ZFS on Linux is a poorly designed software solution to get ZFS up and running in Linux environments. Unlike FreeBSD, ZFS does not work with the Linux kernel natively. The developers of ZFS on Linux come up a creative hack. By injecting the ZFS into the kernel via DKMS, Linux kernel will understand what is ZFS. It works very well, and it really works with a single assumption: The system will never be updated or rebooted after installing ZFS on Linux. So what will happen after you update the system such as kernel or the system got rebooted? There is a good chance that your ZFS module will not be loaded. Otherwise you won’t be reading this article, right?

You just can’t assume that a MINI works like a semi truck. MINI was created for a totally different purposes. If you want to use a MINI like a semi-truck, then you have to accept the corresponding risks.

Long story short, below is how you get your data back:


You reboot your computer after a system upgrade (either updating to a new kernel, or updating the DKMS library, or both), and you notice that the ZFS is not loaded, i.e.,

#zpool import -a
The ZFS modules are not loaded.
Try running '/sbin/modprobe zfs' as root to load them.


#/sbin/modprobe zfs
modprobe: FATAL: Module zfs not found.



#dkms status
spl, 0.7.7, 3.10.0-693.17.1.el7.x86_64, x86_64: installed (original_module exists)
spl, 0.7.7, 3.10.0-693.21.1.el7.x86_64, x86_64: installed
zfs, 0.7.7, 3.10.0-693.17.1.el7.x86_64, x86_64: installed (original_module exists) (WARNING! Diff between built and installed module!) (WARNING! Diff between built and installed module!) (WARNING! Diff between built and installed module!) (WARNING! Diff between built and installed module!) (WARNING! Diff between built and installed module!)
zfs, 0.7.7, 3.10.0-693.21.1.el7.x86_64, x86_64: installed (WARNING! Diff between built and installed module!) (WARNING! Diff between built and installed module!) (WARNING! Diff between built and installed module!) (WARNING! Diff between built and installed module!) (WARNING! Diff between built and installed module!)

What you need to do is to erase all the ZFS and related packages:

yum erase zfs zfs-dkms libzfs2 spl spl-dkms libzpool2 -y

Please reboot the system. This step is very important.

reboot

After that, try to install ZFS again.

yum install zfs -y

If the system complaints about mismatch dependent packages, try to remove the affected packages first and run the installation again.

After the installation, try to start the ZFS module:

/sbin/modprobe zfs

zpool import -a

If the ZFS is up and running, you may move to next step. Otherwise, I suggest you to do the following:

  • Reboot
  • Clear the cache of the yum repository and try to update the system again. (sudo yum clean all)
  • Reboot to the latest kernel
  • Erase the ZFS and related packages and try it again.

ZFS is portable. If you are unable to get it works, try to bring the ZFS disks to other servers, the new server should be able to recognize the ZFS disks. For the original server, you can connect to the ZFS disks on the new server via NFS using the original path. That will minimize the impact of changes.

Assuming that your ZFS is up and running, we will need to check the DKMS status:

#dkms status

If you see no error message, you are good to go.

spl, 0.7.8, 3.10.0-693.21.1.el7.x86_64, x86_64: installed (original_module exists)
zfs, 0.7.8, 3.10.0-693.21.1.el7.x86_64, x86_64: installed (original_module exists)

If you see an error message like the following, you may need to rebuild the modules again:

spl, 0.7.8, 3.10.0-693.21.1.el7.x86_64, x86_64: installed (original_module exists)
zfs, 0.7.8, 3.10.0-693.21.1.el7.x86_64, x86_64: installed (original_module exists) (WARNING! Diff between built and installed module!) (WARNING! Diff between built and installed module!)
sudo dkms remove zfs/0.7.8 --all
sudo dkms remove spl/0.7.8 --all
sudo dkms --force install spl/0.7.8
sudo dkms --force install zfs/0.7.8
sudo dkms status

Now you understand why no professional truckers use MINI for work. Good luck!

Our sponsors:

I always like to experimenting the idea of building a ZFS cluster, i.e., it has the robust of the ZFS with the cluster capacity. So I came up a test environment with this prototype.

The idea is pretty simple. Typically when we build the ZFS server, the members of the RAID are the hard drives. In my experiment, I use files instead of hard drives, where the corresponding files live in a network share (mounted via NFS). Since the bottle neck of the I/O will be limited by the network, I include a network bonding to increase the overall bandwidth.

The yellow servers are simply regular servers running ZFS with NFS service. I use the following command to generate a simple file / place holder for ZFS mounting:

#This will create an empty 1TB file, you can think of it as a 1TB hard drive / place holder.
truncate -s 1000G file.img

Make sure that the corresponding NFS service is serving the file.img to the client (the blue server).


The blue server will be the NFS client of the yellow servers, where I will use it to serve the data to other computers. It has the following features:

It has a network bonding based on three Ethernet adapter:

#cat /proc/net/bonding/bond0


Ethernet Channel Bonding Driver: v3.7.1 (April 27, 2011)

Bonding Mode: adaptive load balancing
Primary Slave: None
Currently Active Slave: enp0s25
MII Status: up
MII Polling Interval (ms): 1
Up Delay (ms): 0
Down Delay (ms): 0

Slave Interface: enp0s25
MII Status: up
Speed: 1000 Mbps
Duplex: full
Link Failure Count: 0
Permanent HW addr: 00:19:d1:b2:1e:0d
Slave queue ID: 0

Slave Interface: enp6s0
MII Status: up
Speed: 1000 Mbps
Duplex: full
Link Failure Count: 0
Permanent HW addr: 00:18:4d:f0:12:7b
Slave queue ID: 0

Slave Interface: enp6s1
MII Status: up
Speed: 1000 Mbps
Duplex: full
Link Failure Count: 0
Permanent HW addr: 00:22:3f:f6:98:03
Slave queue ID: 0

It mounts the yellow servers via NFS

#df
192.168.1.101:/storage/share   25T  3.9T   21T  16%  /nfs/192-168-1-101
192.168.1.102:/storage/share   8.1T  205G  7.9T   3% /nfs/192-168-1-102
192.168.1.103:/storage/share   8.3T  4.4T  4.0T  52% /nfs/192-168-1-103

The ZFS has the following structure:

#sudo zpool status
        NAME                                  STATE     READ WRITE CKSUM
        storage                               ONLINE       0     0     0
          raidz1-0                            ONLINE       0     0     0
            /nfs/192-168-1-101/file.img       ONLINE       0     0     0
            /nfs/192-168-1-102/file.img       ONLINE       0     0     0
            /nfs/192-168-1-103/file.img       ONLINE       0     0     0

or:

zpool create -f storage raidz /nfs/192-168-1-101/file.img \
                              /nfs/192-168-1-102/file.img \
                              /nfs/192-168-1-103/file.img

The speed of the network will be the limitation of the system, I don’t expect the I/O speed goes beyond 375MB/s (125MB/s x 3). Also since it is a file-based ZFS (the ZFS on the blue server is based on files, not disks), so the overall performance will be discounted.

#Write speed
time dd if=/dev/zero of=/storage/data/file.out bs=1M count=1000
1000+0 records in
1000+0 records out
1048576000 bytes (1.0 GB) copied, 3.6717 s, 285 MB/s
#Write speed
time dd if=/storage/data/file.out of=/dev/null
1000+0 records in
1000+0 records out
1048576000 bytes (1.0 GB) copied, 3.9618 s, 265 MB/s

Both read and the write speed are roughly around 75% of the maximum bandwidth, which is not bad at all.

So I decide to make one of the yellow servers offline, let’s see what’s going on:

#sudo zpool status
        NAME                                  STATE     READ WRITE CKSUM
        storage                               ONLINE       0     0     0
          raidz1-0                            ONLINE       0     0     0
            /nfs/192-168-1-101/file.img       ONLINE       0     0     0
            /nfs/192-168-1-102/file.img       ONLINE       0     0     0
            /nfs/192-168-1-103/file.img       UNAVAIL      0     0     0 cannot open

And the pool is still functioning, that’s pretty cool!


Here are some notes that will affect the overall performance:

  • The quality of the Ethernet card matters, which includes PCIe or PCI, 1 lane or 16 lane, total throughput etc.
  • The network traffic. Is the switch busy?
  • How are you connect these servers together? One big switch or multiple switches that are bridged together. If they are bridged, the limitation will be the cable of the bridge, which is 125MB/s for gigabit network.

Again, this is just an for experimental purposes only. If you decide to put this in a production environment, do it on your own risk. Have fun!

Our sponsors:

A friend of mine likes to try ZFS on CentOS 7, therefore I decide to make a guide for him. The following instructions have been well tested on CentOS 7.

Before you decide to put ZFS in a production use, you should be aware of the following:

  • ZFS is originally designed to work with Solaris and BSD system. Because of the legal and licensing issues, ZFS cannot be shipped with Linux.
  • Since ZFS is open source, some developers port the ZFS the Linux, and make it run at the kernel level via dkms. This works great as long as you don’t update the kernel. Otherwise the ZFS will not be loaded with the new kernel.
  • In a ZFS/Linux environment, it is a bad idea to update the system automatically.
  • For some odd reasons, ZFS/Linux will work with server grade or gaming grade computers. Do not run ZFS/Linux on entry level computers.

Instructions

By default, ZFS is not available in the standard CentOS repository. We will need to include some 3rd party repositories here.

sudo rpm -Uvh http://www.elrepo.org/elrepo-release-7.0-2.el7.elrepo.noarch.rpm
sudo rpm -Uvh http://dl.fedoraproject.org/pub/epel/epel-release-latest-7.noarch.rpm
sudo rpm -Uvh https://forensics.cert.org/cert-forensics-tools-release-el7.rpm
sudo rpm -Uvh http://download.zfsonlinux.org/epel/zfs-release.el7_3.noarch.rpm

sudo yum update -y
sudo yum groupinstall -y "Development Tools" "Development Libraries" "Additional Development"
sudo yum install -y kernel-devel kernel-headers

It is very likely that the system will install a new kernel. You may want to reboot the computer before installing the ZFS.

sudo reboot

Please make sure that the system does not update automatically. If you need to update the system, please exclude the kernel and related modules from the update.

sudo nano /etc/yum.conf 
exclude=kernel*

Now you are on the latest kernel. Let’s install the ZFS:

sudo yum install -y zfs
sudo /sbin/modprobe zfs

Now, you can create a simple stripped ZFS. Stripped ZFS gives you the best performances and zero data protections. When referencing the disks, we don’t want to use /dev/sd*, instead, we want to use the device id directly, e.g., /dev/disk/by-id/wwn-0x8000c8004e8ac11a

ls /dev/disk/by-id/


lrwxrwxrwx 1 root root  9 Jan  3 21:49 wwn-0x8000c8004e8ac11a -> ../../sde
lrwxrwxrwx 1 root root  9 Jan  3 21:49 wwn-0x8000c8008ad0a22d -> ../../sdd
lrwxrwxrwx 1 root root  9 Jan  3 21:49 wwn-0x8000c8008b4f6338 -> ../../sda
lrwxrwxrwx 1 root root  9 Jan  3 21:49 wwn-0x8000c8008b52144c -> ../../sdc
lrwxrwxrwx 1 root root  9 Jan  3 21:49 wwn-0x8000c8008b59a553 -> ../../sdb

Once you identify the list of the hard disks, we can create a simple stripped ZFS. This will create a ZFS under /storage. You can replace storage to anything you like.

#We are going to create a ZFS pool with three disks. You can add more if you like. For stripped design, the higher number of disks, the faster the IO speed.
zpool create -f storage /dev/disk/by-id/device1 /dev/disk/by-id/device2 /dev/disk/by-id/device3 

storage is like a big umbrella. Under this umbrella, we will need to create multiple “partitions” for storing data.

zfs create storage/mydata

If you have a fast CPU like i7, you may want to turn on the compression. This will reduce the amount of data write to the system, and it will improve the overall performance.

sudo zfs set compression=lz4 storage

Finally we want to change the ownership and the permissions

#Assuming that you are part of the wheel group
sudo chown -R root:wheel /storage
sudo chmod -R g+rw /storage

Now, run df and you should be able to see the ZFS in your system.

#df -h
Filesystem                   Size  Used Avail Use% Mounted on
storage                      6.8T  128K  6.8T   1% /storage
storage/mydata                13T  6.1T  6.8T  48% /storage/mydata

You can monitor the health of the ZFS system.

#sudo zpool status



  pool: storage
 state: ONLINE
config:

        NAME                        STATE     READ WRITE CKSUM
        storage                     ONLINE       0     0     0
            wwn-0x8000c8004e8ac11a  ONLINE       0     0     0
            wwn-0x8000c8008ad0a22d  ONLINE       0     0     0
            wwn-0x8000c8008b4f6338  ONLINE       0     0     0
            wwn-0x8000c8008b52144c  ONLINE       0     0     0


errors: No known data errors

For some very odd reasons, ZFS will not be loaded automatically. We want to make sure that ZFS will be loaded after reboot.

#sudo nano /etc/crontab

#Add the following:
@reboot         root    sleep 10; zpool import -a;

Now you can try to test the ZFS by running dd or copying a big file to the ZFS. If you are not happy with the configurations, you can always destroy it and re-create the ZFS again.

sudo zpool destroy storage

Further Reading

Have fun!

Our sponsors:

Let’s all agree with this fact: ZFS is foreign to Linux. It is not native. You can’t expect that ZFS on Linux will run smoothly as FreeBSD or Solaris. Having using ZFS on Linux since 2013 (and ZFS on FreeBSD since 2009), I’ve noticed that ZFS does not like Linux (well, at least RHEL 7). Here are some few examples:

  • ZFS is not loaded at the boot time. You will need to manually start it or load it via cron. Good luck if you have other services (like Apache, MySQL, NFS, or even users’ home directories) that depend on the ZFS.
  • Every single time you update the kernel, ZFS will not work after the reboot without some manual work. What if the system runs the update automatically, and one day there is a power failure which makes your server to reboot to a new kernel? Your system will not be able to mount your ZFS volume. If you integrate ZFS with other service applications such as web, database or network drive, oh well, good luck and I hope you will catch this problem fast enough before receiving thousands of emails and calls from your end-users.
  • If you exclude the kernel from the updates (/etc/yum.conf), you will eventually run into trouble, because there are tons of other packages that require the latest kernel. In the other words, running the command: yum update -y will fail. You will need to run yum update –skip-broken, which means you will miss many latest packages. Here is an example:
    --> Finished Dependency Resolution
    Error: Package: hypervvssd-0-0.29.20160216git.el7.x86_64 (base)
               Requires: kernel >= 3.10.0-384.el7
               Installed: kernel-3.10.0-327.el7.x86_64 (@anaconda)
                   kernel = 3.10.0-327.el7
               Installed: kernel-3.10.0-327.22.2.el7.x86_64 (@updates)
                   kernel = 3.10.0-327.22.2.el7
    Error: Package: hypervfcopyd-0-0.29.20160216git.el7.x86_64 (base)
               Requires: kernel >= 3.10.0-384.el7
               Installed: kernel-3.10.0-327.el7.x86_64 (@anaconda)
                   kernel = 3.10.0-327.el7
               Installed: kernel-3.10.0-327.22.2.el7.x86_64 (@updates)
                   kernel = 3.10.0-327.22.2.el7
    Error: Package: hypervkvpd-0-0.29.20160216git.el7.x86_64 (base)
               Requires: kernel >= 3.10.0-384.el7
               Installed: kernel-3.10.0-327.el7.x86_64 (@anaconda)
                   kernel = 3.10.0-327.el7
               Installed: kernel-3.10.0-327.22.2.el7.x86_64 (@updates)
                   kernel = 3.10.0-327.22.2.el7
     You could try using --skip-broken to work around the problem
     You could try running: rpm -Va --nofiles --nodigest
    
  • If you are running the stable Linux distributions like RHEL 7, you can load a more recent kernel like 4.x by installing the package: kernel-ml. However, don’t expect that ZFS will work with version 4:
    Loading new spl-0.6.5.9 DKMS files...
    Building for 4.11.2-1.el7.elrepo.x86_64
    Building initial module for 4.11.2-1.el7.elrepo.x86_64
    configure: error: unknown
    Error! Bad return status for module build on kernel: 4.11.2-1.el7.elrepo.x86_64 (x86_64)
    Consult /var/lib/dkms/spl/0.6.5.9/build/make.log for more information.
    
    

Running ZFS on Linux is like putting a giraffe in the wild in Alaska. It is just not the right thing to do. Unfortunately, there are so many things that only available on Linux so we have to live with it. Just like FUSE (Filesystem in Userspace), many people feel hesitated to run their file systems on the userspace instead of kernel level, but hey, see how many people are happy with GlusterFS, a distributed file system that live on FUSE! Personally I just think it is not a right thing to do, especially in an enterprise environment. Running a production file system at the userspace level, seriously?

Anyway, if you are running into trouble after upgrading your Linux kernel (and you almost had a heart attack when you think your data may be lost), you have two choices:

  1. Simply boot to the previous working kernel if you need to get your data back in quick. However, keep in mind that this will create two problems:
    • Since you already update the system with the new kernel and the new packages, your new packages probably will not work with the old kernel, and that may give you extra headache.
    • Unless you manually overwrite the kernel boot order (boot loader config), otherwise you may get into the same trouble in the next boot.
  2. If you want a more “permanent” fix, you will need to rebuild the dkms ZFS and SPL modules. See below for the instructions. Keep in mind that you will have the same problem again when the kernel receives a new update.

You’ve tried to load the ZFS and realize that it is no longer available:

#sudo zpool import
The ZFS modules are not loaded.
Try running '/sbin/modprobe zfs' as root to load them.

#sudo /sbin/modprobe zfs
modprobe: FATAL: Module zfs not found.

You may want to check the dkms status. Write down the version number. In my case, it is 0.6.5.9

#sudo dkms status
spl, 0.6.5.9, 3.10.0-327.28.3.el7.x86_64, x86_64: installed (WARNING! Diff between built and installed module!) (WARNING! Diff between built and installed module!)
spl, 0.6.5.9, 3.10.0-514.2.2.el7.x86_64, x86_64: installed (WARNING! Diff between built and installed module!) (WARNING! Diff between built and installed module!)
zfs, 0.6.5.9, 3.10.0-327.28.3.el7.x86_64, x86_64: installed (WARNING! Diff between built and installed module!) (WARNING! Diff between built and installed module!) (WARNING! Diff between built and installed module!) (WARNING! Diff between built and installed module!) (WARNING! Diff between built and installed module!) (WARNING! Diff between built and installed module!)

Before running the following commands, make sure that you know what you are doing.


#Make sure that you reboot to the kernel you want to fix.
#Find out what is the current kernel
uname -a
Linux 3.10.0-514.2.2.el7.x86_64 #1 SMP Tue Dec 6 23:06:41 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux

#In my example, it is:
3.10.0-514.2.2.el7.x86_64

#Now, let's get into the fun part. We will remove them and reinstall them.
#Don't forget to match your version, in my base, my version is: 0.6.5.9
sudo dkms remove zfs/0.6.5.9 --all
sudo dkms remove spl/0.6.5.9 --all
sudo dkms --force install spl/0.6.5.9
sudo dkms --force install zfs/0.6.5.9

#or you can run these commands in one line, so that you don't need to wait:
sudo dkms remove zfs/0.6.5.9 --all; sudo dkms remove spl/0.6.5.9 --all; sudo dkms --force install spl/0.6.5.9; sudo dkms --force install zfs/0.6.5.9;

And we will verify the result.

#sudo dkms status
spl, 0.6.5.9, 3.10.0-514.2.2.el7.x86_64, x86_64: installed
zfs, 0.6.5.9, 3.10.0-514.2.2.el7.x86_64, x86_64: installed

Finally we can start the ZFS again.

sudo /sbin/modprobe zfs

Your ZFS pool should back. You can verify it by rebooting your machine. Notice that Linux may not automatically mount the ZFS volumes. You may want to mount it manually or via cron job.

Here is how to mount the ZFS volumes manually.

sudo zpool import -a

You may want to remove all of the old kernels too.

sudo package-cleanup --oldkernels --count=1 -y

Our sponsors:

I had a hard drive sitting around, and I decided to format it such that I could use it in my Linux CentOS box. When I decided to mount it, I got the following error message:

mount: /dev/sdb1: more filesystems detected. This should not happen,
       use -t  to explicitly specify the filesystem type or
       use wipefs(8) to clean up the device.

This message simply tells you that there are two or more file systems sitting in the hard drive partitions, and the system does not know which one to use to mount. We can take a closer look to see what’s going on:

sudo wipefs /dev/sdb1


offset               type
----------------------------------------------------------------
0x2d1b0fa8923        zfs_member   [raid]
                     LABEL: storage
                     UUID:  12661834248699203227

0x951                xfs   [filesystem]
                     UUID:  90295123-2395-7456-8521-9A1EE963ac53

As you can see, we have two file systems here. The easiest way is to wipe out the first few sectors of your disk, i.e.,

sudo dd if=/dev/zero of=/dev/sdb bs=1M count=10

And we will re-do everything again, i.e.,

sudo parted /dev/sdb1
...
...
sudo mkfs.xfs /dev/sdb1
sudo mount /dev/sdb1 /mnt/

That’s it!

Our sponsors:

I put my personal websites on a FreeBSD server. One of my websites is a photo album, which I want to read the content from a Dropbox. That Dropbox primarily runs on Mac, iPhone and iPad. I was trying to explore the possibilities to set up a Dropbox on FreeBSD. Since Dropbox doesn’t support FreeBSD officially, I need to use 3rd party tools, most of them are basically based on the Dropbox developer API.

So I have tried several 3rd party tools, as you expect, none of them works. The primary problem is the synchronization, i.e., if my wife adds or deletes a photo on the Dropbox, I expect that the Dropbox folder on FreeBSD will get updated as well. Another problem is the speed. Looks like the Dropbox API is not as fast comparing to its own native application. On the same network, it took few hours to download the content (around 1GB of jpeg files) from Dropbox on FreeBSD, versus 10 minutes on a Mac/Windows/Linux machine using the native application.

So I came up few alternative solutions:

  1. Hosting my website on CentOS Linux. Since Dropbox supports Linux, I can easily read the Dropbox without any problem.
  2. Push the Dropbox content from Mac/Linux to FreeBSD using Rsync periodically (e.g., every 5 mins, hourly etc). That way FreeBSD will have access the Dropbox files.
  3. Set up a NFS service on a Linux box with access to Dropbox, and let the FreeBSD to mount the corresponding NFS share. This solution is okay if both machines are on the same network. It may raise some security concerns if both machines are connected via the public.

Another solution I think it may work is to install the Dropbox native application on FreeBSD. FreeBSD supports running Linux application via Linux emulation. Back in the old days (FreeBSD 8), it was pretty easy to include the Linux support on FreeBSD (one click in the sysinstall). Since the recent releases, they’ve made it harder because not many people wants to run Linux binary on FreeBSD. Based on my previous experience, I think it should work on the latest FreeBSD, but it may require some works.

Another crazy idea will be running Dropbox with Wine on FreeBSD. But this goes way too far from my original purpose, and I am not a big fan of Wine because it adds too many libraries to the system.

Our sponsors:

Recently, I decided to upgrade a database server from RHEL 6 (CentOS 6) to RHEL 7 (CentOS 7), which involves switching from MySQL 5.5 to MariaDB 5.5. Our server hosts about 100 databases, when I was testing them individually, I didn’t see any problem. However, when I ran the back up all databases one by one using mysqldump (i.e., running mysqldump command for each database, one after one, 100 times), something funny happened. Here is the error message:


#The system was running a brunch of mysqldump commands, one by one (not via background)

Got error: 1016: "Can't open file: './db_my_database/tbl_mytable.frm' (errno: 24)" when using LOCK TAB                                                                                                   LES
mysqldump: Error: 'Out of resources when opening file '/var/tmp/#sql_2d6c_2.MAI' (Errcode: 24)' when trying to dump tablespaces
mysqldump: Error: 'Out of resources when opening file '/var/tmp/#sql_2d6c_2.MAI' (Errcode: 24)' when trying to dump tablespaces
mysqldump: Error: 'Out of resources when opening file '/var/tmp/#sql_2d6c_2.MAI' (Errcode: 24)' when trying to dump tablespaces
mysqldump: Error: 'Out of resources when opening file '/var/tmp/#sql_2d6c_2.MAI' (Errcode: 24)' when trying to dump tablespaces
mysqldump: Error: 'Out of resources when opening file '/var/tmp/#sql_2d6c_2.MAI' (Errcode: 24)' when trying to dump tablespaces
mysqldump: Error: 'Out of resources when opening file '/var/tmp/#sql_2d6c_2.MAI' (Errcode: 24)' when trying to dump tablespaces
mysqldump: Error: 'Out of resources when opening file '/var/tmp/#sql_2d6c_2.MAI' (Errcode: 24)' when trying to dump tablespaces
mysqldump: Error: 'Out of resources when opening file '/var/tmp/#sql_2d6c_2.MAI' (Errcode: 24)' when trying to dump tablespaces
mysqldump: Error: 'Out of resources when opening file '/var/tmp/#sql_2d6c_2.MAI' (Errcode: 24)' when trying to dump tablespaces

At the mean time, I tried to access the database via MySQL terminal,

MariaDB [(none)]> SHOW DATABASES;
ERROR 1018 (HY000): Can't read dir of '.' (errno: 24)

This error message means the MySQL cannot access the file. If you google the message, you will notice that there are tons of solutions, and almost every of them suggests you to increase the open_files_limit variable in my.cnf.

Therefore, I checked my configurations (/etc/my.cnf), and I noticed that the value was already set to 30000. I also checked the lsof command and I found something very interesting. Notice that I have 100 database, each of them contains about 60 tables. Each table has about 3 files. Depending on the timeout settings, if all database and tables are opened, the total number of opened file will be 100x60x3 = 18,000

sudo lsof -u mysql | wc
1045   25811 239248

This result suggests that at the time of crashing, the mysql user (the system user that run the MariaDB service) was accessing 1045 files at the same time.

So I was scratching my head. Why I already set the open_files_limit value to 30000 already, and the system crashed at 1045th files? I also verified the memory (command: free) and current process (command: top), and I didn’t find anything unusual. One last thing, I checked the open_files_limit value using MySQL terminal, and this is what I found:

MariaDB [(none)]> SHOW VARIABLES LIKE 'open_files_limit';
+------------------+-------+
| Variable_name    | Value |
+------------------+-------+
| open_files_limit | 1024  |
+------------------+-------+

It seems that MariaDB didn’t honor the open_files_limit I set in config file, instead it uses the default one, which isn’t right. So after some investigations, I’ve noticed that RHEL 7 set up some security stuffs, such that you will need to set the open_file_limit variable at the system level rather than the application level. In the other words, whatever you put in the /etc/my.cnf, it won’t go through the security check at RHEL.

Here is how to set the equivalent open_files_limit at the system level:

sudo mkdir -p /etc/systemd/system/mariadb.service.d/
sudo nano /etc/systemd/system/mariadb.service.d/limits.conf
#Add the following, for me, I like to set the open_files_limit to 30000:
[Service]
LimitNOFILE=30000
sudo systemctl daemon-reload
sudo systemctl restart mariadb

I tried to rerun the command again and that’s what I got:

MariaDB [(none)]> SHOW VARIABLES LIKE 'open_files_limit';
+------------------+-------+
| Variable_name    | Value |
+------------------+-------+
| open_files_limit | 30000 |
+------------------+-------+
1 row in set (0.00 sec)

That’s it! Did I save you from heart attack?

One of the biggest selling points of RHEL is the stability. When we upgraded from RHEL 6 to RHEL 7 (clean install), we expected that everything should work fine without too much modifications. Unfortunately, what I saw is a broken system. I really don’t expect that this happens in an enterprise class product.

Our sponsors:

This article is mainly for CentOS 6, please visit here for CentOS 7.

After I upgraded the CentOS / RHEL system to the latest kernel, the ZFS failed to start. The system was unable to load the ZFS module, i.e., I could not access my data. Here are some error messages I found on the system:

#sudo zpool status
The ZFS modules are not loaded.
Try running '/sbin/modprobe zfs' as root to load them.
#sudo /sbin/modprobe zfs
FATAL: Error inserting zfs (/lib/modules/2.6.32-573.7.1.el6.x86_64/weak-updates/zfs.ko): Unknown symbol in module, or unknown parameter (see dmesg)
#dmesg
zfs: disagrees about version of symbol vn_openat
zfs: Unknown symbol vn_openat
zfs: disagrees about version of symbol taskq_dispatch_delay
zfs: Unknown symbol taskq_dispatch_delay
zfs: disagrees about version of symbol taskq_cancel_id
zfs: Unknown symbol taskq_cancel_id
zfs: disagrees about version of symbol vn_open
zfs: Unknown symbol vn_open
zfs: disagrees about version of symbol vn_remove
zfs: Unknown symbol vn_remove
zfs: disagrees about version of symbol taskq_dispatch_ent
zfs: Unknown symbol taskq_dispatch_ent
zfs: disagrees about version of symbol taskq_dispatch
zfs: Unknown symbol taskq_dispatch
zfs: disagrees about version of symbol system_taskq
zfs: Unknown symbol system_taskq
zfs: disagrees about version of symbol taskq_wait
zfs: Unknown symbol taskq_wait
zfs: Unknown symbol __cv_wait_interruptible
zfs: disagrees about version of symbol taskq_wait_id
zfs: Unknown symbol taskq_wait_id
zfs: disagrees about version of symbol taskq_destroy
zfs: Unknown symbol taskq_destroy
zfs: disagrees about version of symbol vn_rdwr
zfs: Unknown symbol vn_rdwr
zfs: disagrees about version of symbol taskq_init_ent
zfs: Unknown symbol taskq_init_ent
zfs: disagrees about version of symbol taskq_create
zfs: Unknown symbol taskq_create
zfs: Unknown symbol __cv_timedwait_interruptible
zfs: disagrees about version of symbol taskq_member
zfs: Unknown symbol taskq_member

So what does these messages mean? Before I explain the details, let me explain how ZFS works on Linux. For legal reasons, unlike *BSD, Linux kernel does not support ZFS. In order to make Linux talks to ZFS, some people came up a very smart way: They inject the ZFS library at the kernel level, such that when Linux boots, it knows how to handle the ZFS. It sounds pretty ideal, isn’t it?

And now, we have a problem.

Many system administrators like to let the system upgrade automatically (such as running yum update -y in the cron job etc). Unlike *BSD, Linux bundles the kernel and application update together. In the other words, when you run the yum update, it will update both kernel and applications together, and there is no way for you to pick one and skip the other.

When the system upgrades the kernel, it refreshes everything, i.e., the new kernel will not know what is ZFS, because the process of injecting the ZFS happens when we install the ZFS on Linux. If there is no new version available, this process will not happen. So what happen after you reboot the computer, which by default, load the latest kernel? You got it, the ZFS won’t be loaded and your data is not accessible.

There are few ways to handle this. First, if you really want to keep your system up to dated (which I don’t recommend), exclude the kernel from the system update.

sudo nano /etc/yum.conf
[main]
.....
exclude=kernel*

It doesn’t mean your system is 100% safe from now on. You may still get some chances to break your ZFS. Here is some funny messages after I turn on the exclusion and run the yum update:

Loading new zfs-0.6.5.4 DKMS files...
Building for 2.6.32-504.23.4.el6.x86_64
Building initial module for 2.6.32-504.23.4.el6.x86_64
Done.

Adding any weak-modules
ERROR: modinfo: could not open /lib/modules/2.6.32-358.el6.x86_64/weak-updates/: Is a directory
ERROR: modinfo: could not open /lib/modules/2.6.32-504.23.4.el6.x86_64/zavl.ko: No such file or directory
FATAL: /lib/modules/2.6.32-504.23.4.el6.x86_64/zavl.ko: No such file or directory
Warning: Module zavl.ko from kernel  has no modversions, so it cannot be reused for kernel 2.6.32-358.el6.x86_64
ERROR: modinfo: could not open /lib/modules/2.6.32-358.el6.x86_64/weak-updates/: Is a directory
ERROR: modinfo: could not open /lib/modules/2.6.32-504.23.4.el6.x86_64/znvpair.ko: No such file or directory
FATAL: /lib/modules/2.6.32-504.23.4.el6.x86_64/znvpair.ko: No such file or directory
Warning: Module znvpair.ko from kernel  has no modversions, so it cannot be reused for kernel 2.6.32-358.el6.x86_64
ERROR: modinfo: could not open /lib/modules/2.6.32-358.el6.x86_64/weak-updates/: Is a directory
ERROR: modinfo: could not open /lib/modules/2.6.32-504.23.4.el6.x86_64/zunicode.ko: No such file or directory
FATAL: /lib/modules/2.6.32-504.23.4.el6.x86_64/zunicode.ko: No such file or directory
Warning: Module zunicode.ko from kernel  has no modversions, so it cannot be reused for kernel 2.6.32-358.el6.x86_64
ERROR: modinfo: could not open /lib/modules/2.6.32-358.el6.x86_64/weak-updates/: Is a directory
ERROR: modinfo: could not open /lib/modules/2.6.32-504.23.4.el6.x86_64/zcommon.ko: No such file or directory
FATAL: /lib/modules/2.6.32-504.23.4.el6.x86_64/zcommon.ko: No such file or directory
Warning: Module zcommon.ko from kernel  has no modversions, so it cannot be reused for kernel 2.6.32-358.el6.x86_64
ERROR: modinfo: could not open /lib/modules/2.6.32-358.el6.x86_64/weak-updates/: Is a directory
ERROR: modinfo: could not open /lib/modules/2.6.32-504.23.4.el6.x86_64/zpios.ko: No such file or directory
FATAL: /lib/modules/2.6.32-504.23.4.el6.x86_64/zpios.ko: No such file or directory
Warning: Module zpios.ko from kernel  has no modversions, so it cannot be reused for kernel 2.6.32-358.el6.x86_64

depmod...

DKMS: install completed.

The second thing you will need to do is to increase the /boot partition from the default 200MB to at least 2GB. By default, RHEL will create a 200MB /boot for storing the kernel files. Kernels are small and they rarely go beyond 40MB. However, RHEL will only keep up to 5 recent kernels (40MB x 5 = 200MB), and it will remove the rest. So what happen if it removes the one that works with ZFS? The only thing you can do is to reinstall the system and import your ZFS again.

sudo zpool import

Here is how to modify the number:

sudo nano /etc/yum.conf 
#Tell the system to keep the most 20 recent kernels
installonly_limit=20

Another thing you may want to do is to select the working kernel (instead of the latest) one when boot. Here is how to change it:

sudo nano /boot/grub/grub.conf

Notice that I comment out the most recent kernels:

# grub.conf generated by anaconda
#
# Note that you do not have to rerun grub after making changes to this file
# NOTICE:  You have a /boot partition.  This means that
#          all kernel and initrd paths are relative to /boot/, eg.
#          root (hd0,0)
#          kernel /vmlinuz-version ro root=/dev/sda3
#          initrd /initrd-[generic-]version.img
#boot=/dev/sda
default=0
timeout=5
splashimage=(hd0,0)/grub/splash.xpm.gz
hiddenmenu
#title CentOS (2.6.32-573.7.1.el6.x86_64)
#       root (hd0,0)
#       kernel /vmlinuz-2.6.32-573.7.1.el6.x86_64 ro root=UUID=325cc438-33a6-46ae-8f1a-443ebd77c70a rd_NO_LUKS rd_NO_LVM LANG=en_US.UTF-8 rd_NO_MD SYSFONT=latarcyrheb-sun16 crashkernel=128M  KEYBOARDTYPE=pc$
#       initrd /initramfs-2.6.32-573.7.1.el6.x86_64.img
#title CentOS (2.6.32-573.8.1.el6.x86_64)
#       root (hd0,0)
#       kernel /vmlinuz-2.6.32-573.8.1.el6.x86_64 ro root=UUID=325cc438-33a6-46ae-8f1a-443ebd77c70a rd_NO_LUKS rd_NO_LVM LANG=en_US.UTF-8 rd_NO_MD SYSFONT=latarcyrheb-sun16 crashkernel=128M  KEYBOARDTYPE=pc$
#       initrd /initramfs-2.6.32-573.8.1.el6.x86_64.img
#title CentOS (2.6.32-573.12.1.el6.x86_64)
#       root (hd0,0)
#       kernel /vmlinuz-2.6.32-573.12.1.el6.x86_64 ro root=UUID=325cc438-33a6-46ae-8f1a-443ebd77c70a rd_NO_LUKS rd_NO_LVM LANG=en_US.UTF-8 rd_NO_MD SYSFONT=latarcyrheb-sun16 crashkernel=128M  KEYBOARDTYPE=p$
#       initrd /initramfs-2.6.32-573.12.1.el6.x86_64.img
#title CentOS (2.6.32-573.18.1.el6.x86_64)
#       root (hd0,0)
#       kernel /vmlinuz-2.6.32-573.18.1.el6.x86_64 ro root=UUID=325cc438-33a6-46ae-8f1a-443ebd77c70a rd_NO_LUKS rd_NO_LVM LANG=en_US.UTF-8 rd_NO_MD SYSFONT=latarcyrheb-sun16 crashkernel=128M  KEYBOARDTYPE=p$
#       initrd /initramfs-2.6.32-573.18.1.el6.x86_64.img
title CentOS (2.6.32-573.3.1.el6.x86_64)
        root (hd0,0)
        kernel /vmlinuz-2.6.32-573.3.1.el6.x86_64 ro root=UUID=325cc438-33a6-46ae-8f1a-443ebd77c70a rd_NO_LUKS rd_NO_LVM LANG=en_US.UTF-8 rd_NO_MD SYSFONT=latarcyrheb-sun16 crashkernel=128M  KEYBOARDTYPE=pc$
        initrd /initramfs-2.6.32-573.3.1.el6.x86_64.img
title CentOS (2.6.32-573.1.1.el6.x86_64)
        root (hd0,0)
        kernel /vmlinuz-2.6.32-573.1.1.el6.x86_64 ro root=UUID=325cc438-33a6-46ae-8f1a-443ebd77c70a rd_NO_LUKS rd_NO_LVM LANG=en_US.UTF-8 rd_NO_MD SYSFONT=latarcyrheb-sun16 crashkernel=128M  KEYBOARDTYPE=pc$
        initrd /initramfs-2.6.32-573.1.1.el6.x86_64.img
title CentOS (2.6.32-504.30.3.el6.x86_64)
        root (hd0,0)
        kernel /vmlinuz-2.6.32-504.30.3.el6.x86_64 ro root=UUID=325cc438-33a6-46ae-8f1a-443ebd77c70a rd_NO_LUKS rd_NO_LVM LANG=en_US.UTF-8 rd_NO_MD SYSFONT=latarcyrheb-sun16 crashkernel=128M  KEYBOARDTYPE=p$
        initrd /initramfs-2.6.32-504.30.3.el6.x86_64.img

Do not bother to remove the ZFS libraries and reinstall them again. It won’t work and it will make you system only more messy.

That’s it! Hope this tutorial saves you from heart attack.

–Derrick

Our sponsors:

I was looking for a way to include a directory name with space using rsync. So I google it, found a brunch of suggestions, which turned out that NONE of them really works. As always, I ended up coming the solution on my own. Here is how I did it:

rsync -avr 'username@remotehost:/directory\ abc/' /directory\ abc/

That’s it. Enjoy!

Our sponsors:

FreeBSD or Linux

FreeBSD or Linux (Ubuntu/RHEL)? This is a very old question. It’s like asking iPhone or Android. There is no short answer. It all depends on your situation. To make things easier, I am going to break it down into six simple questions to help you making decision.

My Background
I have been a FreeBSD user since 2003. My usage on FreeBSD mainly on service-oriented stuffs such as web farm, database clusters and file system etc. In short, I mainly use my FreeBSD system via command line. In 2009, I jumped into Linux world (Ubuntu/RHEL) because of my job. As an advanced user on both Operating Systems (FreeBSD and Ubuntu/RHEL Linux), here is my guide on these two systems.

There is only one FreeBSD, but there are many different variants of Linux. The Linux I mention below refers to two popular distributions: RHEL and Ubuntu.

FreeBSD vs Linux: Q.1 How do you describe yourself?

I am a very demanding person. I like to control everything I manage. –> FreeBSD
I don’t care about how a system is run. I am okay as long as it just works. –> Linux / Ubuntu / RHEL

Comment:
FreeBSD gives you freedom to control every single thing. One of its coolest feature is the port tree. You can build every application from source using port tree. In Linux world, you usually install applications from pre-built/pre-compiled package (yum, apt-get etc), which may not be exactly what you need.

Example:
In RHEL and Ubuntu, HTTP load balancer module does not come with Apache by default. You will need to compile Apache from source. What about in FreeBSD? All you need is to check a box (pretty much like shopping cart) and you are done.

FreeBSD vs Linux: Q.2 Do you prefer Ferrari or Hyundai?

Ferrari / BMW / SLR Camera –> FreeBSD
Toyota / Hyundai / Point and Shoot Camera / Phone Camera –> Linux / Ubuntu / RHEL

Comment:
The technology uses by FreeBSD such as kernel, file system, architecture etc are way better and more advanced than Linux. It’s like comparing Ferrari and Hyundai (And no, I am not kidding).

Example 1:
I need to run some extreme applications (e.g., DNA Sequence Alignment) which use all available threads and memory. The default settings of memory management in Linux is very poor. Every time I run my application, the system becomes not usable to other users. However, FreeBSD does not have this server problem. In fact, FreeBSD is smart enough not to cause the system to freeze. Of course you can tweak the memory management settings in Linux, or even run the command along with the nice command. However, these settings are just not available out of the box, and most of the time, you learn these tricks after your system has problem.

Example 2:
I installed FreeBSD 11 and RHEL 7 on two identical computers respectively. Both use default settings and enable similar services, such as enabling the SSH server and disable booting to X-Windows (RHEL). I used these two machines for exact the same purposes: SSH tunneling, with exact the same work load (evenly distributed). After using them for a month, I checked the memory usage. With FreeBSD, the available memory is about 800MB (out of 1GB), while there are only 200MB left (out of 1GB) on RHEL. Yes, Linux (at least with RHEL 7) consumes lots of memory.

Example 3:
FreeBSD comes with ZFS (The next generation file system) by default. Although it has been ported to Linux world, it is definitely unstable. We’ve tried to use it in a production environment. One thing that we’ve learned is that the ZFS may stop working after upgrading to a newer Linux kernel. I’ve received countless of email alert about missing the files (ZFS is not working, of course the files are gone) in the middle of the night. I ended up disable the auto update and disable the reboot after the update. Sounds familiar? That’s a feature in Windows, and for some odd reasons, this feature is available in Linux, a server.

Example 4:
LVM+RAID is an the most advanced storage method in Linux world. Unfortunately it does not do what it promises, i.e., you may lose your data if a hard drive is failure, even if you follow its directions to detach your failed hard drive correctly. Not to mention that the data will get corrupted if the power is down (which has been taken care of in ZFS, available in FreeBSD).

That’s why I prefer ZFS over LVM+RAID here: Building a Super Large and Reliable File Server with Mixed Size of Harddisks. It solves my problem (yes, even the power is failed during writing to the disk, my data is still safe!)

FreeBSD vs Linux: Q.3 Do you have lots of free time?

Yes: FreeBSD
No: Linux / Ubuntu / RHEL

Comment:
Making a production-ready system using FreeBSD can take you days to weeks if you are not an experienced FreeBSD user, while everything works out of the box in Linux. Sometimes, the new upgrade from the port tree can drive you nut, such as package conflicts etc. However, working with Linux is a leisure thing.

Example:
Installing Apache + MySQL + PHP from FreeBSD port (compiling the source) can take at least half day on a computer with a dual core CPU (AMD Athlon 64 X2 Dual Core Processor 4600+), while it takes less than 30 minutes on Linux. That’s because you need to compile the code from source in FreeBSD, while you simply download the packages and extract them in Linux. The time difference is huge.

FreeBSD vs Linux: Q.4 Do you prefer simplicity or complexity?

Adding sugar into water –> FreeBSD
Taking sugar away from soda–> Linux / Ubuntu / RHEL

Comment:
FreeBSD is a very very simple system. Think of it as a bare-bone system that comes with no junk. By default, it comes with no graphic user interface, no unnecessary application. It likes a pure distilled water.

In Ubuntu / RHEL, everything is configured and ready to use. It comes with very attractive, beautiful graphical user interface. Everything just works out of the box, no tuning or tweaking is required. However, it also comes with lots of junk such as Ubuntu One (For Ubuntu Cloud service), SELinux (A program developed by Red Hat where many people don’t use it), etc. It makes your system very bulky and increase the computation resource consumption.

FreeBSD vs Linux: Q.5 Are you going to use the computer as desktop?

Yes: Linux / Ubuntu / RHEL
No: FreeBSD

Comment:
Setting up a desktop-ready system on FreeBSD can take a long time. Main reason is the drivers availability. A lot of hardware such as graphic cards, audio cards or webcams are not supported in FreeBSD natively. If you want to get them working as good as on Windows / Ubuntu, you will need to get the driver first (if available), build it (which may gives error during compiling the codes), and recompile the kernel to make it supports the new driver, which can take few days if you are not experienced with FreeBSD and debugging driver.

On the other side, the Linux driver community is very strong and well developed. Usually they develop drivers for most popular hardware.

Example:

#1: My Logitech Orbit MP webcam (Pan / Tilt / Zoom) is not working on FreeBSD but works like a charm on Linux.

#2: Some vendors such as Highpoint may stop developing drivers for their products for newest version of FreeBSD.

FreeBSD vs Linux: Q.6 Do you need to blame someone when something goes wrong?

Yes: Linux / Ubuntu / RHEL
No: FreeBSD

Comment:

When something goes wrong, you can blame Linux and you can’t blame FreeBSD.

FreeBSD is a community driven operating system, while some Linux distributions such as Ubuntu and RHEL are backed by commercial vendors. In the world of FreeBSD, it is not uncommon that some unskilled developers introduce bugs, troubles to the rest of the world. Yes, we know it is free, so we can’t complaint about it. However, as an IT administrator, you will need to use your judgement to judge whether those new stuffs are safe to use or not. In short, that will increase your workload. It’s more like Windows update. How many people actually read the change log before hitting the update button?

In Linux (e.g., RHEL), that’s a whole different story. Every patches, new updates have been screened by the vendor before hitting to public. So you can trust them in some degree. And the key thing is, you can blame them when something goes wrong.

Conclusion

In short, use FreeBSD for your personal purpose while Linux for your work. Be the top 5%, not the bottom 95%.

Our sponsors: