Ciro Santilli @cirosantilli 37

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Field (mathematics) Updated 2025-07-16

A ring where multiplication is commutative and there is always an inverse.

A field can be seen as an Abelian group that has two group operations defined on it: addition and multiplication.

And then, besides each of the two operations obeying the group axioms individually, and they are compatible between themselves according to the distributive property.

Basically the nicest, least restrictive, 2-operation type of algebra.

Examples:

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Fifth Solvay Conference (1927) Updated 2025-07-16

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Fighting game Updated 2025-07-16

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Omics Updated 2025-07-16

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Each of the omics studies a subset of molecular biology with a data intensive and broad point of view that tries to understand global function or organisms, trying to understand what every biologically relevant molecule does as part of the hole metabolism.

The main omics are:

Omics might be stamp collecting, but maybe it is a bit more like Trading card game/Magic: The Gathering collecting, in which the cards that you are collecting actually have specific uses and interactions, especially considering that most metabolic pathways are analogous across many species.

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Once upon a time in the west (1968) Updated 2025-07-16

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Has the best opening scene of all time.

Top quotes:

3 evil guys: looks like we're short one horse. The good guy, shaking his head: you brought two too many.
"So, you found out you're not a businessman after all." dialogue, see: www.imdb.com/title/tt0064116/characters/nm0000314

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graphviz/node.dot Updated 2025-07-16

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graphviz/quotes.dot Updated 2025-07-16

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js/matterjs/hello.html Updated 2025-07-16

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Hello world adapted from: github.com/liabru/matter-js/wiki/Getting-started/1d138998f05766dc4de0e44ae2e35d03121bb7f2

Also asked at: stackoverflow.com/questions/28079138/how-to-make-minimal-example-of-matter-js-work/76203103#76203103

Renderer questions:

follow object on viewport: codepen.io/csims314/pen/goZQvG
draw text: github.com/liabru/matter-js/issues/321

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File manager Updated 2025-07-16

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Ciro Santilli used to use file managers in the past.

But he finally converted to a shell cd aliases that auto-ls: github.com/cirosantilli/dotfiles/blob/a51bcc324f0cff0eddd4c3bb8654ec223a0adb7b/home/.bashrc#L1058

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Open boundary condition Updated 2025-07-16

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In the context of wave-like equations, an open-boundary condition is one that "lets the wave go through without reflection".

This condition is very useful when we want to simulate infinite domains with a numerical method. Ciro Santilli wants to do this all the time when trying to come up with demos for his physics writings.

Here are some resources that cover such boundary conditions:

www.asc.tuwien.ac.at/~arnold/pdf/graz/graz.pdf lots of slides
hplgit.github.io/wavebc/doc/pub/._wavebc_cyborg002.html mentions them and gives a 1D formula. It mentions that things get complicated in 2D and 3D TODO why.
The other page: hplgit.github.io/wavebc/doc/pub/._wavebc_cyborg003.html shows solution demos.

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OpenShot Updated 2025-07-16

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Ubuntu 20.10 crash...:

  exceptions:ERROR Unhandled Exception
Traceback (most recent call last):
  File "/usr/bin/openshot-qt", line 11, in <module>
    load_entry_point('openshot-qt==2.5.1', 'gui_scripts', 'openshot-qt')()
  File "/usr/lib/python3/dist-packages/openshot_qt/launch.py", line 97, in main
    app = OpenShotApp(argv)
  File "/usr/lib/python3/dist-packages/openshot_qt/classes/app.py", line 218, in __init__
    from windows.main_window import MainWindow
  File "/usr/lib/python3/dist-packages/openshot_qt/windows/main_window.py", line 45, in <module>
    from windows.views.timeline_webview import TimelineWebView
  File "/usr/lib/python3/dist-packages/openshot_qt/windows/views/timeline_webview.py", line 42, in <module>
    from PyQt5.QtWebKitWidgets import QWebView
ImportError: /usr/lib/x86_64-linux-gnu/libQt5Quick.so.5: undefined symbol: _ZN4QRhi10newSamplerEN11QRhiSampler6FilterES1_S1_NS0_11AddressModeES2_, version Qt_5_PRIVATE_API

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nodejs/sequelize/parallel_select_and_update.js Updated 2025-07-16

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This example is the same as nodejs/sequelize/raw/parallel_select_and_update.js, but going through Sequelize rather than with Sequelize raw queries. NONE is not supported for now to not have a transaction at all because lazy.

The examples illustrates: stackoverflow.com/questions/55452441/for-share-and-for-update-statements-in-sequelize

Sample invocation:

node --unhandled-rejections=strict ./parallel_select_and_update.js p 10 100 READ_COMMITTED UPDATE

where:

READ_COMMITTED: one of the keys documented at: sequelize.org/master/class/lib/transaction.js~Transaction.html which correspond to the standard sQL isolation levels. It not given, don't set one, defaulting to the database's/sequelize's default level.
UPDATE: one of the keys documented at: sequelize.org/master/class/lib/transaction.js~Transaction.html#static-get-LOCK. Update generates a SELECT FOR UPDATE in PostgreSQL for example. If not given, don't use any FOR xxx explicit locking.

Other examples:

node --unhandled-rejections=strict ./parallel_select_and_update.js p 10 100 READ_COMMITTED UPDATE

Then, the outcome is exactly as described at: nodejs/sequelize/raw/parallel_select_and_update.js:

READ_COMMITTED: fails
READ_COMMITTED UPDATE: works
REPEATABLE_READ: works, but is a bit slower, as it does rollbacks
This case also illustrates Sequelize transaction retries, since in this transaction isolation level transactions may fail:

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nodejs/sequelize/raw/parallel_select_and_update_deterministic.js Updated 2025-07-16

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This example contains a deterministic demo of when postgreSQL serialization failures may happen.

Tested on PostgreSQL 13.5.

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nodejs/sequelize/raw/parallel_select_and_update.js Updated 2025-07-16

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This example is similar to nodejs/sequelize/raw/parallel_update_async.js, but now we are doing a separate SELECT, later followed by an update:

SELECT FROM to get i
update on Js code newI = i + 1
UPDATE SET the newI

Although this specific example is useless in itself, as we could just use UPDATE "MyInt" SET i = i + 1 as in nodejs/sequelize/raw/parallel_update_async.js, which automatically solves any concurrency issue, this kind of code could be required for example if the update was a complex function not suitably implemented in SQL, or if the update depends on some external data source.

Sample execution:

node --unhandled-rejections=strict ./parallel_select_and_update.js p 2 10 'READ COMMITTED'

which does:

PostgreSQL, see other databases options at SQL example
2 threads
10 increments on each thread

Another one:

node --unhandled-rejections=strict ./parallel_select_and_update.js p 2 10 'READ COMMITTED' 'FOR UPDATE'

this will run SELECT FOR UPDATE rather than just SELECT

Observed behaviour under different SQL transaction isolation levels:

READ COMMITTED: fails. Nothing in this case prevents:
- thread 1: SELECT, obtains i = 0
- thread 2: SELECT, obtains i = 0
- thread 2: newI = 1
- thread 2: UPDATE i = 1
- thread 1: newI = 1
- thread 1: UPDATE i = 1
REPEATABLE READ: works. the manual mentions that if multiple concurrent updates would happen, only the first commit succeeds, and the following ones fail and rollback and retry, therefore preventing the loss of an update.
READ COMMITTED + SELECT FOR UPDATE: works. And does not do rollbacks, which probably makes it faster. With p 10 100, REPEATABLE READ was about 4.2s and READ COMMITTED + SELECT FOR UPDATE 3.2s on Lenovo ThinkPad P51 (2017).
SELECT FOR UPDATE should be enough as mentioned at: www.postgresql.org/docs/13/explicit-locking.html#LOCKING-ROWS
FOR UPDATE causes the rows retrieved by the SELECT statement to be locked as though for update. This prevents them from being locked, modified or deleted by other transactions until the current transaction ends. That is, other transactions that attempt UPDATE, DELETE, SELECT FOR UPDATE, SELECT FOR NO KEY UPDATE, SELECT FOR SHARE or SELECT FOR KEY SHARE of these rows will be blocked until the current transaction ends; conversely, SELECT FOR UPDATE will wait for a concurrent transaction that has run any of those commands on the same row, and will then lock and return the updated row (or no row, if the row was deleted). Within a REPEATABLE READ or SERIALIZABLE transaction, however, an error will be thrown if a row to be locked has changed since the transaction started. For further discussion see Section 13.4.

A non-raw version of this example can be seen at: nodejs/sequelize/parallel_select_and_update.js.

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Gibbs free energy Updated 2025-07-16

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TODO understand more intuitively how that determines if a reaction happens or not.

Δ G = Δ H - T Δ S

(1)

At least from the formula we see that:

the more exothermic, the more likely it is to occur
if the entropy increases, the higher the temperature, the more likely it is to occur
- otherwise, the lower the temperature the more likely it is to occur

A prototypical example of reaction that is exothermic but does not happen at any temperature is combustion.

Video 1.

Lab 7 - Gibbs Free Energy by MJ Billman (2020)

Source. Shows the shift of equilibrium due to temperature change with a color change in a HCl CoCl reaction. Unfortunately there are no conclusions because its student's homework.

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nodejs/sequelize/raw/trigger_count.js Updated 2025-07-16

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In this example we cache track the number of posts per user on a cache column.

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numpy/fft.py Updated 2025-07-16

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Output:

sin(t)
fft
real 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
imag 0 -10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10
rfft
real 0 0 0 0 0 0 0 0 0 0 0
imag 0 -10 0 0 0 0 0 0 0 0 0

sin(t) + sin(4t)
fft
real 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
imag 0 -10 0 0 -10 0 0 0 0 0 0 0 0 0 0 0 10 0 0 10
rfft
real 0 0 0 0 0 0 0 0 0 0 0
imag 0 -10 0 0 -10 0 0 0 0 0 0

With our understanding of the discrete Fourier transform we see clearly that:

the signal is being decomposed into sinusoidal components
because we are doing the Discrete Fourier transform of a real signal, for the fft, $X_{k} = \overset{ˉ}{X_{N - k}}$ so there is redundancy in the. We also understand that rfft simply cuts off and only keeps half of the coefficients

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python/getitem_complex.py Updated 2025-07-16

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python/pytorch/matmul.py Updated 2025-07-16

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Matrix multiplication example.

Fundamental since deep learning is mostly matrix multiplication.

NumPy does not automatically use the GPU for it: stackoverflow.com/questions/49605231/does-numpy-automatically-detect-and-use-gpu, and PyTorch is one of the most notable compatible implementations, as it uses the same memory structure as NumPy arrays.

Sample runs on P51 to observe the GPU speedup:

$ time ./matmul.py g 10000 1000 10000 100
real    0m22.980s
user    0m22.679s
sys     0m1.129s
$ time ./matmul.py c 10000 1000 10000 100
real    1m9.924s
user    4m16.213s
sys     0m17.293s

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python/sphinx Updated 2025-07-16

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To run each example and see the output run:

./build.sh
xdg-open out/index.html

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