EUROFUSION WPISA-REP(16) 16106 R Hatzky et al. HLST Core Team Report 2012 REPORT This work has been carried out within the framework of the EUROfusion Con- sortium and has received funding from the Euratom research and training pro- gramme 2014-2018 under grant agreement No 633053. The views and opinions expressed herein do not necessarily reflect those of the European Commission. This document is intended for publication in the open literature. It is made available on the clear under- standing that it may not be further circulated and extracts or references may not be published prior to publication of the original when applicable, or without the consent of the Publications Officer, EUROfu- sion Programme Management Unit, Culham Science Centre, Abingdon, Oxon, OX14 3DB, UK or e-mail Publications.Offi[email protected] Enquiries about Copyright and reproduction should be addressed to the Publications Officer, EUROfu- sion Programme Management Unit, Culham Science Centre, Abingdon, Oxon, OX14 3DB, UK or e-mail Publications.Offi[email protected] The contents of this preprint and all other EUROfusion Preprints, Reports and Conference Papers are available to view online free at http://www.euro-fusionscipub.org. This site has full search facilities and e-mail alert options. In the JET specific papers the diagrams contained within the PDFs on this site are hyperlinked HLST Core Team Report 2012 Contents 1. Executive Summary .............................................................................. 3 1.1. Progress made by each core team member on allocated projects .... 3 1.2. Further tasks and activities of the core team ..................................... 7 1.2.1. Dissemination ............................................................................. 7 1.2.2. Training ...................................................................................... 7 1.2.3. Internal training ........................................................................... 7 1.2.4. Workshops & conferences .......................................................... 8 1.2.5. Meetings ..................................................................................... 8 1.3. Recommendations for the year 2013 ................................................. 9 2. Report on HLST project EMPHORB ................................................... 10 2.1. Introduction ...................................................................................... 10 2.2. First steps ........................................................................................ 10 2.3. Field evaluation ............................................................................... 11 2.4. Charge assignment.......................................................................... 11 2.5. Weight evolution .............................................................................. 12 2.6. Matrix building ................................................................................. 12 2.7. Complex variables ........................................................................... 14 2.8. Forcheck analysis of the BEUPACK benchmark suite ..................... 15 2.8.1. NEMORB .................................................................................. 15 2.8.2. JOREK ..................................................................................... 16 2.8.3. GYSELA ................................................................................... 16 2.9. FUTILS in EUTERPE code .............................................................. 16 2.10. Summary and Future work .............................................................. 16 2.11. References ...................................................................................... 17 3. Final report on the HLST project GYNVIZ ........................................... 18 3.1. Initial objectives and project evolution ............................................. 18 3.2. File format technology review and initial choice ............................... 18 3.3. Project restructuring ......................................................................... 19 3.4. GYNVIZ project outcomes ............................................................... 20 3.4.1. Visualization cluster at RZG ..................................................... 20 3.4.2. Data transfer between JSC and RZG computer centers .......... 20 3.4.3. 3D+t → 4D conversion tool: gyncompress4d ........................... 20 3.4.4. 4D visualization plug-in for VisIt................................................ 21 3.4.5. Parallel I/O study ...................................................................... 23 3.5. Conclusions ..................................................................................... 23 4. Report on HLST project BLIGHTHO ................................................... 25 4.1. Introduction ...................................................................................... 25 4.2. CSC-Europe file transfer .................................................................. 25 4.3. MPI library behaviour on HPC-FF and HELIOS ............................... 25 4.4. MPI library initialization time ............................................................ 30 4.5. Clone computing strategy ................................................................ 32 4.6. Ideas to circumvent the initialization time issue ............................... 33 4.7. Computer architecture comparison .................................................. 37 4.8. Future work ...................................................................................... 39 5. Final report on HLST project MGTRI ................................................... 40 5.1. Introduction ...................................................................................... 40 5.2. Model problem and discretization scheme ....................................... 41 5.3. Decomposition of the structured triangular grid ............................... 42 5.4. Scaling properties of the multigrid method ....................................... 43 5.5. Domain decomposition method ....................................................... 45 5.6. Conclusions ..................................................................................... 47 6. Report on HLST project KSOL2D-2 .................................................... 49 6.1. Introduction ...................................................................................... 49 6.2. Current status and future work ........................................................ 49 7. Final Report on HLST project ITM-ADIOS .......................................... 51 7.1. Introduction ...................................................................................... 51 7.2. The LUSTRE file system and ADIOS: notation ................................ 51 7.3. The ADIOS library ........................................................................... 52 7.4. Collaboration with other parties ....................................................... 53 7.5. Development of an ADIOS benchmark ............................................ 54 7.6. Serial I/O on HELIOS and HPC-FF's LUSTRE file systems ............ 54 7.7. Parallel I/O on HPC-FF .................................................................... 56 7.8. Parallel I/O on HELIOS .................................................................... 59 7.9. Discussion and extra experiments ................................................... 62 7.10. Comparison of HELIOS to HPC-FF ................................................. 62 7.11. Conclusions ..................................................................................... 64 7.12. Future work ...................................................................................... 65 7.13. References ...................................................................................... 66 8. Report on HLST project PARFS .......................................................... 67 8.1. Introduction ...................................................................................... 67 8.2. Initial activities ................................................................................. 67 8.3. Further activities .............................................................................. 67 9. Final report on HLST project NEMOFFT ............................................. 68 9.1. Introduction ...................................................................................... 68 9.2. NEMORB's 2D Fourier transform algorithm ..................................... 68 9.2.1. Domain decomposition ............................................................. 68 9.2.2. Multi-dimensional Fourier transforms ....................................... 69 9.2.3. XOR/MPI_Sendrecv distributed transpose algorithm ............... 69 9.2.4. Basic algorithm profiling ........................................................... 70 9.3. Index order swapping: local transpose ............................................ 71 9.4. Fourier transform of real data: Hermitian redundancy ..................... 72 9.5. Distributed transpose: XOR/MPI_Sendrecv vs. MPI_Alltoall ........... 73 9.6. Additional transposes: FFTW and MKL libraries .............................. 76 9.7. Optimization of the XOR/MPI_Sendrecv transpose ......................... 77 9.7.1. XOR exchange pattern sequence............................................. 77 9.7.2. Square Fourier filter: partial matrix transposition .....................