Name: FS computing 2023
Start: 2023-11-10T09:00:00+01:00
End: 2023-11-10T15:50:00+01:00
Location: DESY

FS computing 2023

Friday 10 November 2023 - 09:00

Monday 6 November 2023
Tuesday 7 November 2023
Wednesday 8 November 2023
Thursday 9 November 2023
Friday 10 November 2023
09:00 Welcome and introduction - Anton Barty (FS-SC (Scientific computing)) Edgar Weckert (FS (Forschung mit Synchrotronstrahlung))
Welcome and introduction
- Anton Barty (FS-SC (Scientific computing))
- Edgar Weckert (FS (Forschung mit Synchrotronstrahlung))
09:00 - 09:10
Room: FLASH seminar room
09:10 Philipp Neumann - Central IT - Philipp Neumann (IT (Informationstechnik))
Philipp Neumann - Central IT
- Philipp Neumann (IT (Informationstechnik))
09:10 - 09:15
Room: FLASH seminar room
09:15 FS-EC: Software solutions in the critical path for data acquisition - Linus Pithan (FS-EC (Experimente Control))
FS-EC: Software solutions in the critical path for data acquisition
- Linus Pithan (FS-EC (Experimente Control))
09:15 - 09:25
Room: FLASH seminar room Within FS-EC (Experiment Control) we develop and adopt software solutions that cater the data acquisition processes in user operation in FS facilities as well as fundamental background services that are needed for a performant beamline infrastructure. The group covers aspects spanning across high level controls (Sardana), low level controls and hardware abstraction (Tango), detector drivers and adaptors (for high speed cameras), custom firmware for embedded devices (PILC) to beamline specific scripts and user interfaces. Further we are involved in data analysis (Maxwell support) as well as GPFS storage (ASAP3) related activities. As one of the support groups within FS our mission is to contribute to smooth user operation in DESY FS facilities. This involves own developments (e.g. hundreds of Tango servers) as well as the contributions to international collaborations.
09:25 Martin Burger - FS-CI - Martin Burger (FS-CI (Computational Imaging))
Martin Burger - FS-CI
- Martin Burger (FS-CI (Computational Imaging))
09:25 - 09:35
Room: FLASH seminar room
09:35 Protein Machinists: Teasing out the secrets of subtle protein dynamics - Helen Ginn (DESY-FS)
Protein Machinists: Teasing out the secrets of subtle protein dynamics
- Helen Ginn (DESY-FS)
09:35 - 09:45
Room: FLASH seminar room The knowledge gap between what we know about proteins and what we would like to do with them is broadly described as “protein dynamics". The nascent Protein Machinists group tackles this from computational angles: how to mathematically express protein conformations, compare them, establish what is contained within an experimentally observed population and manipulate them. I will also talk about the computational backbone of the scientific work.
09:45 Enabling online phase retrieval for in-situ and operando x-ray holography - Johannes Hagemann (FS-PETRA (PETRA III))
Enabling online phase retrieval for in-situ and operando x-ray holography
- Johannes Hagemann (FS-PETRA (PETRA III))
09:45 - 10:00
Room: FLASH seminar room Applying for measurements at large X-ray sources like PETRA III at DESY or BESSY II at HZB is highly competitive. If granted beam time, numerous samples need to be measured. These measurements often occur under in-situ or operando conditions, such as studying the degradation of a biodegradable Mg wire or structural changes in a battery during charging. These changes happen at a sub-micron scale, requiring computationally intensive techniques like phase-sensitive X-ray microscopy. However, these techniques don’t provide immediate feedback, increasing the risk of failed measurements and wasted beam time. The Helmholtz imaging project SmartPhase aims to address this issue by providing online reconstruction of measurement data. We are implementing self-optimizing phase-retrieval algorithms based on conventional and physics-informed machine learning approaches.
10:00 Modelling the interaction of matter with ultrafast and ultraintense x-ray pulses - Ludger Inhester (CFEL, DESY)
Modelling the interaction of matter with ultrafast and ultraintense x-ray pulses
- Ludger Inhester (CFEL, DESY)
10:00 - 10:15
Room: FLASH seminar room I present an overview over the simulation activities done with the XRAYPAC tookit developed at FS-CFEL-3.
10:15 RIC and open science - Sophie Servan (DESY)
RIC and open science
- Sophie Servan (DESY)
10:15 - 10:25
Room: FLASH seminar room Overview of RIC activities for FS, including e.g. results from EU projects and collaborations with LEAPS and Helmholtz.
10:25 Overview of central IT for FS - Juergen Hannappel (IT (IT Scientific Computing))
Overview of central IT for FS
- Juergen Hannappel (IT (IT Scientific Computing))
10:25 - 10:35
Room: FLASH seminar room A short overview of the services provided by central IT specifically for FS data taking and data processing, especially the ASAP3 framework and related services.
10:35

10:35 - 11:05
Room: FLASH seminar room
11:05 Real-time data processing for serial crystallography at P11 - Thomas White (FS-SC) Tim Schoof (DESY)
Real-time data processing for serial crystallography at P11
- Thomas White (FS-SC)
- Tim Schoof (DESY)
11:05 - 11:20
Room: FLASH seminar room
11:20 Borrowing HEP algorithms for detector alignment in photon science - Thomas White (FS-SC)
Borrowing HEP algorithms for detector alignment in photon science
- Thomas White (FS-SC)
11:20 - 11:30
Room: FLASH seminar room Accurate and precise information about the position of the detector is critical to the success of many types of experiment in photon science. This is particularly true for serial crystallography, which is sensitive to detector misalignments of less than one pixel’s width. However, serial crystallography data is also very useful for refining the detector geometry, consisting of sharp, bright Bragg peaks in regular and geometrically simple patterns. Several methods have been developed for this process over the last decade. The current state of the art involves refining the “global” detector geometry parameters along with the “local” crystal orientation parameters, in one very large least-squares refinement. The joint refinement of local and global parameters is needed to avoid a biased fit and slow convergence. Unfortunately, with a typical serial crystallography dataset consisting of many tens of thousands of crystals, only a fraction of the data can be used before the refinement becomes too computationally demanding. The “Millepede” algorithm was developed in high energy physics to address exactly this problem. The relevant matrix equations can be rearranged such that the full calculation can be performed, without approximations but with vastly reduced memory and CPU requirements. This makes a full joint refinement using tens or even hundreds of thousands of crystals practical. In this contribution, I will describe the ongoing experience of applying the Millepede algorithm to serial crystallography data, and the potential for other applications in photon science.
11:30 Data Handling and Analysis at FLASH - Christopher Passow (FS-FLASH-D (FLASH Photon Diagnostics and Controls))
Data Handling and Analysis at FLASH
- Christopher Passow (FS-FLASH-D (FLASH Photon Diagnostics and Controls))
11:30 - 11:45
Room: FLASH seminar room This presentation offers a succinct examination of FLASH, emphasizing the facility's key features. It outlines the IT infrastructure and collaborative relationships with different DESY groups. Additionally, it delves into the technical aspects of experimental control, data acquisition, and analysis methods. The talk also sheds light on current projects and future directions.
11:45 Data reduction activities in FS-DS (photon science detector systems) - David Pennicard (FS-DS (Detektorsysteme))
Data reduction activities in FS-DS (photon science detector systems)
- David Pennicard (FS-DS (Detektorsysteme))
11:45 - 12:00
Room: FLASH seminar room New detectors produce increasing volumes of data, and so performing data reduction close to the detector (e.g. on detector-specific data acquisition PCs) can potentially reduce the workload on later infrastructure. I will present on current work on this in FS-DS. Also, for historical reasons, FS-DS are responsible for the DESY part of a few collaboration projects on data reduction: Data-X, HIR3X workpackage 2, and LEAPS-INNOV workpackage 7. I will present these projects, and we can discuss how to proceed with them in future.
12:00 X-Environment metadata management - Igor Khokhriakov (FS-SC (Scientific computing))
X-Environment metadata management
- Igor Khokhriakov (FS-SC (Scientific computing))
12:00 - 12:15
Room: FLASH seminar room
12:15 Data processing and management at P06 - Jan Garrevoet (FS-PETRA-S (FS-PET-S Fachgruppe P06))
Data processing and management at P06
- Jan Garrevoet (FS-PETRA-S (FS-PET-S Fachgruppe P06))
12:15 - 12:30
Room: FLASH seminar room
12:30 Posters
Posters
12:30 - 13:50
Room: FLASH seminar room
Contributions

12:30 Real-time data processing for serial crystallography at P11 - Thomas White (FS-SC)

12:35 Shaking out Intrinsic Structural Variation in Femtosecond Protein Crystallography using Deep Learning - Samuel Flewett (FS-SC (Scientific computing))

12:40 DAPHNE4NFDI - Anton Barty (FS-SC (Scientific computing))

12:45 DASHH

12:50 RockIT project - Alexander Schoekel (DESY)

13:05 Computational Imaging @ DESY - Tim Roith (FS-CI (Computational Imaging))

13:10 Molecular states for quantum simulation - Sebastian Trippel (FS-CFEL-CMI (CFEL-CMI Controlled Molecule Imaging))

13:20 Beamline P11

13:30 The imaging program at the SAXSMAT beamline P62 - Sylvio Haas (FS-PETRA-D (FS-PET-D Fachgruppe P62 (SmallAngleSc)))

13:35 The AMARCORD electronic log book - Philipp Middendorf (FS-CFEL-1 (Forschung mit Photonen Experimente 1))

13:40 Start-to-end Wave Propagation Simulations of Beamlines and Coherence Properties using SRW PIV