Merge branch 'master' into gsoc_blog

Author: kr-2003

.github/actions/spelling/allow/names.txt

@@ -32,6 +32,7 @@ Ilieva
 Isemann
 JLange
 Jomy
+Jurgaityt
 Kyiv
 LBNL
 Lattner
@@ -122,6 +123,7 @@ christinakoutsou
 daemond
 daemondzh
 davidlange
+delatorre
 dlange
 efremale
 elrawy
@@ -201,6 +203,7 @@ thakkar
 tharun
 timmaraju
 tlattner
+torre
 vaibhav
 vassil
 vassilev

.github/actions/spelling/allow/terms.txt

@@ -1,5 +1,6 @@
 AARCH
 BGZF
+Caa
 CINT
 CMSSW
 Cppyy
@@ -21,6 +22,7 @@ PTX
 Slib
 Softsusy
 Superbuilds
+TBR
 TFormula
 TTree
 aarch
@@ -35,6 +37,7 @@ gridlay
 gsoc
 gpu
 jit
+jthread
 llm
 llvm
 pushforward
@@ -46,6 +49,7 @@ reoptimize
 samtools
 sitemap
 softsusy
+superbuilds
 vimeo
 www
 xcolors
@@ -60,3 +64,9 @@ xplugin
 youtu
 youtube
 zenodo
+biodynamo
+Caa
+Jurgaityt
+Resugaring
+superbuilds
+TBR

.github/actions/spelling/expect.txt

@@ -1,4 +1,6 @@
 Reoptimization
+Resugaring
+optimizing
 genomics
 reoptimization
 sustainability

_data/contributors.yml

@@ -275,10 +275,34 @@
        potentially establishing a new standard for high-performance genomic data analysis.
       proposal: /assets/docs/Aditya_Pandey_GSoC2025.pdf
       mentors: Martin Vassilev, Jonas Rembser, Fons Rademakers, Vassil Vassilev
+
+- name: Petro Mozil
+  photo: PetroMozil.jpg
+  info: "Google Summer of Code 2025 Contributor"
+  email: [email protected]
+  education: "Bachelor of Computer Science, Ukrainian Catholic University, Ukraine"
+  github: "https://github.com/pmozil"
+  active: 1
+  linkedin: "https://www.linkedin.com/in/petro-mozil-a94583170/"
+  projects:
+    - title: "Enabling support for STL concurrency primitives in CLAD"
+      status: Ongoing
+      description: |
+        Clad recursively iterates over the syntax tree to check whether a given 
+        statement should be differentiated. Each function that is called from 
+        inside of a differentiated function should be differentiated as well, 
+        and so should any object method. The main issue for clad is that std::thread is an object, 
+        and thus as a type that should be differentiated However, std::thread shouldn’t 
+        be differentiated, the function inside of it should. 
+        Some of STL’s concurrency primitives face the same problem - 
+        the methods in them should not be differentiated, 
+        and only the location of where they were called should be preserved.
+      proposal: /assets/docs/petro_mozil_promosal_GSoC_2025.pdf
+      mentors: Martin Vassilev, David Lange
 
 - name: Salvador de la Torre Gonzalez
-  info: "Google Summer of Code 2025 Contributor"
   photo: salva_de_la_torre_gonzalez.jpg
+  info: "Google Summer of Code 2025 Contributor"
   email: [email protected]
   github: "https://github.com/salva24"
   linkedin: "https://www.linkedin.com/in/salva-de-la-torre-gonzalez-7299b6335/"

_data/standing_meetings.yml

@@ -3,6 +3,10 @@
   time_cest: "17:00"
   connect: "[Link to zoom](https://princeton.zoom.us/j/97915651167?pwd=MXJ1T2lhc3Z5QWlYbUFnMTZYQlNRdz09)"
   agenda:
+    - title: "Using ROOT in the field of genome sequencing"
+      date: 2025-05-21 17:00:00 +0200
+      speaker: "Aditya Pandey"
+      link: "[Slides](/assets/presentations/CaaS_Weekly_21_05_2025_Aditya_Pandey_Using_ROOT_for_genome_sequencing.pdf)"
     - title: "Activity Analysis: Summary"
       date: 2025-01-29 17:00:00 +0200
       speaker: "Maksym Andriichuk"
@@ -245,7 +249,7 @@
       date: 2022-09-07 14:00:00 +0200
       speaker: "Anubhab Ghosh"
       link: "[Slides](/assets/presentations/CaaS_Weekly_07_09_2022_Anubhab-Shared_Memory_Based_JITLink_Memory_Manager.pdf)"
-    - title: "Current working status of optmizing ROOT modules"
+    - title: "Current working status of optimizing ROOT modules"
       date: 2022-09-07 14:00:00 +0200
       speaker: "Jun Zhang"
       link: "[Slides](/assets/presentations/CaaS_Weekly_07_09_2022_Jun_Zhang_Current_Working_Status_of_Optimize_Modules_Usage_For_ROOT.pdf)"
@@ -349,3 +353,7 @@
       date: 2022-01-05 14:00:00 +0200
       speaker: "Parth Arora"
       link: "[Slides](/assets/presentations/CaaS_Weekly_05_01_2022_Parth-Add_Support_For_Differentiating_wrt_User_Defined_Types.pdf)"
+    - title: "Agent-Based Simulation of CAR-T Cell Therapy Using BioDynaMo Initial Presentation"
+      date: 2025-05-21 17:00:00 +0200
+      speaker: "Salvador de la Torre Gonzalez"
+      link: "[Slides](/assets/presentations/Salva_initial_presentation_me_and_project_CART.pdf)"

_pages/team/petro-mozil.md

@@ -0,0 +1,10 @@
+---
+title: "Compiler Research - Team - Petro Mozil"
+layout: gridlay
+excerpt: "Compiler Research: Team members"
+sitemap: false
+permalink: /team/PetroMozil
+email: [email protected]
+---
+
+{% include team-profile.html %}

_pages/team/salvador-delatorre.md renamed to _pages/team/salvador-de-la-torre-gonzalez.md

@@ -3,7 +3,7 @@ title: "Compiler Research - Team - Salvador de la Torre Gonzalez"
 layout: gridlay
 excerpt: "Compiler Research: Team members"
 sitemap: false
-permalink: /team/SalvadorDeLaTorreGonzalez
+permalink: /team/SalvadordelaTorreGonzalez
 email: [email protected]
 ---
 

_posts/2025-05-14-biodynamo-cart-simulation.md

@@ -5,7 +5,7 @@ excerpt: "This GSoC 2025 project, Agent-Based Simulation of CAR-T Cell Therapy,
 sitemap: true
 author: Salvador de la Torre Gonzalez
 permalink: blogs/gsoc25_salvador_introduction_blog/
-banner_image: /images/blog/gsoc-banner.png
+banner_image: /images/blog/cart_plasma_gsoc.png
 date: 2025-05-14
 tags: gsoc BioDynaMo c++
 ---
@@ -29,7 +29,7 @@ of microenvironmental factors like hypoxia, regulatory T-cells, and immunosuppre
 
 This project represents an exciting opportunity to apply my dual academic background in mathematics and computer engineering to a highly impactful domain: cancer immunotherapy.
 
-My interest in oncology and CAR-T treatments deepened significantly after attending a course on Mathematical Modeling and Data Analysis in Oncology, taught by researchers from the Mathematical Oncology Laboratory" ([MôLAB](https://molab.es/)) team at the University of Cádiz. During this course, I was introduced to the fundamentals of immunotherapy and CAR-T cell dynamics, and became fascinated by the potential of mathematical and computational tools to contribute to this area.
+My interest in oncology and CAR-T treatments deepened significantly after attending a course on Mathematical Modeling and Data Analysis in Oncology, taught by researchers from the Mathematical Oncology Laboratory" ([MôLAB](https://molab.es/)) team at the University of Cadiz. During this course, I was introduced to the fundamentals of immunotherapy and CAR-T cell dynamics, and became fascinated by the potential of mathematical and computational tools to contribute to this area.
 
 I believe that building a scalable, open-source simulation of CAR-T therapy can become a valuable resource for scientists and clinicians worldwide, helping them to better understand and optimize treatment strategies considering the complex landscape of solid tumors. 
 

_posts/2025-05-18-Supporting-STL-concurrency-primitives-in-clad.md

@@ -0,0 +1,50 @@
+---
+title: "Supporting STL Concurrency Primitives in CLAD"
+layout: post
+excerpt: "Support for STL concurrency features in CLAD is a useful feature for applications utilizing cpu threads. Many applications of autodifferentiation benefit from parallel or concurrent processing, and support for some STL concurrency primitives such as threads and basic synchronization primitives may considerably simplify the user's design."
+sitemap: false
+author: Petro Mozil
+permalink: blogs/gsoc25_/
+banner_image: /images/blog/gsoc-banner.png
+date: 2025-05-18
+tags: gsoc llvm clang auto-differentiation
+---
+
+## About me
+
+I am Petro Mozil, a student participating in the Google Summer of Code program in 2025.
+I will work on adding support of STL concurrency primitives to CLAD.
+
+## Problem description
+
+`Clad` is a plugin for automatic differentiation for the `clang` compiler.
+Automatic differentiation is a term for multiple techniques of deriving a mathematical function analytically. Some of the ways of doing this include simply calculating the derivative numerically or by deriving a function by a set of rules, symbolically.
+
+`Clad` provides an interface that returns an object that contained the derivative of a given function. There might be problems with some functions, if they are to be derived. For example, one would not derive `printf`,  and neither would they derive `std::tread` - those are exceptions, and should be handled differently from mathematical  functions.
+
+The main goals of this project are to implement support for automatically derive functions that contain `std::thread` so that the user wouldn't have to separate the multi-processing logic from the mathematical functions - such a feature would be a great time-saver for production of multi-processing code.
+
+## Objectives
+
+The objectives for this project include adding support for multiple objects in STL, such as `std::thread`, `std::atomic`, `std::mutex`.
+
+The first, and, likely, most important part of the project is to add support for `std::thread` - this will include deriving not the `std::thread` constructor, but deriving the function supplied for the thread.
+
+Support for mutexes is a bit more straightforward - though `clad` creates a second object to represent the derived value, it shouldn't do so for a mutex. It is a matter of having a custom derivative for `std::mutex`.
+
+Atomics will likely involve more effort - they would require custom derivatives for `compare_exchange` functions as well as their methods.
+
+If time allows, I would also like to add support for `std::condition_variable`, `std::lock_guard`, `std::unique_lock` and `std::jthread`, and most of those would also only involve a custom derivative.
+
+
+## Conclusion
+
+A a result of this project, support for the concurrency primitives is expected. Clad should seamlessly derive functions with concurrency primitives in them.
+Though this project does not focus on features immediately required from `clad`, it should result in making easier the lives of those, who use clad for high-perf computing.
+
+## Related links
+
+- [LLVM Repository](https://github.com/llvm/llvm-project)
+- [CLAD repository](https://github.com/vgvassilev/clad)
+- [Project description](https://hepsoftwarefoundation.org/gsoc/2025/proposal_Clad-STLConcurrency.html)
+- [My github](https://github.com/pmozil)