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section .data
    hello_world db "Hello world!", 10
    hello_world_len  equ $ - hello_world
section .text
    global _start
    _start:
        mov rax, 1
        mov rdi, 1
        mov rsi, hello_world
        mov rdx, hello_world_len
        syscall
        mov rax, 60
        mov rdi, 0
        syscall

Compiled with:

nasm -w+all -f elf64 -o 'hello_world.o' 'hello_world.asm'
ld -o 'hello_world.out' 'hello_world.o'

TODO: use a minimal linker script with -T to be more precise and minimal.

Versions:

NASM 2.10.09
Binutils version 2.24 (contains ld)
Ubuntu 14.04

We don't use a C program as that would complicate the analysis, that will be level 2 :-)

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ELF Hello World Tutorial / Object hd by

Ciro Santilli 37 Updated 2025-07-16

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Running:

hd hello_world.o

gives:

00000000  7f 45 4c 46 02 01 01 00  00 00 00 00 00 00 00 00  |.ELF............|
00000010  01 00 3e 00 01 00 00 00  00 00 00 00 00 00 00 00  |..>.............|
00000020  00 00 00 00 00 00 00 00  40 00 00 00 00 00 00 00  |........@.......|
00000030  00 00 00 00 40 00 00 00  00 00 40 00 07 00 03 00  |....@.....@.....|
00000040  00 00 00 00 00 00 00 00  00 00 00 00 00 00 00 00  |................|
*
00000080  01 00 00 00 01 00 00 00  03 00 00 00 00 00 00 00  |................|
00000090  00 00 00 00 00 00 00 00  00 02 00 00 00 00 00 00  |................|
000000a0  0d 00 00 00 00 00 00 00  00 00 00 00 00 00 00 00  |................|
000000b0  04 00 00 00 00 00 00 00  00 00 00 00 00 00 00 00  |................|
000000c0  07 00 00 00 01 00 00 00  06 00 00 00 00 00 00 00  |................|
000000d0  00 00 00 00 00 00 00 00  10 02 00 00 00 00 00 00  |................|
000000e0  27 00 00 00 00 00 00 00  00 00 00 00 00 00 00 00  |'...............|
000000f0  10 00 00 00 00 00 00 00  00 00 00 00 00 00 00 00  |................|
00000100  0d 00 00 00 03 00 00 00  00 00 00 00 00 00 00 00  |................|
00000110  00 00 00 00 00 00 00 00  40 02 00 00 00 00 00 00  |........@.......|
00000120  32 00 00 00 00 00 00 00  00 00 00 00 00 00 00 00  |2...............|
00000130  01 00 00 00 00 00 00 00  00 00 00 00 00 00 00 00  |................|
00000140  17 00 00 00 02 00 00 00  00 00 00 00 00 00 00 00  |................|
00000150  00 00 00 00 00 00 00 00  80 02 00 00 00 00 00 00  |................|
00000160  a8 00 00 00 00 00 00 00  05 00 00 00 06 00 00 00  |................|
00000170  04 00 00 00 00 00 00 00  18 00 00 00 00 00 00 00  |................|
00000180  1f 00 00 00 03 00 00 00  00 00 00 00 00 00 00 00  |................|
00000190  00 00 00 00 00 00 00 00  30 03 00 00 00 00 00 00  |........0.......|
000001a0  34 00 00 00 00 00 00 00  00 00 00 00 00 00 00 00  |4...............|
000001b0  01 00 00 00 00 00 00 00  00 00 00 00 00 00 00 00  |................|
000001c0  27 00 00 00 04 00 00 00  00 00 00 00 00 00 00 00  |'...............|
000001d0  00 00 00 00 00 00 00 00  70 03 00 00 00 00 00 00  |........p.......|
000001e0  18 00 00 00 00 00 00 00  04 00 00 00 02 00 00 00  |................|
000001f0  04 00 00 00 00 00 00 00  18 00 00 00 00 00 00 00  |................|
00000200  48 65 6c 6c 6f 20 77 6f  72 6c 64 21 0a 00 00 00  |Hello world!....|
00000210  b8 01 00 00 00 bf 01 00  00 00 48 be 00 00 00 00  |..........H.....|
00000220  00 00 00 00 ba 0d 00 00  00 0f 05 b8 3c 00 00 00  |............<...|
00000230  bf 00 00 00 00 0f 05 00  00 00 00 00 00 00 00 00  |................|
00000240  00 2e 64 61 74 61 00 2e  74 65 78 74 00 2e 73 68  |..data..text..sh|
00000250  73 74 72 74 61 62 00 2e  73 79 6d 74 61 62 00 2e  |strtab..symtab..|
00000260  73 74 72 74 61 62 00 2e  72 65 6c 61 2e 74 65 78  |strtab..rela.tex|
00000270  74 00 00 00 00 00 00 00  00 00 00 00 00 00 00 00  |t...............|
00000280  00 00 00 00 00 00 00 00  00 00 00 00 00 00 00 00  |................|
00000290  00 00 00 00 00 00 00 00  01 00 00 00 04 00 f1 ff  |................|
000002a0  00 00 00 00 00 00 00 00  00 00 00 00 00 00 00 00  |................|
000002b0  00 00 00 00 03 00 01 00  00 00 00 00 00 00 00 00  |................|
000002c0  00 00 00 00 00 00 00 00  00 00 00 00 03 00 02 00  |................|
000002d0  00 00 00 00 00 00 00 00  00 00 00 00 00 00 00 00  |................|
000002e0  11 00 00 00 00 00 01 00  00 00 00 00 00 00 00 00  |................|
000002f0  00 00 00 00 00 00 00 00  1d 00 00 00 00 00 f1 ff  |................|
00000300  0d 00 00 00 00 00 00 00  00 00 00 00 00 00 00 00  |................|
00000310  2d 00 00 00 10 00 02 00  00 00 00 00 00 00 00 00  |-...............|
00000320  00 00 00 00 00 00 00 00  00 00 00 00 00 00 00 00  |................|
00000330  00 68 65 6c 6c 6f 5f 77  6f 72 6c 64 2e 61 73 6d  |.hello_world.asm|
00000340  00 68 65 6c 6c 6f 5f 77  6f 72 6c 64 00 68 65 6c  |.hello_world.hel|
00000350  6c 6f 5f 77 6f 72 6c 64  5f 6c 65 6e 00 5f 73 74  |lo_world_len._st|
00000360  61 72 74 00 00 00 00 00  00 00 00 00 00 00 00 00  |art.............|
00000370  0c 00 00 00 00 00 00 00  01 00 00 00 02 00 00 00  |................|
00000380  00 00 00 00 00 00 00 00  00 00 00 00 00 00 00 00  |................|
00000390

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ELF Hello World Tutorial / SHT_STRTAB by

Ciro Santilli 37 Updated 2025-07-16

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Sections with sh_type == SHT_STRTAB are called string tables.

They hold a null separated array of strings.

Such sections are used by other sections when string names are to be used. The using section says:

which string table they are using
what is the index on the target string table where the string starts

So for example, we could have a string table containing:

Data: \0 a b c \0 d e f \0
Index: 0 1 2 3  4 5 6 7  8

The first byte must be a 0. TODO rationale?

And if another section wants to use the string d e f, they have to point to index 5 of this section (letter d).

Notable string table sections:

.shstrtab
.strtab

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Astera Institute by

Ciro Santilli 37 Updated 2025-07-16

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astera.org/agi/

By the rich founder of Mt. Gox and Ripple, Jed McCaleb.

Obelisk is the Artificial General Intelligence laboratory at Astera. We are focused on the following problems: How does an agent continuously adapt to a changing environment and incorporate new information? In a complicated stochastic environment with sparse rewards, how does an agent associate rewards with the correct set of actions that led to those rewards? How does higher level planning arise?

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ELF Hello World Tutorial / .shstrtab by

Ciro Santilli 37 Updated 2025-07-16

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Section type: sh_type == SHT_STRTAB.

Common name: "section header string table".

The section name .shstrtab is reserved. The standard says:

This section holds section names.

This section gets pointed to by the e_shstrnd field of the ELF header itself.

String indexes of this section are are pointed to by the sh_name field of section headers, which denote strings.

This section does not have SHF_ALLOC marked, so it will not appear on the executing program.

readelf -x .shstrtab hello_world.o

outputs:

Hex dump of section '.shstrtab':
  0x00000000 002e6461 7461002e 74657874 002e7368 ..data..text..sh
  0x00000010 73747274 6162002e 73796d74 6162002e strtab..symtab..
  0x00000020 73747274 6162002e 72656c61 2e746578 strtab..rela.tex
  0x00000030 7400                                t.

The data in this section has a fixed format: www.sco.com/developers/gabi/2003-12-17/ch4.strtab.html

If we look at the names of other sections, we see that they all contain numbers, e.g. the .text section is number 7.

Then each string ends when the first NUL character is found, e.g. character 12 is \0 just after .text\0.

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ELF Hello World Tutorial / STT_SECTION by

Ciro Santilli 37 Updated 2025-07-16

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There are two such entries, one pointing to .data and the other to .text (section indexes 1 and 2).

Num:    Value          Size Type    Bind   Vis      Ndx Name
  2: 0000000000000000     0 SECTION LOCAL  DEFAULT    1
  3: 0000000000000000     0 SECTION LOCAL  DEFAULT    2

TODO what is their purpose?

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ELF Hello World Tutorial / SHN_ABS by

Ciro Santilli 37 Updated 2025-07-16

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hello_world_len points to the special st_shndx == SHN_ABS == 0xF1FF.

0xF1FF is chosen so as to not conflict with other sections.

st_value == 0xD == 13 which is the value we have stored there on the assembly: the length of the string Hello World!.

This means that relocation will not affect this value: it is a constant.

This is small optimization that our assembler does for us and which has ELF support.

If we had used the address of hello_world_len anywhere, the assembler would not have been able to mark it as SHN_ABS, and the linker would have extra relocation work on it later.

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ELF Hello World Tutorial / SHT_SYMTAB on the executable by

Ciro Santilli 37 Updated 2025-07-16

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By default, NASM places a .symtab on the executable as well.

This is only used for debugging. Without the symbols, we are completely blind, and must reverse engineer everything.

You can strip it with objcopy, and the executable will still run. Such executables are called "stripped executables".

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British political party by

Ciro Santilli 37 Updated 2025-07-16

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ELF Hello World Tutorial / .strtab by

Ciro Santilli 37 Updated 2025-07-16

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Holds strings for the symbol table.

This section has sh_type == SHT_STRTAB.

It is pointed to by sh_link == 5 of the .symtab section.

readelf -x .strtab hello_world.o

outputs:

Hex dump of section '.strtab':
  0x00000000 0068656c 6c6f5f77 6f726c64 2e61736d .hello_world.asm
  0x00000010 0068656c 6c6f5f77 6f726c64 0068656c .hello_world.hel
  0x00000020 6c6f5f77 6f726c64 5f6c656e 005f7374 lo_world_len._st
  0x00000030 61727400                            art.

This implies that it is an ELF level limitation that global variables cannot contain NUL characters.

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ELF Hello World Tutorial / .rel.text by

Ciro Santilli 37 Updated 2025-07-16

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Besides sh_type == SHT_RELA, there also exists SHT_REL, which would have section name .text.rel (not present in this object file).

Those represent the same struct, but without the addend, e.g.:

typedef struct {
    Elf64_Addr  r_offset;
    Elf64_Xword r_info;
} Elf64_Rela;

The ELF standard says that in many cases the both can be used, and it is just a matter of convenience.

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ELF Hello World Tutorial / PT_INTERP by

Ciro Santilli 37 Updated 2025-07-16

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Contains the path to the dynamic loader, i.e. /lib64/ld-linux-x86-64.so.2 in Ubuntu 18.10. Explained at: stackoverflow.com/questions/8040631/checking-if-a-binary-compiled-with-static/55664341#55664341

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ELF Hello World Tutorial / DF_1_PIE by

Ciro Santilli 37 Updated 2025-07-16

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Determines if an executable is a position independent executable (PIE).

Seems to be informational only, since not used by Linux kernel 5.0 or glibc 2.29.

file 5.36 however does use it to display file type as explained at: stackoverflow.com/questions/34519521/why-does-gcc-create-a-shared-object-instead-of-an-executable-binary-according-to/55704865#55704865

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ELF Hello World Tutorial / Program header table by

Ciro Santilli 37 Updated 2025-07-16

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Only appears in the executable.

Contains information of how the executable should be put into the process virtual memory.

The executable is generated from object files by the linker. The main jobs that the linker does are:

determine which sections of the object files will go into which segments of the executable.
In Binutils, this comes down to parsing a linker script, and dealing with a bunch of defaults.
You can get the linker script used with ld --verbose, and set a custom one with ld -T.
do relocation according to the .rela.text section. This depends on how the multiple sections are put into memory.

readelf -l hello_world.out gives:

Elf file type is EXEC (Executable file)
Entry point 0x4000b0
There are 2 program headers, starting at offset 64

Program Headers:
  Type           Offset             VirtAddr           PhysAddr
                 FileSiz            MemSiz              Flags  Align
  LOAD           0x0000000000000000 0x0000000000400000 0x0000000000400000
                 0x00000000000000d7 0x00000000000000d7  R E    200000
  LOAD           0x00000000000000d8 0x00000000006000d8 0x00000000006000d8
                 0x000000000000000d 0x000000000000000d  RW     200000

 Section to Segment mapping:
  Segment Sections...
   00     .text
   01     .data

On the ELF header, e_phoff, e_phnum and e_phentsize told us that there are 2 program headers, which start at 0x40 and are 0x38 bytes long each, so they are:

00000040  01 00 00 00 05 00 00 00  00 00 00 00 00 00 00 00  |................|
00000050  00 00 40 00 00 00 00 00  00 00 40 00 00 00 00 00  |..@.......@.....|
00000060  d7 00 00 00 00 00 00 00  d7 00 00 00 00 00 00 00  |................|
00000070  00 00 20 00 00 00 00 00                           |.. .....        |

and:

00000070                           01 00 00 00 06 00 00 00  |        ........|
00000080  d8 00 00 00 00 00 00 00  d8 00 60 00 00 00 00 00  |..........`.....|
00000090  d8 00 60 00 00 00 00 00  0d 00 00 00 00 00 00 00  |..`.............|
000000a0  0d 00 00 00 00 00 00 00  00 00 20 00 00 00 00 00  |.......... .....|

Structure represented www.sco.com/developers/gabi/2003-12-17/ch5.pheader.html:

typedef struct {
    Elf64_Word  p_type;
    Elf64_Word  p_flags;
    Elf64_Off   p_offset;
    Elf64_Addr  p_vaddr;
    Elf64_Addr  p_paddr;
    Elf64_Xword p_filesz;
    Elf64_Xword p_memsz;
    Elf64_Xword p_align;
} Elf64_Phdr;

Breakdown of the first one:

40 0: p_type = 01 00 00 00 = PT_LOAD: this is a regular segment that will get loaded in memory.
40 4: p_flags = 05 00 00 00 = execute and read permissions. No write: we cannot modify the text segment. A classic way to do this in C is with string literals: stackoverflow.com/a/30662565/895245 This allows kernels to do certain optimizations, like sharing the segment amongst processes.
40 8: p_offset = 8x 00 TODO: what is this? Standard says:
This member gives the offset from the beginning of the file at which the first byte of the segment resides.
But it looks like offsets from the beginning of segments, not file?
50 0: p_vaddr = 00 00 40 00 00 00 00 00: initial virtual memory address to load this segment to
50 8: p_paddr = 00 00 40 00 00 00 00 00: unspecified effect. Intended for systems in which physical addressing matters. TODO example?
60 0: p_filesz = d7 00 00 00 00 00 00 00: size that the segment occupies in memory. If smaller than p_memsz, the OS fills it with zeroes to fit when loading the program. This is how BSS data is implemented to save space on executable files. i368 ABI says on PT_LOAD:
The bytes from the file are mapped to the beginning of the memory segment. If the segment’s memory size (p_memsz) is larger than the file size (p_filesz), the ‘‘extra’’ bytes are defined to hold the value 0 and to follow the segment’s initialized area. The file size may not be larger than the memory size.

60 8: p_memsz = d7 00 00 00 00 00 00 00: size that the segment occupies in memory
70 0: p_align = 00 00 20 00 00 00 00 00: 0 or 1 mean no alignment required. TODO why is this required? Why not just use p_addr directly, and get that right? Docs also say:
p_vaddr should equal p_offset, modulo p_align

The second segment (.data) is analogous. TODO: why use offset 0x0000d8 and address 0x00000000006000d8? Why not just use 0 and 0x00000000006000d8?

Then the:

 Section to Segment mapping:

section of the readelf tells us that:

0 is the .text segment. Aha, so this is why it is executable, and not writable
1 is the .data segment.

TODO where does this information come from? stackoverflow.com/questions/23018496/section-to-segment-mapping-in-elf-files

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Molecular biology feels like systems programming by

Ciro Santilli 37 Updated 2025-07-16

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Whenever Ciro Santilli learns about molecular biology, he can't help but to feel that it feels like programming, and notably systems programming and computer hardware design.

In some sense, the comparison is obvious: DNA is clearly a programmable medium like any assembly language, but still, systems programming did give Ciro some further feelings.

The most important analogy perhaps is observability, or more precisely the lack of it. For the computer, this is described at: The lower level you go into a computer, the harder it is to observe things.
And then, when Ciro started learning a bit about biology techniques, he started to feel the exact same thing.
For example when he played with E. Coli Whole Cell Model by Covert Lab, the main thing Ciro felt was: it is going to be hard to verify any of this data, because it is hard/impossible to know the concentration of each element in a cell as a function of time.
More generally of course, this is exactly why making any biology discovery is so hard: we can't easily see what's going on inside the cell, and have to resort to indirect ways of doing so..
This exact idea was highlighted by I should have loved biology by James Somers:
For a computer scientist, a biologist's methods can seem insane; the trouble comes from the fact that cells are too small, too numerous, too complex to analyze the way a programmer would, say in a step-by-step debugger.
And then just like in software, some of the methods biologists use to overcome the lack of visibility have direct software analogues:
- add instrumentation to cells, e.g. GFP tagging comes to mind
- emulation, e.g. E. Coli Whole Cell Model by Covert Lab
The boot process is another one. E.g. in x86 the way that you start in 16-bit mode, largely compatible into the 70's, then move to 32-bit and finally 64, does feel a lot the way a earlier stages of embryo development looks more and more like more ancient animals.

Ciro likes to think that maybe that is why a hardcore systems programmer like Bert Hubert got into molecular biology.

Some other people who mention similar things:

I should have loved biology by James Somers highlights the computer abstraction layer analogy between the two:
Everywhere you look - the compiler, the shell, the CPU, the DOM - is an abstraction hiding lifetimes of work.

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Virtualization by

Ciro Santilli 37 Updated 2025-07-16

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Docker (software) by

Ciro Santilli 37 Updated 2025-07-16

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Docker is good.

As a lightweight virtualization however, it does break more often than full proper virtualization like QEMU after some updates.

The images also appear to randomly update slightly and break things, even though you've specified e.g.:

FROM ubuntu:20.04

Also, we need more Linux distributions buildable from source, especially with Reproducible builds.

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 Pinned article: Introduction to the OurBigBook Project

Welcome to the OurBigBook Project! Our goal is to create the perfect publishing platform for STEM subjects, and get university-level students to write the best free STEM tutorials ever.

Everyone is welcome to create an account and play with the site: ourbigbook.com/go/register. We belive that students themselves can write amazing tutorials, but teachers are welcome too. You can write about anything you want, it doesn't have to be STEM or even educational. Silly test content is very welcome and you won't be penalized in any way. Just keep it legal!

Video 1.

Intro to OurBigBook

. Source.

We have two killer features:

topics: topics group articles by different users with the same title, e.g. here is the topic for the "Fundamental Theorem of Calculus" ourbigbook.com/go/topic/fundamental-theorem-of-calculus
Articles of different users are sorted by upvote within each article page. This feature is a bit like:
- a Wikipedia where each user can have their own version of each article
- a Q&A website like Stack Overflow, where multiple people can give their views on a given topic, and the best ones are sorted by upvote. Except you don't need to wait for someone to ask first, and any topic goes, no matter how narrow or broad
This feature makes it possible for readers to find better explanations of any topic created by other writers. And it allows writers to create an explanation in a place that readers might actually find it.
Figure 1.
Screenshot of the "Derivative" topic page
. View it live at: ourbigbook.com/go/topic/derivative
Video 2.
OurBigBook Web topics demo
. Source.
local editing: you can store all your personal knowledge base content locally in a plaintext markup format that can be edited locally and published either:
- to OurBigBook.com to get awesome multi-user features like topics and likes
- as HTML files to a static website, which you can host yourself for free on many external providers like GitHub Pages, and remain in full control
This way you can be sure that even if OurBigBook.com were to go down one day (which we have no plans to do as it is quite cheap to host!), your content will still be perfectly readable as a static site.
Figure 2.
You can publish local OurBigBook lightweight markup files to either OurBigBook.com or as a static website
.
Figure 3.
Visual Studio Code extension installation
.
Figure 4.
Visual Studio Code extension tree navigation
.
Figure 5.
Web editor
. You can also edit articles on the Web editor without installing anything locally.
Video 3.
Edit locally and publish demo
. Source. This shows editing OurBigBook Markup and publishing it using the Visual Studio Code extension.
Video 4.
OurBigBook Visual Studio Code extension editing and navigation demo
. Source.
Internal cross file references done right:
Infinitely deep tables of contents:
Figure 6.
Dynamic article tree with infinitely deep table of contents
.
Live URL: ourbigbook.com/cirosantilli/chordate
Descendant pages can also show up as toplevel e.g.: ourbigbook.com/cirosantilli/chordate-subclade

All our software is open source and hosted at: github.com/ourbigbook/ourbigbook

Further documentation can be found at: docs.ourbigbook.com

Feel free to reach our to us for any help or suggestions: docs.ourbigbook.com/#contact

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