The exact format of table entries is fixed by the hardware.

Each page entry can be seen as a struct with many fields.

The page table is then an array of struct.

On this simplified example, the page table entries contain only two fields:so in this example the hardware designers could have chosen the size of the page table to b 21 instead of 32 as we've used so far.

All real page table entries have other fields, notably fields to set pages to read-only for Copy-on-write. This will be explained elsewhere.

It would be impractical to align things at 21 bits since memory is addressable by bytes and not bits. Therefore, even in only 21 bits are needed in this case, hardware designers would probably choose 32 to make access faster, and just reserve bits the remaining bits for later usage. The actual value on x86 is 32 bits.

Here is a screenshot from the Intel manual image "Formats of CR3 and Paging-Structure Entries with 32-Bit Paging" showing the structure of a page table in all its glory: Figure 1. "x86 page entry format".

The fields are explained in the manual just after.

Why are pages 4 KiB anyways?

There is a trade-off between memory wasted in:

This can be seen with the extreme cases:

x86 designers have found that 4 KiB pages are a good middle ground.

Because Ciro's a software engineer, and he's done enough staring in computers for a lifetime already, and he believes in the power of Git, he didn't pay much attention to this part ;-)

According to the eLife paper, the code appears to have been uploaded to: github.com/d-j-k/puntseq. TODO at least mention the key algorithms used more precisely.

Ciro can however see that it does present interesting problems!

Because it was necessary to wait for 2 days to get our data, the workshop first reused sample data from previous collections done earlier in the year to illustrate the software.

First there is some signal processing/machine learning required to do the base calling, which is not trivial in the Oxford Nanopore, since neighbouring bases can affect the signal of each other. This is mostly handled by Oxford Nanopore itself, or by hardcore programmers in the field however.

After the base calling was done, the data was analyzed using computer programs that match the sequenced 16S sequences to a database of known sequenced species.

This is of course not just a simple direct string matching problem, since like any in experiment, the DNA reads have some errors, so the program has to find the best match even though it is not exact.

The PuntSeq team would later upload the data to well known open databases so that it will be preserved forever! When ready, a link to the data would be uploaded to: www.puntseq.co.uk/data

Besides a missing page, a very common source of page faults is copy-on-write (COW).

Page tables have extra flags that allow the OS to mark a page a read-only.

Those page faults only happen when a process tries to write to the page, and not read from it.

When Linux forks a process:

The third one from Cambridge after:

medium.com/left-right/the-education-system-is-about-to-implode-5c95f774b523 The Education System is About to Implode by Nicholas Budny (2020)

Incredible that there hasn't been a Nobel Prize for it as of 2022, e.g. as mentioned at: theconversation.com/no-nobel-but-epigenetics-finally-gets-the-recognition-it-deserves-18970

Some old dudes getting another prize in 2016: www.cuimc.columbia.edu/news/pioneers-epigenetics-awarded-horwitz-prize

The good:

The bad:

Consider the E. Coli K-12 MG1655 operon thrLABC.

That single operon can produce two different mRNA transcription units:

The reason for this appears to be that there is a rho-independent termination region after thrL. But then under certain conditions, that must get innactivated, and then the thrLABC is produced instead.