Notes about open source software, computers, other stuff.

Tag: sysadmin (Page 3 of 5)

Fixing problems after giving your Samba server a new IP address

While moving my DHCP server to a Raspberry Pi I also changed some of the IPs handed out to my (virtual) servers. This lead to problems when I logged into Windows (which is tied to my Samba domain), Windows complained that my roaming profile wasn’t completely synced and browsing network shares didn’t work, copying from (mounted) network shares didn’t work, etc.

In the Samba log files I noticed some references to the old IP address (192.168.10.23), e.g.:

[2014/03/13 16:22:23,  0] nmbd/nmbd_become_dmb.c:237(become_domain_master_query_success)
  become_domain_master_query_success:
  There is already a domain master browser at IP 192.168.10.23 for workgroup SENW registered on subnet UNICAST_SUBNET.

and

  [2014/03/13 16:20:07,  0] nmbd/nmbd_browsesync.c:248(domain_master_node_status_fail)
  domain_master_node_status_fail:
  Doing a node status request to the domain master browser
  for workgroup SENW at IP 192.168.10.23 failed.
  Cannot sync browser lists.

Even after restarting smbd and nmbd, and checking my smb.conf thoroughly, these kept showing up.

It turns out (thanks a lot Matt Godbolt) that nmbd keeps caches in two files (paths as they are on my Ubuntu 12.04 server):

  • /var/cache/samba/browse.dat
  • /var/lib/samba/wins.dat

Simply stop nmbd, delete them, restart nmbd and you’re happy.

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Slackware on the Raspberry Pi

I took some time this week to migrate my DNs and DCHP server from an Ubuntu virtual machine to my Raspberry Pi. I wanted to do this because these two servers are so essential to regular network functioning. Before this change whenever my server was down (for whatever reason) any machine connected to the LAN would stop having a working internet connection. Moreover, since I never got the VM to boot correctly on autostart I had to manually start it every time the server came back up again.
Conclusion: not ideal and pissed of family members ;-).

Since I had my Raspberry Pi lying around and, apart from a few toy projects, hadn’t used it for anything, I decided to use it for this task: low power requirements and hardware that was more than up to the task.

The question was which distribution to use. I could have gone for Raspbian (Debian for the Raspberry Pi), which would have blended well with my otherwise Ubuntu-minded network. However, partly for nostalgic reasons, partly make sure I don’t get too tied to one distribution, I decided to try and install Slackware, the distribution I used for my first steps in Linux Land.

I followed most of the steps from the fatdog.eu tutorial (see link below) to get everything running. It’s a very well written, extensive tutorial. Things where I followed my own judgement/experience were the fact that I didn’t use a USB stick to download the Slackware packages on (I used an NFS share on my server) and the package selection. With a relatively simple selection I now have about 2GB of disk usage.

Only one thing left to migrate to the Pi now: my LDAP server. Unfortunately it’s been several years since I configured OpenLDAP (on Ubuntu) and Slackware doesn’t include the OpenLDAP server by default. So this will be something for a rainy day…

Links:

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Puppet commands change when upgrading to v3.0.0

After upgrading Puppet from versions < v3 to version 3.0.0 or higher, the main commands have changed, keep this in mind when reading my earlier post. From the ChangeLog:

Pre-2.6 Post-2.6
puppetmasterd puppet master
puppetd puppet agent
puppet puppet apply
puppetca puppet cert
ralsh puppet resource
puppetrun puppet kick
puppetqd puppet queue
filebucket puppet filebucket
puppetdoc puppet doc
pi puppet describe

Some examples

To run puppet on a client puppetd --test is changed to:

puppet agent --test

To show a list of clients waiting for signing of their certificates run the following on the master:

puppet cert list

instead of puppet ca -l. To list all certificates, run (on the master):

puppet cert list --all

To completely remove a client’s certificate on the master run:

puppet cert clean client.localdomain

and to sign a client certificate on the master run:

puppet cert sign client.localdomain

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Replacing a character in a Bash variable name

Today I needed to replace a : in a bunch of file names with a -, so I wanted to write a Bash for-loop to do just that. I vaguely remembered that you can do character replacements within variables, but couldn’t remember the details.

This is how it’s done:

for filename in *; do
    mv "$filename" "${filename/:/-}"
done

I put the variables in double quotes, because the file names contained spaces.

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Showing other users (from LDAP) in the LightDM greeter

Ubuntu Linux uses the LightDM greeter (the login screen you see after booting). Since I’m using an LDAP server to store my user accounts and LightDM by default only shows local users I needed to tell LightDM to give me an ‘other user’ option where I can enter a user name and password (I first checked to see if my LDAP connection work by logging in with an LDAP user from the console (tty1).
LightDM is configured in /etc/lightdm/lightdm.conf, but also provides command line tools to set the options. To show the ‘other user’ use:

sudo /usr/lib/lightdm/lightdm-set-defaults --show-manual-login true

This will disable the user list. It adds the line

greeter-show-manual-login=true

to the lightdm.conf file.
If you only want to see the “Other” entry run:

sudo /usr/lib/lightdm/lightdm-set-defaults --hide-users true

And lastly you can turn off guest:

sudo /usr/lib/lightdm/lightdm-set-defaults --allow-guest false

Thanks to mfish at askubuntu.com!

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Growing XFS and still not able to write files, enough free space

One of the XFS filesystems at work almost ran out of space recently, so I extended the Logical Volume it was on, followed by xfs_growfs. This worked fine, df -h showed enough free space for the upcoming data. In the XFS FAQ I read that by default all inodes are placed in the first 1 TB of disk, which could lead to problem. Therefore, I added the inode64 option to the mount options and ran

mount -o remount

on the partition.

While reviewing my log messages this morning I noticed a lot of

No space left on device

messages for that filesystem. Having this inode64 option in mind I wondered what went wrong. Although df -h and df -i showed enough free space and free inodes, respectively, I still couldn’t create a file. Again the XFS FAQ had an entry for that, but it puzzled me, because I was already using the inode64 option. Since the filesystem wasn’t in use I decided to completely unmount it and then mount it again. That worked. Apparently -o remount is not enough to enable the inode64 option.

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Setting up (or fixing) an encrypted swap partition

Today I tried to clone my laptop’s harddrive to a new drive (thanks to Lenovo for sending me a replacement since the old drive was showing signs of breaking down). At first I tried dd, but that failed at around 90%, either because the old disk is indeed failing or because something fishy with the USB connection or enclosure in which I put the new disk. So I started gparted to check which partitions were copied OK and which weren’t. It turns out that all partitions were fine, except for my (encrypted) swap partition. gparted didn’t even recognise the partition type (on the original drive!). So after I replaced the harddrive I wanted to recreate the encrypted swap partition. It turn’s out to be easy if you follow the steps outlined in this blog post from Puny Geek. Thanks Puny Geek!

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Speeding up grep when looking in large files

In my line of work it is not uncommon to have to find out whether a given term is present in a long list. Say, for example you need to look up whether a set of, say 10, SNPs is present in a (possibly annotated) list of SNPs present on a genotyping array (having for example 240k SNPs).
My first instinct in such cases is to use grep, and it’s a good instinct that has served me well over the years.

Recently we had a case that involved quite some larger files. We needed to see whether a set of genomic positions was present in a genome-wide list of such positions. Of course we split the files up per chromosome, but still this took ~ 24 hours for a chromosome when using

grep -w -f short_list long_file > results

I was convinced this could be done faster and googled a bit, read the grep man page to find out that the -F option of grep ensures that the search string is not seen as a (regexp) pattern, but as fixed. This meant an enormous speed improvement. Instead of having to wait for 24 hours we got the output in under a minute!

I did a quick performance comparison: looking up ten items in a ~415MB file with 247,871 rows and 136 columns took ~2 minutes, 3 seconds with out -F and less than a second with the -F option:

$ time grep -w -f shortlist.txt largefile.tsv > out_withoutF
 
real    2m3.181s
user    2m0.780s
sys     0m2.196s
$ time grep -wF -f shortlist.txt largefile.tsv > out_withF
 
real    0m0.568s
user    0m0.500s
sys     0m0.060s

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Fixing the NFS check plugin in Nagios (in Ubuntu)

For some time (probably after an upgrade, I actually don’t remember anymore) we had problems with the NFS check in Nagios on our Ubuntu 12.04 servers. The check would return UNKNOWN: RPC program nfs udp is not running. When running the actual check from the command line:

/usr/lib/nagios/plugins/check_rpc -H '$HOSTADDRESS$' -C nfs -c2,3

the output would be: Can't fork for rpcinfo.
It turns out that the file /usr/lib/nagios/plugins/utils.pm has the wrong path to the rpcinfo binary. Instead of /usr/sbin/rpcinfo it lists /usr/bin/rpcinfo. So, like most of the times, the fix is easy, but pinpointing the exact problem isn’t.

Don’t forget to restart Nagios after changing the path as utils.pm needs to be reloaded.

As Ubuntu is based on Debian, I expect this fix to work there as well. According to this Launchpad bug report this issue was fixed in January in version 1.4.16-1ubuntu1 of the nagios-plugins package, which is not in Ubuntu 12.04.

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Importing a git repo into another one (keeping all history)

Today I wanted to create a new git repository that should contain several subdirectories that each were initially stored as separate git repos. Of course I didn’t want to lose the history. Thanks to user ebneter‘s answer at StackOverflow I was able to do so. These are the steps I took:

mkdir new_combined_repo
git init                           # Make empty new 'container' repo (no need to create a subdir at this point yet)
git remote add oldrepo /path/to/oldrepo
git fetch oldrepo
git checkout -b olddir oldrepo/master
mkdir olddir
git mv stuff olddir/stuff          # as necessary
git commit -m "Moved stuff to olddir"
git checkout master                
git merge olddir                   # should add olddir/ to master
git commit
git remote rm oldrepo
git branch -d olddir               # to get rid of the extra branch before pushing
git push                           # if you have a remote, that is

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