Changes between Version 40 and Version 41 of WorkingGroups/HPC
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- 2017-04-27T20:32:35+02:00 (7 years ago)
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WorkingGroups/HPC
v40 v41 1 [[ TOC(heading=NEMO_HPC,NEMO_HPC/*, depth=1)]]1 [[PageOutline()]] 2 2 3 = ''' NEMO HPC''' =3 = '''HPC WG''' 4 4 Working group leader (and responsible for wiki pages) : Mike Bell 5 5 6 6 ---- 7 == Members of the Working group: == 7 8 == Members of the Working group: 8 9 * Jeremy Appleyards (NVIDIA) 9 10 * Lucien Anton (CRAY) … … 15 16 * Tim Graham (Met Office) 16 17 * Matt Glover (Met Office) 17 * Jason Holt ( NOC)18 * Jason Holt (noC) 18 19 * Dmitry Kuts (Intel) 19 20 * Claire Levy (CNRS) … … 31 32 ---- 32 33 33 == Minutes of Meetings == 34 == Minutes of Meetings 35 [[TOC(WorkingGroups/NEMO_HPC/Mins_2*, depth=1)]] 34 36 [[TitleIndex(WorkingGroups/NEMO_HPC/Mins_2)]] 35 37 36 38 == Minutes of Subgroup Meetings == 39 [[TOC(WorkingGroups/NEMO_HPC/Mins_s*, depth=1)]] 37 40 [[TitleIndex(WorkingGroups/NEMO_HPC/Mins_s)]] 38 41 39 42 ---- 40 == Documents ==41 43 42 * [https://forge.ipsl.jussieu.fr/nemo/wiki/WorkingGroups/NEMO_HPC/Working_document Current version of NEMO HPC working document] 43 ---- 44 == Old version of page == 45 46 Working group leader (and responsible for wiki pages) : Sébastien Masson.[[BR]] 47 44 == Documents 45 * [/WorkingGroups/NEMO_HPC/Working_document Current version of NEMO HPC working document] 48 46 49 47 ---- 50 == Members of the Working group: == 48 49 == Old version of page 50 51 Working group leader (and responsible for wiki pages) : Sébastien Masson. 52 53 ---- 54 55 == Members of the Working group: 51 56 * Sébastien Masson 52 57 * Italo Epicoco … … 58 63 59 64 ---- 60 == Objectives: == 65 66 == Objectives: 61 67 * make short term recommendations for improving the performance of the existing system 62 68 * propose criteria for a taking decisions at Gateway 2025 regarding HPC. … … 65 71 * define a simple configuration (with IO and complex geometry) that will serve as a proof of concept for validating the proposed approach for the future system. 66 72 67 == Some ideas...: ==68 Document by Seb detailing some short term actions to help reduce communications (https://forge.ipsl.jussieu.fr/nemo/attachment/wiki/WorkingGroups/NEMO_HPC/HPC_tasks_Masson.doc).73 == Some ideas...: 74 [attachment:wiki:WorkingGroups/NEMO_HPC:HPC_tasks_Masson.doc Document by Seb] detailing some short term actions to help reduce communications . 69 75 70 76 A strong improvement of NEMO scalability is needed to be able to take advantage of the new machines. This probably means a deep review/rewrite of NEMO code at some point in the future (beyond 5 years from now?). At the same time, we already know that CMIP7 won't use an ocean model that has not been strongly tested and validated and will stick to a NEMO model not so far from the existing one. [[BR]] This means that we need to: 71 77 72 1) keep improving the current structure of NEMO so it works quite efficiently for almost 10 more years (until the end of CMPI7). [[BR]] 2) start to work on a new structure that would fully tested and validated at least for CMIP8 in about 10 years. [[BR]] 78 1. keep improving the current structure of NEMO so it works quite efficiently for almost 10 more years (until the end of CMPI7). 79 2. start to work on a new structure that would fully tested and validated at least for CMIP8 in about 10 years. 73 80 74 Based on this, we propose to divide the work according to 3 temporal windows [[BR]]81 Based on this, we propose to divide the work according to 3 temporal windows 75 82 76 '''0-3 years''': improvements with existing code: [[BR]]83 '''0-3 years''': improvements with existing code: 77 84 78 1) remove solvers and global sums (to be done in 3.7) 1) reduce the number of communications: do less and bigger communications (group communications, use larger halo). main priority: communications in the time splitting and sea-ice rheology. [[BR]] 2) reduce the number of communications: remove useless communications (a lot of them are simply associated with output...) [[BR]] 3) introduce asynchronous communications [[BR]] 4) check code vectorization (SIMD instructions) [[BR]] 85 1. remove solvers and global sums (to be done in 3.7) 1) reduce the number of communications: do less and bigger communications (group communications, use larger halo). main priority: communications in the time splitting and sea-ice rheology. 86 2. reduce the number of communications: remove useless communications (a lot of them are simply associated with output...) 87 3. introduce asynchronous communications 88 4. check code vectorization (SIMD instructions) 79 89 80 '''0-5 years''': improvements through the introduction of OpenMP: [[BR]]90 '''0-5 years''': improvements through the introduction of OpenMP: 81 91 82 92 work initialed by CMCC. implementation such as tiling may be efficient with many cores processors? review lbclnk to be able to deal with MPI and OpenMP OpenMP along the vertical axis? Find a way to remove implicit schemes? test different way to find new sources of parallelism for example with the help of OpenMP4 test OpenACC (not that far from OpenMP)? 83 93 84 '''beyond 5 years''': [[BR]]94 '''beyond 5 years''': 85 95 86 96 GungHo or not GungHo , that is the question... … … 89 99 For the next 2 years, as a start, a workshop to be organized in 2015 on “NEMO in 2025 : routes toward multi-resolution approaches”. 90 100 91 == == 92 == == 93 == Comments of group members : ==94 '''gurvan''' -- (2014 November 11):101 ---- 102 103 == Comments of group members : 104 '''gurvan''' -- (2014 november 11): 95 105 96 106 • improving the code efficiency imply using more processor for a given application. This means breaking the current limit of 35x35 local horizontal domain. The 3 years propositions go in that direction. One point is missing: A target for an ORCA 1/36° is a 10x10 local domain to be able to use 1 Million cores... In this case, the number of horizontal grid points is the same as the vertical one (about 100 levels is currently what we are running). So, do we have to consider a change in the indexation of arrays from i-j-k to k-j-i ? … … 104 114 • Remark: the version of MON currently under development (MOM5: switch to C-grid, use of finit volume approach,...) is using FMS, a GungHo type approach...and "There are ''' dozens''' of scientists and engineers at GFDL focused on meeting the evolving needs of climate scientists pushing the envelope of computational tools for studying climate" 105 115 106 '''Sebastien''' -- (2014 November 17): some ideas I heard about asynchronous communications:116 '''Sebastien''' -- (2014 november 17): some ideas I heard about asynchronous communications: 107 117 108 118 • compute inner domain during communication of the halo: … … 114 124 • in 3D loops: hide communication at each level by the computation of the next level... -> do not do 3D communications but n 2D asynchronous communications. Good only if communications are really hidden by the computation at each level (that will be less and less as the size of the subdomain is decreasing... Is it really a good idea? 115 125 116 '''Silvia''' -- (2014 November 25): about asynchronous communications:126 '''Silvia''' -- (2014 november 25): about asynchronous communications: 117 127 118 • compute inner domain during communication of the halo:128 • compute inner domain during communication of the halo: 119 129 120 In the past, at CMCC we have carried out some optimization activities on a regional configuration (covering the mediterranean basin at 1/16°) of NEMO (v3.2). The performance analysis highlighted the SOR as one of the most computational intensive kernels, so our optimizations have been focused also on it. One activity aimed at overlapping communication and computation changing the algorithm in the following way: (i) halo computation, (ii) asynchronous communications and (iii) computation over the inner domain (overlapped with communication). The new algorithm has been evaluated on the old Mare Nostrum system (dismissed in 2013), in the context of an HPC-Europa application. It has been theoretically evaluated using the Dimemas tool (developed at BSC) showing that the new algorithm performed better than the old one, but the experimental results did not confirm the expectations. However, we can plan to test the communication/computation overlap paradigm on new architectures. The idea could be to extract some kernels characterized by the "do loops" you talked about, to change the communication algorithm and to test it before deciding to extend the modification to the entire the code.130 In the past, at CMCC we have carried out some optimization activities on a regional configuration (covering the mediterranean basin at 1/16°) of NEMO (v3.2). The performance analysis highlighted the SOR as one of the most computational intensive kernels, so our optimizations have been focused also on it. One activity aimed at overlapping communication and computation changing the algorithm in the following way: (i) halo computation, (ii) asynchronous communications and (iii) computation over the inner domain (overlapped with communication). The new algorithm has been evaluated on the old Marenostrum system (dismissed in 2013), in the context of an HPC-Europa application. It has been theoretically evaluated using the Dimemas tool (developed at BSC) showing that the new algorithm performed better than the old one, but the experimental results did not confirm the expectations. However, we can plan to test the communication/computation overlap paradigm on new architectures. The idea could be to extract some kernels characterized by the "do loops" you talked about, to change the communication algorithm and to test it before deciding to extend the modification to the entire the code. 121 131 122 • larger halo: could be done only on some variables that are for example using neighbor of neighbor (see what was done on sor solver).132 • larger halo: could be done only on some variables that are for example using neighbor of neighbor (see what was done on sor solver). 123 133 124 Larger halo allows to decrease the communication frequency in spite of the computation of a larger domain. It is needed to identify the best trade-off between communication time decrease and computation time increase, that is the halo dimension which minimizes the total execution time. This dimension could depend on the number of MPI processes, the domain size and some architectural parameters such as the communication latency, … (we have published a work on this aspect "The performance model for a parallel SOR algorithm using the red-black scheme", Int. J. of High Performance Systems Architecture, 2012 Vol.4, No.2, pp.101 - 109)134 Larger halo allows to decrease the communication frequency in spite of the computation of a larger domain. It is needed to identify the best trade-off between communication time decrease and computation time increase, that is the halo dimension which minimizes the total execution time. This dimension could depend on the number of MPI processes, the domain size and some architectural parameters such as the communication latency, … (we have published a work on this aspect "The performance model for a parallel SOR algorithm using the red-black scheme", Int. J. of High Performance Systems Architecture, 2012 Vol.4, no.2, pp.101 - 109)
