Update documentation

4 files changed, 72 insertions, 4 deletions

diff --git a/issues/database-not-responding.gmi b/issues/database-not-responding.gmi
index 8928d08..8cb5656 100644
--- a/issues/database-not-responding.gmi
+++ b/issues/database-not-responding.gmi
@@ -294,6 +294,49 @@ MariaDB [db_webqtl]> SHOW VARIABLES LIKE '%timeout%';
 
 If you set wait_timeout and interactive_timeout values they get reset after a while.
 
+# Recent crash
+
+```
+| Max_used_connections                          | 1030   |
+| Threads_connected                             | 1030   |
+
+show open tables where in_use > 1;
+
++-----------+----------------+--------+-------------+
+| Database  | Table          | In_use | Name_locked |
++-----------+----------------+--------+-------------+
+| db_webqtl | ProbeFreeze    |    182 |           0 |
+| db_webqtl | ProbeSet       |      3 |           0 |
+| db_webqtl | ProbeSetXRef   |      3 |           0 |
+| db_webqtl | PublishFreeze  |      7 |           0 |
+| db_webqtl | Species        |     94 |           0 |
+| db_webqtl | Tissue         |     94 |           0 |
+| db_webqtl | ProbeSetFreeze |      3 |           0 |
+| db_webqtl | InbredSet      |    108 |           0 |
+| db_webqtl | GenoFreeze     |      7 |           0 |
++-----------+----------------+--------+-------------+
+```
+
+```
+FLUSH NO_WRITE_TO_BINLOG TABLES
+
+Waiting for table flush SELECT confidentiality, AuthorisedUsers FROM ProbeSetFreeze WHERE Name = 'EL_BXDCDScWAT_0216' 0.000
+
+Waiting for table flush SELECT DISTINCT Tissue.Name FROM ProbeFreeze,ProbeSetFreeze, InbredSet, Tissue, Species WHERE Speci  0.000
+```
+
+Another one to check next time is
+
+```
+SHOW ENGINE INNODB STATUS
+```
+
+and
+
+```
+mariabackup --backup --kill-long-query-type=SELECT --kill-long-queries-timeout=120
+```
+
 # Monitor connections
 
 Use the general log as described in
diff --git a/issues/systems/octopus.gmi b/issues/systems/octopus.gmi
index 1420865..bc421eb 100644
--- a/issues/systems/octopus.gmi
+++ b/issues/systems/octopus.gmi
@@ -26,3 +26,14 @@ default via 172.23.16.1 dev ens1f0np0
 172.23.16.0/21 dev eno1 proto kernel scope link src 172.23.18.68
 172.23.16.0/21 dev eno2 proto kernel scope link src 172.23.17.134
 ```
+
+# Current topology
+
+```
+ip a
+ip route
+```
+
+- Octopus01 uses eno1 172.23.18.188/21 gateway 172.23.16.1 (eno1: Link is up at 1000 Mbps)
+- Octopus02 uses eno1 172.23.17.63/21  gateway 172.23.16.1 (eno1: Link is up at 1000 Mbps)
+                      172.23.x.x
diff --git a/topics/octopus/lizardfs/README.gmi b/topics/octopus/lizardfs/README.gmi
index ef8d1aa..078a628 100644
--- a/topics/octopus/lizardfs/README.gmi
+++ b/topics/octopus/lizardfs/README.gmi
@@ -1,6 +1,6 @@
 # Information about lizardfs, and some usage suggestions
 
-On the octopus cluster the lizardfs head node is on octopus01, with disks being added mainly from the other nodes. SSDs are added to the lizardfs-chunkserver.service systemd service and HDDs added to the lizardfs-chunkserver-hdd.service. The storage pool is available on all nodes at /lizardfs, with the default storage option of "slow", which corresponds to two copies of the data, both on HDDs.
+On the octopus cluster the lizardfs head node is on octopus01, with disks being added mainly from the other nodes. SSDs are added to the lizardfs-chunkserver.service systemd service and SDDs added to the lizardfs-chunkserver-hdd.service. The storage pool is available on all nodes at /lizardfs, with the default storage option of "slow", which corresponds to two copies of the data, both on SDDs.
 
 ## Interacting with lizardfs
 
@@ -71,11 +71,12 @@ Chunks deletion state:
         slow    68      15      2081    27598   201022  20      -       -       -       -       -
         fast    12603   720     1880    5377    23902   -       -       -       -       -       -
         2ssd    7984    -       -       -       -       -       -       -       -       -       -
-
 ```
 
 To query how the individual disks are filling up and if there are any errors:
 
+List all disks
+
 ```
 lizardfs-admin list-disks octopus01 9421 | less
 ```
@@ -103,7 +104,7 @@ It should be noted that any goal using erasure_coding is incredibly slow to writ
 ```
 # CHUNKS_SOFT_DEL_LIMIT = 100
 # CHUNKS_HARD_DEL_LIMIT = 250
-# CHUNKS_WRITE_REP_LIMIT = 20 
+# CHUNKS_WRITE_REP_LIMIT = 20
 # CHUNKS_READ_REP_LIMIT = 100
 ```
 
diff --git a/topics/systems/shepherd.gmi b/topics/systems/shepherd.gmi
index d67d9d6..9cf1ed4 100644
--- a/topics/systems/shepherd.gmi
+++ b/topics/systems/shepherd.gmi
@@ -8,6 +8,14 @@
 * status: wip
 * priority: unclear
 
+## Quick overview
+
+Shepherd runs in systemd as a shepherd user
+
+```
+systemctl status user-shepherd.service
+```
+
 ## Description
 
 On Debian based systems we run shepherd as a shepherd user. The service gets started up through systemd.
@@ -17,9 +25,11 @@ repository.
 
 The process for deploying the services:
 
+```
 symlink shepherd-services/shepherd to $HOME/.config/shepherd
 symlink shepherd-services/cron to $home/.config/cron
 symlink shepherd-services/*sh to $HOME
+```
 
 When shepherd starts up it should start all the services. So currently
 that's bnw, gitea, ipfs, power, rn6app, singlecell and the mcron
@@ -28,7 +38,10 @@ services, gitea-dump and pubmed.
 To use shepherd's herd command the command is 'sudo -u shepherd
 /home/shepherd/.guix-profile/bin/herd status'.
 
-: /home/shepherd/.guix-profile/bin/herd status
+```
+su shepherd
+/home/shepherd/.guix-profile/bin/herd status
+```
 
 Adding a bash alias, such as "alias herd-herd='sudo -u shepherd
 /home/shepherd/.guix-profile/bin/herd'", will make it easier to