Cant connect to kopano core

dark957 · November 21, 2018, 9:37am

Hello,
I had a Harddisk size problem on my virtuel disk by copy of mails and now I cant connect via Webapp to my accounts Error message: “Cannot connect to Kopano Core.”.

journalctl -u kopano-server

"Nov 21 09:37:33 mail kopano-server[1784]: Wed Nov 21 09:37:33 2018: [error  ] SQL [00000012] Failed: Disk full (/tmp/#sql_4ec_1.MAI); waiting for someone to free some space... (errno: 28 "No space left on device"), Query Size: 1083, Query: "SELECT count(*),mvproperties.tag,mvproperties.type,group_concat(length(mvproperties.val_ulong),':', mvproperties.val_ulong ORDER BY mvproperties.orderid SEPARATOR ''), group_concat(length(mvproperties.val_string),':', mvproperties.val_string ORDER BY mvproperties.orderid SEPARATOR ''), group_concat(length(mvproperties.val_binary),':', mvproperties.val_binary ORDER BY mvproperties.orderid SEPARATOR ''), group_concat(length(mvproperties.val_double),':', mvproperties.val_double ORDER BY mvproperties.orderid SEPARATOR ''), group_concat(length(mvproperties.val_longint),':', mvproperties.val_longint ORDER BY mvproperties.orderid SEPARATOR ''), group_concat(length(mvproperties.val_hi),':', mvproperties.val_hi ORDER BY mvproperties.orderid SEPARATOR ''), group_concat(length(mvproperties.val_lo),':', mvproperties.val_lo ORDER BY mvproperties.orderid SEPARATOR ''), hierarchyid, names.nameid, names.namestring, names.guid FROM mvproperties LEFT JOIN names ON mvproperties.tag-34049=names.id WHERE hierarchyid=12 AND (tag <= 34048 OR names.id IS NOT NULL)  GROUP BY hierarchyid, tag"

Now I fixed the problem with the size but the kopano core doesnt run

Nov 21 10:08:20 mail systemd[1]: Started Kopano Core Storage Server.
Nov 21 10:08:20 mail kopano-server[1770]: Wed Nov 21 10:08:20 2018: [=======] Starting kopano-server version 8.6.2 (pid 1770)
Nov 21 10:08:20 mail kopano-server[1770]: Wed Nov 21 10:08:20 2018: [error  ] Coredumps will not be generated: kopano-server requires the fs.suid_dumpable sysctl to contain the value 2, not 0. See kopano-coredump(5) for details.
Nov 21 10:08:20 mail kopano-server[1770]: Wed Nov 21 10:08:20 2018: [error  ] KDatabase::Connect(): database access error Unknown error code (0x80000007), mysql error: Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2)
Nov 21 10:08:20 mail kopano-server[1770]: Wed Nov 21 10:08:20 2018: [crit   ] Unable to connect to database: MYSQL not initialized
Nov 21 10:08:20 mail kopano-server[1770]: An error occurred (80000007). Please check logfile "-" for details.
Nov 21 10:08:20 mail kopano-server[1770]: Wed Nov 21 10:08:20 2018: [=======] Server shutdown complete.
Nov 21 10:08:20 mail systemd[1]: kopano-server.service: Main process exited, code=exited, status=255/n/a
Nov 21 10:08:20 mail systemd[1]: kopano-server.service: Unit entered failed state.
Nov 21 10:08:20 mail systemd[1]: kopano-server.service: Failed with result 'exit-code'.
/var/log$ systemctl status apache2
● apache2.service - The Apache HTTP Server
   Loaded: loaded (/lib/systemd/system/apache2.service; enabled; vendor preset: enabled)
   Active: active (running) since Wed 2018-11-21 10:08:25 CET; 19min ago
  Process: 2108 ExecStart=/usr/sbin/apachectl start (code=exited, status=0/SUCCESS)
 Main PID: 2181 (apache2)
    Tasks: 11 (limit: 9830)
   Memory: 74.4M
      CPU: 736ms
   CGroup: /system.slice/apache2.service
           ├─2181 /usr/sbin/apache2 -k start
           ├─2235 /usr/sbin/apache2 -k start
           ├─2236 /usr/sbin/apache2 -k start
           ├─2237 /usr/sbin/apache2 -k start
           ├─2238 /usr/sbin/apache2 -k start
           ├─2239 /usr/sbin/apache2 -k start
           ├─2253 /usr/sbin/apache2 -k start
           ├─2254 /usr/sbin/apache2 -k start
           ├─2255 /usr/sbin/apache2 -k start
           ├─2420 /usr/sbin/apache2 -k start
           └─2421 /usr/sbin/apache2 -k start

Nov 21 10:08:24 mail systemd[1]: Starting The Apache HTTP Server...
Nov 21 10:08:25 mail systemd[1]: Started The Apache HTTP Server.

Is there any Idea how to fix this?

damrose · November 21, 2018, 9:41am

The error message says that the MySQL/MariaDB server is not running. Depending which UCS version you are running, start the appropriate service with the service or systemctl command.

dark957 · November 21, 2018, 9:51am

Hello, Thx for the fast answer! I have the latest version running with all updates (Kopano Core: 8.6.2.1-2). Can you give me the command in detail which I can put in Putty?

damrose · November 21, 2018, 9:55am

To start mariadb on UCS 4.3, use service mariadb start. You can check the service status with service mariadb status

dark957 · November 21, 2018, 9:59am

Thx for the fast answer. It dosent work

/var/log$ service mariadb status
● mariadb.service - MariaDB database server
   Loaded: loaded (/lib/systemd/system/mariadb.service; enabled; vendor preset: enabled)
   Active: failed (Result: exit-code) since Wed 2018-11-21 10:08:20 CET; 49min ago
  Process: 967 ExecStart=/usr/sbin/mysqld $MYSQLD_OPTS $_WSREP_NEW_CLUSTER $_WSREP_START_POSITION (code=exited, status=1/FAILURE)
  Process: 830 ExecStartPre=/bin/sh -c [ ! -e /usr/bin/galera_recovery ] && VAR= ||   VAR=`/usr/bin/galera_recovery`; [ $? -eq 0 ]   && systemctl set-environment _WSREP_START_POSITION=$VAR || exit 1 (code=exited, status=0/SUCCESS)
  Process: 797 ExecStartPre=/bin/sh -c systemctl unset-environment _WSREP_START_POSITION (code=exited, status=0/SUCCESS)
  Process: 787 ExecStartPre=/usr/bin/install -m 755 -o mysql -g root -d /var/run/mysqld (code=exited, status=0/SUCCESS)
 Main PID: 967 (code=exited, status=1/FAILURE)
   Status: "MariaDB server is down"
      CPU: 499ms

Nov 21 10:08:11 mail systemd[1]: Starting MariaDB database server...
Nov 21 10:08:13 mail mysqld[967]: 2018-11-21 10:08:13 139781907026496 [Note] /usr/sbin/mysqld (mysqld 10.1.26-MariaDB-0+deb9u1) starting as process 967 ...
Nov 21 10:08:20 mail systemd[1]: mariadb.service: Main process exited, code=exited, status=1/FAILURE
Nov 21 10:08:20 mail systemd[1]: Failed to start MariaDB database server.
Nov 21 10:08:20 mail systemd[1]: mariadb.service: Unit entered failed state.
Nov 21 10:08:20 mail systemd[1]: mariadb.service: Failed with result 'exit-code'.
/var/log$ service mariadb start
Job for mariadb.service failed because the control process exited with error code.
See "systemctl status mariadb.service" and "journalctl -xe" for details.

damrose · November 21, 2018, 10:07am

The last lines mentions additional logs you can check, with journalctl -xe. You can also have a look at the logfiles in /var/log/mysql/. It may be possible that the MariaDB database was damaged when your disk ran out of space. If that is the case, the MariaDB documentation will hopefully have some information how to proceed - I do not have experience with reconstructing corrupted databases. If you have a backup of the database, you could import the last working version.

dark957 · November 21, 2018, 10:38am

Damrose thank you very much. I will do a rool back to the former VM and rekonfigure the space directly that this problem never happend.

fbartels · November 21, 2018, 12:23pm

there is also a knowledge base entry for this Problem: MySQL Server Does not Start any more

But if you can easily restore to your last snapshot, that is probably the better way.

dark957 · November 23, 2018, 7:41am

Hello Fbartels,
very good hint! Thx! I will try to rebuild the DB!

dark957 · December 19, 2018, 1:29pm

Hello,
question to disk space. I have now the situation that the disk space runs out! I started the VM with 50GB and after the kopano setup I did increase the VM space to 300GB but the system didn’t increase / recognize this, 98% used. Would it be possible to fix this without new installation? It a kind of a partition problem:

Dateisystem Größe Benutzt Verf. Verw% Eingehängt auf
udev 10M 0 10M 0% /dev
tmpfs 787M 16M 772M 3% /run
/dev/mapper/vg_ucs-root 46G 43G 1,1G 98% /
tmpfs 2,0G 56K 2,0G 1% /dev/shm
tmpfs 5,0M 0 5,0M 0% /run/lock
tmpfs 2,0G 0 2,0G 0% /sys/fs/cgroup
/dev/sda1 472M 63M 385M 15% /boot

Christian_Voelker · December 19, 2018, 2:42pm

Hi,

shouldn’t his article help?

/CV

dark957 · December 22, 2018, 8:34pm

Hello Christian,
nice manual which fits on my problem. I tried to execute this but have a poblem. As you can see the VM space (Windows Server 2016) has 300 GB space. But I cant enlarge it. The step 2c (command n) & 2d (command t) dont fits to your manual. Also I couldnt enlarge the space to maybe 250GB. I can create only 49,5GB again as shown. You you have an idea?

Command (m for help): p
Disk /dev/sda: 300 GiB, 322122547200 bytes, 629145600 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disklabel type: dos
Disk identifier: 0xa649a22d

Device Boot Start End Sectors Size Id Type
/dev/sda1 * 2048 999423 997376 487M 83 Linux
/dev/sda2 1001470 104855551 103854082 49,5G 5 Extended
/dev/sda5 1001472 104855551 103854080 49,5G 8e Linux LVM

Command (m for help): d
Partition number (1,2,5, default 5): 5
Partition 5 has been deleted.

Command (m for help): n
Partition type
p primary (1 primary, 1 extended, 2 free)
l logical (numbered from 5)
Select (default p): l

Adding logical partition 5
First sector (1003518-104855551, default 1003520):
Last sector, +sectors or +size{K,M,G,T,P} (1003520-104855551, default 104855551):

Created a new partition 5 of type ‘Linux’ and of size 49,5 GiB.
Partition #5 contains a ext4 signature.

Do you want to remove the signature? [Y]es/[N]o: n

Command (m for help): t
Partition number (1,2,5, default 5): 5
Partition type (type L to list all types): 8e

Changed type of partition ‘Linux’ to ‘Linux LVM’.

Command (m for help): w
The partition table has been altered.
Calling ioctl() to re-read partition table.
Re-reading the partition table failed.: Das Gerät oder die Ressource ist belegt

The kernel still uses the old table. The new table will be used at the next reboot or after you run partprobe(8) or kpartx(8).

root@mail:~# pvresize /dev/sda5
Physical volume “/dev/sda5” changed
1 physical volume(s) resized / 0 physical volume(s) not resized
root@mail:~# lvresize -l +100%FREE /dev/vg_ucs/root
New size (12165 extents) matches existing size (12165 extents).
root@mail:~# resize2fs /dev/vg_ucs/root
resize2fs 1.43.4 (31-Jan-2017)
Das Dateisystem ist bereits 12456960 (4k) Blöcke lang. Nichts zu tun!

Thx a lot!

Christian_Voelker · December 24, 2018, 11:08am

Hi,

updated the article.

Now it takes the extended partition into account.

/CV

dark957 · December 26, 2018, 3:15pm

Hello Again,
Maybe somebody can advice me whats going wrong if I want to increase my stroage size. I stick in step 2e on Christians Workaround (special thx to him!). There isnt the message like shown in that “all space is in use.”

Please see also as shown below what I did. I cant see a mistake.

Additional informtation: the kopano machine run as VM under hyper-v. Maybe here is somethink different.

Step 2e from Christian:

Command (m for help): n
All space for primary partitions is in use.

This is the feedback which I get in step 2e:

Command (m for help): n
Partition type
p primary (1 primary, 1 extended, 2 free)
l logical (numbered from 5)
Select (default p):

If I type l for "logical Partition I get the followed feedback:

Select (default p): l
Adding logical partition 6

No free sectors available.

Complete log from my excecution till 2e:

root@mail:~# fdisk /dev/sda

Welcome to fdisk (util-linux 2.29.2).
Changes will remain in memory only, until you decide to write them.
Be careful before using the write command.

Command (m for help): u

Changing display/entry units to cylinders (DEPRECATED!).

Command (m for help): p
Disk /dev/sda: 220 GiB, 236223201280 bytes, 461373440 sectors
Geometry: 255 heads, 63 sectors/track, 28719 cylinders
Units: cylinders of 16065 * 512 = 8225280 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disklabel type: dos
Disk identifier: 0xa649a22d

Device Boot Start End Cylinders Size Id Type
/dev/sda1 * 1 63 63 487M 83 Linux
/dev/sda2 63 6527 6465 49,5G 5 Extended
/dev/sda5 63 6527 6465 49,5G 8e Linux LVM

Command (m for help): d
Partition number (1,2,5, default 5): 5

Partition 5 has been deleted.

Command (m for help): d
Partition number (1,2, default 2): 2

Partition 2 has been deleted.

Command (m for help): n
Partition type
p primary (1 primary, 0 extended, 3 free)
e extended (container for logical partitions)
Select (default p): e
Partition number (2-4, default 2): 2
First cylinder (63-28719, default 63): 63
Last cylinder, +cylinders or +size{K,M,G,T,P} (63-28719, default 28719): 28719

Created a new partition 2 of type ‘Extended’ and of size 219,5 GiB.

Command (m for help): n
Partition type
p primary (1 primary, 1 extended, 2 free)
l logical (numbered from 5)
Select (default p):

PS.: All the best for X-mas days and thx in advanced for support!

knebb · December 26, 2018, 4:35pm

Can you post what you see when typing “p” after this step?

/KNEBB

dark957 · December 26, 2018, 11:12pm

Dear knebb,
thx for your support! Im not realy sure if you can see something?! This is the feedback on p after step 2d. I see there a different start and end cylinder!?!?!?:

Feedback after step 2d on p command:

Command (m for help): p
Disk /dev/sda: 220 GiB, 236223201280 bytes, 461373440 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disklabel type: dos
Disk identifier: 0xa649a22d

Device Boot Start End Sectors Size Id Type
/dev/sda1 * 2048 999423 997376 487M 83 Linux
/dev/sda2 1001470 104855551 103854082 49,5G 5 Extended
/dev/sda5 1001472 104855551 103854080 49,5G 8e Linux LVM

Command (m for help):

This is the complete log:

root@mail:~# fdisk /dev/sda

Welcome to fdisk (util-linux 2.29.2).
Changes will remain in memory only, until you decide to write them.
Be careful before using the write command.

Command (m for help): u
Changing display/entry units to cylinders (DEPRECATED!).

Command (m for help): p
Disk /dev/sda: 220 GiB, 236223201280 bytes, 461373440 sectors
Geometry: 255 heads, 63 sectors/track, 28719 cylinders
Units: cylinders of 16065 * 512 = 8225280 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disklabel type: dos
Disk identifier: 0xa649a22d

Device Boot Start End Cylinders Size Id Type
/dev/sda1 * 1 63 63 487M 83 Linux
/dev/sda2 63 6527 6465 49,5G 5 Extended
/dev/sda5 63 6527 6465 49,5G 8e Linux LVM

Command (m for help): d
Partition number (1,2,5, default 5): 5

Partition 5 has been deleted.

Command (m for help): d
Partition number (1,2, default 2): 2

Partition 2 has been deleted.

Command (m for help): n
Partition type
p primary (1 primary, 0 extended, 3 free)
e extended (container for logical partitions)
Select (default p): e
Partition number (2-4, default 2): 2
First cylinder (63-28719, default 63): 63
Last cylinder, +cylinders or +size{K,M,G,T,P} (63-28719, default 28719): 28719

Created a new partition 2 of type ‘Extended’ and of size 219,5 GiB.

Command (m for help): p
Disk /dev/sda: 220 GiB, 236223201280 bytes, 461373440 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disklabel type: dos
Disk identifier: 0xa649a22d

Device Boot Start End Sectors Size Id Type
/dev/sda1 * 2048 999423 997376 487M 83 Linux
/dev/sda2 1001470 104855551 103854082 49,5G 5 Extended
/dev/sda5 1001472 104855551 103854080 49,5G 8e Linux LVM

Command (m for help):

This is the feedback afterwards if I try to rewrite the partition table:

Command (m for help): w
The partition table has been altered.
Calling ioctl() to re-read partition table.
Re-reading the partition table failed.: Das Gerät oder die Ressource ist belegt

The kernel still uses the old table. The new table will be used at the next reboot or after you run partprobe(8) or kpartx(8).

root@mail:~# fdisk /dev/sda

Welcome to fdisk (util-linux 2.29.2).
Changes will remain in memory only, until you decide to write them.
Be careful before using the write command.

Command (m for help): p
Disk /dev/sda: 220 GiB, 236223201280 bytes, 461373440 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disklabel type: dos
Disk identifier: 0xa649a22d

Device Boot Start End Sectors Size Id Type
/dev/sda1 * 2048 999423 997376 487M 83 Linux
/dev/sda2 1001470 104855551 103854082 49,5G 5 Extended
/dev/sda5 1001472 104855551 103854080 49,5G 8e Linux LVM

Command (m for help):

Christian_Voelker · December 27, 2018, 8:17am

dark957:

Command (m for help): n
Partition type
p primary (1 primary, 0 extended, 3 free)
e extended (container for logical partitions)
Select (default p): e
Partition number (2-4, default 2): 2
First cylinder (63-28719, default 63): 63
Last cylinder, +cylinders or +size{K,M,G,T,P} (63-28719, default 28719): 28719

Created a new partition 2 of type ‘Extended’ and of size 219,5 GiB.

Command (m for help): p
Disk /dev/sda: 220 GiB, 236223201280 bytes, 461373440 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disklabel type: dos
Disk identifier: 0xa649a22d

Device Boot Start End Sectors Size Id Type
/dev/sda1 * 2048 999423 997376 487M 83 Linux
/dev/sda2 1001470 104855551 103854082 49,5G 5 Extended
/dev/sda5 1001472 104855551 103854080 49,5G 8e Linux LVM

These is NOT the exact output of what you are doing! Is simply does not macht.

Please follow the steps exactly and type “p” after 2d and before 2e.
You output shows it has created the larger partition 2:
Created a new partition 2 of type ‘Extended’ and of size 219,5 GiB.
But then you post the output of “p” which tells us it is not directly afterwards (as the units does not match).

/CV

dark957 · December 27, 2018, 9:12am

Hello Again,
sorry maybe I had a copy past error. I check it again, and of course you are right but I stick on the point 2e further. The system did create a full extented partition but doesnt give me the feedback which you have under 2e. How should I proceed?

After step 2d: Extended stroage created of 219,5GB

Command (m for help): p
Disk /dev/sda: 220 GiB, 236223201280 bytes, 461373440 sectors
Geometry: 255 heads, 63 sectors/track, 28719 cylinders
Units: cylinders of 16065 * 512 = 8225280 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disklabel type: dos
Disk identifier: 0xa649a22d

Device Boot Start End Cylinders Size Id Type
/dev/sda1 * 1 63 63 487M 83 Linux
/dev/sda2 63 28719 28657 219,5G 5 Extended

Step 2e dosent give me the same Feedback like you have (all space is use)

Command (m for help): n
Partition type
p primary (1 primary, 1 extended, 2 free)
l logical (numbered from 5)
Select (default p):

Here is the log again with the status after 2e

fdisk: cannot open /etc/sda: Datei oder Verzeichnis nicht gefunden
root@mail:~# u
-bash: u: Kommando nicht gefunden.
root@mail:~# fdisk /dev/sda

Welcome to fdisk (util-linux 2.29.2).
Changes will remain in memory only, until you decide to write them.
Be careful before using the write command.

Command (m for help): u
Changing display/entry units to cylinders (DEPRECATED!).

Command (m for help): p
Disk /dev/sda: 220 GiB, 236223201280 bytes, 461373440 sectors
Geometry: 255 heads, 63 sectors/track, 28719 cylinders
Units: cylinders of 16065 * 512 = 8225280 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disklabel type: dos
Disk identifier: 0xa649a22d

Device Boot Start End Cylinders Size Id Type
/dev/sda1 * 1 63 63 487M 83 Linux
/dev/sda2 63 6527 6465 49,5G 5 Extended
/dev/sda5 63 6527 6465 49,5G 8e Linux LVM

Command (m for help): d
Partition number (1,2,5, default 5): 5

Partition 5 has been deleted.

Command (m for help): d
Partition number (1,2, default 2): 2

Partition 2 has been deleted.

Command (m for help): n
Partition type
p primary (1 primary, 0 extended, 3 free)
e extended (container for logical partitions)
Select (default p): e
Partition number (2-4, default 2): 2
First cylinder (63-28719, default 63): 63
Last cylinder, +cylinders or +size{K,M,G,T,P} (63-28719, default 28719): 28719

Created a new partition 2 of type ‘Extended’ and of size 219,5 GiB.

Command (m for help): p
Disk /dev/sda: 220 GiB, 236223201280 bytes, 461373440 sectors
Geometry: 255 heads, 63 sectors/track, 28719 cylinders
Units: cylinders of 16065 * 512 = 8225280 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disklabel type: dos
Disk identifier: 0xa649a22d

Device Boot Start End Cylinders Size Id Type
/dev/sda1 * 1 63 63 487M 83 Linux
/dev/sda2 63 28719 28657 219,5G 5 Extended

Command (m for help): n
Partition type
p primary (1 primary, 1 extended, 2 free)
l logical (numbered from 5)
Select (default p):

Christian_Voelker · December 27, 2018, 9:24am

Hi,

well from your latest output everything is working fine. The extended partition is created with the space and now you should re-create the logical partition.
According to this it is waiting four you to type “l”…

Sorry, but to be able to help you should REALLY post helpful things. Up to 2d everything is fine. Make sure you type in “l”, and NOT “p”!

/CV

dark957 · December 27, 2018, 9:57am

Thx a lot for your great support Christian! I learnd something About my mistake! Its really essential to run fdisk in one session. I jumped out for exsample sometimes by wrong typing and than you loose all changes directly which was done with fdisk before!