Posts | Project site in English

Scientific programming languages

Sat, 28 May 2022 18:30:00 +0000

Scientific programming is a field of programming that relies on the use of computers for research purposes. His tasks are often very different from industrial programming – while there is often a focus on code readability and maintainability, here the speed with which the program design can be iterated is more important.

Because of this feature, many programming languages are poorly suited for scientific programming. For example, Rust, with its focus on the formal correctness of all memory usages, often slows down the developer, and Java and other strictly object-oriented languages require a more fundamental architecture than is often possible in scientific programming.

One of the languages that is very often used in scientific programming is Python. It is very popular, has an easy-to-learn syntax, allows many different approaches to solving architectural problems, and also integrates into libraries written in C and C ++, which are faster and implement the most complex parts of the algorithms. This makes the Python language convenient for gluing different data together and processing it in different ways, which is exactly what is useful in scientific programming.

Other languages that are often used for working with data – R, Julia, and Ada – have simple syntax, a rich type system, and links to C/C++ code, and all these features also make them useful in scientific programming.

Among other options, functional languages like Haskell, F#, and Clojure allow algorithms to be described in a more declarative style – don’t say what calculations are to be done, but instead state the formulas that need to be calculated in the end.

Rarer programming paradigms like logic programming – as implemented in Prolog and Erlang, for example – are rarely used in industrial applications, but in scientific programming they are often useful. In logic programming, the programmer specifies statements about terms – for example, “If something is a cat, then it is an animal”, “If something is an animal, then it is alive or dead”, “If something is alive, then it is not dead”, “There is something called Barsik”, “If something is called Barsik, then it is a cat” and “If something is called Barsik, then it is not dead”. After that, you can ask questions like “What things are animals?”, “What things are alive and dead at the same time?”, “Is Barsik a cat and alive?” etc. This kind of reasoning is often called logical propositions, and most programs are difficult to translate into a form that consists entirely of logical propositions. However, in scientific programming, there are often questions that can be framed as logical statements, and such languages help with this.

Thus, scientific programming has tasks that often differ from industrial tasks, so the set of languages and paradigms that find application in scientific programming is very wide.

Weekly post 21

Sat, 28 May 2022 18:30:00 +0000

This is a weekly post that is required by the rules for maintaining a personal project. This post was written on May 28, 2022, and covers 21 weeks of 2022.

How was the week

By all accounts, there are only a few weeks left until the end of this module. This circumstance was surprising to many, including me, who began to perceive what was happening as their personal hell.

Key insights

The level of energy contained in the vault very often does not affect the structure of the vault itself, but can affect the environment if the vault is disturbed.
Lithium-ion batteries should be at a medium charge level in transit to minimize the risk of spontaneous combustion.
USB devices can have up to 16 different virtual devices called “endpoints”. Protocols between them should not be unified.

Main insight

Works - do not touch.

What failed to do

I still haven’t had time to do a full-fledged comparative analysis of 3D printers, which is necessary to determine the most rational choice for our project. This should be done as soon as possible.

Work on mistakes

As before, you need to create a stable task scheduling scheme that would not be disturbed by small changes from the schedule, as well as create a backlog of tasks so that they can be effectively scheduled, delegated or postponed.

Weekly post 20

Fri, 20 May 2022 18:30:00 +0000

This is a weekly post that is required by the rules for maintaining a personal project. This post was written on May 20, 2022, and covers week 20, 2022.

How was the week

During the week, one of the non-standard circumstances was the control work on the subject “programming technology”, where it was necessary to implement some operations on lists and arrays. This was somewhat complicated by the fact that the results of the work had to be written on paper.

Key insights

Depending on the transmission medium used, the uptime of systems can be much more or much less than the uptime of communication lines - in the case of a cellular network, the systems reboot more often, and in the case of Wi-Fi, the link itself reboots more often.
The OpenWRT configuration interface does not support specifying specific DHCP server directives, and they may need to be set through manual editing of configuration files
The sampling rate at which an oscilloscope operates can have a disproportionate effect on the signal content it measures.

Main insight

!( sizeof(long long) > sizeof(long) )

What failed to do

I did not have time to do a full-fledged comparative analysis of 3D printers, which is necessary to determine the most rational choice for our project.

Work on mistakes

Working with bibliographies

Fri, 20 May 2022 18:30:00 +0000

A bibliography is a set of records about the literature that was used in the preparation of a document. It serves as a way to cite past work on the topic and to provide links to sources for further information.

Usually the bibliography is printed at the end of the document, and sometimes there are references to certain entries from the text of the document. For example, if I wanted to say something that can be read about in a certain book, I would write something like:

On systems that support this, the name of the TeX markup language must be written in full capital letters, but the letter E should be shifted down from the baseline (see [TEXBOOK]).

After that, in the bibliography part, I would write:

[TEXBOOK] D.E. Knuth, D. Knuth, D. Bibby, and American Mathematical Society. The TeXbook. Computers & typesetting. Addison-Wesley, 1986.

With this information, the reader of my document can go to the library to find this book and read the part I am talking about in the text.

Such records can be written by hand, but this quickly becomes inconvenient as the number of sources increases. Therefore, scientific writing systems like TeX have mechanisms for managing bibliographies.

For example, BibTeX uses a file containing records of the sources used. The same book will be written in it as follows:

 @book{knuth1986texbook,
  title={The TeXbook},
  author={Knuth, D.E. and Knuth, D. and Bibby, D. and American Mathematical Society},
  isbn={9780201134476},
  lccn={85030845},
  series={Computers\& typesetting},
  url={https://books.google.ru/books?id=zqgQAQAAMAAJ},
  year={1986},
  publisher={Addison-Wesley}
}

This machine-readable format stores information that will then be included in the entry in the bibliography. However, you may notice that not all fields were included in the record. This is because the bibliography entry template I used does not use this information. If a document is published in a journal or other publication, this publication will certainly have its own style of bibliography; if you select this style in the BibTeX settings, the record will look different.

BibTeX is one of the bibliography management systems. There are others like EndNote, Mendeley, RefWorks, Zotero, etc. They differ in their interface, supported citation formats, supported data attachments, etc., but most have BibTeX export options. Using such systems, it is possible to structure the set of literature used in the text, which makes it possible to write scientific articles with the correct references quickly and conveniently.

Markup languages, LaTeX

Sat, 14 May 2022 18:30:00 +0000

A markup language is a way of writing text in a format that is suitable for machine processing and often contains, in addition to the text, instructions for displaying that text. There are many different markup languages that work well for different tasks.

We will consider the LaTeX language, which is most often used for writing scientific papers. It is an extension of the TeX layout language, invented by Donald Knuth in 1978. Backslashes are used to call commands, and curly braces are used to specify arguments:

This text is \emph{in italics}.
This text is in \textbf{bold}.
\begin{large}This text is larger than usual.\end{large}
\begin{Large}This text is even larger than usual.\end{Large}
\begin{LARGE}This text is STILL larger than usual.\end{LARGE}
\begin{huge}This text is huge.\end{huge}
\begin{Huge}This text is Huge.\end{Huge}

One of the most famous features of the LaTeX language is the ability to enter complex mathematical formulas. For example, this code:

\begin{equation}
\Delta M_i^{-1} = - \alpha \sum_{n=1}^N D_i \left[ n \right] \left[ \sum_{j \in C \left[ i \right]}^{} F_{ji} \left[ n -1 \right] + Fext_i \left[ n^{-1} \right] \right]
\end{equation}

…displayed as follows:

(This expression is the title of one of Aphex Twin’s tracks.)

Because of this capability, LaTeX remains the gold standard for formatting mathematical texts, and it is not uncommon for other document authoring environments (such as Microsoft Word) to copy some of the syntax. Some programs even use the LaTeX engine as part of their work – for example, Pandoc uses it to convert documents to PDF, and Manim’s programmable animation library uses it to display mathematical formulas in SVG format.

LaTeX also has a wide standard library that allows you to use it to display pictures, graphs, code blocks, and more. Thus, LaTeX is one of the most important markup languages for scientific documents, and it is worth knowing for anyone who plans to write documents with mathematical formulas or other complex display elements.

Weekly post 19

Sat, 14 May 2022 18:30:00 +0000

This is a weekly post that is required by the rules for maintaining a personal project. This post was written on May 14, 2022, and covers week 19, 2022.

How was the week

It is impossible to provide special important reports for this week, as well as for the previous one. This is because we are now in a cycle of work that seems to be endless, and it is becoming more and more difficult to tell one week from the next.

Key insights

Macros in Rust should have a form in which, even without expanding the macro, the code represents a valid syntax tree. This distinguishes them from macros in C/C++, where they only perform text replacement.
The amount of disk space occupied by video recordings of work in progress exceeds the usefulness of these videos by several orders of magnitude. Under the current circumstances, the amount used for these videos should be reduced.
The use of Rutube - the Russian platform - in industrial activities is contraindicated, since it is not able to withstand the SLA that can be expected from alternative platforms.

Main insight

As part of this personal project, we learn how to find ways to optimize work. These methods sometimes lead to lower quality, but following the classic trichotomy of requirements, we can sacrifice this for the greater good.

What failed to do

Fairly poor progress on a robotics project that was assigned to me in an elective course. One of the main reasons for this is that the power supply of the robot consists of 18650 batteries, and the ones that are available to me are quite broken.

Work on mistakes

Version control and Git

Sat, 07 May 2022 18:30:00 +0000

Modification Control Systems (VCS) allow you to track changes in your code, look through history to look for specific changes, and coordinate work on the same code base between multiple developers. Today we will look at how one of the most popular VCS, Git, works.

Story

Git was developed in 2005 by Linus Torvalds to help develop the Linux kernel. Shortly before this, there was a scandal with Bitkeeper, a proprietary version control system that was used by many developers, but was no longer available for free after the copyright holder found out that it was reverse-engineered to create SourcePuller.

The goals of the project were: to make a distributed VCS that could support a procedure similar to Bitkeeper, but was also fast (no more than three seconds to apply a patch) and had strong protection against errors and unintentional modifications.

Principles

Git’s primitive data structures do not necessarily implement VCS. There are two places where information is stored – a dynamic index that describes the state of the working tree, and an immutable object database. The latter stores the following five types of objects:

BLOB – the content of the file, denoted by its hash. Each BLOB is a separate version of a file.
a tree is analogous to a directory, which has links to sub-trees and BLOBs to represent one version of the working tree.
A commit is a history element pointing to the tree it describes and one or more previous commits.
tag - an object that has a link to some other object and some additional information about this object. Most commonly used to add digital signatures to commits.
packfile – a file containing several other objects in a compressed format for compactness.

Because of this design, each repository contains the entire history and can be viewed locally. This is what makes Git distributed VCS.

The commit history is structured as a singly-linked tree, and because the identifiers are based on a cryptographic hash of the content, this can also be thought of as a blockchain instance. Each commit can have a parent, the commit that the changes are based on. With the help of them you can go back to the history of changes. Since each commit is identified by its hash, any change in history requires the hash of each object to be recalculated further, which provides cryptographic protection against changes.

In addition to this, Git maintains a linkbase. Head objects point to the latest commit on a branch, they call the branch, and are in fact branches. One special head, called HEAD, points to the current branch from which the comparison to the working tree is being made. There are also tags, which, like head, indicate commits, but unlike them do not move, and can instead be used to mark important points in the project’s history.

History keeping process

Git does not dictate how a project’s history should be maintained. One option that is supposed to be used in the OS course involves short-lived branches within which work is done to implement a new feature, and then this branch is merged into the main tree when the feature is completed. Other options include long-lived branches ranked by code stability, or branches assigned to specific team members.

Different methods have their pros and cons, which are more or less obvious depending on the type of project and the development methodology that the team uses.

Conclusions

Git is one of the most popular VCS, and for good reason. It was written to solve problems with existing SLEs, and it was able to solve them much more effectively than any other solution at the time.

One of the factors behind its popularity has been the rise of Git hosting services such as GitHub, GitLab, and BitBucket. These services allow you to publish a Git repository and make it available from the web, and their convenience has led many users to now associate Git with GitHub.

With such popularity, ease of casual use, and yet depth of functionality for advanced use, Git is now a must for any kind of code development. That is why in the OS course we learn the basics of using Git.

Weekly post 18

Sat, 07 May 2022 18:30:00 +0000

This is a weekly post that is required by the rules for maintaining a personal project. This post was written on May 7, 2022, and covers week 18, 2022.

How was the week

Overall, week 18 was similar to week 17, and both were more productive than week 16. This is because the format of this course is still unfamiliar and goes against my previous experience. Therefore, according to the sensations, it turned out only to do the work at the rate of the OS and nothing more useful.

Key insights

The AVR architecture has three system timers. The first one is usually used for real time tracking, the second one for precise PWM signals, and the third one for approximate PWM signals.
As before, the model of reality based on the theory of complete determinism with the addition of randomness through quantum mechanics seems to be the most accurate description of reality.
The video game The Stanley Parable: Ultra Deluxe (2022) puts forward a model of reality based on the central thesis that everything (with the possible exception of the narrator and the player character) is a bucket, and therefore any attempt to limit the number of buckets in the world inevitably leads to the destruction of the world in the current understanding. This model must be carefully considered by the engineers of metaphysics to determine its scope.

Main insight

With the understanding that all timing in the AVR is done with three timers, it is now possible to write code that connects one of the timers to the pins on the chip, allowing you to implement PWM signals from scratch as part of the Rust Arduino environment project.

What failed to do

As in weeks 16 and 17, there is a feeling that almost nothing can be done from the plans. This feeling is based on the fact that the work on the OS course takes a very long time and requires full concentration (due to the fact that the video is being recorded), and after completing one stage, it is difficult to convince yourself to do the next. It basically boils down to the fact that I have not yet developed a stable strategy for allocating work and rest time, which, combined with the drastic change in the load profile, leads to this feeling of lack of progress.

Work on mistakes

In order to solve the above problems, the most promising solution is to develop task allocation schemes that are comfortable enough for everyday use and that allow active tasks to be solved more efficiently.

Welcome to Wowchemy, the website builder for Hugo

Sun, 13 Dec 2020 00:00:00 +0000

Overview

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Hugo Academic CLI: Automatically import publications from BibTeX

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Posts | Project site in English

Scientific programming languages

Weekly post 21

How was the week

Key insights

Main insight

What failed to do

Work on mistakes

Weekly post 20

How was the week

Key insights

Main insight

What failed to do

Work on mistakes

Working with bibliographies

Markup languages, LaTeX

Weekly post 19

How was the week

Key insights

Main insight

What failed to do

Work on mistakes

Version control and Git

Story

Principles

History keeping process

Conclusions

Weekly post 18

How was the week

Key insights

Main insight

What failed to do

Work on mistakes

Welcome to Wowchemy, the website builder for Hugo

Overview

Get Started

Crowd-funded open-source software

❤️ Click here to become a sponsor and help support Wowchemy’s future ❤️

Ecosystem

Inspiration

Features

Themes

License