BeatificaBytes

If you are connected on your NAS via a SSH console, the file to be edited is located in /var/services/web/phpMyAdmin/synology_server_choice.json.

But you should also be able to access it from a Windows PC on \\<YourNAS>\web\phpMyAdmin\synology_server_choice.json on DSM 6.x or \\<YourNAS>\web_packages\phpmyadmin on DMS 7.x\synology_server_choice.json

To add a server, simply duplicate the first statement of the json file, separated with a comma:

[
{"verbose":"Server 1","auth_type":"cookie","host":"localhost","connect_type":"socket","socket":"\/run\/mysqld\/mysqld10.sock","compress":false,"AllowNoPassword":false},
{"verbose":"Server 2","auth_type":"cookie","host":"192.168.0.20","connect_type":"socket","socket":"\/run\/mysqld\/mysqld10.sock","compress":false,"AllowNoPassword":false},
{"verbose":"Server 3","auth_type":"cookie","host":"192.168.0.100","connect_type":"socket","socket":"\/run\/mysqld\/mysqld10.sock","compress":false,"AllowNoPassword":false}
]

Et voilà.

This is a summary of my attempts. It is based on various posts found on the web:

• https://superuser.com/questions/834100/shrink-raid-by-removing-a-disk
• https://unix.stackexchange.com/questions/67702/how-to-reduce-volume-group-size-in-lvm#67707
• https://blog.reboost.net/manually-removing-a-disk-from-a-synology-raid/

Notice that xfs File System only supports “extend” and not “reduce”. So, I only tried with etx4 and btrfs.

Although I used a DSM with a video station, a photo station, the web station and wordpress, this was not a “real case” (most of the data were still on the first sectors of the disks). So, I would really not recommend to do this on a real NAS !!!

 

Open a SSH console and enter root mode (sudo -i) to execute the commands here after.

To identify which process is accessing a volume, we possibly need lsof (only if umount fails)

Install OPKG : See https://www.beatificabytes.be/use-opkg-instead-of-ipkg-on-synology/

Install lsof: /opt/bin/opkg install lsof

Layout of the Physical Volume/Volume Group/ Logical Volumes :

Find the Filesytem of /volume1:

df -h

Filesystem      Size  Used Avail Use% Mounted on
/dev/md0        2.3G 1016M  1.2G  46% /
none            2.0G     0  2.0G   0% /dev
/tmp            2.0G  536K  2.0G   1% /tmp
/run            2.0G  3.2M  2.0G   1% /run
/dev/shm        2.0G  4.0K  2.0G   1% /dev/shm
none            4.0K     0  4.0K   0% /sys/fs/cgroup
cgmfs           100K     0  100K   0% /run/cgmanager/fs
/dev/vg1000/lv   14G  3.2G  9.9G  25% /volume1

• Show Physical Volume: pvdisplay
• Show Volume Group: vgdisplay
• Show Logical Volume: lvdisplay
• Show Disks: fdisk -l

Check if one can umount the volume1 :

umount /dev/vg1000/lv

umount: /volume1: target is busy
        (In some cases useful info about processes that
         use the device is found by lsof(8) or fuser(1).)

Stop all services :

synopkg onoffall stop

/usr/syno/etc.defaults/rc.sysv/S80samba.sh stop

/usr/syno/etc.defaults/rc.sysv/S83nfsd.sh stop

/usr/syno/etc.defaults/rc.sysv/pgsql.sh stop

/usr/syno/etc.defaults/rc.sysv/synomount.sh stop

check which daemons are still using volume1 :

/opt/bin/lsof | grep volume1

COMMAND    PID  TID     USER  FD        TYPE                          DEVICE SIZE/OFF       NODE NAME
s2s_daemo 10868         root    8u      REG               0,30    11264        608 /volume1/@S2S/event.sqlite
synologan  8368         root  3u        REG               0,30       3072        654 /volume1/@database/synologan/alert.sqlite
synoindex  8570         root  mem       REG               0,28                  7510 /volume1/@appstore/PhotoStation/usr/lib/libprotobuf-lite.so (path dev=0,30)
synoindex  8570         root  mem       REG               0,28                 30143 /volume1/@appstore/VideoStation/lib/libdtvrpc.so (path dev=0,30)
lsof       8585         root  txt       REG               0,30     147560      32161 /volume1/@entware-ng/opt/bin/lsof

Kill those daemons :

initctl list | grep synoindex

synoindexcheckindexbit stop/waiting
synoindexd start/running, process 11993

killall synoindexd

initctl list | grep synologan

synologand start/running, process 8368

killall synologand

This is not working… synologand  restart immediately ☹

chmod u-x /usr/syno/sbin/synologand

killall synologand 

killall s2s_daemon

Shrink the ext2 or ext4 Filesystem :

Only do the steps here under if using ext2 or ext4 instead of btfrs

Resize the File System :

umount -d /dev/vg1000/lv

e2fsck -C 0 -f /dev/vg1000/lv

e2fsck 1.42.6 (21-Sep-2012)
Pass 1: Checking inodes, blocks, and sizes
Pass 2: Checking directory structure
Pass 3: Checking directory connectivity
/lost+found not found. Create<y>? yes
Pass 4: Checking reference counts
Pass 5: Checking group summary information

1.42.6-23739: ***** FILE SYSTEM WAS MODIFIED *****
1.42.6-23739: 30742/889440 files (0.7% non-contiguous), 734048/3553280 blocks

NB. If you want to stop e2fsck : killall -USR2 e2fsck
NB. If you want to get a progress from e2fsck : killall -USR1 e2fsck

resize2fs -p -M /dev/vg1000/lv

resize2fs 1.42.6 (21-Sep-2012)
Resizing the filesystem on /dev/vg1000/lv to 702838 (4k) blocks.
The filesystem on /dev/vg1000/lv is now 702838 blocks long.

If you see the error message here under, you possibly have another file system than ext2 or ext4 (E.g.: btfrs, …):

resize2fs: Bad magic number in super-block while trying to open /dev/vg1000/lv
Couldn't find valid filesystem superblock.

If you have this error message although having ext2 or ext4, try: lvm lvchange –refresh /dev/vg1000/lv

Check the results :

mount /dev/vg1000/lv /volume1
df -h

Filesystem Size Used Avail Use% Mounted on
/dev/md0 2.3G 968M 1.3G 44% /
none 2.0G 0 2.0G 0% /dev
/tmp 2.0G 512K 2.0G 1% /tmp
/run 2.0G 3.0M 2.0G 1% /run
/dev/shm 2.0G 4.0K 2.0G 1% /dev/shm
none 4.0K 0 4.0K 0% /sys/fs/cgroup
cgmfs 100K 0 100K 0% /run/cgmanager/fs
/dev/vg1000/lv 2.6G 2.5G 0 100% /volume1

Resize the Logical Volume :

Resize the logical volume a bit larger than the file system (See the outcome of df -h above)

umount /dev/vg1000/lv
lvm lvreduce -L 2.7G /dev/vg1000/lv

Rounding size to boundary between physical extents: 2.70 GiB
WARNING: Reducing active logical volume to 2.70 GiB
THIS MAY DESTROY YOUR DATA (filesystem etc.)
Do you really want to reduce volume_1? [y/n]: y
Size of logical volume vg1/volume_1 changed from 13.55 GiB (3470 extents) to 2.70 GiB (692 extents).
Logical volume volume_1 successfully resized.

NB: to get a progress, use : LV=/dev/vg1000/lv; echo `lvdisplay -v $LV | grep current | wc -l` `lvdisplay -v $LV | grep stale | wc -l` | awk ‘{printf ( “%3d percent Complete \n”, 100-$2/$1*100) }’

Shrink a BTRFS File System :

Only do the steps here under if using btfrs

Resize the File System :

btrfs filesystem resize 2.7G /volume1

You can restore max size if required: btrfs filesystem resize max /volume1

df -h

Filesystem      Size  Used Avail Use% Mounted on
/dev/vg1000/lv  2.6G  2.5G  1.4G  71% /volume1

Resize the Logical Volume:

umount -d /dev/vg1000/lv

lvm lvreduce -L 2.7G /dev/vg1000/lv

 

Next steps :

The steps here under are both for ext2/ext4 and btfrs

Resize the Physical Volume :

Look for the device and if blocks must be moved:

pvdisplay -C

PV VG Fmt Attr PSize PFree
/dev/md2 vg1 lvm2 a-- 13.57g 10.85g

pvs -v –segments /dev/md2

    Using physical volume(s) on command line.
    Wiping cache of LVM-capable devices
  PV         VG     Fmt  Attr PSize  PFree   Start SSize LV   Start Type   PE Ranges
  /dev/md2   vg1000 lvm2 a--  14.00g 440.00m     0  3473 lv       0 linear /dev/md2:0-3472
  /dev/md2   vg1000 lvm2 a--  14.00g 440.00m  3473   110          0 free

If there is a bloc trailing after the “free” part (I had not), use:

lvm pvmove –alloc anywhere /dev/md2:xxx-xxx

 

Resize the device a bit larger than the logical volume. If you don’t use a sufficient size, you will get an error message:

pvresize –setphysicalvolumesize 2.7G /dev/md2

/dev/md2: cannot resize to 691 extents as 695 are allocated.
0 physical volume(s) resized / 1 physical volume(s) not resized

pvresize –setphysicalvolumesize 2.8G /dev/md2

Physical volume "/dev/md2" changed
1 physical volume(s) resized / 0 physical volume(s) not resized

 

Resize the array to use less disks:

Reduce the array to use 3 disks (-n3)

mdadm –grow -n3 /dev/md2

mdadm: this change will reduce the size of the array.
       use --grow --array-size first to truncate array.
       e.g. mdadm --grow /dev/md2 --array-size 7114624

You have first to reduce the array size.

mdadm –grow /dev/md2 –array-size 7114624

mdadm –grow -n3 /dev/md2 –backup-file /root/mdam.md2.backup &

 

Monitor the progress of the resizing with:

cat /proc/mdstat

Personalities : [linear] [raid0] [raid1] [raid10] [raid6] [raid5] [raid4] [raidF1]md2 : active raid5 sdak5[4] sdaj5[3] sdai5[2] sdah5[1] sdag5[0]7114624 blocks super 1.2 level 5, 64k chunk, algorithm 2 [3/3] [UUU][======>..............] reshape = 31.7% (1129600/3557312) finish=0.3min speed=112960K/sec

md1 : active raid1 sdak2[4] sdaj2[3] sdai2[2] sdah2[1] sdag2[0]2097088 blocks [12/5] [UUUUU_______]
md0 : active raid1 sdak1[4] sdaj1[3] sdag1[0] sdah1[1] sdai1[2]2490176 blocks [12/5] [UUUUU_______]
unused devices: <none>

This can take a lot of time, but you can continue (I did wait 😉 )

Finalize

pvresize /dev/md2

Physical volume "/dev/md2" changed
1 physical volume(s) resized / 0 physical volume(s) not resized

lvextend -l 100%FREE /dev/vg1000/lv

Size of logical volume vg1/volume_1 changed from 2.70 GiB (692 extents) to 4.07 GiB (1041 extents).
Logical volume volume_1 successfully resized.

for btrfs:

btrfs filesystem resize max /volume1

for ext2/ext4:

e2fsck -f /dev/vg1000/lv

e2fsck 1.42.6 (21-Sep-2012)
Pass 1: Checking inodes, blocks, and sizes

Running additional passes to resolve blocks claimed by more than one inode...
Pass 1B: Rescanning for multiply-claimed blocks
Multiply-claimed block(s) in inode 13: 9221
Pass 1C: Scanning directories for inodes with multiply-claimed blocks
Pass 1D: Reconciling multiply-claimed blocks
(There are 1 inodes containing multiply-claimed blocks.)

File /@tmp (inode #13, mod time Sat May 23 23:00:14 2020)
  has 1 multiply-claimed block(s), shared with 0 file(s):
Multiply-claimed blocks already reassigned or cloned.

Pass 2: Checking directory structure
Pass 3: Checking directory connectivity
Pass 4: Checking reference counts
Pass 5: Checking group summary information
1.42.6-23739: 30742/179520 files (0.7% non-contiguous), 685397/720896 blocks

Hope that no nodes are corrupted. Otherwise… well… accept to fix them.

resize2fs /dev/vg1000/lv

resize2fs 1.42.6 (21-Sep-2012)
Resizing the filesystem on /dev/vg1/volume_1 to 1065984 (4k) blocks.
The filesystem on /dev/vg1/volume_1 is now 1065984 blocks long.

mount /dev/vg1000/lv /volume1

Restart services:

/usr/syno/etc.defaults/rc.sysv/S80samba.sh start

/usr/syno/etc.defaults/rc.sysv/S83nfsd.sh start

/usr/syno/etc.defaults/rc.sysv/pgsql.sh start

/usr/syno/etc.defaults/rc.sysv/synomount.sh start

 

synopkg onoffall start

 

Remove the new  spare disks from the volume

mdadm –detail –scan

ARRAY /dev/md0 metadata=0.90 UUID=3b122d95:7efea8ff:3017a5a8:c86610be

ARRAY /dev/md1 metadata=0.90 UUID=bd288153:d00708bf:3017a5a8:c86610be

ARRAY /dev/md2 metadata=1.2 spares=2 name=DS3617_62:2 UUID=875ad2d6:956306b7:8c7ba96b:4287f6e6

mdadm –detail /dev/md2

/dev/md2:
        Version : 1.2
  Creation Time : Sat May 23 14:00:02 2020
     Raid Level : raid5
     Array Size : 7114624 (6.79 GiB 7.29 GB)
  Used Dev Size : 3557312 (3.39 GiB 3.64 GB)
   Raid Devices : 3
  Total Devices : 5
    Persistence : Superblock is persistent

    Update Time : Sat May 23 18:54:30 2020
          State : clean
 Active Devices : 3
Working Devices : 5
 Failed Devices : 0
  Spare Devices : 2

         Layout : left-symmetric
     Chunk Size : 64K

           Name : DS3617_62:2  (local to host DS3617_62)
           UUID : 875ad2d6:956306b7:8c7ba96b:4287f6e6
         Events : 56

    Number   Major   Minor   RaidDevice State
       0       8        5        0      active sync   /dev/sda5
       1       8       37        1      active sync   /dev/sdc5
       2       8       53        2      active sync   /dev/sdd5
       3       8       69        -      spare   /dev/sde5
       4       8       85        -      spare   /dev/sdf5

Here above, we see that sde5 and sdf5 are unused

 

mdadm –fail /dev/md2 /dev/sde5

mdadm: set /dev/sde5 faulty in /dev/md2

mdadm –fail /dev/md2 /dev/sdf5

mdadm: set /dev/sdf5 faulty in /dev/md2

mdadm –remove /dev/md2 /dev/sde5

mdadm: hot removed /dev/sde5 from /dev/md2

mdadm –remove /dev/md2 /dev/sdf5

mdadm: hot removed /dev/sdf5 from /dev/md2

 

Et voilà.

DS3617xs is a model where SHR is not enabled:

To enable it:

1. Open a SSH console and enter root mode.
2. Edit the file  /etc.defaults/synoinfo.conf
3. At the end, you should find: supportraidgroup=”yes”
4. Comment that line with a #
5. Next to it, add a new line with: support_syno_hybrid_raid=”yes”
6. Reboot your Synology

You can use “vi” to edit the file: sudo vi /etc.defaults/synoinfo.conf,

• Press i or the insert key to make your modifications, then “Esc” to end the modifications.
• After that type :x! to save and exit. Ot :q! to exit without saving.

Et voilà, your DS3617xs offers now the option for SHR

This list is now reduced to the minimum as I use the following search engine for third-party packages to Synology’s DSM : https://search.synopackage.com/home

Here are the servers not referenced by the search engine:

• http://www.pulse-station.com/repo/
• …

 

First, open a SSH console on your Synology and enter the root (See here)

Notice that you cannot change the config file of nginx (/etc/nginx/nginx.conf). Even if you do so, your changes will be removed automatically. But in the config file of nginx, for the server listening on the port of your WebStation (port 80 by default), you can see it is loading extra config named www.*.conf under the folder /usr/syno/share/nginx/conf.d/

include /usr/syno/share/nginx/conf.d/www.*.conf;

So, go to that folder : cd /usr/syno/share/nginx/conf.d

There, create a password file with your login and password

Type : htpasswd -c -b .htpasswd YourLogin YourPassword

the parameter -c is to create the file. Only use it if the file does not yet exist otherwise you will clean its current content!!

Look at the content if the file: cat .htpasswd

It should be similar to this: 

YourLogin:$apr3$hUZ87.Mo$WUHtZHjtPWbBCD4jezDh72

Now, create and edit a file name like : www.protected.conf (Ex.: using vi)

Assuming that you want to protect a subfolder You/Sub/Folder existing in the root of your WebStation, you should theoretically this into www.protected.conf :

location /Your/Sub/Folder {
auth_basic “Any Prompt Message You Want”;
auth_basic_user_file /usr/syno/share/nginx/conf.d/.htpasswd;
}

Next, you have to restart nginx with the command : nginx -s reload

Or even better to be 100% sure: synoservicecfg –restart nginx

 

But for some reason, this is not working on Synology (at least on mine ?!). It seems that the block location does not work without a modifier like = or ~

It searched for hours why it was not working, without answer. 

For example, I tested first that the following webpage was working fine on my NAS: http://MyNas/SubFolder/index.php

Next, I edited the www.protected.conf with the following block before restarting nginx, deleting the cache ofh my browser and restarting my browser (THIS IS MANDATORY each time one changes the location):

location /SubFolder/index.php {
return 301 https://www.google.be/search;
}

But opening http://MyNas/SubFolder/index.php didn’t return me to Google.

Next, I tried with :

location = /SubFolder/index.php {
return 301 https://www.google.be/search;
}

And this was working! So, I thought that the path used as location was possibly was incorrect. To see the path capture as location I tried next with 

location ~ (/SubFolder/index.php) {
return 301 http://Fake$1;
}

Opening now http://MyNas/SubFolder/index.php, I got the (unvailable) page  http://Fake/SubFolder/index.php

So, the path /SubFolder/index.php was definitively correct. 

I think that my directive is included before another one which overwrite it. Possibly this one, found in /etc/nginx.nginx.conf:

location / {
rewrite ^ / redirect;
}

So, I have no choice but use the modifier = (exact match) or ~ (matching a regular expression). Unfortunately, doing so, another problem arise… the php pages are not reachable anymore 🙁

If you look at the log file of nginx: cat /var/log/nginx/error.log

You see:

2019/11/30 21:22:12 [error] 25657#25657: *50 open() “/etc/nginx/html/SubFolder/index.php” failed (2: No such file or directory), client: 192.168.0.1, server: _, request: “GET /SubFolder/index.php HTTP/1.1”, host: “MyNas”

This is because nginx is using its default root folder /etc/nginx/html/ instead of inheriting the one define for the WebStation.

The solution is to simply specify the root in the location block : root /var/services/web;

But now, instead of being executed, the php script is downloaded.. Harg !

The following location works, by redefining the execution of the php page:

location = /SubFolder/index.php {
  root /var/services/web;

  try_files $uri /index.php =404;
  fastcgi_pass unix:/var/run/php-fpm/php73-fpm.sock;
  fastcgi_index index.php;
  include fastcgi.conf;
}

Pay attention, corrupting the config of nginx will make you DSM unable to run anymore ! Always check that your config is correct with the command : nginx -t

 

Ok, now, to handle both folders and php pages, one can use this variant of the location above:

location ~ /SubFolder/ {
  root /var/services/web;

  location ~ \.php$ {
    try_files $uri /index.php =404;
    fastcgi_pass unix:/var/run/php-fpm/php73-fpm.sock;
    fastcgi_index index.php;
    include fastcgi.conf;
  }
}

In the sub-location above, use php73-fpm.sock, php70-fpm.sock, php50-fpm.sock, etc… according to the version of php used by default with your nginx in your WebStation !

This is more or less working fine… I still have issues as some server variables are not passed to the php pages… But it’s working enough for my purpose. We are now only missing the basic authentication !!! Here is the final location block:

location ~ /You/Sub/Folder/ {
  root /var/services/web;

  location ~ \.php$ {
    try_files $uri /index.php =404;
    fastcgi_pass unix:/var/run/php-fpm/php73-fpm.sock;
    fastcgi_index index.php;
    include fastcgi.conf;
  }

  auth_basic “Any Prompt Message You Want”;
  auth_basic_user_file /usr/syno/share/nginx/conf.d/.htpasswd;

}

Once in place, nginx restarted, your browser cleaned and restarted too, you finally got the prompt for your login and password.

If you type a wrong login or password, you could see the error in the nginx log file: cat /var/log/nginx/error.log

2019/11/30 17:51:47 [error] 12258#12258: *145 user “mystery” was not found in “/usr/syno/share/nginx/conf.d/.htpasswd”, client: 192.168.0.1, server: _, request: “GET /err/You/Sub/Folder/ HTTP/1.1”, host: “MyNas”

2019/11/30 17:59:52 [error] 20130#20130: *3 user “mystery”: password mismatch, client: 192.168.0.1, server: _, request: “GET /You/Sub/Folder/ HTTP/1.1”, host: “MyNas”

Et voilà… Not perfect, not clear why it’s not wokring out of the box as documented here… But