
@NicolasCARPi
I love it when community takes over support and I can just sit back and watch issues get resolved. Thanks @alexander-haller ;)
nmontua
@nmontua
Hi. I tried to update to the most current version, but I get an error about incorrect time format that is not covered by any Github issue etc. as far as I have found. The db:update command throws the following error: SQLSTATE[22007]: Invalid datetime format: 1292 Incorrect datetime value: '0
000-00-00 00:00:00' for column 'datetime' at row 1
Is there a way to roll back to a previous version?
nmontua
@nmontua
I did that, thank you for the link, however not when I run docker exec -it elabftw bin/console db:update, I get a different error :(
SQLSTATE[42S02]: Base table or view not found: 1146 Table 'elabftw.notifications' doesn't exist
nmontua
@nmontua
I have rolled back for now. Maybe I will have time to play around some more at a later date
Nicolas CARPi
@NicolasCARPi
the notifications table is created in schema70.sql, I don't see how it could have been skipped
also if you want support please open a proper github issue with all information so it's easier to debug
nmontua
@nmontua
Absolutely, if on my next attempt this occurs again, I will make a proper github issue. Thank you for your time.
nmontua
@nmontua
Okay, I tried again and this time everything worked fine. Again, I followed the instructions you linked, only this time I did not do "After, manually run the last lines of schema71:". Thats the only thing I did differently really. In any case, happy it worked and thank you for the troubleshooting guide.
Nicolas CARPi
@NicolasCARPi
ok cool
HClO4
@HClO4
I'm just trying to set up a elabftw instance on a Kubuntu VM to test the utf8 stuff prior to the update to 4.3.x. Did elabctl install and elabctl start but all I get is "ERROR: The Compose file '/etc/elabftw.yml' is invalid because:
services.web.depends_on contains an invalid type, it should be an array" with the last command. What is wrong?
Nicolas CARPi
@NicolasCARPi
@HClO4 you are asking what is wrong but you are not showing that part of your config file! So it's hard to say. Does it look exactly like this? https://github.com/elabftw/elabimg/blob/1338801d49fdd3c4ac8e71f58cc5b64b04799235/src/docker-compose.yml-EXAMPLE#L26-L28 If yes, upgrade your docker-compose version.
Nicolas CARPi
@NicolasCARPi
also note that it's perfectly fine to simply remove this part that is causing problem
taitlab
@taitlab
Hello! Silly question - how can I resize a picture in Markdown mode? I think I've done it before, but I forgot the syntax :)
Nicolas CARPi
@NicolasCARPi
You can't (AFAIK)
4 replies
plasmapper
@plasmapper
Hello everyone! I don't know if anyone here is using LabVIEW, but just in case I've made a LabVIEW client library for eLabFTW using API v1 documentation and testing it on https://demo.elabftw.net.