Notes about open source software, computers, other stuff.

Tag: nfs

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/ 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 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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Comparing rsnapshot and obnam for scheduled large backups


The home directories of the servers I administer at work total about 6.5TB of data. The home directories are stored on a file server (using ext4 partitions) and served to the other server over NFSv3 with a bonded 1Gbps LAN link.

As you all know backups are a good idea but how to implement a backup strategy for this kind of data? We decided quite early that using tapes as backup medium was out of the question. We simply can’t afford them given the amount of disk space we need. Moreover, tapes usually require operator involvement and neither me nor my colleague feels like going to the data centre every week. Our idea was to back up to another server with enough disk space in a different part of the data centre. For off-site backups we can always make an annual (maybe monthly) backup either on tape at SurfSARA/BigGrid or on a remote server.

Before implementing a given strategy several things need to be known and tested. The major questions we wanted to have an answer to were:

  1. How often do we want to backup the data? Daily snapshots? Weekly? Monthly?
  2. How many of the backups mentioned above do we want to keep? And for how long?
  3. In order to answer these questions (given a roughly fixed amount of backup space) we need to know
    • How much data changes per night/week/etc.
    • How much duplication is there in the data? How many people store the same file (or blocks, if you go for block-level deduplication)?
  4. Is NFS/network speed a limiting factor when running the backups?
  5. Can the tool preserve additional file system attributes like POSIX ACLS?


After looking around the web and looking back at my own experiences I came up with three possible candidates. Each of them allows for backup rotation and preserves Posix ACLs (so points 1 and 5 above have been taken care of).

  1. Bacula: enterprise-level backup application that I’ve used in combination with tapes in the past. Easily supports multiple clients, tape robots, etc. No deduplication. All metadata etc. are stored in a (MySQL) database, so restoring takes some effort (and don’t forget to make a backup of the database as well!).
  2. rsnapshot: based on rsync, makes snapshots using hard links. Easy to restore, because files are simply copied to the backup medium.
  3. rdiff-backup: similar to rsnapshot, but doesn’t allow for removal of intermediate backups after a given time interval. Consequently it was the first candidate to fall of my list.
  4. Obnam: a young tool that promises block level data deduplication. Stores backed up data in its own file format. Tools for browsing those archives are not really well developed yet.


Because I already had quite some experience with Bacula but none with the other two candidates (although I use rsync a lot) I decided to start a test run with Obnam, followed by a run with rsnapshot. These are the results:


After backing up /home completely (which took several days!), a new run, several days later took (timing by the Linux time command):

Backed up 3443706 files, uploaded 94.0 GiB in 127h48m49s at 214.2 KiB/s average speed830 files; 1.24 GiB (0 B/s)

real    7668m56.628s
user    4767m16.132s
sys     162m48.739s

From the obname log file:

2012-11-17 12:41:34 INFO VFS: baseurl=/home read=0 written=0
2012-11-21 23:09:36 INFO VFS: baseurl=/backups/backup_home read=2727031576964 written=150015706142
2012-11-21 23:09:36 INFO Backup performance statistics:
2012-11-21 23:09:36 INFO * files found: 3443706
2012-11-21 23:09:36 INFO * uploaded data: 100915247663 bytes (93.9846482715 GiB)
2012-11-21 23:09:36 INFO * duration: 460128.627629 s
2012-11-21 23:09:36 INFO * average speed: 214.179341663 KiB/s
2012-11-21 23:09:36 INFO Backup finished.
2012-11-21 23:09:36 INFO Obnam ends
2012-11-21 23:09:36 INFO obnam version 1.2 ends normally

So: ~5 days for backing up ~100 GB of changed data… Load was not high on the machines, neither in terms of CPU, nor in terms of RAM. Disk usage in /backups/backup_home was 5.7T, disk usage of /home was 6.6T, so there is some dedup, it seems.


A full backup of /home to (according to the log file):

[27/Nov/2012:12:55:31] /usr/bin/rsnapshot daily: started
[27/Nov/2012:12:55:31] echo 17632 > /var/run/
[27/Nov/2012:12:55:31] mkdir -m 0700 -p /backups/backup_home_rsnapshot/
[27/Nov/2012:12:55:31] mkdir -m 0755 -p /backups/backup_home_rsnapshot/daily.0/
[27/Nov/2012:12:55:31] /usr/bin/rsync -a --delete --numeric-ids --relative --delete-excluded /home /backups/backup_home_rsnapshot/daily.0/localhost/
[28/Nov/2012:23:16:16] touch /backups/backup_home_rsnapshot/daily.0/
[28/Nov/2012:23:16:16] rm -f /var/run/
[28/Nov/2012:23:16:16] /usr/bin/rsnapshot daily: completed successfully

So: ~1.5 days for a full backup of 6.3TB. An incremental backup a
day later took:

[29/Nov/2012:13:10:21] /usr/bin/rsnapshot daily: started
[29/Nov/2012:13:10:21] echo 20359 > /var/run/
[29/Nov/2012:13:10:21] mv /backups/backup_home_rsnapshot/daily.0/ /backups/backup_home_rsnapshot/daily.1/
[29/Nov/2012:13:10:21] mkdir -m 0755 -p /backups/backup_home_rsnapshot/daily.0/
[29/Nov/2012:13:10:21] /usr/bin/rsync -a –delete –numeric-ids –relative –delete-excluded –link-dest=/backups/backup_home_rsnapshot/daily.1/localhost/ /home /backups/backup_home_rsnapshot/daily.0/localhost/
[29/Nov/2012:13:25:09] touch /backups/backup_home_rsnapshot/daily.0/
[29/Nov/2012:13:25:09] rm -f /var/run/
[29/Nov/2012:13:25:09] /usr/bin/rsnapshot daily: completed successfully

So: 15 minutes… and the changed data amounted to 21GB.

This gave me a clear winner: rsnapshot! Not only is it very fast, but given its simple way of storing data restoring a backup of any file is quickly done.

We now also have answers to our questions: Our daily changing volume is of the order of ~ 100GB, there isn’t much data that can be deduplicated. We also monitored the network usage and, depending on the server load it can be limiting, but since a daily differential backup takes only 15-30 minutes that isn’t a problem.
For a remote backup sever that was connected with a 100Mbps line we did see that the initial backup took a very long time. We should try to get a faster connection to that machine.

The future

The next challenge we face is how to back up some of the large data sets we have/produce. These include aligned BAM files of next-generation sequencing data, VCF files of the same data, results from genomic imputations (both as gzip-ed text files and as binary files in DatABEL format). This also totals several TB. Luckily these files usually don’t change on a daily basis.

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Cloning Ubuntu virtual machines: some problems (and solutions)

Yesterday I set up a KVM virtual machine on my new Ubuntu 9.10 server. The VM also ran Ubuntu 9.10 server. In order to do some performance tests (what would be the speed up of having the VM’s disks on an LVM LV on the host, compared to having them in a file on the host) I used virt-clone to clone the machine:

virt-clone --connect=qemu:///system -o testldap -n testldap-lvm -f testldap-lvm/ubuntu-kvm/disk0.img

This clones the VM named testldap to testldap-lvm and put its disk file in the subdirectory testldap-lvm/ubuntu-kvm/. After that I still had to convert this image file to it’s location in an LV, but that’s not what this post is about.

As the machine is cloned, the MAC address of its virtual NIC is also changed. The ‘source’ VM had 52:54:00:f2:cc:40, the new VM was given 00:16:36:46:34:42. As I booted the new VM I noticed it wouldn’t come up as expected. I couldn’t reach it via the fixed IP that I had given the source VM (even though the source VM was shut down, of course). Closer inspection revealed that the interface name for the NIC in the new VM had changed. I vaguely remembered that Debian-derived distro’s do that: because they don’t want NIC name assignments (eth0, eth1, etc.) to change if a new network adapter is added, they tie a name to a MAC address. And, as noted, the MAC address had indeed changed in the cloning process.

The assignments between MAC and eth? name are recorded in the file /etc/udev/rules.d/70-persistent-net.rules. They are set by the script /lib/udev/write_net_rules, so I removed the execute permissions on that file. However, this was not a clean solution, since it resulted in an error on start up. I found that editing /lib/udev/rules.d/75-persistent-net-generator.rules is a far better solution. Adding the lines

# ignore KVM virtual interfaces
ENV{MATCHADDR}=="52:54:00:*", GOTO="persistent_net_generator_end"
# This seems to be the range used by Xen, but also by virt-clone
ENV{MATCHADDR}=="00:16:36:*", GOTO="persistent_net_generator_end"

seems to do the trick (don’t forget to remove the rules already added in /etc/udev/rules.d/70-persistent-net.rules). Make sure to add them after the lines

# read MAC address

so that the variable MATCHADDR has a value. I documented this solution in the Ubuntu bug report that seemed the most appropriate as well.

This solved one problem. Then the next problem reared its ugly head: Both the source VM and the clone refused to finish their boot process, they kept hanging on the NFS mounts defined in /etc/fstab. The only option mountall gave was to enter the root password (after pressing ESC) or type Crtl-D to continue. Doing the latter resulted in nothing but an infinite wait. In an Ubuntu bug report I found that using DHCP for the network interface would solve the problem. And, indeed it did. However, since I want static IP addresses for my servers this was not a solution that I liked. Much to my surprise the NFS mounts worked perfectly after changing the interface (in /etc/network/interfaces) back to static. I don’t know why, but on both VMs I set the configuration for eth0 from static to dhcp, rebooted, changed it back to static and rebooted again to find the problem solved… Strange!

Update 2009-12-18:
As it turns out, the solution to the mount problem doesn’t always work. I tried it again, but now it failed to work after switchting back from DHCP to a static IP. I guess it has something to do with the lease time of the IP, because in the case I described above there was a night between using the DHCP IP and turning static back on. So somewhere, something needs to time out before switching back from DHCP to static IPs works again.

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