While updating our network on the Rocks Cluster, the nodes had to reinstall (this is default protocol). Now however the nodes got stuck during PXE (over the net automatic installation) on the setting of the language.

This is annoying as it would mean connect a screen and a keyboard to every node to install. This however is an indication that something is wrong all together, however finding what proved a little bit tricky, that’s why I share it here.

To find if you face the same issue, execute :

sudo -u apache /opt/rocks/bin/rocks list host profile compute-0-0

This will show the configuration the node pulled from the head-node.  In my case it looked like :

Traceback (most recent call last):
  File "/opt/rocks/bin/rocks", line 301, in <module>
    command.runWrapper(name, args[i:])
  File 
"/opt/rocks/lib/python2.6/site-packages/rocks/commands/__init__.py", 
line 2194, in runWrapper
    self.run(self._params, self._args)
  File 
"/opt/rocks/lib/python2.6/site-packages/rocks/commands/list/host/profile/__init__.py", 
line 301, in run
    for host in self.getHostnames(args):
  File 
"/opt/rocks/lib/python2.6/site-packages/rocks/commands/__init__.py", 
line 773, in getHostnames
    min,max = self.db.fetchone()
TypeError: 'NoneType' object is not iterable

While this should be a large XML file structure like. After allot of extensive google skills (and this 2013 topic) I found out that a simple MySQL update had dropped the root password out of the global configuration, this can be found :

/opt/rocks/etc/my.cnf

a update, generally saves it here :

/opt/rocks/etc/my.cnf.rpmsave

it should look like this :

[mysqld]
user            = rocksdb
port            = 40000
socket          = /var/opt/rocks/mysql/mysql.sock
datadir         = /var/opt/rocks/mysql

[client]
user            = rocksdb
port            = 40000
socket          = /var/opt/rocks/mysql/mysql.sock
password        = <password>

You don’t have to restart the MySQL or the service, just let the node reboot and it will install properly 🙂

Good luck

Rocks distro is a cluster system. It comes with SNMP configured out of the box. It is polled using Ganglia. Which is working nicely, but I like to have all SNMP data in my favorite SNMP system, LibreNMS. Changing the SNMP configuration to be able to poll from LibreNMS should be a rather straight forward process, however those nodes have no connection to the public network. They have a private VLAN to talk to the head-node and a private VLAN to communicate with the storage array. So to get the SNMP data to Librenms we will have to get crafty with Iptables to get this data to LibreNMS on the public net.

Configuration

First let’s check the /etc/snmp/snmpd.conf file from the Rocks installation :

com2sec        notConfigUser   default         public
group  notConfigGroup  v1              notConfigUser
group  notConfigGroup  v2c             notConfigUser
view    all             included        .1             80

access  notConfigGroup  "" any noauth exact all all all

This config is a bit complex and I figure I won’t go back, so I commented it. I decided not to remove it completely, since I don’t want to break the possibility to go back to Ganglia should it be an important system in Rocks. (note : it’s not) I added :

# this create a  SNMPv1/SNMPv2c community named "my_servers"
# and restricts access to LAN adresses 192.168.0.0/16 (last two 0's are ranges)
rocommunity my_servers <our_public_net>/16
rocommunity my_servers 10.1.0.0/16

# setup info
syscontact  "svennD"

# open up
agentAddress  udp:161

# run as
agentuser  root

# dont log connection from UDP:
dontLogTCPWrappersConnects yes

Important here is, that I added two IP ranges, I’m not sure if the private VLAN (10.1.0.0/16) is even required, but since traffic is going over those devices I just added it.

Next thing is setting up the Iptables on the head-node. Since Rocks is already pretty protective (good !) I had to add an extra rule to even allow SNMP polling from the device :

-A INPUT -p udp -m udp --dport 161 -j ACCEPT

Allow the head-node to be polled by LibreNMS by accepting incoming UDP packets over port 161.

To receive packets send from the node on port 161 to the head-node, but forward this to port 3161 externally to LibreNMS (circumventing most known ports and the REJECT rule in Rocks for port 1-1023.) can be done with prerouting rule :

-A PREROUTING -i eth1 -p udp -m udp --dport 3161 -j DNAT --to-destination 10.1.255.244:161
-A POSTROUTING -o eth1 -j MASQUERADE

Note : 10.1.255.244 is the private IP of the node.

So from now on packets should come in, this can be checked using tcpdump, which came in handy during the debugging of this project : (on the node)

tcpdump 'port 161'

To be able to let snmpd answer we needed the information to be forwarded on the head-node, this can be done with a forward rule :

-A FORWARD -d 10.1.255.244/32 -p udp -m udp --dport 161 -m state --state NEW,RELATED,ESTABLISHED -j

note : again 10.1.255.244 is the ip of the node.

Surprisingly the node was unable to answer to the incoming requests. This was due to the fact that, the default route (route -n) was pointing towards one of the storage servers. To add a default gateway we can add it using route :

route add default gw 10.1.1.1 eth0

note : 10.1.1.1 is the private VLAN ip of the head-node.

Conclusion

Bam! LibreNMS can talk to the node using the public IP of the head-node on port 3161 and to the head-node on port 161. One issue that remains unsolved is on reboot, this setup is lost. Rocks by default will reinstall nodes that reboot. This can be resolved by adapting the configurations on Rocks and rebuild the distribution (rocks create distro). However this is rather advanced and (IMHO) difficult to debug. So I did not use that system for this project. Another problem is that its rather work-intense to add all the configuration to all the nodes. (this is only for a single node) This can be resolved most easily using scripts and using rocks run host to execute bits on all the nodes. I decided that I only want one node to be polled as a sample. I already track opengridscheduler using an extend on the head-node. So this is mostly for debugging. Good luck !

Oh noes, while starting a container, it failed cause of a corrupt quota file…

Starting container ...
vzquota : (error) quota file is corrupted
vzquota on failed [4]
TASK ERROR: command 'vzctl start 114' failed: exit code 60

The fix is to remove it and rebuild it (this takes a long time, depending on the size of the container)

# this failed
vzquota off 114

# delete the quota
quota drop 114

We can rebuild the quota using vzquota but that is done automatically if you restart the container :

# vzctl start 114
Starting container ...
Initializing quota ...

The vzquota currently running is : (for reference)

/usr/sbin/vzquota init 114 -b 8388608100 -B 9227468900 -i 1600000100 -I 1760000100 -p /data/private/114 -e 0 -n 0 -s 0

Sit back and relax, cause this will take time.

Got this error :

mount.nfs: rpc.statd is not running but is required for remote locking.
mount.nfs: Either use '-o nolock' to keep locks local, or start statd.
mount.nfs: an incorrect mount option was specified

You forgot the rpcbind service !

yum install rpcbind
service rpcbind start
chkconfig rpcbind on

Glad to help 😉

In order to increase the size of files you can upload in WordPress, we need to adapt the software powering the software.

Let’s begin with PHP, I use Nginx + php-fpm to run PHP, so I need to edit

/etc/php.ini

on line 799, upload_max_filesize determines the maximum allowed size a PHP file will accept for upload.

upload_max_filesize = 2M

This should not be to big, but a few megabytes will work just fine. I increased this to 10M (~10MB)

After that its time to update Nginx to allow larger upload body’s, this I already had an error documented in the past. So in short :

/etc/nginx/nginx.conf

add after the

http {

# increase upload size to 10MB
client_max_body_size 10M;

Once that is done, just restart Nginx and php-fpm.

systemctl restart nginx
systemctl restart php-fpm

And voila

Some powerful and or useful find commands; As with anything on the web, test before running ! (I forget the syntax so this is mainly self-documenting)

 

 

Find all *.tsv larger 1Mb, compress them with the super fast lz4 on high compression and remove the source file after this.

find . -name "*.tsv" -size +1M -exec lz4 -9 --rm '{}' \;

In the same line; compress all files ending with *.fastq and gzip them, also they cannot end with *.gz (in this case redundant but its an extra safety)

find . -type f -name "*.fastq" ! -name '*.gz' -exec gzip "{}" \;

 

Recursive remove all directory’s matching the name *.tsv.index in a rm or echo single command. This makes it possible to easily swap out rm for echo as a test.

find . -type d -name "*.tsv.index" -exec echo {} +
find . -type d -name "*.tsv.index" -exec rm -rf {} +

A combination of a few commands, calculate the storage use from all files size larger then 1M, with no hardlinks, ending with *.tsv.

find . -name "*.tsv" -size +1M -links 1 -print0 | du -hc | tail -n 1

(edit: might not work as intended)

find . -name "log_jobs" -exec du -hc {} +

 

Find files, that are newer then 5 minutes :

find . -type f -mmin -5

and older :

find . -type f -mmin +5

Hard links are nice, but also a (enter curse-word) to track, luckily we have find to locate it :

find /data -samefile file.txt -xdev

This would find all the files that are exactly the same as file.txt (so only hard links, no soft links or copy’s) considering hard links can only be in one file system its logical to add -xdev which tells find not to enter other file-systems since hard links can not be across file-systems. If you are also looking for soft links remove -xdev and add -L

Generate a md5sum for every file in this current directory except files “mylog.log” and “md5.lst”.

find . -type f ! -name "mylog.log" ! -name "md5.lst" -exec md5sum "{}" + > md5.lst

 

A quick and dirty way to find directories (=experiments) that have been made in the last 90 days, sorted on date (removing hard linked .save dirs) This is a sort.

find . -maxdepth 1 -name "*_machine_ID_*" -type d -ctime -90 | grep -v .save | sort -t_ -k 2

 

Ignore certain files, can be done using ! -name “*file” for example. This finds all directories starting with 17, and not ending with .save (hard link for us) and shows the size of those directories.

find . -maxdepth 1 -name "17*" ! -name "*.save" -type d -exec du -hs '{}' +