Human mitochondrion Updated +Created
Great doubt Updated +Created
The type of feeling of confusion and distrut for your sense that some Koans attempt to instill.
Ciro Santilli's preferred version of it is physics and the illusion of life.
Some notable references:
Market liquidity Updated +Created
Existence of the matrix logarithm Updated +Created
en.wikipedia.org/wiki/Logarithm_of_a_matrix#Existence mentions it always exists for all invertible complex matrices. But the real condition is more complicated. Notable counter example: -1 cannot be reached by any real .
The Lie algebra exponential covering problem can be seen as a generalized version of this problem, because
  • Lie algebra of is just the entire
  • we can immediately exclude non-invertible matrices from being the result of the exponential, because has inverse , so we already know that non-invertible matrices are not reachable
James Howells Updated +Created
MJCF Updated +Created
JavaScript memory usage benchmark Updated +Created
In this section we will use the file nodejs/bench_mem.js, tests are run on Node.js v16.14.2 from NVM, Ubuntu 21.10, on Lenovo ThinkPad P51 (2017) which has 32 GB RAM.
A C hello world with an infinite loop at the end has:
  • 2.7 MB
  • 770 KB
For a Node.js infinite loop nodejs/infinite_loop.js
topp infinite_loop.js
This gives approximately:
  • RSS: 20 MB
  • VSZ: 230 MB
Adding a single hello world to it as in nodejs/infinite_hello.js and running:
topp infinite_hello.js
leads to:
  • RSS: 26 MB
  • VSZ: 580 MB
We understand that Node.js preallocates VSZ wildly. No big deal, but it does mean that VSZ is a useless measure for Node.js.
Forcing garbage collection as in nodejs/infinite_hello.js brings it down to 20 MB however:
topp node --expose-gc infinite_hello_gc.js
Finally let's see a baseline for process.memoryUsage nodejs/infinite_memoryusage.js:
node --expose-gc infinite_memoryusage.js
which gives initially:
{
  rss: 23851008,
  heapTotal: 6987776,
  heapUsed: 3674696,
  external: 285296,
  arrayBuffers: 10422
}
but after a few seconds randomly jumps to:
{
  rss: 26005504,
  heapTotal: 9084928,
  heapUsed: 3761240,
  external: 285296,
  arrayBuffers: 10422
}
so we understand that
  • heapUsed seems constant at 3.7 MB
  • heapTotal is a very noisy, as it starts at 7 MB, but randomly jumps to 9 MB at one point without apparent reason
Now let's run our main test program.
First a baseline case with an array of length 1:
node --expose-gc bench_mem.js n 1
This gives the same results as node --expose-gc infinite_memoryusage.js. The same result is obtained by doing:
a = undefined
with:
node --expose-gc bench_mem.js dealloc
Not let's vary the size of n a bit with:
node --expose-gc bench_mem.js n N
which gives:
NheapUsedheapTotalrssheapUsed per elemrss per elem
1 M14 MB48 MB56 MB1030
10 M122 MB157 MB176 MB1815
100 M906 MB940 MB960 MB99.3
"rss per elem" is calculated as: rss - 26 MB, where 26 MB is the baseline RSS seen on n 1.
Similarly "heapUsed per elem" deduces the 4 MB (approximation of the above 3.7 MB) seen on n 1.
Note that to reach MAX_SAFE_INTEGER we would need 8 bytes per elem worst case.
Everything below 100 million (8) is therefore very memory wasteful in terms of RSS.
If we use Int32Array typed array buffers instead of a simple Array:
node --expose-gc bench_mem.js array-buffer n N
we see that the memory is now, unsurprisingly, accounted for under arrayBuffers, e.g. for N 1 million:
{
  rss: 31776768,
  heapTotal: 6463488,
  heapUsed: 3674520,
  external: 4285296,
  arrayBuffers: 4010422
}
Results for different N:
|| N
|| `arrayBuffers`
|| `rss`
|| `rss` per elem

| 1 M
| 4 MB
| 31 MB
| 5

| 10 M
| 40 MB
| 67 MB
| 4.6

| 100 M
| 40 MB
| 427 MB
| 4
We see therefore that typed arrays are much closer to what they advertise (4 bytes per element), even for smaller element counts, as expected.
Now let's try one million objects of type { a: 1, b: -1 }:
node --expose-gc bench_mem.js obj
gives:
{
  rss: 138969088,
  heapTotal: 105246720,
  heapUsed: 70103896,
  external: 285296,
  arrayBuffers: 10422
}
Disaster! Memory usage is up to 70 MB! Why?? We were expecting only about 24, 4 baseline + 2 * 10 for each million int?!
And now an equivalent version using class:
node --expose-gc bench_mem.js class
gives the same result.
Let's try Array:
node --expose-gc bench_mem.js arr
is even worse at 78 MB!! OMG why.
{
  rss: 164597760,
  heapTotal: 129363968,
  heapUsed: 78117008,
  external: 285296,
  arrayBuffers: 10422
}
Let's change the number of fields on the object? First as a sanity check:
node --expose-gc bench_mem.js obj 2
produces as expected the smae result as:
node --expose-gc bench_mem.js obj
so adding properties one by one doesn't change anything from creating the literal all at once. Good.
Now:
node --expose-gc bench_mem.js obj N
gives heapUsed:
  • 1: 70M
  • 2: 70M
  • 3: 70M
  • 4: 70M
  • 5: 110M
  • 6: 110M
  • 7: 110M
  • 8: 134M
  • 9: 134M
  • 10: 134M
  • 11: 158M
Node.js standard library Updated +Created
Express.js Updated +Created
This doesn't do a hole lot. Ciro Santilli wouldn't really call it a web framework. It's more like a middleware. Real web frameworks are built on top of it.
Examples under: nodejs/express:
  • nodejs/express/min.js: minimal example. Visit localhost:3000 and it shows hello world. It is a bit wrong because the headers say HTML but we return plaintext.
  • nodejs/express/index.js: example dump with automated tests where possible. The automated tests are run at startup after the server launches. Then the server keeps running so you can interact with it.
A live example on Heroku can be seen at: github.com/cirosantilli/heroku-node-min
FeathersJS Updated +Created
Looks interesting.
It seems to abstract the part about the client messaging the backend, which focuses on being able to easily plug in a number of Front-end web framework to manage client state.
Has the "main web API is the same as the REST API" focus, which is fundamental 2020-nowadays.
Uses Socket.IO, which allows the client Javascript to register callbacks when data is updated to achieve Socket.IO, e.g. their default chat app does:
client.service('messages').on('created', addMessage);
so that message appear immediately as they are sent.
Their standard template from feathers generate app on @feathersjs/cli@4.5.0 includes:
  • several authentication methods, including OAuth
  • testing
  • backend database with one of several object-relational mapping! However, they don't abstract across them. E.g., the default Chat example uses NeDB, but a real app will likely use Sequelize, and a port is needed
which looks promising! They don't have a default template for a Front-end web framework however unfortunately: docs.feathersjs.com/guides/frameworks.html#the-feathers-chat lists a few chat app versions, which is their hello world:
But it is in itself a completely boring app with a single splash page, and no database interaction, so not a good showcase. The actual showcase app is feathersjs/feathers-chat.
And there is no official example of the chat app that is immediately deployable to Heroku: FeathersJS Heroku deployment, all setups require thinking.
Global source entry point: determine on package.json as usual, defaults to src/index.js.
Meteor (web framework) Updated +Created
The idea is cool. It really unifies front-and back end.
But Ciro Santilli feels the approach proposed by FeathersJS of being a glue between bigger third-party Front-end web frameworks like React and backend (object-relational mapping) is more promising and flexible.
LK-99 Updated +Created
bkill all jobs Updated +Created
By the current user:
bkill 0
M. genitalium whole cell model by Covert lab Updated +Created
www.wholecellviz.org/viz.php awesome visualization of simtk, paper: www.ncbi.nlm.nih.gov/pmc/articles/PMC3413483/ A Whole-Cell Computational Model Predicts Phenotype from Genotype - 2013 - Jonathan R. Karr.
ARTIQ Updated +Created
M. mycoides JCVI strain Updated +Created
www.newyorker.com/magazine/2022/03/07/a-journey-to-the-center-of-our-cells A Journey to the Center of Our Cells (2022) by James Somers comments on M. genitalium in general, and in particular on the JCVI strains.
Dan Jewett Updated +Created
MacKenzie Bezos' new husband after she divorced Bezos.
Science teacher at the Lakeside School in Seattle.

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