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University of Hamburg PUMA User's Guide Version 15.0

1. draw title yr ny set vpage 0 5 5 0 4 25 set gxout contour if setlevs 1 set clevs 990 995 1000 1005 1010 1015 1020 endif set ccols 1 set grads off set t 3 d c151 100 draw title yr ny JJA set vpage 5 5 11 0 4 25 set gxout contour if setlevs 1 set clevs 990 995 1000 1005 1010 1015 1020 endif set ccols 1 set grads off set t 4 d c151 100 draw title yr ny SON print disable print Igxps c i print mf o slp_sm ps 7 2 Vis5D Vis5D is a system for interactive visualization of large 5 D gridded data sets such as those produced by numerical weather models One can make isosurfaces contour line slices colored slices volume renderings etc of data in a 3 D grid then rotate and animate the images in real time There s also a feature for wind trajectory tracing a way to make text annotations for publications support for interactive data analysis etc from the Vis5D home page http www ssec wisc edu billh vis5d html This powerful visualisation tool together with its documentation is available through the above home page Vis5D uses its own data format which makes it necessary to transform your data Depending on their format and the flowchart on http puma dkrz de puma download map you have the following choices If e your data is raw PUMA output you need to process it with
2. Options Debug mode Orography Start year Parallelism Resolution T21 64x32 0 Change gpm Um ui pherical Harmonics mode selector Write Output Run with GUI finnual cucle Diurnal cycle Simulation Years to run CHAPTER 5 GRAPHICAL USER INTERFACE ave Save amp amp Abort xit Run Mars Toggle mode Toggle column 3 Toggle line Zonal Wavenumber Figure 5 1 Zonal Wind m s Zonal Wind Level 2 m s 9 Mar 0001 4 88 EP Il Grid Screenshot of Model Starter MoSt Temperature K SES sol Lid EQ i 995 m1000 m1005 m1010 210 m 220 m 230 m 240 250 Ps Hovmoeller 45N 5 days T I H ftol 985 990 m 995 m1000M 1005 m1010 91015 m1020 m1025 X Zonal Wind m s Moridional Wind m s Temperature K Xlsurface Pressure hPa Zonal Wind Level 2 m s Meridional Wind Level 2 m s Hovmoeller 45N 5 days M Timeseries 5 days Ies Hoc 11 mt 1022 hi 16 092004 Tables CE on Bl vacan ai TOT edi on bisce X Puma 7 a AN Figure 5 2 Screenshot of Graphical User Interface GUI 5 2 GUI CONFIGURATION 3l Horizontal global fields in cylinder projection e Horizontal global fields in polar projection Time longitude Hovm
3. 3 7 pumamod f90 General The module pumamod f90 contains all parameters and variables which may be used to share information between puma f90 and other modules No subroutines or programs are included Input Output pumamod f90 does not use any extra input file or output file No namelist input is required Structure Internally pumamod f90 is FORTRAN 90 module named pumamod Names for global parameters scalars and arrays are declared and if possible values are preset 21 22 CHAPTER 3 MODULES 3 8 resmod f90 General The module resmod f90 defines horizontal and vertical resolution together with the number of processes Creation This file is created by the model starter MoSt If you don t use MoSt copy the file resmod def f90 to resmod f90 and edit the file resmod f90 to fit your needs Structure The default values are set to T21 NLAT_ATM 32 and 10 level NLEV_ATM 10 The number of processes to use is set to 1 no parallel pro cessing module resmod will be overwritten by MoSt parameter NLAT ATM 32 parameter NLEV ATM 10 parameter NPRO ATM 1 end module resmod All other resolution dependent parameters like NTRU NLON NHOR etc are derived from the values set in resmod f90 23 3 9 restartmod f90 General The module restartmod f90 contains routines for opening reading and writ ing restart files The scalars and array of the restart files are
4. 400 3 2 fileseek f90 fseek64 f90 fseek f90 3 guimod f90 5 90 34 Wega AAN ne er Sa 3 5 mpimod f90 mpimod stub f90 a ae en a A a ese Be a oe a Pe Br ae ee a 3 7 pumamod f90 Loi de Ge hd at 38 sus x o4 930 35 3 od we E dE AUR EUR E e ES HE SES 3 9 90 4 Parallel Program Execution ss se oP Se o Bee ee a oa eee a ee Usa hh bee eo Be HO Bee a a o ee ee 5 45 Source codel e ee 5 Graphical User Interface 5 1 Graphical user interface AAA EE ee Pes EE Aa As egar a a as as bei 522 Blot gee tras E heh et ee ee ee n a ee ia inus fe SEO abe cs ed ee A ee ee ee AE s op ered UB de OH oe Sw a 10 10 11 18 13 14 15 16 17 19 21 22 28 25 25 25 26 26 27 4 CONTENTS 35 6 1 Introductionl 2 2 2m a 35 ee ee te ents oe de 35 6 8__ 36 o4 HYPE ge Lu ds ee ee we y SR SOEs 36 65 a a Wwe 3 36 CD 36 MeL CRITICIS 3T 68 LATS and LONS 3T 69 MEAN 3
5. 5 5 1 0 ps 0 0 Figure 8 3 Vertical geometry of with associated variables 5 level version The model is represented by finite differences in the vertical as shown in figure The number of the levels in the vertical is variable The vertical coordinate is defined as o p ps The prognostic variables C D and T are calculated at full levels At the half levels 0 upper boundary and 1 lowerboundary the vertical velocity is set to zero The vertical advection at level r is approximated as follows 1 Be r 2 2 Ag e Ao 55 02 8 22 The tendencies of temperature divergence and surface pressure are solved by the implicit time step The vorticity equation is approximated by the centred differences intime Hoskins and Simmons 1975 8 5 PUMA FLOW DIAGRAM 53 8 5 PUMA Flow Diagram The diagram shows the route through the main program PUMA with the names of the most important subroutines Puma is the main program It calls the three subroutines Prolog Master and Epilog Prolog does all initialization It calls the following subroutines gauaw computes gaussian abscissas and weights inilat initializes some utility arrays like square of cosine of latitude etc legpri prints the arrays of gauaw and inilat readnl reads the namelist from standard input initpm initializes most vertical arrays and some in the spectral domain initsi computes arrays for the semi implicit scheme legini computes
6. A J Simmons B J Hoskins and D M Burridge Stability of the Semi Implicit Method of Time Integration Mon Wea Rev 106 405 412 1978 97 98 BIBLIOGRAPHY Appendix A List of Constants and Symbols Symbol Definition Value Unit a earth radius 6371 10 m A D V Vinp Es A absorptivity emissivity As surface emissivity B T Planck function Wm cc cloud cover Conon Charnock constant 0 018 Ch transfer coefficient for heat Cin drag coefficient for momentum 6 specific heat of moist air at constant pressure Ike bx Cpd specific heat of dry air at constant pressure 1005 46 Jkg oy specific heat of water vapor at constant pressure 1869 46 Jhg ke om specific heat of sea ice 2070 Wskg K specific heat of snow 2090 Wskg es specific heat of sea water 4180 Wskg K Cw coefficient for the deep ocean heat flux 4 Wm K wetness factor D scaled divergence E evaporation ms Eo extrateristical solar flux density Wm f Coriolis parameter 20 sin y gs Fp tendency of the first moment Kms Fa tendency of the zeroth moment long E surface moisture flux kgm 28 Fr surface sensible heat flux Wm E surface zonal wind stress Pa F surface meridional wind stress Pa put long wave radiation flux density Wm FSW short wave radiation flux density Wm g gravitational acceleration 9 81 m Amir mixed layer depth m Pr climatological mixed layer d
7. http puma dkrz de puma download map If you chose to compile it yourself please read the comments in the first few lines of the program text Sometimes the srv2gra tool has difficulties to calculate an appropriate time increment from the date headers of the data records so you should check this In this example the file puma m ct1 should look like this DSET puma m gra UNDEF 9e 09 XDEF 64 LINEAR 0 0000 5 6250 OPTIONS YREV YDEF 32 LEVELS 41 42 CHAPTER 7 GRAPHICS 85 7606 80 2688 74 7445 69 2130 63 6786 58 1430 52 6065 47 0696 41 5325 35 9951 30 4576 24 9199 19 3822 13 8445 8 3067 2 7689 2 7689 8 3067 13 8445 19 3822 24 9199 30 4576 35 9951 41 5325 47 0696 52 6065 58 1430 63 6786 69 2130 74 7445 80 2688 85 7606 ZDEF 1 LINEAR 1 1 TDEF 12 LINEAR 00 00Z01jan0001 imo VARS 3 c139 0 99 139 0 0 c151 0 99 151 0 0 c175 0 99 175 0 0 ENDVARS Here the line starting with TDEF ends with 1mo since we are handling monthly mean data When the PUMA output is used without averaging this should correspond to the output interval given by the nafter variable used in the namelist of your PUMA run see section C The number of variables depends on how the pumaburner was called In this example only 3 variables were processed i e the surface temperature c139 the sea level pressure c151 and the albedo c175 refer to appendix B for a list of codes The GrADS program is started by typing grads in a terminal wi
8. Oz the vertical restoration temperature gradient Tr gra and the restoration temperature at the surface and at the global isothermal tropopause respectively S provides a smoothing of the profile at the tropopause z o is determined by an iterative method The profile is determined by setting the parameters gra Zp L and S Figure shows the vertical profile for the standard parameter values 50 CHAPTER 8 MODEL DYNAMICS The temperature contrast between low and high latitudes due to the differential radiative energy balance which drives the general circulation is described by the meridional form of the restoration temperature sin Tr 6 ATR Ns 5 1 sin 6 3 8 12 The meridional gradient decreases with height and vanishes at the tropopause sin Ecce if o gt Op 2 11 05 8 13 0 if o lt Op with the height of the tropopause TR gra In equation 8 12 ATR represents the constant part of the meridional temperature con trast ATr ws the variable part corresponding to the annual cycle Figure shows the meridional and vertical form of the restoration temperature field see eqn Usually for the lower model levels the time scale is set to less values stronger diabatic heating than for the upper levels to account for the stronger impact of the turbulent heat fluxes near the surface A standard setting for is TR i 1 3 30d Tr i 4 10d TR 5 5d
9. a University of Hamburg Zonal Wind m s 995 m1000 M1005 m1010 990 995 1000 1005 01010 Timeseries 5 days H Zonal Wind m s Mar 0001 4 00 DISP 9 00 Meridional Mind u s emperature ll DTEP 70 00 Surface Pressure hPa DTNS 53 00 Zonal Wind Level 2 m s Meridional Wind Level 2 m s X Grid Ps Hovmoeller 45N 5 days lt Timeseries 5 days Tables MAMADAS Da ee 08 38 54 16 09 2004 User s Guide Version 15 0 Klaus Fraedrich Simon Blessing Edilbert Kirk Torben Kunz Ute Luksch Frank Lunkeit Frank Sielmann The PUMA User s Guide is a publication of the Theoretical Meteorology at the Meteorological Institute of the University of Hamburg Address Prof Dr Klaus Fraedrich Meteorological Institute University of Hamburg Bundesstrasse 55 D 20146 Hamburg Contact Klaus Fraedrich zmaw de Frank Lunkeit zmaw de E KirkOgmx de Contents 1 Installation a oo ee a UR MEHR SERERE 2 Introduction 3 2 1 Training of junior scientists and students rn nn nn 2 2 Compatibility with other models os 24m a2 E EU a ze e 2 3 24 Red irements s ss sea tes ektar AAA 2 5 SON d epe ee rede un Rub ee ARA Modules 3 1 90 991
10. redirected lt stdin gt printout redirected lt stdout gt 35 36 CHAPTER 6 POSTPROCESSOR PUMABURNER 6 3 Namelist The namelist values control the selection coordinate system and output format of the post processed variables Names and values are not case sensitive You can assign values to the following names Name Def Type Description Example HTYPE S char Horizontal type HTYPE G VTYPE S char Vertical type VTYPE P MODLEV 0 int Model levels MODLEV 2 3 4 hPa O real Pressure levels hPa 500 1000 LATS 0 int No of latitudes for output grid LATS 40 LONS 0 int No of longitudes for output grid LONS 80 CODE 0 int ECMWF field code CODE 130 152 NETCDF 0 int NetCDF output selector NETCDF 1 CYCLICAL 0 int Add data for longitude 360 CYCLICAL 0 MEAN 1 int Compute monthly means MEAN 0 HHMM 1 int Time format in Service format HHMM 0 HEAD7 0 int User parameter HEAD7 0815 MARS 0 int Use constants for planet Mars MARS 1 MULTI 0 int Process multiple input files MULTI 12 6 4 HTYPE HTYPE accepts the first character of the following string Following settings are equivalent HTYPE S HTYPE Spherical Harmonics HTYPE Something Blanks and the equal sign are optional Possible Values are Setting Description Dimension for T21 resolution HTYPE S Spherical Harmonics 506 22 23 coefficients HTYPE Fourier Coefficients 32 42 latitudes wavenumber HTY
11. CHAPTER 3 MODULES 3 2 fileseek f90 fseek64 f90 fseek f90 General The module fileseek f90 is used by the restartmod f90 for file positioning Most compiler have FORTRAN callable routines fseek and ftell in their runtime libraries The gfortran has ftell but not fseek In this case a subroutine defined in fileseek f90 is used instead fseek64 f00 is a variant with a 64bit filepointer that can address filepositions beyond 2 GBytes though the PUMA restart files will never be that large The configure script tries to figure out which of these three variants to use and writes an entry to the file most compiler Code This is a listing of the default fseek f90 use this routine with FORTRAN compilers that support fseek subroutine fileseek kunit kptr implicit none integer kunit kptr call fseek kunit kptr 0 return end 3 3 guimod f90 guimod stub f90 General The module guimod f90 contains subroutines for communication with the GUI On operating systems that don t support the Xlib X11R6 e g Windows guimod_stub f90 may be used as a stub replacement Structure The following subroutines are included in guimod f90 Subroutine guistart guistop guistep puma guistep plasim guips guihor guigu change_disp change_dtep change_dtns change_co2 change_gsol0 change_dawn Purpose initialize GUI finalize GUI called every timestep from PUMA called every timestep from PLASIM
12. POSTPROCESSOR PUMABURNER e Not all combinations of HTYPE VTYPE and CODE are valid Try to use HTYPE Grid and VTYPE Pressure before switching to exotic parameter combinations Chapter 7 Graphics 7 1 Grads In this section visualisation using the graphics package GrADS is described A useful Internet site for reference and installation instructions is lt http grads iges org grads grads html gt Latest versions of GrADS can handle data in NETCDF format via the command sdfopen Any file produced by the pumaburner with the option NETCDF 1 can be read directly from GrADS An alternate way for files in SERVICE format is to use a converter which translates the SERVICE format to NETCDF In the following it is assumed that the PUMA output has been converted to SERVICE format with the pumaburner and the resulting file is called puma srv Monthly mean data is either obtained directly from the pumaburner namelist parameter MEAN 1 see section 6 or via a PINGO command srv monmeans puma srv puma_m srv Information on the PINGO package can be found in DKRZ report 11 at lt http www mad zmaw de Pingo repdl html gt The SERVICE file has to be converted to GrADS s native format by the command srv2gra puma_m srv which results in the files puma_m gra and puma m ctl The first file contains the data the latter one information on the grid time steps and variable names The program srv2gra is one of the postprocessing tools available at
13. for a horizontal resolution of T21 a vertical resolution of 10 levels and 2 CPU s The executable is copied to the model s bin directory at the end of the build Each time Most is used to setup a new experiment it checks the bin directory for a matching executable If it exists it is used without rebuilding otherwise a new executable with the selected parameters is created Rebuilding may be forced by using the cleanpumacommand in the Most directory The build directory is not cleared after usage The user may want to modify the makefile or the build script for his own purposes and start the building directly by executing most puma build For permanent user modifications the contents of the bld directories have to be copied elsewhere because each usage of Most overwrites the contents of bld 1 4 MODEL RUN PHASE 7 1 4 Model run phase After building the model with the selected configuration Most writes or copies all necessary files to the model s run directory These are the executable initial and boundary data namelist files containing the parameter and finally the run script itself Depending on the exit from Most either Save amp Exit or Run amp Exit the run script is started from Most and takes control of the model run A checkmark on GUI invokes also the the Graphical User Interface for user control and display of variables during the run Again all contents of the run directory are subject of chan
14. for n 5 levels om eue 8 14 8 2 3 Diffusion The parameterizations 8 7 8 8 and further contain the hyperdiffusion terms H Hp and Ar respectively The hyperdiffusion parameterizes both subgrid scale horizontal mixing a a r 14 1 1 12 n2 E E 10 04 E m B gt E ef up bt ri En The NEN oe 4 oa hy as a 2 E N LU i i i i i i LA LO N i i i i i _ 70 B50 5m 3n 20 10 10 T 50 50 0 50 20 10 10 1 Ter Figure 8 1 Vertical profile of the restoration temperature as function of the geometric height z left and as function of the dimensionless vertical coordinate c right for standard parameter values 288 K Zip 12km L 6 5 K km S 2 K 8 2 PARAMETERIZATIONS 51 Sigma Level 4 oo 505 305 EQ 30N BON e Figure 8 2 Restoration temperature field in C as function of latitude and the o level for standard parameter values as in figure and with ATg gp 70 K ATR ns 0K and the energy cascade into these scales and its subsequent dissipation because the dissipative range of the wavenumber energy spectrum is not included with the relatively coarse model resolution If Q is one of the model variables D or then the hyperdiffusion is given by equation for grid point representation and by equation for spectral representation see also eqn 8
15. identified by name This enables adding or removing variables from the restart file without loosing com patibility There s also no dependence on the sequence of variables In parallel runs these routines are either called from the root process which takes care of broadcast ing or from subroutines of the mpimod f90 which gather before writing or scatter after reading arrays Structure Subroutine Purpose restart ini Scan restart file and store pointer restart prepare Open file for restart ouput restart stop Close files get restart integer read integer scalar get_restart_array read real array put_restart_integer write integer scalar put_restart_array write real array 24 CHAPTER 3 MODULES Chapter 4 Parallel Program Execution 4 1 Concept PUMA is coded for parallel execution on computers with multiple CPU s or networked ma chines The implementation uses MPI Message Passage Interface that is available for nearly every operating system In order to avoid maintaining two sets of source code for the parallel and the single CPU version all calls to the MPI routines are encapsulated into a module Users that want to compile and execute the parallel version use the module mpimod f90 and the commands mpif90 for compiling and mpirun for running If MPI is not implemented or the single CPU version is sufficient the module mpimod_dummy f90 is used instead of mpimod f90 Also remove or comment the line use mpi and
16. in the spectral domain the non linear contributions in grid point space Therefor at every time step the necessary model variables are transformed from spectral to grid point representation by Legendre transforma tion and Fast fourier transformation FFT and then the calculated tendencies are transformed back into the spectral domain where the time step is carried out for the transform method see Orszag Eliasen et al 1970 Because of the semi implicit time integration scheme Hoskins and Simmons 1975 Simmons Hoskins and Burridge 1978 the terms due to gravity wave propagation are integrated in time implicitly the remaining terms are integrated explicitly the latter with a leap frog time step In the standard model version a time step of one hour is used A Robert Asselin time filter Haltiner and Williams 1982 is applied to avoid decoupling 8 2 PARAMETERIZATIONS 49 of the two leap frog time levels The contributions to the tendencies due to vertical advection are calculated by an energy and angular momentum conserving vertical finite difference scheme Simmons and Burridge 1981 8 2 Parameterizations 8 2 1 Friction The dissipative processes in the atmosphere are parameterized by a linear approach Rayleigh friction describing the effect of surface drag and vertical transport of horizontal momentum due to small scale turbulence in the boundary layer For this purpose vorticity and divergence D are damped t
17. set the number of processors to 1 parameter NPRO 1 4 2 Parallelization in Gridpoint Domain The data arrays in gridpoint domain are either three dimensional e g gt NLON NLEV referring to an array organized after longitudes latitudes and levels or two dimensional e g gp NLON NLAT The code is organized such that there are no dependencies in latitudinal direction while in gridpoint domain Such dependencies are resolved during the Legendre Transformations So the the partitioning of the data is done in latitudes The program can use as many CPU s as latitudes with the extreme of every CPU doing the computations for a single latitude There is the restriction however that the number of latitudes NLAT divided by the number of processors NPRO giving the number of latitudes per process NLPP must have zero remainder E g A T31 resolution uses NLAT 48 Possible values for NPRO are then 1 2 3 4 6 8 12 16 24 and 48 All loops dealing with a latitudinal index look like do jlat 1 NLPP enddo There are however many subroutines with the most prominent called calcgp that can fuse latitudinal and longitudinal indices In all these cases the dimension NHOR is used NHOR is defined as NHOR NLON x NLPP in the pumamod module The typical gridpoint loop that looks like 25 26 CHAPTER 4 PARALLEL PROGRAM EXECUTION do jlat 1 NLPP do jlon 1 NLON gp jlon jlat enddo enddo is then repla
18. some Linux distributions e g Fedora 7 It s also available from http directory fsf org devel compilers gfortran html 2 5 History The PUMA version at the University of Hamburg originates from the Hoskins and Simmons SGCM Simple General Circulation Model version Hoskins and Simmons 1975 The major differences between PUMA and its predecessor SGCM are e The code is rewritten in portable FORTRAN 90 code which removes problems associated with machine specific properties like word lengths floating point precision output etc All necessary routines are in the source code even the FFT Fast Fourier Transformation and the Legendre transformation The model can be run on any computer with a standard FORTRAN 90 compiler The MPI library is needed to run PUMA on parallel machines see below The Xlib X11R6 library is needed for the graphical user interface e The truncation scheme is changed from jagged triangular truncation to standard trian gular truncation that is compatible to other T models like ECHAM e The PUMA Pumaburner system is data compatible to ECHAM Afterburner Thus all other diagnostic software can be used on PUMA data e PUMA is fully parallelized and can use as many CPU s as latitudes e g 32 in T21 resolution It uses the MPI Message Passing Interface library while running on parallel systems or cluster MPI is not needed for running PUMA on a single CPU 12 CHAPTER 2 INTRODUCTION Chapter 3 Module
19. the pumaburner postprocessor see section 6 in order to transform it to either NETCDF option n or namelist parameter NETCDF 1 or GRIB option g or namelist parameter GRIB 1 and proceed from there e your data is in SERVICE format you need to convert it to either GRIB for instance with the PINGOs 7 2 VIS5D 45 grb copy2 data srv data with grib metainfo grb output grb or NETCDF using the program puma2cdf which is available with the PUMA postprocessing tools Despite of its name this program cannot process raw PUMA output but takes SERVICE format as input It can as well be called as srv2cdf which changes its behaviour oddities of model output such as the existence of February 30 are then no longer removed Once the format is changed proceed from there e your data is in NETCDF format it can easily transformed to Vis5D s native format by means of the program cdf2v2d which is available with the PUMA postprocessing tools e your data is in GRIB format you can find a transformation tool named Grib2V5d at lt http grib2v5d sourceforge net gt which offers various practical features Once the conversion to Vis5D s native format is achieved please follow the instructions from the Vis5D documentation or if Vis5D is already installed on your system try finding your own way by typing visbd my data v5d 46 CHAPTER 7 GRAPHICS Chapter 8 Model Dynamics 8 1 Model equations and numerics Core of the model are th
20. used The postprocessor Pumaburner differs from ECHAM s Afterburner only in respect to the format of the model s raw data which overcomes some problems of ECHAM s data format PUMA uses a more compact though more precise format compared to the GRIB GRIdded Binary that is used for ECHAM output The Pumaburner supports the output formats SERVICE or NetCDF All diagnostics and graphics software that is applied on ECHAM Afterburner data can be used for PUMA Pumaburner in exactly the same way 10 CHAPTER 2 INTRODUCTION Processes in Processes in PUMA comprehensive GCMs EM Ed procemes w Figure 2 1 Processes in ECHAM left and PUMA right 2 3 Scientific applications The PUMA code is the dynamical core of a GCM forced by Newtonian cooling and Rayleigh friction such as proposed by Held and Suarez 1994 to evaluate the dynamical cores of GCMs It forms the basis for various applications e The code can be utilized to build and test new numerical algorithms like semi Langrangian techniques e Idealized experiments can be performed to analyze nonlinear processes arising from in ternal atmospheric systems life cycles etc e Data assimilation techniques can be incorporated to interpret results from GCM simula tions or observations Figure left demonstrates the complexity of interactions in a full size climate model which leads to similar complex response patterns on small parameter cha
21. 0 min for T42 The values are not checked So take care not to violate the CFL Courant Friedrichs Levy crite tion NYEARS Integer Number of years to be run 1 NMONTHS Integer Number of months to be run 0 NYEARS and NMONTHS may be used together The simulation length in days is NYEARS 360 NMONTHS 30 NOUTPUT Integer NOUTPUT is a global switch for enabling 1 or disabling 0 writ ing to puma_output NWPD Integer NWPD Number of Writes Per Day defines the output interval for writing model arrays to the file puma output Possible val ues range from 1 daily output to 24 hourly NDIAG Integer NDIAG sets the interval in timesteps for printing out some diagnostic arrays and values to the standard output 19 20 CHAPTER 3 MODULES Parameter Type Purpose Default NDL NLEV Integer Array Switch for diagnostic print NLEV 0 out of a level 0 off 1 on DTEP Real Equator to pole tempera 60 0 ture difference K for New tonian cooling DTNS Real North to South pole tem 0 0 perature difference K for Newtonian cooling DTROP Real Tropopause height m for 12000 0 Newtonian cooling DTTRP Real Smoothing of the 2 tropopause K for Newto nian cooling TGR Real Surface temperature K for 288 Newtonian cooling TDISS Real time scale d for the hori 0 25 zontal diffusion PSURF Real Global mean sea level pres 101100 00 sure Pa RESTIM NLEV Real Array Time scale d for Newto 0 0 ni
22. 155 NLEV s divergence 1 s 156 NLEV geopotential height gpm s PUMA spectral field g PUMA grid point field c computed by PUMA burner a accumulated 63 64 APPENDIX B PUMA CODES FOR VARIABLES Appendix C Namelist Name Default Type Description kick 1 integer 0 no initial noise p const 1 initial random white noise 2 equator symmetric random white noise 3 mode 1 2 reproducable initialization mpstep 60 integer timestep minutes per step 60 min for T21 ncoeff 0 integer number of coefficients to print in wrspam ncu 0 integer gt 0 write debug info to file unit ncu ndel 6 integer order of hyperdiffusion for each level 2 h ndiag 12 integer output interval for diagnostics timesteps ngui 0 integer 1 run with GUI nhz 0 integer nhz gt 0 Held amp Suarez setups nkits 3 integer number of short initial timesteps nlevt 0 integer number of tropospheric levels if nvg 1 nextout 0 integer l extended output entropy production noutput 1 integer 1 write model output to file puma output nruido 0 integer l add noise on every timestep ntspd 24 integer number of timesteps per day nmonths 0 integer simulation time in months nyears 1 integer simulation time in years nsymm 0 integer 1 use strict symmetric transformations nvg 0 integer vertical grid type O linear 1 Scinocca 2 Polvani nwpd 1 integer number of writes per da
23. 6 H 1K V QA ut 8 15 R V YQ t Y A 8 16 The hyperdiffusion for one spectral mode y is then 1992 AYKV Q O YQ p 8 17 242 QOYA n 8 18 With the condition that the spectral modes with n nr are damped with a prescribed time scale Tp 1 H QuE Y Au AE nen 8 19 H substitution into equation 8 18 yields 1 2 k a 8 20 nr nr 1 Thus from equation 8 18 follows 1 n n 1 TH nr nr 1 9 00 YQ p 821 In the model the hyperdiffusion is applied in the form 8 21 For the shortest waves n nr the damping is maximal for the mean n 0 the damping vanishes The integer exponent with the standard value h 4 leads to an additional reduction of the damping at little wavenumbers The diffusion time scale is usually set to Ty 1 44 52 CHAPTER 8 MODEL DYNAMICS 8 3 Scaling of Variables The variables are rendered dimensionless using the following characteristic scales Variable Scale Scale description Divergence Q Q angular velocity Vorticity Q Q angular velocity Temperature a 0 R a planet radius R gas constant Pressure 101100 Pa PSURF mean sea level pressure Orography aQ g g gravity 8 4 Vertical Discretization Level Variables 0 5 0 0 p 0 0 0 oe DO 15 02 la 2 5 0 4 Y Mae CIT 3 5 0 6 4 07 nn Cu 4 5 0 8 5
24. 7 a ee ee eee a 38 6 11 SERVICE forma 38 TD 38 6 I9 zt amp pr amp vene ect we S we 38 PP 39 6 15 MULTI ws ee bow ae oe ee de 39 T LIT 39 6 17 Troubleshooting s gue wa ses AR AAA CH de 39 41 41 ee 44 4T Cr 47 2__ 5 49 8 21 Brietion no eoe voe 4X 9 Yee Re SMe OER X ER dee Neg 49 8 2 2 Diabstc heating oc oc a kx owe aa dad asea REE OES 49 Wurm 50 52 2 Be Ye E Aa RA Pe 52 a ado ad A ee 53 58 dds gis A ad 54 59 63 65 Chapter 1 Installation The whole package containing the models Planet Simulator and along with MoSt the model starter comes in a single file named Most n tgz with n specifying a version number The following subsection shows the commands to use assuming the version number is 15 1 1 Quick Installation tar zxvf Most15 tgz cd Mosti5 configure sh most x If your tar command doesn t support the z option e g on Sun UNIX type instead gunzip Most15 tgz tar xvf Most15 tar cd Most15 configure sh most x If this sequence of commands produces error messages consult the FAQ Frequent Asked Questions and README files in the Most15 directory They are in plain text that can be read with the command more or opened by a text editor 1 2 M
25. PE Z Zonal Means 32 levels latitudes levels HTYPE Gauss Grid 64 32 longitudes latitudes 65 VTYPE VTYPE accepts the first character of the following string Following settings are equivalent VTYPE S VTYPE Sigma VTYPE Super Blanks and the equal sign are optional Possible Values are Setting Description Remark VTYPE S Sigma model levels Some derived variables are not available VTYPE P Pressure levels Interpolation to pressure levels 6 6 MODLEV MODLEV is used in combination with VI YPE S If VTYPE is not set to Sigma the contents of MODLEV are ignored MODLEV is an integer array that can get as many values as there are levels in the model output The levels are numbered from top of the atmo sphere to the bottom The number of levels and the corresponding sigma values are listed in the pumaburner printout The outputfile orders the level according to the MODLEV values 6 7 HPA 37 MODLEV 1 2 3 4 5 produces an output file of five model levels sorted from top to bottom while MODLEV 5 4 3 2 1 sorts them from bottom to top 6 7 hPa hPa is used in combination with VTYPE P If VTYPE is not set to Pressure the contents of hPa are ignored hPa is a real array that accepts pressure values with the units hectoPascal or millibar All output variables will be interpolated to the selected pressure levels There is no extrapolation on the top of the atmosphe
26. a records The header record is an integer array of 8 elements head 1 head 2 head 3 head 4 head 5 head 6 head 7 head 8 ECMWF field code modellevel or pressure in Pa date yymmdd yymmOO for monthly means time hhmm or hh for HHMM 0 1 dimension of data array 2 dimension of data array may be set with the parameter HEAD7 experiment number extracted from filename Example for reading the SERVICE format NETCDF 0 INTEGER HEAD 8 REAL FIELD 64 32 dimensions for T21 grids READ 10 ERR 888 END 999 HEAD READ 10 ERR 888 END 999 FIELD 888 STOP I 0 999 STOP EOF ERR 6 12 HHMM Setting Description HHMM 0 head 4 shows the time in hours HH HHMM 1 head 4 shows the time in hours and minutes HHMM 6 13 HEAD7 The 7th element of the header is reserved for the user It may be used for experiment numbers flags or anything else Setting HEAD7 to a number exports this number to every header record in the output file SERVICE format only 6 14 MARS 39 6 14 MARS This parameter is used for processing simulations of the Mars atmosphere Setting MARS 1 switches gravity gas constant and planet radius to the correct values for the planet Mars 6 15 MULTI The parameter MULTI can bes used to process a series of input data within one run of the pumaburner Setting MULTI to a number n tells the pumaburner to procees n input files The inp
27. all polynomials needed for the Legendre transformation restart starts the model from the restart file of a previous run if selected initfd initializes spectral arrays setzt sets up the restoration temperature array noise puts a selectable form of noise into InPs setztex is a special version of setzt for dipole experiments Master On initial runs master does some initial timesteps then it runs the timeloop for the selected integration time It calls the following subroutines makebm constructs the array bm gridpoint does all transformations and calculations in grid point domain sp2fc spectral to Fourier coefficients inverse Legendre transf dv2uv divergence vorticity to u and v im plies spectral to fourier fc2gp Fourier coefficients to grid points fast Fourier transformation calcgp calculations in grid point space gp2fc grid points to Fourier coefficients fast Fourier transformation fc2sp Fourier coefficients to spectral direct Legendre transf mktend make tendencies implies fourier to spectral spectral does all calculations in the spectral domain outsp writes spectral fields in physical dimensions on an output file diag writes selected fields and parameters to standard output Epilog writes the restart file 8 6 Initialization The model starts either from a restart file or with an atmosphere at rest The defaults make the initial state a motionless stable stratified atmosphere For an initial start thedivergence and the relativ
28. an cooling TOK NLEV Real Array Reference temperature used 250 0 in the discretization scheme TFRC NLEV Real Array Time scale d for Rayleigh 0 0 friction 0 0 off Structure After starting MPI the main program puma calls prolog for initializing the model Then master is called to do the time stepping Finally subroutine epilog finishes the run In subroutine prolog calls to different subroutines which are part of puma f90 or are provided by other modules initialize various parts of the model gauaw and inilat build the grid readnl reads the namelist and sets some parameter according to the namelist input initpm and initsi initialize some parameter for the physics and the semi implicit scheme respectively outini starts the output The prgram then checks for the existence of a file named puma restart If the file can be opened then the restart record is read by restart otherwise initfd sets the prognostic variables to their initial values Finally the global averaged surface pressure is set according to PSURF and the orography Subroutine master controls the time stepping First if its not a restart initial NKITS explicit forward timesteps are performed The main loop is defined by calling gridpoint for the adiabatic tendencies and spectral to add the adiabatic tendencies interface routines to the output module outmod f90 The run is finalized by subroutine epilog which writes the restart records and finalizes MPI
29. anged to perform as a circulation model For example James and Gray 1986 studied the influence of surface friction on the circulation of a baroclinic atmosphere James and James 1992 and James et al 1994 investigated ultra low frequency variability and Mole and James 1990 analyzed the baroclinic adjustment in the context of a zonally varying flow Frisius et al 1996 simulated an idealized storm track by embedding a dipole structure in a zonally symmetric forcing field and Lunkeit et al 1998 investigated the sensitivity of GCM scenarios by an adaption technique applicapable to SGCMs The Storm track dynamics and low frequency variability was investigated by Fraedrich et al 2005 PUMA is introduced with following aims in mind Training of junior scientists compatibility with ECHAM European Centre HAMburg and scientific applications 2 1 Training of junior scientists and students PUMA contains only the main processes necessary to simulate the atmosphere The source code is short and clearly arranged A student can learn to work with PUMA within few weeks whereas full size GCMs require a team of specialists for maintenance experiment design and diagnostics 2 2 Compatibility with other models PUMA is designed to be compatible with other circulation models like Planet Simulator and ECHAM The same triangular truncation is employed and analogous transformation techniques like the Legendre and Fast Fourier transformation are
30. ations contains the four prognostic equations 8 1 8 2 8 4 and 8 5 Vorticity and divergence D are scaled by angular velocity of the earth pressure p and by the global mean surface pressure P 1011 hPa temperatures T and To by a20 R geopotential by a Q g and time t by Q1 where a is the radius of the earth R the gas constant of dry air and g the gravitational acceleration For the parameterizations Pp and Pr see section The model can be run with or without orography The horizontal representation of any model variable is given by a series of spherical har monics If Q is an arbitrary model variable then its spectral representation has the form Q0 1 t QE Ys 8 6 Here Y are the spherical harmonics and Q the corresponding complex amplitudes where y n m designates the spectral modes n 1 2 3 total wave number m 0 1 2 3 zonal wave number with m n 1992 The latter condition follows from the tri angular truncation in wave number space The truncation is done at the total wave number nr which can be set to nr 21 31 42 85 127 170 i e the model can be used with the T21 T170 spectral resolution The vertical resolution is given by nr equidistant o levels with the standard value 5 At the upper 0 and lower boundary 1 of the model domain the vertical velocity is set to zero 0 The linear contributions to the tendencies are calculated
31. bin lt model executables 1824 bld lt build directory 280 dat lt initial and boundary data 80 doc lt documentation user s guide reference manual 928 run lt run directory 1744 src lt source code drwxr xr x drwxr xr x drwxr xr x drwxr xr x drwxr xr x drwxr xr x After installation only dat doc and src contain files All other directories are empty Running Most to setup a model configuration and define an experiment uses the directo ries in the following manner 1 3 Model build phase Most writes an executable shell script to the bld directory and ithen executes it First it copies all necessary source files from src to bld and modifies them according to the selected parameter configuration Modification of source code is necessary for vertical and horizontal resolution change and when using more than 1 processor parallel program execution The original files in the src directory are not changed by Most The program modules are then compiled and linked using the make command also issued by Most Most provides two different makefiles one for the single CPU version and the other or the parallel version using MPI Message Passing Interface The resolution and CPU parameters are coded into the filename of the executable in order that there are different names for different versions E g the executable most puma t21 110 p2 x is an executable compiled
32. ced by the faster executing loop do jhor 1 NHOR gp jhor Pers enddo I 4 3 Parallelization in Spectral Domain The number of coefficients in spectral domain NRSP is divided by the number of processes NPRO giving the number of coefficients per process NSPP The number is rounded up to the next integer and the last process may get some additional dummy elements if there is a remainder in the division operation All loops in spectral domain are organized like do jsp 1 NSPP sp jsp enddo 4 4 Synchronization points All processes must communicate and have therefore to be synchronized at following events e Legendre Transformation This involves changing from latitudinal partitioning to spectral partitioning and such some gather and scatter operations e Inverse Legendre Transformation The partitioning changes from spectral to latitudinal by using gather broadcast and scatter operations e Input Output All read and write operations must be done only by the root process who gathers and broadcasts or scatters the information as desired Code that is to be executed by the root process exclusively is written like if mypid NROOT then endif NROOT is typically 0 in MPI implementations mypid My process identification is assigned by MPI 4 5 SOURCE CODE 27 4 5 Source code It needs some discipline in order to maintain parallel code Here are the most important rules for changing or adding
33. code to PUMA Adding namelist parameters All namelist parameters must be broadcasted after reading the namelist Subroutines mpbci mpbcr mpbcin mpbcrn Adding scalar variables and arrays Global variables must be defined in a module header and initialized Initialization code Initialization code that contains dependencies on latitude or spectral modes must be done by the root process only and then scattered from there to all child processes Array dimensions and loop limits Always use parameter constants NHOR NLAT NLEV etc as defined in pumamod f90 for array dimensions and loop limits Testing After significant code changes the program should be tested in single and in multi CPU configuration The results of a single CPU run is usually not exactly the same as the result of a multi CPU run due to effects in rounding But the results should show only small differences during the first timesteps Synchronization points The code is optimzed for parallel execution and minimizes there fore communication overhead The necessary communication code is grouped around the Legendre transformations If more scatter gather operations or other communica tion routines are to be added they should be placed just before or after the execution of the calls to the Legendre Transformation Any other place would degrade the overall performance in introducing additional process synchronization 28 CHAPTER 4 PARALLEL PROGRAM EXECUTION Chapt
34. e model s namelist file Depending on all settings MoSt generates a runscript for the simulation The user has the choice of leaving MoSt and continue with the simulation under control of a GUI right away or to exit MoSt with the scripts prepared to run The second alternative is useful for users who want to modify the setup beyond the scope of MoSt or want to run the Planet Simulator without GUI There s also a simple graphical editor for topograpy Check the box Orography and then use the mouse to mark rectangular areas in the topography display Enter a value for rising positive or lowering the area and press the button labelled Preprocess The preprocessor will be built and executed a new topography will be computed and written to a start file Another editor is the mode editor for spherical harmonics Green modes are enabled red modes are disabled This feature can be used to make runs with only certain modes of spherical harmonics being active MB1 MB2 MB3 refer to the left middle and right mouse button You may toggle individual modes or whole lines and columns Currently this mode editor can only be used for PUMA in the T21 resolution The GUI for running PUMA screenshot in 5 2 has two main purposes The first one is to display model arrays in suitable representations Current implementations are e Zonal mean cross sections 29 30 PUMA Planet Simulator Earth of CPUs
35. e primitive equations They describe the conservation of momentum mass and thermal energy In spherical coordinates and in the sigma system and with the aid of the equation of state they can be written in the dimensionless form as follows Conservation of momentum Vorticity equation C f 1 OF OF ze LP at 1 42 Ou Divergence equation 1 OF OF U V b Tolnp P t 1 02 OX s p a Hydrostatic approximation Od T Olmo Conservation of mass Continuity equation Conservation of energy First law of thermodynamics OT _ 1 O UT AVE T J Ot 1 12 cl Pe with QU Olnp F M jede E Va 890 TUS OV bnt P UEH P TO A D V Vinp and U ucosd V vcos Here the variables denote 47 8 4 48 CHAPTER 8 MODEL DYNAMICS temperature To reference temperature T T temperature deviation from To relative vorticity D divergence Ps surface pressure p pressure geopotential t time A longitude latitude 5 pip sigma vertical coordinate do dt vertical velocity in o system w dp dt vertical velocity in p system u V zonal meridional component of horizontal velocity V horizontal velocity with components U V f Coriolis parameter J diabatic heating rate Cp specific heat of dry air at constant pressure K adiabatic coefficient The set of differential equ
36. e vorticity are set to zero only mode 1 0 of vorticity is set tothe planetary vorticity The temperature is initialized as a horizontal constant field thevertical distribution is adopted from the restoration temperature usually a stablestratification The initialization of the logarithm of the surface pressure is controlled by the namelist variable kick kick 0 sets all modes to zero the model runs zonally constant without eddies kick 1 generates random white noise kick 2 generates random white noise that is symmetric to the equator Runs started with kick 1 or 2 are irreproducible due to the randomization For reproducible runs with eddies use kick 3 which initializes only mode 1 2 of InPs with a small constant The amplitude of the noise perturbation is normalized to 0 1 hPa 1 e 4 of the mean surface pressure A radiative equilibrium temperature field for the run is set up by setzt First a global mean radiative equilibrium temperature profile T a c is defined A hyperbolic function of height is used to provide as illustrated in Fig 4 1 With z oo the profile tends to a uniform laps rate alr passing through the temperature tgr at z 0 With z the profile becomes isothermal The transition takes place at a height ztrop The sharpness of the tropopause is controlled by the parameter dttrp When dttrp 0 the lapse rate changes discontinuously at ztrop For dttrp small but positive thetransition is
37. ength for heat m Am asymptotic mixing length for momentum m A longitude sin Y Ho cosine of the solar zenith angle APPENDIX A LIST OF CONSTANTS AND SYMBOLS Symbol Definition Value Unit p density of air kg m Pi density of sea ice 920 kg m Ps density of snow 330 kg m Pw density of sea water 1030 kg m Po density of fresh water 1000 kg m normalized pressure coordinate vertical velocity in o system OSB Stefan Bolzmann constant 5 67 1078 Wm gt K TN cloud optical depth TF time scale for RF time scale for NC time scale for temperature flux correction S time scale for depth flux correction S geopotential height g z mos scaled geopotential height latitude scaled velocity potential scaled streamfunction angular velocity of the earth 7 292 1075 s7 single scattering albedo ee Appendix B PUMA Codes for Variables Codes available from PUMA burner Code Levels Type Variable Unit 129 1 S surface geopotential m s 130 NLEV 5 temperature K 131 u velocity m s 132 NLEV c v velocity m s 135 NLEV c vertical velocity Pa s 138 NLEV s vorticity 1 s 148 NLEV c horizontal streamfunktion m s 149 NLEV c velocity potential m s 151 1 mean sea level pressure Pa 152 1 5 In surface pressure 154 NLEV 5 restoration temperature K
38. epth m H effective mixed layer depth TT m H reduced center of gravity A m 59 60 APPENDIX A LIST OF CONSTANTS AND SYMBOLS Symbol Definition Value Unit Ju vertical turbulent moisture flux kg m s7 Jr vertical turbulent temperature flux Kms Ji vertical turbulent flux of zonal momentum Pa Jy vertical turbulent flux of meridional momentum Pa k von Karman constant 0 4 Kn exchange coefficient for heat Km exchange coefficient for momentum L latent heat Ike L latent heat of fusion L L 3 28 10 Jkg In mixing length for heat m Im mixing length for momentum m Ls latent heat of sublimation 2 8345 109 Jkg Js latent heat of vapourization 2 5008 109 Jkg P convective precipitation mar P large scale precipitation ms P u associated Legendre function of the first kind p pressure Pa ps surface pressure Pa De scaled surface pressure specific humidity kg kg Q total heat flux through sea ice Wm Q flux correction heat flux through sea ice Wm Qa total atmospheric heat flux Wm Qe conductive heat flux through sea ice Wm Qf heat flux available for freezing sea ice Wm Q heat flux into the soil Wm Qm snow melt heat flux Wm Qo oceanic heat flux Wm ds surface specific humidity kg kg Gent saturation specific humidity kg kg R refexivity albedo Rs surface albedo Ra gas constant for dry air 287 05 Jkeg k surface long wave radiation Wm Rs sur
39. er 5 Graphical User Interface 5 1 Graphical user interface GUI PUMA may be used in the traditional fashion with shell scripts batch jobs and network queuing systems This is acceptable for long running simulations on complex machines and number crunchers like vector computers massive parallel computers and workstation clusters There is now however a much more convenient method by using a graphical user interface GUI for model setup with parameter configurations and for interaction between user and model PUMA is configured and setup by the first GUI module named MoSt Model Starter screen shot in B 1 MoSt is the fastest way to get the model running It gives access to the most important parameters of the model preset to the most frequently used values The model can be started with a mouse click on the button labelled Save amp Run either with the standard paramater setting or after editing some of the parameters in the MoSt window Some param eters like horizontal and vertical resolution or the number of processors require the building compile link and load of new executables MoSt achieves this by generating and execut ing build scripts that perform the necessary code changes and create the required executable Other parameters define startup and boundary conditions or settings for parameterisations They can be edited in MoSt and after a check for correct range and consistency with other parameters are written to th
40. face short wave radiation Wm R gas constant for water vapor 461 51 Jkg7t K7 Ro zeroth moment of the temperature distribution Km R first moment of the temperature distribution Km Ri Richardson number ui salinity of sea water 34 7 psu 61 Symbol Definition Value Unit t time S t scaled time step T transmissivity temperature K JY temperature anomaly Tp Ta deep ocean temperature at 400m K T sea ice surface temperature K freezing temperature 271 25 K T surface temperature K To d sea surface temperature K melting point 273 16 K dass mixed layer temperature K Trze climatological mixed layer temperature K Tref asymptotic reference temperature K Top oceanic temperature profile K To reference temperature profile 250 0 K U scaled zonal wind u cosy u zonal wind ms Ux friction velocity ms V scaled meridional wind v cosy U meridional wind ms 0 horizontal wind vector nig W cloud liquid water path gm Wenow mass of snow water kg W Loi soil water m 2 height m 20 roughness length m At time increment S Az height increment m a thermal expansion coefficient a 2 41 10 Kc 16 back scattering coefficient Ba diffusivity factor 1 66 scaled vorticity 0 potential temperature K K Ra Cpa K mean heat conductivity in ice and snow Wm heat conductivity in ice 2 03 Kis heat conductivity in snow 0 31 An asymptotic mixing l
41. gather scale and send surface pressure to GUI gather scale and send a gridpoint array to GUI gather scale and send wind components to GUI called for user input in GUI called for user input in GUI called for user input in GUI called for user input in GUI called for user input in GUI called for user input in GUI 15 CHAPTER 3 MODULES 3 4 legmod f90 General The module legmod f90 contains all subroutines necessary to perform the Legendre transformation and its inverse The interface to the main PUMA module puma f90 is given by the subroutines legini inigau fc2sp fc3sp and sp2gp which are called in puma f90 from the subroutines prolog and gridpoint Input Output legmod f90 does not use any extra input file or output file No namelist input is required The following subroutines are included in legmod f90 Subroutine Purpose inigau compute Gaussian abscissas and weights legini compute Legendre polynomials fs2sp Fourier to Spectral transformation sp2fc Spectral to Fourier transformation sp fc Simultaneous transformation of T Div and Vort mktend Compute and transform tendencies 3 5 mpimod f90 mpimod stub f90 General The module mpimod f90 contains interface subroutines to the MPI Mes sage Passing Interface needed for massive parallel computing Several MPI rou tines are called from the module The interface to other modules are given by numer ous subroutines which name star
42. ge for the user But it would be wise to keep changed run setups in other user created directories because each usage of Most will overwrite the contents of the run directory Another concept could be to rename user changed files because Most always generated files starting with most and leaves other files untouched 1 5 Running long simulations For long simulations make a new directory on a filesystem that has enough free disk space to store the results You may use the df command to check filesystems Hint 1 Don t use your home directory if there are filequotas Your run may crash due to file quota exceeded Hint 2 Use a local disk not NFS mounted filesystems if possible The model runs much faster writing output to local disks Example e cd Most15 e most x e Select model and resolution e Switch GUI off e Switch Output on e Edit number of years to run e Click on Save amp Exit e Make a directory e g mkdir data longsim e cp puma run data longsim e cd data longsim e edit most puma run for experiment name e edit namelist files if necessary e start simulation with most puma run amp CHAPTER 1 INSTALLATION Chapter 2 Introduction The Portable University Model of the Atmosphere PUMA is based on the multi level spectral model SGCM Simple Global Circulation Model described by Hoskins and Simmons 1975 and James and Gray 1986 Originally developed as a numerical prediction model it was ch
43. itesp mpi_info mpgetsp mpgetgp mpputsp mpputgp mpmazval mpsumval Purpose read and scatter grid point field gather and write grid point field gather and write with header grid point field read and scatter spectral field gather and write spectral field give information about setup read spectral array from restart file read gridpoint array from restart file write spectral array to restart file write gridpoint array to restart file compute maximum value of an array compute sum of all array elements 3 6 puma f90 General The module puma f90 is the main module of the model It includes the main program puma and controls the run From puma f90 the interface routines to all other modules are called The output is done by calling the subroutine to outsp In addition the adiabatic tendencies and the horizontal diffusion are computed in puma f90 To do the necessary transformations calls to the modules fftmod f90 and legmod f90 are used Input Output puma f90 A diagnostic printout is written on standard output usu allay redirected with the operator gt to a file puma f90 is controlled by the namelist np which is part of the namelist file puma namelist For a complete list of namelist variables see appendix Here is a table of the most important ones Parameter Type Purpose Default MPSTEP Integer MPSTEP Minutes Per STEP 60 defines the length of the timestep Recommended values are 60 min for T21 and 2
44. ma data Write diagnostics to standard output Perform spectral calculations and time step Write restart file puma status MP finalize end all processes Figure 8 4 Flow diagram of main routines 56 CHAPTER 8 MODEL DYNAMICS Bibliography E Eliasen B Machenhauer and E Rasmussen On a Numerical Method for Integration of the Hydrodynamical Equations with a Spectral Representation of the Horizontal Fields Inst of Theor Met 1970 Univ Copenhagen K Fraedrich E Kirk U Luksch and F Lunkeit The Portable University Model of the Atmo sphere PUMA Storm track dynamics and low frequency variability Meteorol Zeitschrift 14 735 745 2005 G J Haltiner and R T Williams Numerical Prediction and Dynamic Meteorology John Wiley and Sons New York 1982 477 S J R Holton An Introduction to Dynamic Meteorology Academic Press San Diego 3 edition 1992 507 S B J Hoskins and A J Simmons A multi layer spectral model and the semi implicit method Quart J Roy Meteor Soc 101 637 655 1975 S A Orszag Transform Method for the Calculation of Vector Coupled Sums Application to the Spectral Form of the Vorticity Equation J Atmos Sci 27 890 895 1970 A J Simmons and D Burridge An Energy and Angular Momentum Conserving Vertical Finite Difference Scheme and Hybrid Vertical Coordinates Mon Wea Rev 109 758 766 1981
45. ndow Then data is visualised either by typing commands line by line or preferably by using scripts The following script called tglob gs displays the monthly mean surface temperature tglob gs function pass m reinit open puma_m enable print print mf set t m set gxout shaded d c139 273 16 cbar gs set gxout contour d c139 273 16 draw title Surface Temperature deg C month m print disable print Igxps i print mf o tglob m ps The variable m at the beginning of the script defines the month which should be displayed It is passed from the terminal with the script call Note that in this line no quotation marks are present since only GrADS specific commands are framed by quotation marks Script commands like variable definitions if clauses etc are used without quotation marks The script is executed by typing its name without the ending and the number of the month to be shown For example tglob 7 displays the monthly mean surface temperature in July The resulting output file is called tglob7 ps The following script thh displays the time dependent surface temperature of Hamburg Here two variables are passed to GrADS the first and last day to plot note that here the file puma gra is opened which contains data on a daily basis The call thh 91 180 displays the surface temperature of Hamburg for the spring season from April 1
46. nges The same diagram for PUMA figure 2 1 right shows the direct paths which allow the easy identification of effects 2 4 Requirements PUMA is free of licenses anyone may download and use it But keep in mind that it is not a toy model The design of experiments and the interpretation of the results requires a thorough knowledge of atmospheric sciences PUMA is available as FORTRAN 90 source code So all that is needed to use PUMA on any computer is a FORTRAN 90 compiler The GUI requires additionally a C compiler and the graphical library X11 which is standard on any UNIX Linux system and available for other operating systems like MAC OS and Windows 2 5 HISTORY 11 The program was developed and tested with several operating systems like LINUX Solaris Windows and Unicos Main development is done with Linux and the Intel FORTRAN 90 compiler which is freely available for non commercial usage The postprocessor Pumaburner requires a C compiler There are several compilers available for the Linux operating system Most PUMA and Planet Simulator was successfully tested with e SunStudiol2 development environment including FORTRAN 90 C C and Debug ger for Solaris and Linux SunStudiol2 can be downloaded for free from e Intel FORTRAN 90 compiler There is a cost free version of the Intel compiler for non commercial use http www intel com e Gnu FORTRAN gfortran This free and open FORTRAN 90 compiler is part of
47. nt enable 1 or disable 0 zonal waves nspecsel NCSP 1 int enable 1 or disable 0 modes
48. oeller diagrams Amplitudes of coefficients of spherical harmonics e Time series e Numerical values In case of horizontal global grids pressing the MMB Middle Mouse Button toggles between cylinder and polar projection If the grid is just one level from many of a three dimensional field like u or v the level shown can be decreased by the LMB or increased by the RMB For Hovmoeller and longitude height sections the LMB and RMB can be used to select the latitude The second purpose is the interaction part of the GUI which allows the user to change selected model variables during the model run It is not necessary though possible to pause the model while changing variables Changes to model variables are of course monitored in the outputfile and checked by GUI for the appropriate range of values and maximum possible change per timestep because otherwise a rapid parameter change or a choice of values beyond the normal range may blow up the model All model variables which are candidates for the display or interactive changes have a special code to communicate with the Planet Simulator The experienced modeller can add new code for more variables using the existing communication code as template Thus all model fields or even fields received via coupling with other models can be put on the GUI display Both MoSt and GUI are implemented using the Xlib X11R5 which is a library of routines for graphics and event communication As this librar
49. ost15 directory home Most15 gt ls 1G rw r r 1 1548 cc check c lt Used by configure sh rwxr xr x 1 57 cleanplasim Delete run bld and bin for PLASIM rwxr xr x 1 51 cleanpuma Delete run bld and bin for PUMA drwxr xr x 2 4096 common lt Topography files rwxr xr x 1 3911 configure sh The configure script rwor rp e 1 308 csub c Currently unused rw f r 1 234 f90check f90 lt Used by configure sh rw r r 1 3033 FAQ Frequently Asked Questions drwxr xr x 2 4096 images Directory for images 6 CHAPTER 1 INSTALLATION Dbw r r 1 154 makecheck lt Used by configure sh rw r r 1 85 makefile lt Used to make most x rw r r 1 107844 most c lt Source for MoSt Model Starter rw r r 1 6399 NEW_IN_VERSION_15 lt New in this version drwxr xr x 8 4096 plasim lt Planet Simulator directory drwxr xr x 2 4096 postprocessor lt Postprocessor directory drwxr xr x 8 4096 puma PUMA directory rw r r d 839 README lt Read this first fw f r 1 191 README MAC USER Notes for MAC user Irw cr rb 1 698 README WINDOWS USER Notes for Windows user The directory structure must not be changed Even empty directories must be kept as they are because the Most program relies on their existence For each model currently Planet Simulator and PUMA there exists a directory plasim or puma with the following subdirectories Most15 puma gt 1s lg 128
50. owards the state of rest 0 D 0 with the time scale The parameterization terms and Pp appear in the model equations resp 8 2 and have the form Lg 8 7 TF D Pp Hn 8 8 TF The time scale depends on the o level l 1 1 n Usually for the upper levels 1 1 n 1 it is set to rr oo no friction and for the lowest layer nj a typical value is Tr 1d An explanation of the hyperdiffusion terms and Hp follows in section 8 2 3 8 2 2 Diabatic heating All diabatic processes considered in the model are parameterized by a linear approach Newto nian cooling too including the diabatic heating due to absorption and emission of short and longwave radiation as well as latent and sensible heat fluxes convection The temperature T relaxes towards the restoration temperature with the time scale The parameterization term in the thermal energy equation 8 5 is given by J Tr Pr Cp TR For the hyperdiffusion Hr see section Tg depends on the o level l on the latitude amp and on the vertical coordinate The restoration temperature field has the form Tr amp 0 Tr o Ho 8 10 The vertical profile is described by 2 Tr o EG 0 52 a 2 0 8 11 with TR gra L 22 Here z denotes the geometric height z the global constant height of the tropopause L OTg
51. re For pressure values that are lower than that of the model s top level the top level value of the variable is taken The variables tem perature and geopotential height are extrapolated if the selected pressure is higher than the surface pressure All other variables are set to the value of the lowest mode level for this case The outputfile contains the levels in the same order as set in hPa Example hpa 100 300 500 700 850 900 1000 6 3 LATS and LONS The pumaburner defaults to the dimension of the model run E g Lats 32 and Lons 64 for a T21 resolution Note however that this results in Gaussian grids with non equidistant latitudes Selecting for Lats and Lons values that are different from the internal resolution produces equidistant lat lon grids Lats sets the number of latitudes from North to South with the northpole at index 1 and the southpole at index Lats Delta Phi is therefore 180 degrees Lats 1 Lons sets the number of gridpoints on every latitude circle Delta Lambda is 360 Lons Index 1 is on Greewich 0 degrees while the last index denotes the point 360 degrees Delta Lambda Technical note Variables that are stored as spherical harmonics Temperature vorticity divergence etc are calculated on the user grid by setting up the Legendre transformation and the FF T accordingly Variables that are stored on Gaussian grids are interpolated with a bilinear interpolation Note Lats 8 and Lons 16 due to
52. s This is a technical documentation of the PUMA model In the following the purposes of the in dividual modules is given and the general structure and possible input and output opportunities namelist files are explained 3 1 fftmod f90 fft991mod f90 General The module fftmod f90 contains all subroutines necessary to perform the fast fourier transformation and its inverse The interface to the main PUMA module puma f90 is given by the subroutines gp2fc and fc2gp which are called in puma f90 from the subroutine gridpoint Input Output fftmod f90 does not use any extra input file or output file No namelist input is required Structure Internally fftmod f90 uses the FORTRAN 90 module fftmod which uses no other modules Subroutine gpZfc performs the transformation from grid point space into fourier space while the subroutine fc2gp does the transformation from fourier space into grid point space Both routines use several subroutines to do the direct or indirect transformation for different factors When gp2fc or fc2gp is called the first time fftini is called to do the initialization of the FFT The alternate module fft991mod f90 may be used instead of fftmod f90 While fft mod f90 runs faster fft991mod f90 can be used for resolutions that are not supported by fftmod f90 e g T63 or T106 Edit the file Most15 puma src make puma for module selection Use either FFTMOD fftmod or FFTMOD fft991mod 13
53. solines and colouring of longitude height section 5 2 GUI CONFIGURATION 33 5 2 3 Palette Name Range Description AUTO automatic rainbow colours U 10 50 rainbow colours V 10 10 rainbow colours T 50 50 blue red 985 1025 blue red Q 0 60 rainbow colours MARST 90 0 blue red AMPLI 0 12 blue green red VEG 0 100 shades of green 5 2 4 Title The title item may contain any text but keep it short the length of the window s title bar is limited The words Latitude and Level have special features in conjunction with threedimen sional arrays where the user may scroll the level or latitude The GUI will insert the level number after the world Level or the latitude after the word Latitude 5 2 5 Geometry The four integers following the geometry item describe the size and screen position of the window The first two parameters refer to width and height in screen pixel These are the sizes of the inner window title bar border and other decorations are not counted The third and fourth parameter set the coordinates of the upper left corner of the window x and y again without borders If the geometry item is not defined the GUI will initialize the window s geometry depending on the screen size 34 CHAPTER 5 GRAPHICAL USER INTERFACE Chapter 6 Postprocessor Pumaburner 6 1 Introduction The Pumaburner is a postprocessor for the Planet Simulator and
54. spread The hydrostatic relation is used to determine the heights andhence the temperatures of the model levels 54 CHAPTER 8 MODEL DYNAMICS 8 7 Computations in spectral domain The subroutine spectral performs one timestep Details of the time stepping schemeare given in Hoskins and Simmons 1978 The adiabatic tendencies advection etc are used The normal timestep is centered in time and includes a Robert time filter tocontrol time splitting For the first nkits timesteps short initial timesteps an initialforward timestep followed centred step each twice its predecessor are taken in orderto initiate a run from data at only one time level No Robert filter is included in the shortsteps The subroutine calculates the spectral tendencies due to Newtonian cooling Rayleigh friction and hyperdiffusion 8 7 COMPUTATIONS IN SPECTRAL DOMAIN 55 time Main program Multi processing startup Call initialization routines Perform time loop for NRUN time steps Call transformation and gridpoint routines Inverse Legendre transformation Divergence and vorticity to u v wind components Fourier coefficients to grid points Inverse FFT Calculations in grid point space Grid point to Fourier coefficients FFT Make tendencies for spectral domain MP sum and scatter Write prognostic fields to file pu
55. st to June 30th 7 1 GRADS 43 thh gs function pass d1 d2 reinit open puma enable print print mf set lat 53 set lon 10 set t di d2 D d c139 273 16 draw title Surface Temperature deg C in Hamburg print disable print Igxps i print mf o thh ps It is possible to have more than one figure in a plot which is illustrated in the following script It plots seasonal means of the sea level pressure The data file is prepared like this srv selcode 151 puma srv slp srv Srv seasmean slp srv slp_sm srv srv2gra slp_sm srv The commands set vpage sets virtual pages inside the graphic window The full window is 11 inch wide and 8 5 inch high so set vpage 0 5 5 4 25 8 5 defines the upper left corner If setlevs 1 is specified the pressure levels as given are used Otherwise GrADS defines contour levels depending on the data set slp sm gs setlevs 1 reinit open slp sm enable print print mf de set vpage 0 5 5 4 25 8 5 set gxout contour if setlevs 1 set clevs 990 995 1000 1005 1010 1015 1020 endif set ccols 1 set grads off set t 1 d c151 100 draw title SLP hPa yr ny DJF set vpage 5 5 11 4 25 8 5 set gxout contour if setlevs 1 set clevs 990 995 1000 1005 1010 1015 1020 endif set ccols 1 set grads off 44 CHAPTER 7 GRAPHICS set t 2 d c151 100
56. technical reasons 6 9 MEAN MEAN can be used to compute montly means and or deviations The Pumaburner reads date and time information from the model file and handles different lengths of months and output intervals correctly Setting Description MEAN 0 Do no averaging all terms are processed MEAN 1 Compute and write monthly mean fields Not for spherical har monics Fourier coefficients or zonal means on sigma levels MEAN 2 Compute and write monthly deviations Not for spherical harmon ics Fourier coefficients or zonal means on sigma levels Deviations are not available for NetCDF output MEAN 3 Combination of MEAN 1 and MEAN 2 Each mean field is fol lowed by a deviation field with an identical header record Not for spherical harmonics Fourier coefficients or zonal means on sigma levels 38 CHAPTER 6 POSTPROCESSOR PUMABURNER 6 10 Format of output data The pumaburner supports three different output formats e NetCDF Network Common Data Format e Service Format for user readable data see below For more detailed descriptions see for example http www nws noaa gov om ord iob NOAAPORT resources Setting Description NetCDF 1 The output file is written in NetCDF format NetCDF 0 The output file is written in Service format 6 11 SERVICE format The SERVICE format uses the following structure The whole file consists of pairs of header records and dat
57. the PUMA model family It s the only interface between raw model data output and diagnostics graphics and user software The output data of the Planet Simulator are stored as packed binary 16 bit values using the model representation Prognostic variables like temperature divergence vorticity pressure and humidity are stored as coefficients of spherical harmonics on levels Variables like radi ation precipitation evaporation clouds and other fields of the parameterization package are stored on Gaussian grids The tasks of the Pumaburner are e Unpack the raw data to full real representation e Transform variables from the model s representation to a user selectable format e g grids zonal mean cross sections fourier coefficients e Calculate diagnostic variables like vertical velocity geopotential height wind compo nents etc e Transfrom variables from o levels to user selectable pressure levels e Compute monthly means and standard deviations e Write selected data either in SERVICE or NetCDF format for further processing 6 2 Usage burn5 options InputFile OutputFile lt namelist gt printout option h help this output option c print available codes and names option d debug mode verbose output option n NetCDF output override namelist option option m Mean 1 output override namelist option InputFile Planet Simulator or PUMA data file OutputFile SERVICE or NetCDF format file namelist
58. ts with mp Subroutines from mpimod f90 are called in sveral other modules There are no direct calls to MPI other than in mpimod f90 This encapsulation makes it possible to use mpimod stub f90 for single CPU runs without changing any other part of the model code The selection is done auto matically by using MoSt or manually by editing Most15 puma src make Input Output mpimod f90 and mpimod stub do not use any extra input file or output file No namelist input is required Structure Internally mpimod f90 uses the FORTRAN 90 module mpimod which uses the global common module pumamod from pumamod f90 and the MPI module mpi mpimod stub f90 does not use any module The following subroutines are included in mpimod f90 Subroutine Purpose mpbci broadcast 1 integer mpbcin broadcast n integers mpber broadcast 1 real mpbern broadcast n reals mpbel broadcast 1 logical mpscin scatter n integers mpscrn scatter n reals mpscgp scatter grid point field mpgagp gather grid point field mpgallgp gather grid point field to all mpscsp scatter spectral field mpgasp gather spectral field mpgacs gather cross section mpgallsp gather spectral field to all mpsum sum spectral field mpsumsc sum and scatter spectral field mpsumr sum n reals mpsumbcr sum and broadcast n reals mpstart initialize MPI mpstop finalize MPI 17 18 CHAPTER 3 MODULES Subroutine mpreadgp mpwritegp mpwritegph mpreadsp mpwr
59. ult for following runs just copy this file like Most15 puma run cp dat GUI cfg dat GUI cfg old Most15 puma run cp GUI last used cfg dat GUI cfg 32 MoSt will then copy your new layout to the run directory at the next invocation The GUI cfg is a text file that may be also edited manually There is a section for each CHAPTER 5 GRAPHICAL USER INTERFACE window counting from 0 to 8 which looks like Window 00 window number 0 8 Array CSU lt array name Plot ISOCS lt picture type Palette U lt colour palette Title Zonal Wind m s lt window title Geometry 529 299 2 3 lt width height left top Window 01 Array SPAN Plot ISOSH Palette AMPLI Title Spherical Harmonics Ps Geometry 529 299 535 3 Possible values for these items are 5 2 1 Array Name Description CSU Cross Section U Zonal mean zonal wind CSV Cross Section V Zonal mean meridional wind CST Cross Section T Zonal mean temperature SPAN Spherical harmonics coefficients of surface pressure GU Three dimensional grid of zonal wind GV Three dimensional grid of meridional wind GP Grid of surface pressure SCALAR Selected scalars for timeseries and tables 5 2 2 Plot Name Description ISOHOR Isolines and colouring of horizontal grids ISOCS Isolines and colouring of cross sections ISOHOV Colouring of Hovmoeller diagram ISOTS Timeseries ISOTAB Tables ISOSH Coloured amplitudes ISOLON I
60. ut files must follow one of the following two rules e YYMM rule The last four characters of the filename contain the data in the form YYMM e NNN rule The last four characters of the filename consist of a dot followed ny a 3 digit sequence number Examples Namelist contains MULTI 3 Command pumaburn namelist gt printout run 005 out pumaburn processes the files lt run 005 gt lt run 006 gt lt run 007 gt Namelist contains MULTI 4 Command pumaburn namelist gt printout exp0211 out pumaburn processes the files lt exp0211 gt lt exp0212 gt lt exp0301 gt lt exp0302 gt 6 16 Namelist example VTYPE Pressure HTYPE Grid CODE 130 131 132 hPa 200 500 700 850 1000 MEAN 0 NETCDF 0 This namelist will write Temperature 130 u 130 and v 131 on pressure levels 200hPa 500hPa 700hPa 850hPa and 1000hPa The output interval is the same as found on the model data e g every 12 or every 6 hours MEAN 0 The output format is SERVICE format 6 17 Troubleshooting If the pumaburner reports an error or doesn t produce the expected results try the following e Check your namelist especially for invalid codes types and levels e Run the pumaburner in debug mode by using the option d Example pumaburn namelist gt printout d data in data out This will print out some details like parameters and memory allocation during the run The additional information may help to detect the problem 40 CHAPTER 6
61. y to puma output nwspini 1 integer 1 Write initial sp to file puma sp ini 65 66 APPENDIX C NAMELIST Name Default Type Description disp 0 0 real noise amplitude for nruido 1 dtns 0 0 real temperature difference at surface for North pole South pole season simulation dtep 60 0 real temperature difference at surface for equator pole forcing dttrp 2 0 real temperature increment controlling the sharpness of the tropopause in dtrop 12000 0 real height of tropopause m dvdiff 0 0 real vertical diffusion coefficient psurf 101100 0 real global mean sea level pressure Pa rotspd 1 0 real Earth rotation speed factor sigmax 0 0 real sigma value of top half level tac 0 0 real length of annual cycle in days pac 0 0 real phase of annual cycle in days tauta 40 0 real far surface heating time scale nhz gt 0 tauts 0 0 real near surface heating time scale nhz gt 0 tdiss 0 2 real diffusion time scale for divergence days tgr 288 0 real global mean temperature of ground used to set Tr ndl NLEV 0 int 1 activate spectral printouts for this level restim NLEV 15 0 real restoration timescale for each level sigmah NLEV 0 0 real define your own half level layout tOk NLEV 250 0 real reference T r temperature profile tfrc NLEV 0 0 0 1 int Rayleigh friction timescale in days for each level nselect NTP1 1 i
62. y is part of every UNIX Linux operating system and base of all desktop environments there is no need to install additional software for running MoSt and GUI Another important property of Xlib is the full network transparency The display of MoSt and GUI is not locked to the machine running the programs or the model In fact the best performance is obtained in running the Planet Simulator on two or four CPUs of a remote server while displaying the GUI on the user s workstation In summarizing the MoSt and GUI programs automate many tedious tasks minimize the time to become familiar with the Planet Simulator and make debugging and parameter tuning much easier More kinds of presentations coordinate projections and interactivity are being developed A graphical preprocessor with editor for boundary conditions and a graphical postprocessor are future expansions to build an almost complete environment for modellers 5 2 GUI configuration On initialization the GUI reads its configuration from a file GUI cfg which must be present in the current directory MoSt copies the file GUI cfg from the dat directory to the run directory while building PUMA After reading GUI cfg an attempt is made to read the file GUI_last_used cfg This file is always written at the end of a GUI controlled simulation So one may rearrange and position GUI windows during a run and the new layout will be saved to the file GUI last used cfg In order to make this user layout defa

University of Hamburg PUMA User's Guide Version 15.0

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