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Antarctic Climate & Ecosystems Cooperative Research Centre The The CSIRO Mk3L Climate System Model Steven J. Phipps Antarctic Climate & Ecosystems CRC University of Tasmania - Institute of Antarctic & Southern Ocean Studies Antarctic Climate & Ecosystems Cooperative Research Centre Technical Report No. 3 Steven J Phipps Antarctic Climate & Ecosystems CRC University of Tasmania Private Box 80 Hobart, Tasmania 7001, Australia. email: [email protected] © Cooperative Research Centre for Antarctic Climate & Ecosystems 2006 ISSN: 1833-2404 ISBN: 1-921197-03-X October 2006 Published by The Antarctic Climate & Ecosystems Cooperative Research Centre, Hobart, Tasmania, Australia, 236 pp. Established and supported under the Australian Government’s Cooperative Research Centres Programme. The CSIRO Mk3L Climate System Model Contents Acknowledgements 8 List of Acronyms 9 1 Introduction 11 1.1 The CSIRO Mk3L climate system model . ............ 11 1.2 Overview ........................................ ....... 12 2 Model description 13 2.1 Introduction.................................... .......... 13 2.2 Atmospheremodel................................. ......... 14 2.2.1 Atmospheric general circulation model . ............... 14 2.2.2 Seaicemodel ................................... ..... 15 2.2.3 Landsurfacemodel .............................. ....... 17 2.3 Oceanmodel ...................................... ....... 18 2.4 Coupledmodel .................................... ........ 22 2.5 Fluxadjustments ................................. .......... 22 3 Compiling and running Mk3L 25 3.1 Introduction.................................... .......... 25 3.2 Systemrequirements .............................. .......... 25 3.3 Installation .................................... .......... 26 3.4 Compilation..................................... ......... 26 3.4.1 At the APAC National Facility . ........... 26 3.4.2 Onotherfacilities.. .. .. .. .. .. .. .. .. .. .. .. .......... 26 3.5 Testing the installation . .............. 32 3.6 Runningthemodel................................. ......... 32 3.6.1 Thebasics ..................................... ..... 32 3.6.2 Queueingsystems............................... ....... 32 3.6.3 Advanced...................................... ..... 35 4 The control file 37 4.1 Introduction.................................... .......... 37 4.2 Atmospheremodel................................. ......... 37 4.2.1 control ........................................... 38 4.2.2 diagnostics ........................................ 43 4.2.3 statvars .......................................... 48 4.2.4 histvars .......................................... 48 4.3 Oceanmodel ...................................... ....... 53 4.3.1 Overview ...................................... ..... 54 Antarctic Climate & Ecosystems CRC 4.3.2 Basicfeatures ................................. ....... 54 4.3.3 Physical configuration . .......... 55 5 Input files 61 5.1 Introduction.................................... .......... 61 5.2 Overview ........................................ ....... 61 5.2.1 Atmospheremodel............................... ....... 62 5.2.2 Oceanmodel.................................... ..... 63 5.2.3 Coupledmodel.................................. ...... 64 5.3 Defaultinputfiles................................ ........... 64 5.3.1 Atmospheremodel............................... ....... 65 5.3.2 Oceanmodel.................................... ..... 66 5.3.3 Coupledmodel.................................. ...... 68 5.4 Generatingrestartfiles. ............. 68 5.4.1 Atmospheremodel............................... ....... 68 5.4.2 Oceanmodel.................................... ..... 69 5.4.3 Coupledmodel.................................. ...... 69 5.5 Generating auxiliary files . .............. 69 5.5.1 Atmospheremodel............................... ....... 69 5.5.2 Oceanmodel.................................... ..... 70 5.5.3 Coupledmodel.................................. ...... 71 6 Outputfiles 73 6.1 Introduction.................................... .......... 73 6.2 Overview ........................................ ....... 73 6.2.1 Diagnostic information . ........... 73 6.2.2 Atmosphere model output . ......... 74 6.2.3 Oceanmodeloutput .............................. ....... 74 6.2.4 Restartfiles................................... ....... 74 6.3 Processing of ocean model output . ............. 74 6.3.1 convert averages .................................... 74 6.3.2 overturning ........................................ 75 6.3.3 annual averages ..................................... 76 6.3.4 annual overturning ................................... 76 6.4 Analysis........................................ ........ 76 A Porting and optimisation 81 A.1 Introduction .................................... .......... 81 A.2 Theoriginalsourcecode. ............ 81 A.2.1 Detection of machine type . .......... 82 A.2.2 Platform-specific source code . ............ 83 A.2.3 Proprietary compiler directives . .............. 84 A.2.4 Compilers and compiler options . ............ 87 A.3 Hardwareused .................................... ........ 87 A.4 Porting......................................... ........ 88 A.4.1 Minimising the dependence on external libraries . ................. 89 4 The CSIRO Mk3L Climate System Model Antarctic Climate & Ecosystems CRC A.4.2 Removing proprietary compiler directives . ................ 91 A.4.3 Removing platform-specific source code . .............. 92 A.4.4 Compilation................................... ....... 92 A.4.5 Checkingthesourcecode. ......... 93 A.4.6 Conversionofrestartfiles . ...........101 A.4.7 Conversion of auxiliary files . ............102 A.5 Overview of code optimisation . .............102 A.5.1 Serial and parallel optimisation . ..............103 A.5.2 Coarse-grain and fine-grain parallelism . ...............103 A.5.3 The atmosphere and ocean models . .........103 A.6 Serialoptimisation .............................. ............104 A.6.1 Oceanmodel.................................... 105 A.6.2 Coupledmodel.................................. 108 A.6.3 Compilation for serial execution . ..............108 A.7 Parallel optimisation . .............109 A.7.1 Atmospheremodel............................... .......109 A.7.2 Oceanmodel.................................... 114 A.7.3 Compilation for parallel execution . ...............115 A.8 Modifiedsourcecode ............................... .........116 A.9 Benchmarks ...................................... .......116 A.10Reproducibility ................................ ............118 A.10.1AlphaServerSC ................................ .......119 A.10.2LinuxCluster ................................. ........119 A.10.3Summary ...................................... 119 A.11 Scope for further optimisation . ................119 A.11.1MPI .......................................... 120 A.11.2 Preprocessor directives . ............120 A.11.3FFTW......................................... 120 A.11.4Looprestructuring . ..........121 A.11.5Masking...................................... 121 B Modifications to the atmosphere model 123 B.1 Introduction .................................... ..........123 B.2 Modelphysics.................................... .........123 B.2.1 Insolation .................................... .......123 B.2.2 Cloudalbedo ................................... 125 B.2.3 Seaicemodel ................................... 127 B.2.4 Numerical instabilities . ............131 B.3 I/O............................................. 135 B.3.1 Inputfiles ..................................... 135 B.3.2 Outputfiles .................................... 136 C Modifications to the ocean model 139 C.1 Introduction .................................... ..........139 C.2 Modelphysics.................................... .........139 C.2.1 Mixing across unresolved straits . .............139 The CSIRO Mk3L Climate System Model 5 Antarctic Climate & Ecosystems CRC C.2.2 Density calculations . ..........144 C.2.3 Fourierfiltering ............................... .........145 C.2.4 Eddy diffusion in the Arctic Ocean . ............146 C.2.5 Relaxation timescale . ..........150 C.3 I/O............................................. 150 C.3.1 Inputfiles ..................................... 150 C.3.2 Outputfiles .................................... 151 C.4 Utilities ....................................... .........152 C.4.1 Monthly-mean model output . ..........152 C.4.2 Meridional overturning streamfunctions . ................152 C.4.3 Annual-mean model output . .........154 D Modifications to the coupled model 155 D.1 Introduction .................................... ..........155 D.2 Coupling between the AGCM and OGCM . ..........157 D.2.1 Fields passed from the AGCM to the OGCM . .........157 D.2.2 Fields passed from the OGCM to the AGCM . .........160 D.3 Assessingthecoupling . .. .. .. .. .. .. .. .. .. .. .. ...........160 D.3.1 Interpolation ................................. ........160 D.3.2 The surface salinity tendency . ............165 D.3.3 The role of flux adjustments . ..........170 D.4 Modifications to the coupling . .............170 D.4.1 Conservation .................................. .......171 D.4.2 Surface salinity tendency . ...........172 E Restart and auxiliary files 175 E.1 Introduction .................................... ..........175 E.2 Generation of auxiliary files . ..............175 E.2.1 Datasets ...................................... 175 E.2.2 The definition of “surface” . ...........176 E.2.3 Conservation .................................. .......177
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