Do initrd dance before turning Linux physical server into VM

If one day you decide to convert your physical server to a VM, which could be easily achieved if all its disks are presented from SAN, then don’t forget to rebuild initrd beforehand. Otherwise you would see something similar to this:

No device found
Scanning and configuring dmraid supported devices
Scanning logical volumes
  Reading all physical volumes. This may take a while...
  No volume groups found
Activating logical volumes
  Volume group "VolGroup00" not found
Trying to resume from /dev/VolGroup00/LogVol01
Unable to access resume device (/dev/VolGroup00/LogVol01)
Creating root device.
Mounting root filesystem.
mount: could not find filesystem '/dev/root'
Setting up other filesystems.
Setting up new root fs
setuproot: moving /dev failed: No such file or directory
no fstab.sys, mounting internal defaults
setuproot: error mounting /proc: No such file or directory
setuproot: error mounting /sys: No such file or directory
Switching to new root and running init
unmount old /dev
unmount old /proc
unmount old /sys
switchroot: mount failed: No such file or directory 
Kernel panic - not syncing: Attempted to kill init! 

Also, if your SAN disks are multipathed, which is an obvious and the only correct choice, then you must (according to RedHat note) to disable multipath by editing /etc/sysconfig/mkinitrd/multipath, otherwise the system won’t boot:

# vi /etc/sysconfig/mkinitrd/multipath MULTIPATH=no

Root Cause
The multipath option should only be set to YES if you your root volume (/) is on a multipathed device
If multipath is enabled with root (/) on a local device, multipathing will enable at boot time and lock down the device
If the device is locked down, fsck will be unable to open it for checking

There are two options to rebuild initrd:

  1. Use mkinitrd or dracut, depending on the OS version you’re currently on, and pre-build a new initrd before detaching the disks from the old system.
  2. If the system has been already converted to a VM, .i.e. all disks from the old system have been detached and presented as RDMs to a new VM, then boot from a rescue disk, and chroot to /mnt/sysimage (if you are running RedHat or CentOS) and run mkinitrd or dracut from their. Keep in mind that /boot partition as well as /sys must be mounted in the chrooted environment or, again, your system will not fly.
  3. mount --bind /proc /mnt/sysimage/proc
    mount --bind /dev /mnt/sysimage/dev
    mount --bind /sys /mnt/sysimage/sys

Good luck.

Workaround for Tomcat7 on Linux, JDBC and javax.naming.NamingException

A few days ago I was dabbling with JDBC and Tomcat7 and the configuration that seemingly had no issues resulted in the following error in the log file:

org.apache.catalina.core.NamingContextListener addResource
WARNING: Failed to register in JMX: javax.naming.NamingException: Could not create resource factory instance
[Root exception is java.lang.ClassNotFoundException: org.apache.tomcat.dbcp.dbcp.BasicDataSourceFactory]

Thankfully, Google pointed me to this post at which had both the solution and the link to the details behind this behaviour.

In the nutshell, the workaround looks like the following:

  1. Grab tomcat-dbcp-version.jar from Maven that
    matches the version of Tomcat you are running and place it in $CATALINA_HOME/lib. Copying it somewhere else and creating a link also works.
  2. Update <Resource/> section in context.xml file by adding the following line:
  3. Restart Tomcat


P.S. Did a quick test and it looks like that FreeBSD distributes tomcat-dbcp.jar as part of its tomcat package:

# pkg query %Fp tomcat7 | grep dbcp

“Change master” to the rescue or how to revive MySQL replication

Sometime ago had an issue with MySQL replication that consecutively faulted with two different errors. Initially with this one:

Last_Error: Relay log read failure: Could not parse relay log event entry. The possible reasons are: the master’s binary log is corrupted (you can check this by running ‘mysqlbinlog’ on the binary log), the slave’s relay log is corrupted (you can check this by running ‘mysqlbinlog’ on the relay log), a network problem, or a bug in the master’s or slave’s MySQL code. If you want to check the master’s binary log or slave’s relay log, you will be able to know their names by issuing ‘SHOW SLAVE STATUS’ on this slave.

Thankfully, this error was easy to fix with the help of change master SQL statement:

change master to master_log_file='mysql-bin.000047', master_log_pos=152667618;

However, the second error kicked in immediately right after that:

Got fatal error 1236 from master when reading data from binary log: ‘Client requested master to start replication from impossible position; the first event ‘mysql-bin.000048’ at 223481321, the last event read from ‘/var/log/mysql/mysql-bin.000048’ at 4, the last byte read from ‘/var/log/mysql/mysql-bin.000048′ at 4.’

This one was also a no-brainer if you know how to fix them

Armed with mysqlbinlog it was easy to verify that there were no logs past 223481321 position:

mysqlbinlog --base64-output=decode-rows --verbose --start-position=223481321 ./mysql-bin.000048 
/*!40019 SET @@session.max_insert_delayed_threads=0*/;
# End of log file
ROLLBACK /* added by mysqlbinlog */;

Thus the proper solution in that case was to manually point the slave to the next available bin log:

change master to master_log_file='mysql-bin.000049', master_log_pos=4;

DTrace is limping when rootless is enabled

Just learnt that DTrace can’t be run at full pelt when rootless Mac OS X feature is enabled. For example, iotop ends like this:

: probe description io:::start does not match any probes

And it seems that the only way out is to boot into a rescue mode and run csrutil disable to turn off the protection mode. Only after that you could call your best friends like iotop, iosnoop and many others which are published at DTrace Book page.
Btw, if you haven’t bought it yet I highly recommend to do so.

Interview fizzle as a chance to get better

Not a long ago I had one of those humiliating moments when a simple question makes you numb a or even worse – you begin to mumble an absolute rubbish. That what exactly what has happened to me recently and being an afterthought person (which, of course, doesn’t give me any advantage) I decided to do some homework/recap o the questions I’ve failed misarebly.

  • Linux PIPE
  • – Read “man 2 pipe” as it basically says it all in a single sentene:

    pipe() creates a pair of file descriptors, pointing to a pipe inode, and places them in the array pointed to by filedes. filedes[0] is for reading, filedes[1] is for writing.

    – Want to go deeper then the source code is the best place to start:

  • Linux VM overcommit
  • – Again, start from reading the documentation.
    – Take a look at the code to figure out how the heuristic overcommit handling works. Especially, __vm_enough_memory() which is run by security_vm_enough_memory_mm(), which in turn could be called from different places, e.g. mmap_region(), acct_stack_growth(), do_brk(), insert_vm_struct(), dup_mmap().

  • – “man 3 malloc”, “man 2 mallopt”
    – Go through do_brk() code.

  • Swappiness
    – Read vm sysctl documentation about the swappiness parameter.
    – swappiness comes into play in get_scan_count() which is called from shrink_lruvec().
    – If the code looks murky, take a look at the answer published at which goes in a greater details about vm.swappiness.
    – Read about Split LRU

And of course, buy, read and re-read Understanding the Linux Kernel even if it’s a bit dated.

Expanding ZFS rpool in Solaris 10

I was really bad at googling the steps to grow ZFS rpool online without using zpool append, so here is my little story how I’ve done it.
Before I begin, please, note that everything said below applies only to the configurations where rpool consumes a whole disk. If there is another partition sitting right after (or with some gap) your rpool, you’re risking to corrupt the data. So don’t blindly use the last cylinder (or “$”) when it’s time to modify the partition table.

  1. Here is the rpool:
  2. # zpool list rpool
    rpool  31.1G  23.6G  7.52G  75%  ONLINE  -
  3. Saving the partition table first so later this information could be used to correctly re-lable (re-partition) the expanded disk. Btw, use “zpool status rpool -v” to find the device name:
  4. # prtvtoc /dev/dsk/c4t60060E80167D3C0000017D3C000010CAd0s2
    * /dev/dsk/c4t60060E80167D3C0000017D3C000010CAd0s2 partition map
    * Dimensions:
    *     512 bytes/sector
    *     512 sectors/track
    *      15 tracks/cylinder
    *    7680 sectors/cylinder
    *    8533 cylinders
    *    8531 accessible cylinders
    * Flags:
    *   1: unmountable
    *  10: read-only
    *                          First     Sector    Last
    * Partition  Tag  Flags    Sector     Count    Sector  Mount Directory
           0      2    00          0  65518080  65518079
           2      5    01          0  65518080  65518079
  5. Behind the scene LUN was expanded. To confirm that luxadm could be quite handy (pay attention to “Unformatted capacity”) field:
  6. # luxadm display /dev/rdsk/c4t60060E80167D3C0000017D3C000010CAd0s2
    DEVICE PROPERTIES for disk: /dev/rdsk/c4t60060E80167D3C0000017D3C000010CAd0s2
      Vendor:               HITACHI
      Product ID:           OPEN-V      -SUN
      Revision:             7006
      Serial Num:           50 17D3C10CA
      Unformatted capacity: 36864.000 MBytes
      Read Cache:           Enabled
        Minimum prefetch:   0x0
        Maximum prefetch:   0x0
      Device Type:          Disk device
  7. Time for the scariest part, i.e. re-lable the disk by installing a new partition table.
    To be able to do that a new disk’s geometry must be somehow conveyed to the format utility and that’s surprisingly easy to achieve. Just run format, select the disk and use “type” option to autoconfigure it:
  8. # format
    Searching for disks...done
           0. c1t0d0 
           1. c4t60060E80167D3C0000017D3C000010CAd0 
    Specify disk (enter its number): 1
    selecting c4t60060E80167D3C0000017D3C000010CAd0
    [disk formatted]
    /dev/dsk/c4t60060E80167D3C0000017D3C000010CAd0s0 is part of active ZFS pool rpool. Please see zpool(1M).
            disk       - select a disk
            type       - select (define) a disk type
            partition  - select (define) a partition table
            current    - describe the current disk
            format     - format and analyze the disk
            repair     - repair a defective sector
            label      - write label to the disk
            analyze    - surface analysis
            defect     - defect list management
            backup     - search for backup labels
            verify     - read and display labels
            save       - save new disk/partition definitions
            inquiry    - show vendor, product and revision
            volname    - set 8-character volume name
            !     - execute , then return
    format> type
            0. Auto configure
            1. Quantum ProDrive 80S
            2. Quantum ProDrive 105S
            3. CDC Wren IV 94171-344
            4. SUN0104
            5. SUN0207
            6. SUN0327
            7. SUN0340
            8. SUN0424
            9. SUN0535
            10. SUN0669
            11. SUN1.0G
            12. SUN1.05
            13. SUN1.3G
            14. SUN2.1G
            15. SUN2.9G
            16. Zip 100
            17. Zip 250
            18. Peerless 10GB
            19. HITACHI-OPEN-V-SUN-7005
            20. SUN300G
            21. other
    Specify disk type (enter its number)[19]: 0
    c4t60060E80167D3C0000017D3C000010CAd0: configured with capacity of 35.99GB
    selecting c4t60060E80167D3C0000017D3C000010CAd0
    [disk formatted]
  9. Notice that now it’s configured with a new capacity.
  10. Don’t leave the format prompt yet since we are not done. Next step is to carve out the partition table. Remember, that I only had two partitions (0 for root and 2 for backup) and your situation might be completely different, so don’t copy/paste rashly.
  11. Use the numbers from the menu to select the partition you’re willing to modify:
  12. format> partition
            0      - change `0' partition
            1      - change `1' partition
            2      - change `2' partition
            3      - change `3' partition
            4      - change `4' partition
            5      - change `5' partition
            6      - change `6' partition
            7      - change `7' partition
            select - select a predefined table
            modify - modify a predefined partition table
            name   - name the current table
            print  - display the current table
            label  - write partition map and label to the disk
  13. For me, it was enough to set the size of all partitions to zero except the two: 0 (tagged as root) and 2 (tagged as backup). As you can see below wm (write-mountable) flag was set only for partition 0, whilst the rest have wu (write-unmountable):
  14. partition> print
    Current partition table (unnamed):
    Total disk cylinders available: 9828 + 2 (reserved cylinders)
    Part      Tag    Flag     Cylinders        Size            Blocks
      0       root    wm       0 - 9827       35.99GB    (9828/0/0) 75479040
      1 unassigned    wu       0               0         (0/0/0)           0
      2     backup    wu       0 - 9827       35.99GB    (9828/0/0) 75479040
      3 unassigned    wu       0               0         (0/0/0)           0
      4 unassigned    wu       0               0         (0/0/0)           0
      5 unassigned    wu       0               0         (0/0/0)           0
      6 unassigned    wu       0               0         (0/0/0)           0
      7 unassigned    wu       0               0         (0/0/0)           0
  15. Label the disk and quit the format tool:
  16. partition> label
    Ready to label disk, continue? yes
    partition> q
    format> q

  17. Finally it’s time to grow ZFS rpool and to confirm we’re golden:
  18. # zpool online -e rpool /dev/dsk/c4t60060E80167D3C0000017D3C000010CAd0s0
    # zpool list rpool
    rpool  35.9G  23.6G  12.3G  65%  ONLINE  -

Good luck and safe expanding your pools.

mysqldump causes error 2006

Hot on the heels of the recent mysqldump I’ve been running on MySQL 5.5 which ended with the following error:

Got error: 2006: MySQL server has gone away when selecting the database 

Turned out that this error is quite common and there is a quick work around for that – increase max_allowed_packet. In my case going from 16M to 128M was enough.

P.S. There is a helpful thread at DBA Stackexchange which is worth reading too.

What unites DEFINER, “show table status” and ERROR 1143 (42000) in MySQL

For the very first time I had seen this error a couple of days ago:

mysql> show table status;
ERROR 1143 (42000): SELECT command denied to user ''@'some_host_name_here' for column 'sid' in table 'masking'

What the heck was that?!
Turned out that a colleague of mine was doing a cleanup in mysql.user table a day before and deleted a number of non-existent users. So what? Well, the database I was working with didn’t have only “plain” tables:

mysql> show full tables in database_name_here where table_type not like '%table%';
| Tables_in_infra | Table_type |
| v_pool          | VIEW       |
| v_pool_pivot    | VIEW       |
2 rows in set (0.00 sec)

Aha moment! So we had two views. Checked if there was a proper“DEFINER”:

mysql> select TABLE_NAME, DEFINER from information_schema.views;
| TABLE_NAME   | DEFINER                                    |
| v_pool       | some_user@some_host                        |
| v_pool_pivot | some_user@some_host                        |
10 rows in set (0.00 sec)

Of course, that was exactly the user which was deleted and thankfully, that was very easy to fix.
Just had to run “show create view” query to figure out how the view was created in the first place:

mysql> show create view v_pool_pivot\G
*************************** 1. row ***************************
                View: v_pool_pivot
         Create View: CREATE ALGORITHM=UNDEFINED DEFINER=`some_user@some_host` SQL SECURITY DEFINER VIEW `v_pool_pivot` AS (select followed by several lines of spaghetti SQL)
character_set_client: utf8
collation_connection: utf8_general_ci
1 row in set, 1 warning (0.00 sec)

And after that just altered it:

mysql> alter DEFINER=CURRENT_USER view v_pool_pivot AS (select ...)

Puzzle solved.

Bryan Cantrill in BSD Now podcast

The lastest episode of BSD Now (103) podcast brought in a fantastic and hilarious interview with Bryan Cantrill who is well known for his wit and right on the bullseye rants. It’s been awhile since I cried laughing so unquestionably this video is a highly recommended. Not to mention that his talk was very educational both from the technical (epoll, kqueue) and historical point of views. Bookmarked and added to the favorites.