HPC Application Support

HPC Application Support

The MPCDF provides consulting and dedicated high-level support for the development, optimization, analysis and visualization of high-performance-computing (HPC) and high-performance data-analytics (HPDA) applications. This comprises the development and optimization of codes in collaboration with Max-Planck scientists, scientific visualization of data from simulations and experiments, and technical consulting, e.g. on programming techniques and models, like for the use  of  hardware accelerators (e.g. GPU).

Support

 For dedicated project support, please contact HPC) or

 Technical documentation (MPCDF hardware and software) can be found at the MPCDF user documentation.

Ongoing projects and long-term collaborations

  • GENE (Max-Planck Institute for Plasmaphysics, Garching)
  • GVEC (Max-Planck Institute for Plasmaphysics, Garching)
  • GRILLIX (Max-Planck Institute for Plasmaphysics, Garching)
  • JOREK (Max-Planck Institute for Plasmaphysics, Garching)
  • FHI-aims (Fritz-Haber Institute of the MPG, Berlin)
  • NECI (Max-Planck Institute for Solid State Research, Stuttgart)
  • ELPA (MPCDF, Garching)
  • OCTOPUS (Max-Planck Institute for the Structure and Dynamics of Matter, Hamburg)
  • VERTEX (Max-Planck Institute for Astrophysics, Garching)
  • ESPResSo++ (Max-Planck Institute for Polymer Research, Mainz)
  • IDE/GPEC (Max-Planck Institute for Plasmaphysics, Garching)
  • SeLaLib (Max-Planck Institute for Plasmaphysics, Garching)
  • CHIEF (Max-Planck Institute for Solar System Research, Goettingen)
  • MagIC (Max-Planck Institute for Solar System Research, Goettingen)
  • NSCOUETTE (Max-Planck Institute for Dynamics and Self-Organization, Goettingen)
  • TurTLE (Max-Planck Institute for Dynamics and Self-Organization, Goettingen)
  • BioEM (Max-Planck Institute for Biophysics, Frankfurt)
  • Complexes++ (Max-Planck Institute for Biophysics, Frankfurt)
  • GROMACS (together with Max-Planck Institute for Biophysical Chemistry, Goettingen)
  • DIAMOND (Max-Planck Institute for Developmental Biology, Tuebingen)

See also MPG Projects

People

Members of the HPC Application Support Division

  • Dr. Tilman Dannert (coordinator HPC training and academic collaborations)
  • Dr. Sebastian Eibl
  • Meisam Farzalipour-Tabriz
  • Dr. Sebastian Kehl
  • Dr. Cristian Lalescu
  • Dr. Carlos Lopez
  • Dr. Sebastian Ohlmann
  • Dr. Markus Rampp (leader)
  • Dr. Klaus Reuter (deputy leader)
  • Dr. Soheil Soltani
  • Dr. Florian Merz (Lenovo, associated)
  • Dr. Alexander Poeppl (Intel, associated)

 See also: Staff

Former Members

  • Dr. Rafael Lago (ACH at IPP)
  • Dr. Ihor Holod (ACH at IPP)
  • Dr. Andreas Marek (head of MPCDF AI & HPDA division)
  • Dr. Timoteo Colnaghi (MPCDF AI & HPDA division)
  • Dr. Michele Compostella (MPCDF systems division)
  • Dr. Cesar Allande Alvarez (Industry)
  • Dr. Luka Stanisic (Industry)
  • Dr. Lorenz Hüdepohl (MPCDF systems division)
  • Dr. Renate Dohmen (MPCDF systems division)
  • Dr. Pavel Kus (University of Prague)
  • Dr. Berenger Bramas (INRIA Strassbourg)
  • Dr. Werner Nagel (Retired)
  • Elena Erastova (MPCDF systems division)
  • Dr. Fabio Baruffa (Intel)
  • Reinhard Tisma (Retired)

Students

  • Yi Ju (PhD thesis supervised by Prof. E. Laure, MPCDF)
  • Carolin Penke (PhD thesis in collaboration with Prof. P. Benner, MPI for Dynamics of Complex Technical Systems; co-supervisors: T. Dannert, A. Marek)
    • Numerical solvers for the Bethe-Salpeter Eigenvalue problem
  • Matthias Albert (Bachelor thesis in collaboration with Prof. D. Kranzlmueller, LMU; co-supervisor: M. Rampp)
    • Visualizing Big Data in Virtual Reality – Interactive Analysis of Large Scale Turbulence Simulations (completed in 2018)
  • Victor Artigues (Master thesis in collaboration with Prof. O. Lafitte, Universite Paris 13 & Prof. E. Sonnendruecker, IPP; co-supervisors: K. Reuter, M. Rampp)
    • Evaluation of novel, high-level programming frameworks for exascale HPC architectures and their application in numerical plasma physics. (completed in 2018)

Open Positions

We are always looking for highly skilled computational scientists or HPC or HPDA application experts with profound knowledge in parallel programming (ideally with modern Fortran, C or C++, together with MPI, OpenMP, and GPU programming models) and/or data analytics. We offer the opportunity to work on state-of-the-art numerical algorithms, leading HPC codes and HPDA applications, latest supercomputer technology and to maintain close collaborations with the code owners and domain scientists from various Max-Planck-Institutes e.g. in astrophysics, fusion research, materials and bio sciences, polymer research, and theoretical chemistry. Applications are welcome and should be directed to .

See also: Career

Talks and training material

 

See also Training & Education

Selected publications

See also: Publications by MPCDF

2021

  • Toward exascale whole-device modeling of fusion devices: Porting the GENE gyrokinetic microturbulence code to GPU. Germaschewski, K.; Allen, B.; Dannert, T; Hrywniak, M.; Donaghy, J.; Merlo, G.; Ethier, S.; D'Azevedo, E.; Jenko, F.; Bhattacharjee, A. Physics of Plasmas 28, 062501 (2021)
  • Transitions of turbulent superstructures in generalized Kolmogorov flow. Lalescu, C. L.; Wilczek, M. :  Physical Review Research 3 (2), L022010 (2021)
  • Sensitive protein alignments at tree-of-life scale using DIAMOND. B. Buchfink, K. Reuter & H.-G. Drost . Nature Methods 18, 366–368 (2021)
  • Self-consistent potential correction for charged periodic systems. da Silva, M. C.; Lorke, M.; Aradi, B.; Farzalipour Tabriz, M.; Frauenheim, T.; Rubio, A.; Rocca, D.; Deák, P. Physical Review Letters 126, 076401 (2021)
  • Convolutional neural network-assisted recognition of nanoscale L12 ordered structures in face-centred cubic alloys. Li, Y.; Zhou, X.; Colnaghi, T.; Wei, Y.; Marek, A.; Li, H.; Bauer, S.; Rampp, M.; Stephenson, L. T. npj Computational Materials vol 7 article 8 (2021)

2020

  • FaVAD: A software workflow for characterization and visualizing of defects in crystalline structures. von Toussaint, U.; Domínguez-Gutiérrez, F.J.; Compostella, M.; Rampp, M.: Computer Physics Communications 262, 107816 (2020)
  • Intermediate mass black hole formation in compact young massive star clusters. Rizzuto, F. P.; Naab, T.; Spurzem, R.; Giersz, M.; Ostriker, J. P.; Stone, N. C.; Wang, L.; Berczik, P.; Rampp, M.: Monthly Notices of the Royal Astronomical Society 501 (4), pp. 5257 - 5273 (2020)
  • Formation of sdB-stars via common envelope ejection by substellar companions. Kramer, M.; Schneider, F. R. N.; Ohlmann, S. T.; Geier, S.; Schaffenroth, V.; Pakmor, R.; Röpke, F. K.:  Astronomy and Astrophysics 642, A97 (2020)
  • Common-envelope evolution with an asymptotic giant branch star. Sand, C.; Ohlmann, S. T.; Schneider, F. R. N.; Pakmor, R.; Röpke, F. K.:Astronomy and Astrophysics 644, A60 (2020)
  • Validation tests for cryo-EM maps using an independent particle set. S. Ortiz, L. Stanisic, B. A Rodriguez, M. Rampp, G. Hummer, P. Cossio Journal of Structural Biology: X 4, 100032 (2020). preprint: arXiv:1908.01054
  • NECI: N-Electron Configuration Interaction with emphasis on state-of-the-art stochastic methods. Kai Guther, Robert J. Anderson, Nick S. Blunt, Nikolay A. Bogdanov, Deidre Cleland, Nike Dattani, Werner Dobrautz, Khaldoon Ghanem, Peter Jeszenski, Niklas Liebermann, Giovanni Li Manni, Alexander Y. Lozovoi, Hongjun Luo, Dongxia Ma, Florian Merz, Catherine Overy, Markus Rampp, Pradipta K. Samanta, Lauretta R. Schwarz, James J. Shepherd, Simon D. Smart, Eugenio Vitale, Oskar Weser, George H. Booth, Ali Alavi. Journal of Chemical Physics 152,12 (2020). preprint: arXiv:2006.14956
  • SNe Ia from double detonations: Impact of core-shell mixing on the carbon ignition mechanism, S. Gronow, C. Collins, S. T.  Ohlmann, R. Pakmor, M. Kromer, I. R. Seitenzahl, S. A. Sim, F. K. Röpke, A&A 635, A169 (2020)
  • GENE-3D: A global gyrokinetic turbulence code for stellarators. Maurer, M.; Bañón Navarro, A.; Dannert, T.; Restelli, M.; Hindenlang, F.; Görler, T.; Told, D.; Jarema, D.; Merlo, G.; Jenko, F.:  Journal of Computational Physics 420, 109694 (2020)
  • Long-term evolution of a magnetic massive merger product, F R N Schneider, S T Ohlmann, Ph Podsiadlowski, F K Röpke, S A Balbus, R Pakmor, MNRAS 495, 2796–2812 (2020)
  • Intrinsic defects of GaSe. P. Deák, M. Han, M. Lorke, M. Farzalipour Tabriz, Th. Frauenheim. J. Phys.: Condens. Matter 32 (2020) 285503.
  • Octopus, a computational framework for exploring light-driven phenomena and quantum dynamics in extended and finite systems. N. Tancogne-Dejean, M. J. T. Oliveira, X. Andrade, H. Appel, C. H. Borca, G. Le Breton, F. Buchholz, A. Castro, S. Corni, A. A. Correa, U. De Giovannini, A. Delgado, F. G. Eich, J. Flick, G. Gil, A. Gomez, N. Helbig, H. Hübener, R. Jestädt, J. Jornet-Somoza, A. H. Larsen, I. V. Lebedeva, M. Lüders, M. A. L. Marques, S. T. Ohlmann, S. Pipolo, M. Rampp, C. A. Rozzi, D. A. Strubbe, S. A. Sato, C. Schäfer, I. Theophilou, A. Welden, A. Rubio. Journal of Chemical Physics 152,12 (2020) arXiv:1912.07921
  • nsCouette -- A high-performance code for direct numerical simulations of turbulent Taylor-Couette flow. J.-M. Lopez, D. Feldmann, M. Rampp, A. Vela-Martin, L. Shi, M. Avila. SoftwareX, 11, 100395 (2020) arXiv:1908.00587
  • Evaluation of performance portability frameworks for the implementation of a particle-in-cell code V. Artigues, K. Kormann, M. Rampp, K. Reuter. Concurrency and Computation: Practice and Experience 32:e5640 (2020). arXiv:1911.08394
  • MPCDF HPC Performance Monitoring System: Enabling Insight via Job-Specific Analysis. Stanisic L., Reuter K. (2020)  In: Schwardmann U. et al. (eds) Euro-Par 2019: Parallel Processing Workshops. Euro-Par 2019. Lecture Notes in
    Computer Science, vol 11997. Springer, Cham. doi.org/10.1007/978-3-030-48340-1_47 arXiv:1909.11704 (2019)

2019

  • Discovery of an Exceptionally Strong β-Decay Transition of 20F and Implications for the Fate of Intermediate-Mass Stars, Kirsebom, O. S., Jones, S., Strömberg, D. F., Martínez-Pinedo, G., Langanke, K., Röpke, F. K., Brown, B. A., Eronen, T., Fynbo, H. O. U., Hukkanen, M., Idini, A., Jokinen, A., Kankainen, A., Kostensalo, J., Moore, I., Möller, H., Ohlmann, S. T., Penttilä, H., Riisager, K., Rinta-Antila, S., Srivastava, P. C., Suhonen, J., Trzaska, W. H., & Äystö, J. Phys. Rev. Lett. 123, 262701 (2019)
  • Defect calculations with hybrid functionals in layered compounds and in slab models, P. Deák, E. Khorasani, M. Lorke, M. Farzalipour-Tabriz, B. Aradi & Th. Frauenheim, Phys. Rev. B 100, 235304 (2019)
  • Current profile tailoring with the upgraded ECRH system at ASDEX Upgrade, R. Fischer, A. Bock, A. Burckhart, L. Giannone, A. Gude, R.M. McDermott, M. Rampp, M. Reisner, J. Stober, M. Weiland, M. Willensdorfer, and the ASDEX Upgrade Team 46th EPS Conference on Plasma Physics (2019)
  • Efficient Ensemble Refinement by Reweighting, J. Köfinger, L. Stelzl, K. Reuter, C. Allande, K. Reichel, G. Hummer, J. Chem. Theory Comput. ( 2019) , 15, 5, 3390-3401doi: 10.1021/acs.jctc.8b01231( preprint )
  • A massively parallel semi-Lagrangian solver for the six-dimensional Vlasov-Poisson equation. Kormann, K., Reuter, K., Rampp, M.International Journal of High Performance Computing Applications (2019) ( arXiv:1903.00308)
  • Remnants and ejecta of thermonuclear electron-capture supernovae - Constraining oxygen-neon deflagrations in high-density white dwarfs. S. Jones, F. K. Röpke, C. Fryer, A. J. Ruiter, I. R. Seitenzahl, L. R.  Nittler, S. T. Ohlmann, R. Reifarth, M. Pignatari and K. Belczynski. Astronomy & Astrophysics 622, A74 (2019)
  • Increasing the degree of parallelism using speculative execution in task-based runtime systems. B. Bramas. PeerJ Computer Science 5, e183 (2019), doi: 10.7717/peerj-cs.18

2018

  • CADISHI: Fast parallel calculation of particle-pair distance histograms on CPUs and GPUs. Reuter, K., Koefinger, J. Computer Physics Communications (2018)
  • Current distribution reconstruction for plasma scenario development at ASDEX Upgrade. Fischer, R., Bock, A., Burckhart, A., Denk, S., Dunne, M., Ford, O., Giannone, L., Gude, A., Maraschek, M., McDermott, R., Mlynek, A., Poli, E., Rampp, M., Rittich, D., Weiland, M., Willensdorfer, M. 45th EPS Conference on Plasma Physics (2018)
  • Rotation-supported Neutrino-driven Supernova Explosions in Three Dimensions and the Critical Luminosity Condition.Summa A., Janka H.Th., Melson T. and Marek A. Astrophysical Journal, 852 (2018).

2017

2016

  • GPEC, a real-time capable tokamak equilibrium code. M. Rampp, R. Preuss, R. Fischer & ASDEX Upgrade Team. Fusion Science & Technology, 70(1) (2016) (arXiv:1511.04203)
  • Coupling of the flux diffusion equation with the equilibrium reconstruction at ASDEX Upgrade. R. Fischer, A. Bock, M. Dunne, J. C. Fuchs, L. Giannone, K. Lackner, P. J. McCarthy, E. Poli, R. Preuss, M. Rampp, M. Schubert, J. Stober, W. Suttrop, G. Tardini, M. Weiland & ASDEX Upgrade Team. Fusion Science & Technology, 69(2) 526-536 (2016).
  • Summa A., Hanke F., Janka H.-Th., Melson T., Marek A., and Müller B.: Progenitor-dependent Explosion Dynamics in Self-consistent, Axisymmetric Simulations of Neutrino-driven Core-collapse Supernovae, Astrophysical Journal, 825, 2016
  • Ertl T., Ugliano M., Janka H.-Th., Marek A., and Arconnes A.: Erratum: Progenitor-explosion Connection and Remnant Birth Masses for Neutrino-driven Supernovae of Iron-core Progenitors, Astrophysical Journal, 821, 2016

2015

  • The 3D MHD code GOEMHD3 for astrophysical plasmas with large Reynolds numbers. Code description, verification, and computational performance. Skála, J.; Baruffa, F.; Büchner, J.; Rampp, M.Astronomy & Astrophysics, 580, A48  (2015) ( arXiv:1411.1289).
  • A hybrid MPI-OpenMP parallel implementation for pseudospectral simulations with application to Taylor-Couette flow. Shi, L.; Rampp, M.; Hof, B.; Avila, M. Computers & Fluids, 106, 1-11 (2015) ( arXiv:1311.2481).
  • Melson T., Janka H.-Th., Bollig R., Hanke F., Marek A., and Müller B.: Neutrino-driven Explosion of a 20 Solar-mass Star in Three Dimensions Enabled by Strange-quark Contributions to Neutrino-Nucleon Scattering, Astrophysical Journal, 808, 2015
  • Melson T., Janka H.-Th., and Marek A.: Neutrino-driven Supernova of a Low-mass Iron-core Progenitor Boosted by Three-dimensional Turbulent Convection, Astrophysical Journal, 801, 2015

2014

  • Porting Large HPC Applications to GPU Clusters: The Codes GENE and VERTEX. Dannert, T.; Marek, A., Rampp, M., in Advances in Parallel Computing, 25, 305-314 (2014) ( arXiv:1310.1485).
  • Towards Petaflops Capability of the VERTEX supernova Code. Marek, A., Rampp, M., Hanke, F., Janka, H.-Th., in Advances in Parallel Computing, 25, 712-721 (2014). (arXiv:1404.1719).
  • Tamborra I., Hanke F., Janka H.Th., Müller B., Raffelt G., and Marek A.: Self-sustained Asymmetry of Lepton-number Emission: A New Phenomenon during the Supernova Shock-accretion Phase in Three Dimensions, Astrophysical Journal, 792, 2014
  • Marek A., Blum V., Johanni R., Havu V., Lang B., Auckenthaler T., Heinecke A., Bungartz H.-J, and Lederer H.: The ELPA library - Scalable parallel Eigenvalü Solutions for Electronic Structure Theory and Computational Science, Journal of Physics Condensed Matter, 26, 2014

2013

  • A data acquisition system for real-time magnetic equilibrium reconstruction on ASDEX Upgrade and its application to NTM stabilization experiments. L. Giannone et al. (including M. Rampp). Fusion Engineering and Design, 88 3299-3311 (2013)
  • Optimization strategy for the VMEC stellarator equilibrium code. Merz, F.; Geiger, J.; Rampp, M.IPP-Report R/48 (2013)
  • Dnmt2-dependent methylomes lack defined DNA methylation patterns
    G. Raddatz, P. M. Guzzardo, N. Olova, M. R. Fantappié, M. Rampp, M. Schaefer, W. Reik, G. J. Hannon, F. Lyko PNAS (2013). doi:10.1073/pnas.1306723110
  • Genome of the Haloarchaeon Natronomonas moolapensis, a Neutrophilic Member of a Previously Haloalkaliphilic Genus.
    Dyall-Smith M.L., Pfeiffer F., Oberwinkler T., Klee K., Rampp M., Palm P., Gross K., Schuster S.C., Oesterhelt D. Genome Announc. (2013). doi: 10.1128/genomeA.00095-13
  • Chloride & organic osmolytes: a hybrid strategy to cope with elevated salinities by the moderately halophilic, chloride-dependent bacterium Halobacillus halophilus. Saum S., Pfeiffer F., Palm P., Rampp M., Schuster S., Mueller V., Oesterhelt D., Environmental Microbiology (2013). doi: 10.1111/j.1462-2920.2012.02770.x
  • Marek A., Blum V., Johanni R., Havu V., Lang B., Auckenthaler T., Heinecke A., Bungartz H.-J, and Lederer H.: The ELPA library - Scalable parallel Eigenvalü Solutions for Electronic Structure Theory and Computational Science, psi-k.org, Scientific Highlight, 2013
  • Hanke F., Müller B., Wongwathanarat A., Marek A., and Janka H.-Th..: SASI Activity in Three-dimensional Neutrino-hydrodynamics Simulations of Supernova Cores, Astrophysical Journal, 770, 2013
  • Müller B., Janka H.-Th., Marek A.: A New Multi-Dimensional General Relativistic Neutrino Hydrodynamics Code of Core-Collapse Supernovae III. Gravitational Wave Signals from Supernova Explosion Models, Astrophysical Journal, 766, 2013

2012

  • A parallel Grad-Shafranov solver for real-time control of tokamak plasmas . Rampp, M.; Preuss, R.; Fischer, R.; Hallatschek, K.; Giannone, L. Fusion Science & Technology, 62(3) 409-418 (2012).
  • Parallel equilibrium algorithm for real-time control of tokamak plasmas. Preuss, R.; Fischer, R.; Rampp, M.; Hallatschek, K.; von Toussaint, U.; Giannone, L.; McCarthy, P., IPP-Report R/47 (2012)
  • Ugliano M., Janka H.-Th., Marek A., Arcones, A: Progenitor-explosion Connection and Remnant Birth Masses for Neutrino-driven Supernovae of Iron-core Progenitors, APJ, vol 757, 2012
  • Müller B., Janka H.-Th., Marek A.: A New Multi-dimensional General Relativistic Neutrino Hydrodynamics Code for Core-collapse Supernovae. II. Relativistic Explosion Models of Core-collapse Supernovae, APJ, vol 756, 2012
  • Hanke F., Marek A., Müller B., Janka H.-Th.: Is Strong SASI Activity the Key to Successful Neutrino-driven Supernova Explosions?, APJ, vol 755, 2012

2011 and earlier

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