CERN SFT Gsoc 2013 ideas page

29th of September 2013

After experiencing great Google Summer of Code in 2011 and 2012 we have decided to apply again!

As last year, the project ideas are grouped into categories (ideas related to CERN Virtual Machine, Geant 4 related ideas, and ROOT related ideas). We also have a so-called 'Blue sky' ideas which are rather raw and must be worked on further before they become projects. The list of ideas is by no means complete, so if you think you have have a great idea regarding our projects we are certainly certainly looking forward to hear from you. The list of our mentors (and their areas of expertise) can be found below.

LHC Experiment Software Stack

The project ideas are (almost) as diverse as the software stack for LHC experiments is, ranging from twisting the Linux file system layer to the tracking of an electron through a silicon detector.  All experiments have software frameworks that make themselves use of common scientific software libraries for high-energy physics (HEP).  CernVM and CernVM-FS provide a uniform runtime environment based on Scientific Linux.  The software stack is fully open sourced and many of its bits and pieces are used outside the world of particle physics.

 

We encourage students who are planning to apply to do that (and contact us) as early as possible because we have learned from our previous GSoC experience that an initial student application often needs to be reworked in close collaboration with a future mentor. Please do not forget to provide us with some relevant information about yourself (for example CV, past projects, personal page or blog, linkedin profile, github account, etc.).

 

Before submitting an application please consult the official GSoC FAQ where you can find some good advice on writing a successful application. The application should be submitted through the GSoC webapp before the 3rd of May (19:00 UTC).

Project ideas

ROOT Object-Oriented data analysis framework

The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data in a very efficient way. Having the data defined as a set of objects, specialized storage methods are used to get direct access to the separate attributes of the selected objects, without having to touch the bulk of the data. Included are histograming methods in an arbitrary number of dimensions, curve fitting, function evaluation, minimization, graphics and visualization classes to allow the easy setup of an analysis system that can query and process the data interactively or in batch mode, as well as a general parallel processing framework, PROOF, that can considerably speed up an analysis. Thanks to the built-in C++ interpreter the command language, the scripting, or macro, language and the programming language are all C++. The interpreter allows for fast prototyping of the macros since it removes the, time consuming, compile/link cycle. It also provides a good environment to learn C++. If more performance is needed the interactively developed macros can be compiled.

ROOT's new C++11 standard-compliant interpreter is Cling, an interpreter built on top of Clang (www.clang.llvm.org) and LLVM (www.llvm.org) compiler infrastructure. Cling is being developed at CERN as a standalone project. It is being integrated into the ROOT data analysis (root.cern.ch) framework, giving ROOT access to an C++11 standards compliant interpreter.

ROOT is an open system that can be dynamically extended by linking external libraries. This makes ROOT a premier platform on which to build data acquisition, simulation and data analysis systems. ROOT is the de-facto standard data storage and processing system for all High Energy Phyiscs labs and experiments world wide. It is also being used in other fields of science and beyond (e.g. finance, insurance, etc).

 

Extend Cling's Language Support

Description: Clang (the underlying compiler library) supports various programming languages besided C and C++. It offers OpenCL, CUDA, ObjectiveC and ObjectiveC++.  Cling's design and implementation are not bound to support only C/C++.  We propose to improve the inherited language support in the interpreter by supporting as many languages as the underlying compiler library (clang) supports.
Expected results: adjustment of cling's custom AST transform passes, implementing loading of the corresponding language runtime environment and adding corresponding test cases.
Required knowledge: intermediate C++, Clang abstract syntax tree (AST), basic ObjectiveC/C++.

MentorFons Rademakers

 

Implement Pre-run Verification In Cling

Description: The cling interpreter's interactive prompt allows a user to type statements and see the results of their execution. We propose to enhance Cling's execution engine with pre-run verification, including the detection of a dereference of a null pointer.

Expected results: the execution of a NULL pointer dereference does not causes a crash.

Mentor: Vassil Vassilev

Required knowledge: intermediate C++,  knowledge of Clang AST and LLVM IR.

 

ROOT  R interface

Description: Develop an interface in ROOT to call R function using the R C++ interface  (Rcpp, see http://dirk.eddelbuettel.com/code/rcpp.html). As a proof of concept implement the Minimizer interface of ROOT to use a R package for minimization. Developing this interface opens the possibility in ROOT to use the very large set of mathematical and statistical tools provided by R.

Implement C++ class(es) to perform a conversion of ROOT C++ object to R objects, transform the returned R objects into ROOT C++ objects. 

Expected Results: One or more C++ classes which perform the conversion of ROOT C++ object to R objects, able to call R functions and transform the returned R objects in ROOT C++ objects. The class(es) should implement some of the existing algorithm interface in ROOT, so that the R functionality can be used directly for fitting or statistical studies in ROOT.

MentorLorenzo Moneta

Requirements: Basic knowledge of C++.  Knowledge of ROOT and/or R would be advantages.

 

New Formula class

Description: Develop a new parallel version of the TFormula class in ROOT using the capabilities of the new Cling interpreter. Having such a class will allow the user to introduce more complex code, even based on C++ 11, in defining a formula for a function class.

Expected Results: Provide a complete new TFormula class capable of creating a function with and without parameters from C++ code which can be parsed and compiled on the fly using Cling.

MentorLorenzo Moneta

Requirements: Basic knowledge of C++.

 

Implement Automatic Differentiation library using Cling

Description: In mathematics and computer algebra, automatic differentiation (AD) is a set of techniques to numerically evaluate the derivative of a function specified by a computer program. Automatic differentiation is an alternative technique to Symbolic differentiation and Numerical differentiation (the method of finite differences). The automatic differentiation library is to be based on Cling which will provides the necessary facilities for code transformation.
Expected Result:  - The AD library is able to differentiate non trivial functions, to find a partial derivative for trivial cases and has good unit test coverage.
Mentors: Vassil Vassilev, Lorenzo Moneta.
Required knowledge: advanced C++, Clang abstract syntax tree (AST), basic math.
 

CernVM & CernVM-FS

CernVM is a Virtual Software Appliance designed to provide a complete and portable environment for developing and running the data analysis of the CERN Large Hadron Collider (LHC) on any end-user computer (laptop, desktop) as well as on the Grid and on Cloud resources, independently of host operating systems. This "thin" appliance contains only a minimal operating system required to bootstrap and run the experiment software. The experiment software is delivered using the CernVM File System (CernVM-FS),  a Fuse file system developed to deliver High Energy Physics (HEP) software stacks onto (virtual) worker nodes.

CernVM-FS is used for instance by LHC experiments on their world-wide distributed computing infrastructure. HEP software is quite complex with tens of gigabytes per release and 1-2 releases per week while, at the same time, almost all the individual files are very small resulting in hundreds of thousands of files per release. CernVM-FS uses content addressable storage (like the GIT versioning system). For distribution it uses HTTP. File meta data are organized in trees of SQlite file catalogs. Files and file meta data are downloaded on demand and aggressively cached. The CernVM File System is part of the CernVM appliance but it compiles and runs on physical Linux/OS X boxes as well. It is mostly BSD licensed with small GPL parts. CernVM-FS source code of the current development branch can be downloaded from here, the documentation is available here.

 

Marketplace for VM Contextualization Artifacts

Description: The versatility required to run many different tasks using the very same virtual machine hard disk image is provided by "contextualization".  By contextualizing a CernVM, one can for instance specify that a specific virtual machine instance should run simulation jobs for the ATLAS experiment, or it should connect to the analysis task queue of the CMS experiment, or it should act as a storage proxy for other CernVMs.  The contextualization is typically a brief, textual specification of key value pairs (environment variables), kernel settings, services to start and scriptlets to run at boot.
One can easily imagine that quickly one needs to deal with very many contextualization artifacts, in particular given that not only a single CernVM can be contextualized but also ensembles of virtual machines can be defined by contextualization.  Often, the same work has to be done multiple times by multiple users.  It would be better to consolidate the contextualization artifacts on a common marketplace.  Contextualization artifacts could be described, rated, exchanged, and indexed, similar to an app store, to the recipe repository on puppet forge, or to the collection of virtual machines provided by TurnKey.

Expected Result: Extension of the cernvm-online.cern.ch web application by functionality to index, exchange, rate, and find contextualization artifacts.
Mentors: Jakob Blomer, Predrag Buncic

Requirements: Good knowledge of web technologies. Experience with virtualization and virtual machines will be an asset.

 

CernVM Zookeeper

A virtual analysis facility (VAF) is an ensemble of virtual machines running on IaaS resources which, as a whole, offer a data analysis cluster to physicists.  Such a virtual analysis facility comprises several virtual machine types, e.g. a storage proxy, a job server, and worker nodes that do the actual number crunching.  While such an ensemble of virtual machines can be relatively easily bootstrapped using the right contextualization artifacts, it is more difficult to maintain and monitor the cluster, in particular as every physicist might have several VAFs on several independent IaaS clouds running in parallel.  On top of that, not all virtual machines have public IP addresses.
Description: This project should extend CernVM by a XMPP component that, upon boot, connects to an XMPP server and joins a group chat.  This group chat can then be used by a physicists to control and monitor its virtual machines, possibly through a web interface but also through his or her instant messaging client.  (This project can benefit from previous work on the CernVM Co-Pilot system, a job server for CernVM based on XMPP.)

Mentors: Jakob Blomer, Predrag Buncic
Requirements: Good knowledge of XMPP and scripting lanugages (Perl, Python). Experience with virtualization and virtual machines will be an asset.

 

Garbage Collection for the CernVM File System

Context: In the CernVM-FS internal storage, every file is addressed by its cryptographic content hash.  Whenever a file is modified, a new file with a new content is stored internally.  Naturally, this design results in a versioning file system, i.e. previous versions of files remain accessible.  In many cases, this can be considered a desirable feature.
In some cases, however, it would be better to automatically remove previous file system versions. Such a case is the hosting of nightly snapshots of an experiment software development tree on CernVM-FS. The problem of gathering and removing older revisions of the file system is amplified by the fact that CernVM-FS repositories can grow to a large number of files (tens or hundreds of millions) and that any automatic garbage collection need to be performed online.  Possible approaches can be the implementation of reference counting or a mark and sweep algorithm on the CernVM-FS storage.

Expected Result: Extension of the CernVM-FS server toolkit (C++ and bash) that is able to detect garbage generation during regular file system updates and incrementally removes garbage.
Mentors: Jakob Blomer
Requirements: Good knowledge of C++, file systems, and storage technologies.
 

 

The Geant4 toolkit simulates the interactions of elementary particles and radiation with matter. It is used to simulate the detectors of the LHC and other High Energy Physics (HEP) experiments. It finds application in other areas, from assessing the effects of radiation on the electronics of satellites to improving the design of medical detectors with the custom GATE application. LHC experiments use Geant4 to compare the signatures of rare events from new physics (such as the Higgs boson) to those coming from known interactions. The open source toolkit is developed by the Geant4 collaboration, which brings together 90 physicists and engineers from laboratories and universities around the world. Developments are ongoing to improve its precision and scope of application, and to better utilise current and emerging computer architectures. The simulation programs of the LHC experiments use the Geant4 simulation toolkit to produce simulated LHC events continuously running with on about 100,000 CPU cores throughout the year. These statistics remain a limitation in the analysis potential for some interesting types of new physics. As a result the goal of the project is to explore different ways to reduce the execution time of Geant4 on today’s complex commodity CPUs, and to prototype how to use it efficiently on the many-core hardware of the future (tens, hundreds of cores, threads or ‘warps’). The code required to model diverse types of particles and interactions, and to model the complex geometries of detectors is large. Due to this it overwhelms the caches of current CPUs, significantly reducing the efficiency of utilisation of today’s hardware. This effort is focused on identifying ways to spread the work between threads and/or to reorganise the work. By using less code in each core we aim to use the memory architectures of today’s hardware better. At the same time we prepare the way to obtain good performance on tomorrow’s hardware.

Improve Geometry Navigation in Sequential and GPU versions

Description: Locating the volume which corresponds to a position, and the next boundary along a ray are computationally expensive operations in a complex geometry.  Geant4 uses a voxelisation technique which precompute the volumes in 3-d slices of a setup. The first objective of this project is to investigate how to speedup the sequential Geant4 navigation. The second objective is to refine the algorithms used for navigation in a voxelised geometry in the GPU version of Geant4.

Mentors: John Apostolakis, Gabriele Cosmo 
Requirements: Good knowledge of C++, Object-Oriented Programming, parallel programming using GPUs are needed. Knowledge of ray tracing algorithms will be very beneficial.

 

Evaluate language or annotation options for Simulation kernels

Description: Port key kernels of simulation code to a parallel C++ variant ( Cilk+, SplitC ) and/or OpenAcc/OpenMP and benchmark the effort and computing speedup obtained.
Mentors: John Apostolakis 

 

Requirements: Good knowledge of C++ and exposure to parallel/vector programming are needed. Experience with OpenMP or similar technologies, or a parallel C++ variant will be beneficial. 

 

Vectorised implementations of Solids

Description: create vectorised versions of the implementations of new library of solides (USolids), which is the future library of Solids for Geant4 and Root.

Expected result: Vector versions of UBox and UTubs solid.

Mentors: John Apostolakis, Gabriele Cosmo

Requirements: Knowledge of C++ and vectorisation.

 

Performance Monitoring

Linux-perf is a performance tuning component of the Linux kernel. It is the go-to system for performance tuning activities on Linux, ranging from software events such as OS context switches to the hardware counter level (instructions executed, cache misses, etc). CERN, as numerous other large organizations and companies, makes extensive use of such performance monitoring features in its daily work. Large portions of the software powering the Large Hadron Collider science go through systems such as linux-perf every day.

The main components of a setup with linux-perf are a kernel part and a userspace tool called “perf”, supported by the libpfm library. Work on the project will provide world-class experience in performance tuning, Linux software architecture and computer architecture. The student(s) can also find out how CERN uses its computers to further large-scale scientific goals.

Performance Self Monitoring

Description: While external tools for tuning exist today, some applications need to have performance monitoring facilities built in. That means that the application - by itself – can report on its usage of various hardware features of the platform it runs on. This project will involve a design and implementation of a C/C++ API to linux-perf and to libpfm that will allow applications to monitor their own behavior. Software developments will be preceded by performance studies of the linux-perf system itself, to establish practical bounds of such improvements. All work will involve and impact real-world High Energy Physics software.
MentorVincenzo Innocente, Andrzej Nowak
Requirements: Knowledge of C/C++ programming and understanding of Linux programming and software execution in Linux are required. Experience with perf and Python is beneficial.

Performance tuning: organizing performance data

Description: The goal of this project is to design and develop efficient mechanisms to organize performance data. One problem is that collected performance data can only be referenced by its location in the code, but cannot be described by user-defined names or in any other way. Another issue is that data is collected on the whole program rather than only some pre-selected routines – improvements on this will help focus performance studies. The work will involve developing software solutions to these challenges, in close collaboration with CERN experts. All work will focus on and impact real-world High Energy Physics software.
MentorVincenzo Innocente, Andrzej Nowak

Requirements: Knowledge of C/C++ programming and understanding of Linux programming and software execution in Linux are required. Experience with perf and Python is beneficial.
 

Miscellaneous

CERN app on Android

Description: A prototype iOS app was created by a GSoC student in 2012 (see http://ph-news.web.cern.ch/content/new-ios-application-cern ) which provides a wide range of (real-time) information on CERN, the accelerators, the detectors, the physics, the history, the latest news, etc. This project foresees to create a similar app for Android. One goal is to make it extensible so that additional aspects relevant to CERN and particle physics could be added in future, including displays of LHC events, mini-simulations or science quizzes. There is the potential for tens to hundreds of thousands of downloads as the public follows the restart of the upgraded LHC in 2015.

Mentors: Fons Rademakers, Timur Pocheptsov

Requirements: Experience with Android development.

 

Parallelisation of Core Services for High Energy Physics Data Processing

 The software frameworks for High Energy Physics (HEP) data processing are C++ programs of millions of lines of code which transform the electric signals coming from the particle detectors into the building blocks of exciting discoveries. Frameworks such as Gaudi (cern.ch/proj-gaudi/) provide a variety of services: from connection to databases, the management of the execution of physicists' code to the interaction with accelerators and coprocessors.
With multiple petabytes of experiment data recorded each year, the overall performance of such frameworks is essential. The partially interdependent services mentioned above are rather complex entities, which need considerable time for their initialization, before the actual physics data processing can start.

Description: As the parallelisation of the physics processing improves, the overhead due to sequential startup becomes an important issue.  To address this we propose to parallelise the service initialization in the widely used,  in the GaudiHive (concurrency.web.cern.ch/GaudiHive) multi-threaded extension of the cross-experiment HEP framework Gaudi.
The task should be accomplished using the functionalities offered by the C++ language (C++11 standard) and taking advantage of highly optimised, lock free algorithms and data structures.

Mentors: Danillo Piparo, Benedikt Hegner

Requirements: Good knowledge of C++ and parallel programming. Experience with Python is a plus.

 

Extending Indico

Indico (http://indico-software.org<http://indico-software.org/>) is a web-based event lifecycle management system, room booking application and collaboration hub (video conference, chat, webcast and others). It is used at many High Energy Physics laboratories for long term archival of documents and metadata related to all kinds of events.  CERN installation  (http://indico.cern.ch<http://indico.cern.ch/>), hosts more than 210.000 events, more than 1 million uploaded files and receives around 14.000 visitors per day. It is installed in more than 100 institutes world-wide (http://indico-software.org/wiki/IndicoWorldWide). This generates a need for permanent improvement and development.

The student will gain expertise in web development, acquiring skills in software engineering good practices, and both development of front-end (using modern JavaScript-based web technologies and libraries) and back-end web (Python programming language, Object Oriented Database (ZODB), Flask, WSGI,...).  Indico's GitHub address is https://github.com/indico/indico.

 

Indico: Abstract editor

Description: Indico is mainly used for events by the physics community. Physicists, like some other scientists, often need to write very complex formulas in their paper abstracts, as well adding images and other types of content. Indico currently provides only a simple web form to submit plain-text abstracts for a conference. The project is to enable users to write in different formats (Markdown + MathJax for formulas, LaTeX, etc) that will allow the generation of beautiful conference abstracts, which can be published in a Book of Abstracts.

MentorJose Benito Gonzalez Lopez, Pedro Ferreira

Requirements: Knowledge of Web development and Javascript (jQuery) technologies are required. Knowledge of Python, git, Markdown, MathJax for formulas, and/or LaTeX would be beneficial.

 

Indico: On-line Proceedings

Description: The final step for almost every big conference is the publication of the conference's proceedings. Basically, this means a big book with all the accepted papers of a conference. This final step is the only one that Indico is missing in order to provide the full functionality needed to complete the lifecycle of conference organization. We do not intend to be able to publish a real book but instead to create digital proceedings. The goal would be to be able to retrieve all the papers of a given conference and build a very user-friendly interface with all the publications as well as many different indexes, filters and search capabilities by content.

MentorJose Benito Gonzalez Lopez, Pedro Ferreira

Requirements: Knowledge of Web development and Javascript (jQuery) technologies are required. 

 

'Blue sky' ideas

  • "HEPunion" filesystem implementation as Linux module: Adapt and extend union file system to address the requirements of a HEP experiment's dedicated farm.
    Mentors: Pierre Schweitzer, Loic Brada
    Requirements: Good knowledge of C, Linux and (Linux) Kernel development.

  • Extend Geant 4 on GPUs: Extend the Geant4 GPU prototype's geometry or physics.  Geometry navigation can be extended by devoloping additional types of volumes, starting from the geometry developed by Otto Seiskari (2010) and Dhruva Tirumala (GSoC 2012) in OpenCL/Cuda.  Extending physics can create new processes or integrate models from other authors.

Mentor: John Apostolakis
Requirements: Experience with C/C++, OpenCL/Cuda

  • General GPU-vectorized solid: Create a vectorised/GPU-capable solid that can be used in place of the most popular existing solids (box, tube, conical & spherical shells), for use in Geant4-GPU and vector simulation. Inspired by the approach of James Tickner (see article in Computer Physics Communications, Vol 181, Issue 11, Nov 2010, pages 1821–1832 available at http://dx.doi.org/10.1016/j.cpc.2010.07.001).

Mentor: John Apostolakis, Gabriele Cosmo
Requirements: Experience with C/C++, vectorization

  • New simulation engine: Create a prototype geometry navigation for one particle type with a limited geometry choice (1-2 types of volume types) using a high-productivity parallel language ( Chapel, X10 ). Benchmark this against existing solutions for the same problem. Document the development effort and the pitfalls of the language, tools and implementation (potential for a scientific report on the coding experience, in addition to the results).

Mentor: John Apostolakis
Requirements: Experience with C/C++ and either Chapel, X10, Cilk+, SplitC or a similar language is required.

 

Mentors

Here is the list of our mentors and their areas of experitse:

 

Contact information

Please do not hesitate to contact us if you are planning to apply for any of the above projects:

  • SFT GSoC mailing list: sft-gsoc-AT-cern-DOT-ch (no subscription needed).
  • SFT GSoC Jabber/XMPP chat room: gsoc-sft@conference.jabber.org . We noticed that Gmail/Gtalk XMPP accounts have problems posting messages to the chat room, so please register yourself an XMPP account on some other server (it takes no time to register an account at http://www.jabber.org).
  • IRC is restricted at CERN - please use Jabber instead.

You are here