Let’s take a look at the gzip format. Why might you want to do this?

1. Maybe you’re curious how gzip works
2. Maybe you’re curious how DEFLATE works. DEFLATE is the “actual” compression method inside of gzip. It’s also used in zip, png, git, http, pdf… the list is pretty long.
3. Maybe you would like to write a gzip/DEFLATE decompressor. (A compressor is more complicated–understanding the format alone isn’t enough)

Let’s work a few examples and look at the format in close detail. For all these examples, I’m using GNU gzip 1.10-3 on an x86_64 machine.

I recommend checking out the linked resources below for a deeper conceptual overview if you want to learn more. That said, these are the only worked examples of gzip and/or DEFLATE of which I’m aware, so they’re a great companion to one another. In particular, you may want to learn what a prefix code is ahead of time.

References:
[1] RFC 1951, DEFLATE standard, by Peter Deutsch
[2] RFC 1952, gzip standard, by Peter Deutsch
[3] infgen, by Mark Adler (one of the zlib/gzip/DEFLATE authors), a tool for dis-assembling and printing a gzip or DEFLATE stream. I found this useful in figuring out the endian-ness of bitfields, and somewhat in understanding the dynamic huffman decoding process. Documentation is here.
[4] An explanation of the ‘deflate’ algorithm by Antaeus Feldspar. A great conceptual overview of LZ77 and Huffman coding. I recommend reading this before reading my DEFLATE explanation.
[5] LZ77 compression, Wikipedia.
[6] Prefix-free codes generally and Huffman‘s algorithm specifically
[7] After writing this, I learned about puff.c, a reference (simple) implementation of a DEFLATE decompressor by Mark Adler.

Gzip format: Basics and compressing a stream

Let’s take a look at our first example. If you’re on Linux, feel free to run the examples I use as we go.

echo "hello hello hello hello" | gzip

The bytes gzip outputs are below. You can use xxd or any other hex dump tool to view binary files. Notice that the original is 24 bytes, while the compressed version is 29 bytes–gzip is not really intended for data this short, so all of the examples in this article actually get bigger.

The beginning and end in bold are the gzip header and footer. I learned the details of the format by reading RFC 1952: gzip

• Byte 0+1 (1f8b): Two fixed bytes that indicate “this is a gzip file”. These file-type indicators are also called “magic bytes”.
• Byte 2 (08): Indicates “the compression format is DEFLATE”. DEFLATE is the only format supported by gzip.
• Byte 3 (00): Flags. 8 single-bit flags.
  • Not set: TEXT (indicates this is ASCII text. hint to the decompressor only. i think gzip never sets this flag)
  • Not set: HCRC (adds a 16-bit CRC to the header)
  • Not set: EXTRA (adds an “extras” field to the header)
  • Not set: NAME (adds a filename to the header–if you compress a file instead of stdin this will be set)
  • Not set: COMMENT (adds a comment to the header)
  • There are also three reserved bits which are not used.
• Byte 4-7 (00000000): Mtime. These indicate when the compressed file was last modified, as a unix timestamp. gzip doesn’t set an associated time when compressing stdin. Technically the standard says it should use the current time, but this makes the output the same every time you run gzip, so it’s better than the original standard.
• Byte 8 (00): Extra flags. 8 more single-bit flags, this time specific to the DEFLATE format. None are set so let’s skip it. All they can indicate is “minimum compression level” and “max compression level”.
• Byte 9 (03): OS. OS “03” is Unix.
• Byte 10-20: Compressed (DEFLATE) contents. We’ll take a detailed look at DEFLATE below.
• Byte 21-24 (0088590b): CRC32 of the uncompressed data, “hello hello hello hello\n”. I assume this is correct. It’s worth noting, there are multiple things called “CRC32”.
• Byte 25-28 (18000000): Size of the uncompressed data. This is little-endian byte order, 0x00000018 = 16*1+1*8 = 24. The uncompressed text is 24 bytes, so this is correct.

DEFLATE format: Basics and fixed huffman coding

DEFLATE is the actual compression format used inside gzip. The format is detailed in RFC 1951: DEFLATE. DEFLATE is a dense format which uses bits instead of bytes, so we need to take a look at the binary, not the hex, and things will not be byte-aligned. The endian-ness is a little confusing in gzip, so we’ll usually be looking at the “reversed binary” row.

• As a hint, whenever we read bits, we use the “reverse” binary order. For Huffman codes, we keep the bit order in reverse. For fixed-length fields like integers, we reverse again into “normal” binary order. I’ll call out the order for each field.
• Byte 10: 1 1010011. Is it the last block? Yes.
  • 1: Last block. The last block flag here means that after this block ends, the DEFLATE stream is over

• Byte 10: 1 10 10011. Fixed huffman coding. We reverse the bits (because it’s always 2 bits, and we reverse any fixed number of bits) to get 01.

  • 00: Not compressed

  • 01: Fixed huffman coding.

  • 10: Dynamic huffman coding.
  • 11: Not allowed (error)
• So we’re using “fixed” huffman coding. That means there’s a static, fixed encoding scheme being used, defined by the DEFLATE standard. The scheme is given by the tables below. Note that Length/Distance codes are special–after you read one, you may read some extra bits according to the length/distance lookup tables.

• Now we read a series of codes. Each code might be
  • a literal (one binary byte), which is directly copied to the output
  • “end of block”. either another block is read, or if this was the last block, DEFLATE stops.
  • a length-distance pair. first code is a length, then a distance is read. then some of the output is copied–this reduces the size of repetitive content. the compressor/decompressor can look up to 32KB backwards for duplicate content. This copying scheme is called LZ77.
• Huffman codes are a “prefix-free code” (confusingly also called a “prefix code”). What that means is that, even though the code words are different lengths from one another, you can always unambigously tell which binary codeword is next. For example, suppose the bits you’re reading starts with: 0101. Is the next binary codeword 0, 01, 010, or 0101? In a prefix-free code, only one of those is a valid codeword, so it’s easy to tell. You don’t need any special separator to tell you the codeword is over. The space savings from not having a separator is really important for good compression. The “huffman” codes used by DEFLATE are prefix-free codes, but they’re not really optimal Huffman codes–it’s a common misnomer.
• Byte 10-11: 110 10011000 10010: A literal. 10011000 (152) minus 00110000 (48) is 104. 104 in ASCII is ‘h’.
• Byte 11-12: 000 10010101 10011: A literal. 10010101 (149) minus 00110000 (48) is 101. 101 in ASCII is ‘e’.
• Byte 12-13: 101 10011100 10011: A literal. 10011100 (156) minus 00110000 (48) is 108. 108 in ASCII is ‘l’.
• Byte 13-14: 100 10011100 10011: Another literal ‘l’
• Byte 14-15: 100 10011111 01010: A literal. 10011111 (159) minus 00110000 (48) is 111. 111 in ASCII is ‘o’.
• Byte 15-16: 111 01010000 10011: A literal. 01010000 (80) minus 00110000 (48) is 32. 32 in ASCII is ‘ ‘ (space).
• Byte 16-17: 000 10011000 00010: Another literal ‘h’.
• Byte 17: 000 0001011: A length. 0001011 (11) minus 0000001 (1) is 10, plus 257 is 267. We look up distance 256 in the “length lookup” table. The length is 15-16, a range.
• Byte 18: 1 00100: Because the length is a range, we read extra bits. The “length lookup” table says to read 1 extra bit: 1. The extra bits need to be re-flipped back to normal binary order to decode them, but 0b1 flipped is still 0b1. 15 (bottom of range) plus 0b1 = 1 (extra bits) is 16, so the final length is 16.
• Byte 18-19: 111 00100 10011101: After a length, we always read a distance next. Distances are encoded using a second huffman table. 00100 is code 4, which using the “distance lookup” table is distance 5-6.
• Byte 18-19: 11100100 1 0011101. Using the “distance lookup” table, we need to read 1 extra bit: 0b1. Again, we reverse it, and add 5 (bottom end of range) to 0b1 (extra bits read), to get a distance of 6.
• We copy from 6 characters ago in the output stream. The stream so far is “hello h”, so 6 characters back is starting at “e”. We copy 16 characters, resulting in “hello hello hello hello“. Why this copy didn’t start with the second “h” instead of the second “e”, I’m not sure.
• Byte 19-20: 1 00111010 0000000: A literal. 00111010 (58) minus 00110000 (48) is 10. 10 in ASCII is “\n” (new line)
• Byte 20: 0 0000000: End of block. In this case we ended nicely on the block boundry, too. This is the final block, so we’re done decoding entirely.
• At this point we’d check the CRC32 and length match what’s in the gzip footer right after the block.

Our final output is “hello hello hello hello\n”, which is exactly what we expected.

Gzip format: Compressing a file

Let’s generate a second example using a file.

echo -en "\xff\xfe\xfd\xfc\xfb\xfa\xf9\xf8\xf7\xf6\xf5\xf4\xf3\xf2\xf1" >test.bin
gzip test.bin

This input file is pretty weird. In fact, it’s so weird that gzip compression will fail to reduce its size at all. We’ll take a look at what happens when compression fails in the next DEFLATE section below. But first, let’s see how gzip changes with a file instead of a stdin stream.

Okay, let’s take a look at how the header and footer changed.

• Byte 0+1 (1f8b): Two fixed bytes that indicate “this is a gzip file”. These file-type indicators are also called “magic bytes”.
• Byte 2 (08): Indicates “the compression format is DEFLATE”. DEFLATE is the only format supported by gzip.
• Byte 3 (08): Flags. 8 single-bit flags.
  • Not set: TEXT (indicates this is ASCII text. hint to the decompressor only. i think gzip never sets this flag)
  • Not set: HCRC (adds a 16-bit CRC to the header)
  • Not set: EXTRA (adds an “extras” field to the header)
  • Set: NAME (adds a filename to the header)
  • Not set: COMMENT (adds a comment to the header)
  • There are also three reserved bits which are not used.
• Byte 4-7 (9f08ea60) . Mtime. This is in little-endian order: 0x60ea089f is 1625950367. This is a unix timestamp — 1625950367 seconds after midnight, Jan 1, 1970 is 2021-07-10 20:52:47 UTC, which is indeed earlier today. This is the time the original file was last changed, not when compression happened. This is here so we can restore the original modification time if we want.
• Byte 8 (00): Extra flags. None are set.
• Byte 9 (03): OS. OS “03” is Unix.
• Byte 10-18 (74 65 73 74 2e 62 69 6e 00): Zero-terminated string. The string is “test.bin”, the name of the file to decompress. We know this field is present because of the flag set.
• Byte 19-38: The compressed DEFLATE stream.
• Byte 39-42 (c6d3157e): CRC32 of the uncompressed data. Again, I’ll just assume this is correct.
• Byte 25-28 (0f000000): Size of the uncompressed data. 0x0000000f = 15 bytes, which is correct.

DEFLATE format: Uncompressed data

Uncompressed data is fairly rare in the wild from what I’ve seen, but for the sake of completeness we’ll cover it.

• Again, we start reading “r. binary” — the binary bits in reversed order.
• Byte 19: 10000000. The first three bits are the most important bits in the stream:
  • 1: Last block. The last block flag here means that after this block ends, the DEFLATE stream is over

• Byte 19: 100 00000. Not compressed. For a non-compressed block only, we also skip until the end of the byte.

  • 00: Not compressed

  • 01: Fixed huffman coding.

  • 10: Dynamic huffman coding.
• Byte 20-21: 11110000 00000000. Copy 15 uncompressed bytes. We reverse the binary bits as usual for fixed fields. 0b0000000000001111 = 0x000f = 15.
• Byte 22-23: 00001111 11111111. This is just the NOT (compliment) of byte 20-21 as a check. It can be ignored.
• Byte 24-38: ff fe fd fc fb fa f9 f8 f7 f6 f5 f4 f3 f2 f1: 15 literal bytes of data, which are directly copied to the decompressed output with no processing. Since we only have one block, this is the whole of the decompressed data.

DEFLATE format: Dynamic huffman coding

Dynamic huffman coding is by far the most complicated part of the DEFLATE and gzip specs. It also shows up a lot in practice, so we need to learn this too. Let’s take a look with a third and final example.

echo -n "abaabbbabaababbaababaaaabaaabbbbbaa" | gzip

The bytes we get are:

• Byte 0-9 (1f 8b 08 00 00 00 00 00 00 03): Header
• Byte 10-32 (1d c6 49 01 00 00 10 40 c0 ac a3 7f 88 3d 3c 20 2a 97 9d 37 5e 1d 0c): DEFLATE contents
• Byte 33-40 (6e 29 34 94 23 00 00 00): Footer. The uncompressed data is 35 bytes.

We’ve already seen everything interesting in the gzip format, so we’ll skip the header and footer, and move straight to looking at DEFLATE this time.

• As usual, we read “r. binary” — the binary bits in reversed order.
• Byte 10: 10111000. Last (only) block. The DEFLATE stream is over after this block.

• Byte 10: 10111000. 10=Dynamic huffman coding

  • 00: Not compressed

  • 01: Fixed huffman coding.

  • 10: Dynamic huffman coding.

Which parts are dynamic?

Okay, so what does “dynamic” huffman coding mean? A fixed huffman code had several hardcoded values defined by the spec. Some are still hardcoded, but some will now be defined by the gzip file.

1. The available literals are all single-byte literals. The literals remain fixed by the spec.
2. There is a “special” literal indicating the end of the block in both.
3. The lengths (how far to look backwards when copying) were given as ranges whose size was a power of two. For example, there would be one binary code (0001011) for the length range 15-16. Then, we would read one extra bit (because the range is 2^1 elements long) to find the specific length within that range. In a dynamic coding, the length ranges remain fixed by the spec. (“length lookup” table)
4. Again, the actual ranges and literals are fixed by the spec. The binary codewords to represent (lengths/literals/end-of-block) are defined in the gzip stream instead of hardcoded. (“literal/end-of-block/length huffman codes” table)
5. Like the literal ranges, the distance ranges remain fixed by the spec. (“distance lookup” table)
6. Although the distance ranges themselves are fixed, the binary codewords to represent distance ranges are defined in the gzip stream instead of hardcoded. (“distance huffman codes” table)

So basically, the possible lengths and distances are still the same (fixed) ranges, and the literals are still the same fixed literals. But where we had two hardcoded tables before, now we will load these two tables from the file. Since storing a table is bulky, the DEFLATE authors heavily compressed the representation of the tables, which is why dynamic huffman coding is so complicated.

Aside: Storing Prefix-Free Codewords as a List of Lengths

Suppose we have a set of prefix-free codewords: 0, 10, 1100, 1101, 1110, 1111. Forget about what each codeword means for a second, we’re just going to look at the codewords themselves.

We can store the lengths as a list: 1, 2, 4, 4, 4, 4.

• You could make another set of codewords with the same list of lengths. But for our purposes, as long as each value gets the same length of codeword, we don’t really care which of those codes we pick–the compressed content will be the same length.
• Since we don’t really care how if the bits change, any code is fine. For simplicity, we pick a unique “standard” code. When we list the codewords, the standard one can be listed BOTH in order of length, AND in normal sorted order. That is, the those two orders are the same. The example code above is a standard code. Here’s one that isn’t: 1, 01, 00.
• It turns out that if we have the lengths, we can generate a set of prefix-free codewords with those lengths. There’s an easy algorithm to generate the “standard” code from the list of lengths (see RFC 1951, it’s not very interesting)
• Since we picked the standard codewords, we can switch back and forth between codewords and codeword lengths without losing any information.
• It’s more compact to store the codeword lengths than the actual codewords. DEFLATE just stores codeword lengths everywhere (and uses the corresponding generated code).

Finally, we need to make them correspond to symbols, so we actually store

• We store lengths for each symbol: A=4, B=1, C=4, D=4, E=2, F=4
• We can get the correct codewords by going through the symbols in order, and grabbing the first available standard codeword: A=1100, B=0, C=1101, D=1110, E=10, F=1111.

Dynamic Huffman: Code Lengths

What’s a “code length”? It’s yet another hardcoded lookup table, which explains how to compress the dynamic huffman code tree itself. We’ll get to it in a second–the important thing about it for now is that there are 19 rows in the table. The binary column (not yet filled in) is what we’re about to decode.

• Byte 10: 101 11000. Number of literal/end-of-block/length codes (257-286). Read bits in forward order, 0b00011=3, plus 257 is 260 length/end-of-block/literal codes.
• Byte 11: 01100 011. Number of distance codes (1-32). Read bits in forward order, 0b00110=6, plus 1 is 7 distance codes.
• Byte 11-12: 01100 0111 0010010. Number of code length codes used (4-19). Read bits in forward order, 0b1110=14, plus 4 is 18.
• Byte 12-18 1 001 001 010 000 000 000 000 000 000 000 000 001 000 000 000 100 000 001 1: There are 18 codes used (out of 19 available). For each code length code, we read a 3-bit number (in big-endian order) called the “code length code length”, and fill the end with 0s: 4, 4, 2, 0, 0, 0, 0, 0, 0, 0, 0, 4, 0, 0, 0, 1, 0, 4[, 0]
• Next, we re-order the codes in the order 16, 17, 18, 0, 8, 7, 9, 6, 10, 5, 11, 4, 12, 3, 13, 2, 14, 1, 15. This re-order is just part of the spec, don’t ask why–it’s to save a small amount of space.
  The old order is: 16: 4, 17: 4, 18: 2, 0:0, 8:0, 7:0, 9:0, 6:0, 10:0, 5:0, 11:0, 4:4, 12:0, 3:0, 13:0, 2:1, 14:0, 1:4, 15:0
  The new order is: 0:0, 1:4, 2:1, 3:0, 4:4, 5:0, 6:0, 7:0, 8:0, 9:0, 10:0, 11:0, 12:0, 13:0, 14:0, 15:0, 16: 4, 17: 4, 18: 2
• 0s indicate the row is not used (no codeword needed). Let’s re-write it without those.
  1:4, 2:1, 4:4, 16: 4, 17: 4, 18: 2
• Now we assign a binary codewords of length N, to each length N in the list.
  1:1100,2:0,4:1101,16:1110,17:1111,18:10
• Finally, let’s take a look at the whole table again.

• Great, we’ve parsed the code lengths table.

Dynamic Huffman: Parsing the Huffman tree

• As a reminder, in bytes 10-12 we found there was a 260-row literal/end-of-block/length table and a 7-row distance table. Let’s read 267 numbers: the lengths of the codeword for each row.
• Byte 18-19: 0000001 10 0110101. Copy “0” code length 11-138 times
  0b1010110=86, plus 11 is 97. Literals 0-96 are not present.
• Byte 20: 1100 0101: Literal 1. Literal 97 (‘a’) has a codeword of length 1.
• Byte 20: 1100 0 101: Literal 2. Number 98 (‘b’) has a codeword of length 2.
• Byte 20-21: 11000 10 1111111 10. Copy “0” code length 11-138 times. 0b1111111=127, plus 11 is 138. Literals 99-236 are not present.
• Byte 21-22: 111111 10 0001000 1. Copy “0” code length 11-138 times. 0b0001000=8, plus 11 is 19. Literals 237-255 are not present.
• Bytes 22-23: 0001000 1101 11100. Literal 256 (end-of-block) has a codeword of length 4.
• Byte 23-24: 101 1110 00 0111100. Copy previous code 3-6 times. 0b00=0, plus 3 is 3. “Literals” 257-259 (all lengths) have codewords of length 4.
• We read 260 numbers, that’s the whole literal/end-of-block/length table. Assign the “standard” binary codewords based on the lengths to generate the following table:

• Now we read 7 more numbers in the same format: the 7-row distances table.
• Byte 24: 0 0 111100. Distance 0 has a codeword of length 2.
• Byte 24-25: 00 1111 000 0000100. Copy “0” code length 3-10 times. 0b000=0, plus 3 is 3. Distances 1-3 are not present.
• Byte 25: 0 0 0 0 0100: Distances 4-6 have length 2.
• We read 7 numbers, that’s the whole distances table. Assign the “standard” binary codewords to generate the following table:

Dynamic Huffman: Data stream decoding

• Now we’re ready to actually decode the data. Again, we’re reading a series of codes from the literal/end-of-block/length Huffman code table.
• Byte 25: 00000 10 0: Literal ‘a’, ‘b’, ‘a’
• Byte 26: 0 10 10 10 0: Literal ‘a’, ‘b’, ‘b’, ‘b’, ‘a’.
• Byte 27: 1110 10 0 1. Length 4. Whenever we read a length, we read a distance. The distance is a range, 7-8. The extra bit we read is 0b0=0, plus 7 is Distance 7. So we look back 7 bytes and copy 4. The new output is: baabbbabaab
• Byte 27-28: 1110100 1101 11 00 1: Length 3, Distance 9. We look back 9 bytes and copy 3. The new output is: abbabaababb
• Byte 28-29: 1011100 1111 01 1 00. Length 5, Distance 6. We look back 6 bytes and copy 5. The new output is: aababbaabab
• Byte 29: 111011 0 0. Literal ‘a’, ‘a’.
• Byte 30: 0 1111010. Literal ‘a’.
• Byte 30: 0 1111 01 0. Length 5, Distance 5. We look back 5 bytes and copy 5. The new output is: abaaaabaaa
• Byte 31: 10 111000: Literal ‘b’
• Byte 31: 10 1110 00: Length 4, Distance 1. We look back 1 byte and copy 4. The new output is: bbbbb
• Byte 32: 0 0 110000: Literal ‘a’, ‘a’.
• Byte 32: 00 1100 00: End-of block. Since this is the final block it’s also the end of the stream. This didn’t come up in the first example, but we zero-pad until the end of the byte when the block ends.
• The final output is a b a a b b b a baab abb aabab a a a abaaa b bbbb a a (spaces added for clarity), which is exactly what we expected.

I want my debian boot to work as follows:

1. If it’s in my house, it can boot without my being there. To make that happen, I’ll put the root disk key on a USB stick, which I keep in the computer.
2. If it’s not in my house, it needs a password to boot. This is the normal boot process.

As in part 1, this guide is debian-specific. To learn more about the Linux boot process, see part 1.

First, we need to prepare the USB stick. Use ‘dmesg’ and/or ‘lsblk’ to make a note of the USB stick’s path (/dev/sdae for me). I chose to write to a filesystem rather than a raw block device.

sudo mkfs.ext4 /dev/sdae # Make a filesystem directly on the device. No partition table.
sudo blkid /dev/sdae # Make a note of the filesystem UUID for later

Next, we’ll generate a key.

sudo mount /dev/sdae /mnt
sudo dd if=/dev/urandom of=/mnt/root-disk.key bs=1000 count=8

Add the key to your root so it can actually decrypt things. You’ll be prompted for your password:

sudo cryptsetup luksAddKey ROOT_DISK_DEVICE /mnt/root-disk.key

Make a script at /usr/local/sbin/unlockusbkey.sh

#!/bin/sh
USB_DEVICE=/dev/disk/by-uuid/a4b190b8-39d0-43cd-b3c9-7f13d807da48 # copy from blkid's output UUID=XXXX

if [ -b $USB_DEVICE ]; then
  # if device exists then output the keyfile from the usb key
  mkdir -p /usb
  mount $USB_DEVICE -t ext4 -o ro /usb
  cat /usb/root-disk.key
  umount /usb
  rmdir /usb
  echo "Loaded decryption key from USB key." >&2
else
  echo "FAILED to get USB key file ..." >&2
  /lib/cryptsetup/askpass "Enter passphrase"
fi

Mark the script as executable, and optionally test it.

chmod +x /usr/local/sbin/unlockusbkey.sh
sudo /usr/local/sbin/unlockusbkey.sh | cmp /mnt/root-disk.key

Edit /etc/crypttab to add the script.

root PARTLABEL=root_cipher none luks,keyscript=/usr/local/sbin/unlockusbkey.sh

Finally, re-generate your initramfs. I recommend either having a live USB or keeping a backup initramfs.

sudo update-initramfs -u

[1] This post is loosely based on a chain of tutorials based on each other, including this
[2] However, those collectively looked both out of date and like they were written without true understanding, and I wanted to clean up the mess. More definitive information was sourced from the actual cryptsetup documentation.

In this article, I migrate an existing debian 10 buster release, from an unencrypted root drive, to an encrypted root. I used a second hard drive because it’s safer–this is NOT an in-place migration guide. We will be encrypting / (root) only, not /boot. My computer uses UEFI. This guide is specific to debian–I happen to know these steps would be different on Arch Linux, for example. They probably work great on a different debian version, and might even work on something debian-based like Ubuntu.

In part 2, I add an optional extra where root decrypts using a special USB stick rather than a keyboard passphrase, for unattended boot.

Apologies if I forget any steps–I wrote this after I did the migration, and not during, so it’s not copy-paste.

Q: Why aren’t we encrypting /boot too?

1. Encrypting /boot doesn’t add much security. Anyone can guess what’s on my /boot–it’s the same as on everyone debian distro. And encrypting /boot doesn’t prevent tampering–someone can easily replace my encrypted partition by an unencrypted one without my noticing. Something like Secure Boot would resist tampering, but still doesn’t require an encrypted /boot.
2. I pull a special trick in part 2. Grub2’s has new built-in encryption support, which is what would allow encrypting /boot. But grub2 can’t handle keyfiles or keyscripts as of writing, which I use.

How boot works

For anyone that doesn’t know, here’s how a typical boot process works:

1. Your computer has built-in firmware, which on my computer meets a standard called UEFI. On older computers this is called BIOS. The firmware is built-in, closed-source, and often specific to your computer. You can replace it with something open-source if you wish.
2. The firmware has some settings for what order to boot hard disks, CD drives, and USB sticks in. The firmware tries each option in turn, failing and using the next if needed.
3. At the beginning of each hard disk is a partition table, a VERY short info section containing information about what partitions are on the disk, and where they are. There are two partition table types: MBR (older) and GPT (newer). UEFI can only read GPT partition tables. The first thing the firmware does for each boot disk is read the partition table, to figure out which partitions are there.
4. For UEFI, the firmware looks for an “EFI” partition on the boot disk–a special partition which contains bootloader executables. EFI always has a FAT filesystem on it. The firmware runs an EFI executable from the partition–which one is configured in the UEFI settings. In my setup there’s only one executable–the grub2 bootloader–so it runs that without special configuration.
5. Grub2 starts. The first thing Grub2 does is… read the partition table(s) again. It finds the /boot partition, which contains grub.cfg, and reads grub.cfg. (There is a file in the efi partition right next to the executable, which tells grub where and how to find /boot/grub.cfg. This second file is confusingly also called grub.cfg, so let’s forget it exists, we don’t care about it).
6. Grub2 invokes the Linux Kernel specified in grub.cfg, with the options specified in grub.cfg, including the an option to use a particular initramfs. Both the Linux kernel and the initramfs are also in /boot.
7. Now the kernel starts, using the initramfs. initramfs is a tiny, compressed, read-only filesystem only used in the bootloading process. The initramfs’s only job is to find the real root filesystem and open it. grub2 is pretty smart/big, which means initramfs may not have anything left to do on your system before you added encryption. If you’re doing decryption, it happens here. This is also how Linux handles weird filesystems (ZFS, btrfs, squashfs), some network filesystems, or hardware the bootloader doesn’t know about. At the end of the process, we now have switched over to the REAL root filesystem.
8. The kernel starts. We are now big boys who can take care of ourselves, and the bootloading process is over. The kernel always runs /bin/init from the filesystem, which on my system is a symlink to systemd. This does all the usual startup stuff (start any SSH server, print a bunch of messages to the console, show a graphical login, etc).

Setting up the encrypted disk

First off, I used TWO hard drives–this is not an in-place migration, and that way nothing is broken if you mess up. One disk was in my root, and stayed there the whole time. The other I connected via USB.

Here’s the output of gdisk -l on my original disk:

Number  Start (sector)    End (sector)  Size       Code  Name
   1            2048         1050623   512.0 MiB   EF00  # EFI, mounted at /boot/efi
   2         1050624       354803711   168.7 GiB   8300  # ext4, mounted at /
   3       354803712       488396799   63.7 GiB    8200  # swap

Here will be the final output of gdisk -l on the new disk:

Number  Start (sector)    End (sector)  Size       Code  Name
   1            2048          526335   256.0 MiB   EF00  efi # EFI, mounted at /boot/efi
   2         1050624       135268351   64.0 GiB    8200  swap # swap
   3       135268352       937703054   382.6 GiB   8300  root_cipher # ext4-on-LUKS. ext4 mounted at /
   4          526336         1050623   256.0 MiB   8300  boot # ext4, mounted at /boot

1. Stop anything else running. We’re going to do a “live” copy from the running system, so at least stop doing anything else. Also most of the commands in this guide need root (sudo).
2. Format the new disk. I used gdisk and you must select a gpt partition table. Basically I just made everything match the original. The one change I need is to add a /boot partition, so grub2 will be able to do the second stage. I also added partition labels with the c gdisk command to all partitions: boot, root_cipher, efi, and swap. I decided I’d like to be able to migrate to a larger disk later without updating a bunch of GUIDs, and filesystem or partition labels are a good method.

3. Add encryption. I like filesystem-on-LUKS, but most other debian guides use filesystem-in-LVM-on-LUKS. You’ll enter your new disk password twice–once to make an encrypted partition, once to open the partition.

   cryptsetup luksFormat /dev/disk/by-partlabel/root_cipher
   cryptsetup open /dev/disk-by-partlabel/root_cipher root
   

4. Make the filesystems. For my setup:

   mkfs.ext4 /dev/disk/by-partlabel/root
   mkfs.ext4 /dev/disk/by-partlabel/boot  
   mkfs.vfat /dev/disk/by-partlabel/efi
   

5. Mount all the new filesystems at /mnt. Make sure everything (cryptsetup included) uses EXACTLY the same mount paths (ex /dev/disk/by-partlabel/boot instead of /dev/sda1) as your final system will, because debian will examine your mounts to generate boot config files.

   mount /dev/disk/by-partlabel/root /mnt
   mkdir /mnt/boot && mount /dev/disk/by-partlabel/boot /mnt/boot 
   mkdir /mnt/boot/efi && mount /dev/disk/by-partlabel/efi /mnt/boot/efi
   mkdir /mnt/dev && mount --bind /dev /mnt/dev # for chroot
   mkdir /mnt/sys && mount --bind /sys /mnt/sys
   mkdir /mnt/proc && mount --bind /dev /mnt/proc
   

6. Copy everything over. I used rsync -axAX, but you can also use cp -ax. To learn what all these options are, read the man page. Make sure to keep the trailing slashes in the folder paths for rsync.

   rsync -xavHAX / /mnt/ --no-i-r --info=progress2
   rsync -xavHAX /boot/ /mnt/boot/
   rsync -xavHAX /boot/efi/ /mnt/boot/efi/
   

7. Chroot in. You will now be “in” the new system using your existing kernel.
   chroot /mnt

8. Edit /etc/crypttab. Add:
   root PARTLABEL=root_cipher none luks

9. Edit /etc/fstab. Mine looks like this:

   /dev/mapper/root / ext4 errors=remount-ro 0 1
   PARTLABEL=boot /boot ext4 defaults,nofail 0 1
   PARTLABEL=efi /boot/efi vfat umask=0077,nofail
   PARTLABEL=swap none swap sw,nofail 0 0
   tmpfs /tmp tmpfs mode=1777,nosuid,nodev 0 0
   

10. Edit /etc/default/grub. On debian you don’t need to edit GRUB_CMDLINE_LINUX.

    GRUB_DISABLE_LINUX_UUID=true
    GRUB_ENABLE_LINUX_PARTLABEL=true
    

11. Run grub-install. This will install the bootloader to efi. I forget the options to run it with… sorry!

12. Run update-grub (with no options). This will update /boot/grub.cfg so it knows how to find your new drive. You can verify the file by hand if you know how.
13. Run update-initramfs (with no options). This will update the initramfs so it can decrypt your root drive.
14. If there were any warnings or errors printed in the last three steps, something is wrong. Figure out what–it won’t boot otherwise. Especially make sure your /etc/fstab and /etc/crypttab exactly match what you’ve already used to mount filesystems.
15. Exit the chroot. Make sure any changes are synced to disk (you can unmount everything under /mnt in reverse order to make sure if you want)
16. Shut down your computer. Remove your root disk and boot from the new one. It should work now, asking for your password during boot.
17. Once you boot successfully and verify everything mounted, you can remove the nofail from /etc/fstab if you want.
18. (In my case, I also set up the swap partition after successful boot.) Edit: Oh, also don’t use unencrypted swap with encrypted root. That was dumb.

If you want a really good source of random numbers, you should get a hardware generator. But there’s not a lot of great options out there, and most people looking into this get (understandably) paranoid about backdoors. But, there’s a nice trick: if you combine multiple random sources together with xor, it doesn’t matter if one is backdoored, as long as they aren’t all backdoored. There are some exceptions–if the backdoor is actively looking at the output, it can still break your system. But as long as you’re just generating some random pads, instead of making a kernel entropy pool, you’re fine with this trick.

So! We just need a bunch of sources of randomness. Here’s the options I’ve tried:

• /dev/urandom (40,000KB/s) – this is nearly a pseudo-random number generator, so it’s not that good. But it’s good to throw in just in case. [Learn about /dev/random vs /dev/urandom if you haven’t. Then unlearn it again.]
• random-stream (1,000 KB/s), an implementation of the merenne twister pseudo-random-number generator. A worse version of /dev/urandom, use that unless you don’t trust the Linux kernel for some reason.
• infnoise (20-23 KB/s), a USB hardware random number generator. Optionally whitens using keccak. Mine is unfortunately broken (probably?) and outputs “USB read error” after a while
• OneRNG (55 KiB/s), a USB hardware random number generator. I use a custom script which outputs raw data instead of the provided scripts (although they look totally innocuous, do recommend
• /dev/hwrng (123 KB/s), which accesses the hardware random number generator built into the raspberry pi. this device is provided by the raspbian package rng-tools. I learned about this option here
• rdrand-gen (5,800 KB/s), a command-line tool to output random numbers from the Intel hardware generator instruction, RDRAND.

At the end, you can use my xor program to combine the streams/files. Make sure to use limit the output size if using files–by default it does not stop outputting data until EVERY file ends. The speed of the combined stream is at most going to be the slowest component (plus a little slowdown to xor everything). Here’s my final command line:

#!/bin/bash
# Fill up the folder with 1 GB one-time pads. Requires 'rng-tools' and a raspberry pi. Run as sudo to access /dev/hwrng.
while true; do
  sh onerng.sh | dd bs=1K count=1000000 of=tmp-onerng.pad 2>/dev/null
  infnoise --raw | dd bs=1K count=1000000 of=tmp-infnoise.pad 2>/dev/null
  xor tmp-onerng.pad tmp-infnoise.pad /dev/urandom /dev/hwrng | dd bs=1K count=1000000 of=/home/pi/pads/1GB-`\date +%Y-%m-%d-%H%M%S`.pad 2>/dev/null;
done

Great, now you have a good one-time-pad and can join ok-mixnet 🙂

P.S. If you really know what you’re doing and like shooting yourself in the foot, you could try combining and whitening entropy sources with a randomness sponge like keccak instead.

I added a software section to my website. It lists all the software I’ve made over the years (well not all of it, but what I think is most useful to others).

I updated the archive page as well, mostly to remove the software that was there. As usual, I try to make sure all links to my website are good forever.

I participate in a mentoring program, and recently one of the people I mentor asked me about whether it was okay to crawl something. I thought I would share my response, which is posted below nearly verbatim.

For this article, I’m skipping the subject of how to scrape websites (as off-topic), or how to avoid bans.

People keep telling me that if I scrape pages like Amazon that I’ll get banned. I definitely don’t want this to happen! So, what is your opinion on this?

Generally bans are temporary (a day to two weeks). I’d advise getting used to it, if you want to do serious scraping! If it would be really inconvenient, either don’t scrape the site or learn to use a secondary IP, so when your scraper gets banned, you can still use the site as a user.

More importantly than getting banned, you should learn about why things like bans are in place, because they’re not easy to set up–someone decided it was a good idea. Try to be a good person. As a programmer, you can cause a computer to blindly access a website millions of times–you get a big multiplier on anything a normal person can do. As such, you can cause the owners and users of a site problems, even by accident. Learn scraping etiquette, and always remember there’s an actual computer sitting somewhere, and actual people running the site.

That said, there’s a big difference between sending a lot of traffic to a site that hosts local chili cookoff results, and amazon.com. You could cause make the chili cookoff site hard to access or run up a small bill for the owners if you screw up enough, while realistically there’s nothing you can do to slow down Amazon.com even if you tried.

Here are a couple reasons people want to ban automated scraping:

1. It costs them money (bandwidth). Or, it makes the site unusable because too many “people” (all you) are trying to access it at once (congestion). Usually, it costs them money because the scaper is stupid–it’s something like a badly written search engine, which opens up every comment in a blog as a separate page, or opens up an infinite series of pages. For example, I host a bunch of large binaries (linux installers–big!), and I’ve had a search engine try to download every single one, once an hour. As a scraper, you can can avoid causing these problems by
   • rate-limiting your bot (ex. only scraping one page every 5-10 seconds, so you don’t overload their server). This is a good safety net–no matter what you do, you can’t break things too badly. If you’re downloading big files, you can also rate-limit your bandwidth or limit your total bandwidth quota.
   • examining what your scraper is doing as it runs (so you don’t download a bunch of unncessessary garbage, like computer-generated pages or a nearly-identical page for every blog comment)
   • obeying robots.txt, which you can probably get a scraping framework to do for you. you can choose to ignore robots.txt if you think you have a good reason to, but make sure you understand why robots.txt exists before you decide.
   • testing the site while you’re scraping by hand or with a computerized timer. If you see the site do something like load slower (even a little) because of what you’re doing, stop your scraper, and adjust your rate limit to be 10X smaller.
   • make your scraper smart. download only the pages you need. if you frequently stop and restart the scraper, have it remember the pages you downloaded–use some form of local cache to avoid re-downloading things. if you need to re-crawl (for example to maintain a mirror) pass if-modified-since HTTP headers.
   • declare an HTTP user-agent, which explains what you’re doing and how to contact you (email or phone) in case there is a problem. i’ve never had anyone actually contact me but as a site admin I have looked at user agents.
   • probably some more stuff i can’t think of off the top of my head
2. They want to keep their information secret and proprietary, because having their information publicly available would lose them money. This is the main reason Amazon will ban you–they don’t want their product databases published. My personal ethics says I generally ignore this consideration, but you may decide differently
3. They have a problem with automated bots posting spam or making accounts. Since you’re not doing either, this doesn’t really apply to you, but your program may be caught by the same filters trying to keep non-humans out.

For now I would advise not yet doing any of the above, because you’re basically not doing serious scraping yet. Grabbing all the pages on xkcd.com is fine, and won’t hurt anyone. If you’re going to download more than (say) 10,000 URLs per run, start looking at the list above. One exception–DO look at what your bot does by hand (the list of URLs, and maybe the HTML results), because it will be educational.

Also, in my web crawler project I eventually want to grab the text on each page crawled and analysis it using the requests library. Is something like this prohibited?

Prohibited by whom? Is it against an agreement you signed without reading with Amazon? Is it against US law? Would Amazon rather you didn’t, while having no actual means to stop you? These are questions you’ll have to figure out for yourself, and how much you care about each answer. You’ll also find the more you look into it that none of the three have very satisfactory answers.

The answer of “what bad thing might happen if I do this” is perhaps less satisfying if you’re trying to uphold what you perceive as your responsibilities, but easier to answer.

These are the things that may happen if you annoy a person or company on the internet by scraping their site. What happens will depend both on what you do, and what entity you are annoying (more on the second). Editor’s note: Some of the below is USA-specific, especially the presence/absence of legal or government action.

• You may be shown CAPTCHAs to see if you are a human
• Your scaper’s IP or IP block may be banned
• You or your scraper may be blocked in some what you don’t understand
• Your account may be deleted or banned (if your scraper uses an account, and rarely even if not)
• They may yell at you, send you an angry email, or send you a polite email asking you to stop and/or informing you that you’re banned and who to contact if you’d like to change that
• You may be sent a letter telling you to stop by a lawyer (a cease-and-desist letter), often with a threat of legal action if you do not
• You may be sued. This could be either a legitimate attempt to sue you, or a sort of extra-intimidating cease-and-desist letter. The attempt could be successful, unsuccessful but need you to show up in court, or could be something you can ignore althogether.
• You may be charged with some criminal charge such as computer, wire, or mail fraud. The only case I’m aware of offhand is Aaron Swartz
• You may be brought up on some charge by the FBI, which will result in your computers being taken away and not returned, and possibly jailtime. This one will only happen if you are crawling a government site (and is not supposed to happen ever, but that’s the world we live in).

For what it’s worth, so far I have gotten up to the “polite email” section in my personal life. I do a reasonable amount of scraping, mostly of smaller sites.

[… section specific to Amazon cut …]

Craigslist, government sites, and traditional publishers (print, audio, and academic databases) are the only companies I know of that aggressively goes after scrapers through legal means, instead of technical means. Craigslist will send you a letter telling you to stop first.

What a company will do once you publicly post all the information on their site is another matter, and I have less advice there. There are several sites that offer information about historical Amazon prices, for what that’s worth.

You may find this article interesting (but unhelpful) if you are concerned about being sued. Jason Scott is one of the main technical people at the Internet Archive, and people sometimes object to things he posts online.

In my personal opinion, suing people or bringing criminal charges does not work in general, because most people scraping do not live in the USA, and may use technical means to disguise who they are. Scrapers may be impossible to sue or charge with anything. In short, a policy of trying to sue people who scape your site, will result in your site still being scraped. Also, most people running a site don’t have the resources to sue anyone in any case. So you shouldn’t expect this to be a common outcome, but basically a small percentage of people (mostly crackpots) and companies (RIAA and publishers) may.

I made a site for your constant refresh needs: http://isrickandmortyout.com/

I made a new project called qr-backup. It’s a command-line program to back up any file to physical paper, using a number of QR codes. You can then restore it, even WITHOUT the qr-backup program, using the provided instructions.

I’m fairly satisfied with its current state (can actually back up my files, makes a PDF). There’s definitely some future features I’m looking forward to adding, though.

I’ve had pretty irregular sleep schedules at times, so I have some tricks for making it more regular, or moving it back/forwards. Take everything here with a spoonful of salt. All of these tricks are relatively long term (1-4 weeks) and won’t instantly fix your schedule. Most of them are from experience, with some knowledge backing them.

Also, as a note, I wake up whenever I feel like it (I don’t have a day job). I have used many of these same tricks with an alarm and a day job when I had those, but I might be forgetting some details.

Quality of sleep. First off, make sure the sleep you are getting, is good. I recommend something like a Zeo ideally, because it’s hard to get a subjective feel for how well you’re sleeping. Ultimately, it’s important to you to sleep enough and sleep well. Sleeping at the right times is important to other people.

Quantity of sleep. Get enough sleep. Enough said. If you have a good quality of sleep, you don’t use an alarm, and you’re waking up relaxed, you’re probably fine.

Here are some things I’ve found screw up my sleep schedule and affect my quality of sleep.

• Caffein affects schedule AND quality. Caffein at 2pm, affected my quality of sleep at 2am. This is something I just COULD NOT have figured out without a Zeo. Quality of sleep is hard to diagnose.
• Bright/blue light late affects schedule. Use f.lux or a similar program for your computer. Be aware that most programs of this kind don’t actually WORK for your phone–I don’t use a smartphone, personally. Don’t turn on room lights late at night. I find I’m good if I turn lights off about 3 hours before I want to sleep. Turning on lights very late at night (when you’d usually be asleep), even briefly, screws up your circadian rhythm.
• Light pollution affects quality. Light while you sleep sucks. I sleep next to a big window, and I often get poor sleep based on whether neighbors have their lights on. Or sometimes, I just need to sleep during the day.
  • A sleep mask gives you EXCELLENT quality of sleep, but can screw up your schedule because you don’t get early-morning light–you’ll sleep longer and drift forward.
  • Blackout curtains are like a sleep mask, but worse, because they don’t block light as well and they’re expensive. They could be better if you have light pollution from one window only, and they’re okay in combination with a timer light (see below).
  • Cover any electronics with lights, especially blinking or blue LEDs. I use black electrical tape.
• Allergens affect quality
  • Air quality massively affected my sleep. I’d wake up with my throat scratchy, but it took a while to figure out it was affecting my sleep. I now use an ionizing air filter. The trick to air filters is that you have to regularly (once a month) clean the prefilter, and replace the main filter every 6-12 months.
  • Itching. Sometimes this was just mold, which other than an air filter there’s not much I can do about, but also make sure to regularly wash your sheets. Food (don’t eat in bed!) or dust mites can make me itchy.
• Other drugs may affect schedule and quality. When I started on marijuana I found it massively screwed up my sleep schedule. YMMV. Some foods can too, especially before bed.
• Relaxation level affects quality. If you’re tense (neurotic especially), you’ll sleep poorly. I haven’t done a lot of experimentation with this one, because it comes up rarely for me. Deliberate relaxation and self-love (the hippie kind, not the sexual kind) before bed can give nice dreams, though.
• Exercise before bed, or working right before bed, affects at least schedule. Both tend to keep me up.
• Playing videos before bed affects quality. I might RIGHT before, like 2 minutes–I have some maybe bad habits as a bachelor. I think this doesn’t let your brain relax properly, you need more “down” time.
• Working in bed may affect schedule. As a general tip, it may be better to avoid working or otherwise being in bed during the day, to cue your body that bed=sleep.
• Nightmares affects quality. Unfortunately, I can’t be much help on this one. I rarely remember my dreams.
• Depression affects schedule and possibly quality. Depression makes you sleep more, mania makes you sleep less. If like me you become depressed when you don’t get enough sunlight, you can end up stuck nocturnal. A bright artificial light during the day is a partial solution.
• Having a regular schedule is self-reinforcing. If you regularly go to bed at the same time or wake up at the same time, you’ll keep doing it. Also, you’ll get cranky if you don’t. [A similar principle applies to dieting–if you eat meals at the same time each day, you’ll get a sudden appetite then. If you don’t eat meals regularly, you won’t have an appetite, or will have one only when actually hungry. But for sleep, regular is good]
• Age. At 20, I needed 12 hours of sleep a day. At 30, I need only 8-10. This varies a LOT per-person, too. Some people just need more/less sleep.

If you want to move your sleep schedule forward, it’s fairly easy. Just stay up later. I have only performed the “roll forward until you’re the right time” operation once, and don’t recommend it. Normally I hit a wall at dawn. Go forward by no more than 1 hour a day, preferably half that, or it won’t stick. If you do it for more than a few days, you’ll feel weird and sleep deprived.

If you want to move your sleep schedule back a significant amount (more than just undoing a recent 1-hour forward shift) I recommend:

• Do it gradually. Half an hour a day, probably more like 15 minutes. Don’t bother trying to schedule it.
• Have caffein AS SOON as you get up (within 15-30 minutes, the sooner the better). This moves your circadian rhythm back, and also stops you falling back asleep. Again I don’t use alarms these days, but it’s a great combo to set a schedule.
• You can try adjusting it by taking small (0.5mg) melatonin supplements before your usual bedtime, if you’ve just drifted forward a bit
• Make sure you are getting natural light if possible. If you aren’t, or if it’s winter and you want extra help: hook up your lights, especially a sun lamp, to an automated timer so you get bright white light in your room around when you’d like to wake up. This can fix problems caused by blackout curtains.

Finally, I’ll leave you with a horrifying trick I learned while sleep-deprived at my first job after college. To get up while incredibly sleep deprived, set two alarms, about 30 minutes apart. After the first one, hit the alarm, chug significant portions of an energy drink on reflex while mostly asleep, then immediately fall back sleep. On the second one, actually wake up–the caffein will help keep you awake.

I made a new cryptosystem called OK-Mixnet. It has “perfect” security, as opposed to the usual pretty-good security. (Of course, it’s not magic–if your computer is hacked, the cryptosystem isn’t gonna protect your data). Despite the name, it’s not really a mixnet per se, it just similarly defends against SIGINT.

A writeup is here: https://za3k.com/ok-mixnet.md

The alpha codebase is here: https://github.com/za3k/ok-mixnet

Let me know if you’d like to join the open alpha. Email me your username and IP (you’ll need to forward a port).