I remember studying this book in my undergrad which was pretty good and covered how programs look in assembly (calling conventions, call frames, data representation, assembly ...) along with whatever hardware architecture knowledge you require.

Also, to get better understanding of x86 ISA I followed the old i386 manual[2]. Its old but much more smaller. Perhaps once you feel comfortable, you can move to newer manuals. I never read newer ones (because I never actually needed assembly for any project, was just studying for fun).

[1] http://www.amazon.com/Computer-Systems-Programmers-Perspecti...

[2] http://css.csail.mit.edu/6.858/2015/readings/i386.pdf

I highly recommend Computer Systems: A Programmer's Perspective

http://www.amazon.com/Computer-Systems-Programmers-Perspecti...

Some resources on making tiny Hello World programs down to the kernel level that may be useful:

https://blogs.oracle.com/ksplice/entry/hello_from_a_libc_fre...

http://www.muppetlabs.com/~breadbox/software/tiny/teensy.htm...

http://timelessname.com/elfbin/

A wee bit heavy, but it's comprehensive. It deals with what happens when you run code, how the architecture of the computer works (by and large) including at the logic level:

http://www.amazon.co.uk/Computer-Systems-Programmers-Randal-...

If you want to go lower (and higher).. look at Understanding the Linux kernel for a good understanding of how an OS is put together, with specific examples i.e. Linux.

Code, by Petzold, deals with logic and computers from the ground up. It starts with relays and builds them up into gates and usable arithmetic blocks.

http://www.amazon.co.uk/Code-Language-Computer-Hardware-Soft...

http://www.amazon.co.uk/Understanding-Linux-Kernel-Daniel-Bo...

The physics is fairly simple, at least from a CRT or LED display perspective. Gets more tricky dealing with interconnecting microprocessors because a good chunk is vendor specific.

I think this kind of project is well suited to a guide on how to build a computer from the ground up, starting with logic gates, writing a real time OS and developing a scripting language that will run and compile on it. Then you can skip a lot of largely extraneous stuff and have a solid understanding of how the hardware works.

Oops!

http://www.amazon.com/Computer-Systems-Programmers-Perspecti...

Building a CPU in a circuit simulation framework[1] was one of my favorite, and most illuminating, projects I've done.

A great book to learn more: http://www.amazon.com/Computer-Systems-Programmers-Perspecti...

[1] http://tams-www.informatik.uni-hamburg.de/applets/hades/webd...

OK, if you don't have any real experience in low-level embedded coding (relevant to device drivers), RTOS or OS design in general, file systems, data structures, algorithms, interfaces, etc. And, if you have "hobby level" experience with Assembler, C and C++. And, if your intent is to write a desktop OS, from the ground up, without making use of existing technologies, drivers, file systems, memory management, POSIX, etc. Here's a list of books that could be considered required reading before you can really start to write specifications and code. Pick twenty of these and that might be a good start.

In no particular order:

1- http://www.amazon.com/C-Programming-Language-2nd-Edition/dp/...

2- http://www.amazon.com/The-Answer-Book-Solutions-Programming/...

3- http://www.amazon.com/The-Standard-Library-P-J-Plauger/dp/01...

4- http://www.amazon.com/C-Traps-Pitfalls-Andrew-Koenig/dp/0201...

5- http://www.amazon.com/Expert-Programming-Peter-van-Linden/dp...

6- http://www.amazon.com/Data-Structures-In-Noel-Kalicharan/dp/...

7- http://www.amazon.com/Data-Structures-Using-Aaron-Tenenbaum/...

8- http://www.amazon.com/Mastering-Algorithms-C-Kyle-Loudon/dp/...

9- http://www.amazon.com/Code-Complete-Practical-Handbook-Const...

10- http://www.amazon.com/Design-Patterns-Elements-Reusable-Obje...

11- http://www.amazon.com/The-Mythical-Man-Month-Engineering-Ann...

12- http://www.amazon.com/The-Programming-Language-4th-Edition/d...

13- http://www.amazon.com/The-Standard-Library-Tutorial-Referenc...

14- http://www.amazon.com/API-Design-C-Martin-Reddy/dp/012385003...

15- http://www.amazon.com/The-Linux-Programming-Interface-Handbo...

16- http://www.amazon.com/Computer-Systems-Programmers-Perspecti...

17- http://www.amazon.com/System-Programming-Unix-Adam-Hoover/dp...

18- http://www.amazon.com/Memory-Programming-Concept-Frantisek-F...

19- http://www.amazon.com/Memory-Management-Implementations-Prog...

20- http://www.amazon.com/UNIX-Filesystems-Evolution-Design-Impl...

21- http://www.amazon.com/PCI-System-Architecture-4th-Edition/dp...

22- http://www.amazon.com/Universal-Serial-System-Architecture-E...

23- http://www.amazon.com/Introduction-PCI-Express-Hardware-Deve...

24- http://www.amazon.com/Serial-Storage-Architecture-Applicatio...

25- http://www.amazon.com/SATA-Storage-Technology-Serial-ATA/dp/...

26- http://www.amazon.com/Beyond-BIOS-Developing-Extensible-Inte...

27- http://www.amazon.com/Professional-Assembly-Language-Program...

28- http://www.amazon.com/Linux-Kernel-Development-3rd-Edition/d...

29- http://www.amazon.com/Version-Control-Git-collaborative-deve...

30- http://www.amazon.com/Embedded-Software-Primer-David-Simon/d...

31- http://www.amazon.com/Programming-Embedded-Systems-C/dp/1565...

32- http://www.amazon.com/Making-Embedded-Systems-Patterns-Softw...

33- http://www.amazon.com/Operating-System-Concepts-Abraham-Silb...

34- http://www.amazon.com/Performance-Preemptive-Multitasking-Mi...

35- http://www.amazon.com/Design-Operating-System-Prentice-Hall-...

36- http://www.amazon.com/Unix-Network-Programming-Sockets-Netwo...

37- http://www.amazon.com/TCP-Illustrated-Volume-Addison-Wesley-...

38- http://www.amazon.com/TCP-IP-Illustrated-Vol-Implementation/...

39- http://www.amazon.com/TCP-Illustrated-Vol-Transactions-Proto...

40- http://www.amazon.com/User-Interface-Design-Programmers-Spol...

41- http://www.amazon.com/Designing-Interfaces-Jenifer-Tidwell/d...

42- http://www.amazon.com/Designing-Interfaces-Jenifer-Tidwell/d...

43- http://www.amazon.com/Programming-POSIX-Threads-David-Butenh...

44- http://www.intel.com/p/en_US/embedded/hwsw/software/hd-gma#d...

45- http://www.intel.com/content/www/us/en/processors/architectu...

46- http://www.intel.com/p/en_US/embedded/hwsw/hardware/core-b75...

47- http://www.hdmi.org/index.aspx

48- http://en.wikipedia.org/wiki/Digital_Visual_Interface

49- http://www.amazon.com/Essential-Device-Drivers-Sreekrishnan-...

50- http://www.amazon.com/Making-Embedded-Systems-Patterns-Softw...

51- http://www.amazon.com/Python-Programming-Introduction-Comput...

52- http://www.amazon.com/Practical-System-Design-Dominic-Giampa...

53- http://www.amazon.com/File-Systems-Structures-Thomas-Harbron...

54- ...well, I'll stop here.

Of course, the equivalent knowledge can be obtained by trial-and-error, which would take longer and might result in costly errors and imperfect design. The greater danger here is that a sole developer, without the feedback and interaction of even a small group of capable and experienced programmers could simply burn a lot of time repeating the mistakes made by those who have already trenched that territory.

If the goal is to write a small RTOS on a small but nicely-featured microcontroller, then the C books and the uC/OS book might be a good shove in the right direction. Things start getting complicated if you need to write such things as a full USB stack, PCIe subsystem, graphics drivers, etc.

I believe that

  Computer Systems: A Programmer's Perspective

http://www.amazon.com/dp/0136108040

is superior to the widely mandated

  Computer Architecture: A Quantitative Approach

for software engineers and programmers. The former has less hardcoded numbers than the latter and more timeless principles.

Along with the usual classics, I highly recommend Computer Systems: A Programmer's Perspective by Randal E. Bryant and David R. O'Hallaron of Carnegie Mellon. The authors wrote it after teaching a class on the subject. It's extremely readable and gives you an excellent introduction of machine level code, processor architecture and memory as well as a solid foundation of higher level concepts including networking and concurrency. If you're considering programming as a career, I'd say this book (or something similar, probably spread across multiple books) is a must-read. It's used by CMU, Stanford, Caltech, UIUC, Harvard and dozens of other schools.

http://csapp.cs.cmu.edu/ http://www.amazon.com/Computer-Systems-Programmers-Perspecti...

If you want to get into architecture in its own right, Hennessy/Patterson. But I think a far better book on the subject for programmers is "Computer Systems: A Programmer's Perspective."

This is a textbook out of Carnegie Mellon that I was exposed to in grad school. It goes into all kinds of details of processor architecture, memory, I/O, assembly programming, etc. while staying focused on its audience of a systems programmer in C. It's wonderful.

http://www.amazon.com/Computer-Systems-Programmers-Perspecti...