[DRAFT] User Manual for the LMD Martian Mesoscale Model
Contents
1. CHAPTER I INTRODUCING THE MODEL t Please first read the document Design and Performance of the LMD Martian Mesoscale Model to know what the model is what kind of results can be obtained and how these results compare with available data or independant simulations To be completed with description of the dynamics physics driver User Manual for the LMD Martian Mesoscale Model CHAPTER II FIRST STEPS TOWARD RUNNING THE MODEL This chapter is meant for first time users of the LMD Martian Mesoscale Model We describe how to install the model on your system compile the program and run a test case Experience with either the terrestrial WRF mesoscale model or the LMD Martian GCM is not absolutely required although it would help you getting more easily through the installation process II 1 PREREQUISITES 1 1 GENERAL REQUIREMENTS In order to install the LMD Martian Mesoscale Model please ensure that your computer is connected to the internet your OS is Linux with a decent set of basic commmands sed awk your Fortran compiler is the PGI commercial compiler pgf90 or the GNU free compilef 595 your compiler is gcc and development libraries are included bash m4 and perl are installed on your computer OF NETCDF libraries have been compiled on your system t You might also find useful though not mandatory to install on your system the ncview utility which is a nice t2. number of longitude grid points e_sn 61 number of latitude grid points geog_data_res gcm choice of static data sources NB possible 64ppd 32ppd NB please glance at geogrid GEOGRID TBL dx 20000 resolution meters in the x dimension dy 20000 resolution meters in the y dimension map proj mercator map projection mercator lambert or polar ref lat 0 125 north latitude of the center of the domain ref lon 239 east longitude of the center of the domain truelati lambert or polar lat position of projection cone l ooo WPS GEOG User Manual for the LMD Martian Mesoscale Model 23 amp metgrid fg name WPSFEED LMD 1 do not modify symbolic link in the WPS folder io_form_metgrid 2 1 do not modify choice of NETCDF outputs opt output from metgrid path WRFFEED current do not modify symbolic link t No input meteorological data are actually needed to execute geogrid exe rx More details about the database and more options of interpolation could be found in the file geogrid GEOGRID TBL t Defining several domains yields distinct files geo em d01 nc geo em d02 nc geo em d03 nc Once the geo en file s are generated the metgrid exe program performs a similar horizontal inter polation of the meteorological fields to the mesoscale domain as the one performed by geogrid exe for the surface data Then
3. 2 Pa Can I use the two way nesting To be completed 29 30 User Manual for the LMD Martian Mesoscale Model
4. User Manual for the LMD Martian Mesoscale Model calldifv call turbulent vertical diffusion calladj call convective adjustment 7 F callcond call C02 condensation 7 T callsoil call thermal conduction in the soil 7 T calllott call Lott s gravity wave subgrid topography scheme 7 F Radiative transfer options iradia the rad transfer is computed every iradia physical timestep 37 callg2d Output of the exchange coefficient mattrix for diagnostic only F rayleigh Rayleigh scattering should be F for now F Tracer dust water ice and or chemical species options use if tracer T dustbin DUST Transported dust if gt 0 uses q 1 to q dustbin 0 active DUST Radiatively active dust uses q 1 to q dustbin F doubleq DUST needs dustbin 1 use mass q 1 and nb q 2 mr to predict dust size F lifting DUST lifted by GCM surface winds 7 F dustdevil DUST lifted by dust devils 7 F scavenging DUST Scavenging by C02 snowfall 7 F sedimentation DUST WATERICE Gravitationnal sedimentation 7 F iceparty WATERICE Water cycle includes water ice mixing ratio q nqmx 1 F activice WATERICE Radiatively active transported atmospheric water ice 7 F water WATER Compute water cycle using q nqmx F caps WATER put the current permanent caps at both poles F photochem PHOTOCHEMISTRY chemical species included F Thermospheric options relevant if tracer T
5. a corresponding directory LMDMOD LMD_MM_MARS DIRCOMP t For example a DIRCOMP directory named g95 32 single is created if the user requested a 595 compilation of the code for single domain simulations on a 32bits machine generate with copy_model a directory DIRCOMP WRFV2 containing links to SRC WRFV2 sources t This method ensures that any change to the model sources would be propagated to all the different DIRCOMP installation folders execute the WRF configure script with the correct option tweak the resulting configure wrf file to include a link towards the Martian physics calculate the total number of horizontal grid points handled by the LMD physics duplicate LMD physical sources if nesting is activated t The model presently supports nests but more nests can be included by adaptating the following files LMDMOD LMD_MM_MARS SRC WRFV2 call_meso_inifis3 inc LMDMOD LMD_MM_MARS SRC WRFV2 call_meso_physiq3 inc LMDMOD LMD_MM_MARS SRC WRFV2 mars_lmd 1ibf duplicate3 LMDMOD LMD MM MARS SRC WRFV2 mars 1md libf generate3 LMDMOD LMD MM MARS SRC WRFV2 mars lmd makegcm search for nest 5This necessary recompilation each time the number of grid points tracers and domains is modified is imposed by the LMD physics code The WRF dynamical core alone is much more flexible User Manual for the LMD Martian Mesoscale Model 7 o compile the LMD physical packages with the appropriate makegcm command and collect the com
6. of the parameters labelled with p1 p2 or p3 implies the initial and boundary conditions and or the domain definition to be recomputed prior to running the model again As a result you were probably unable to change many of the parameters of the Arsia Mons test case proposed in section IT 3 in which the initial and boundary conditions as well as the domain of simulation were predefined In this chapter we describe the installation and use of the preprocessing tools to define the domain of simulation calculate an initial atmospheric state and prepare the boundary conditions for the chosen simulation time This necessary step would eventually allow you to run your own simulations at the specific season and region you are interested in with a complete ability to modify any of the parameters in namelist input IV 1 INSTALLING THE PREPROCESSING UTILITIES First and foremost since the preprocessing utilities could generate or involve files of quite signif icant sizes it is necessary to define a directory where these files would be stored Such a directory e g bigdisk user must be linked as follows sf bigdisk user LMDMOD TMPDIR A second prerequisite to the installation of the preprocessing tools is that the LMD Martian Mesoscale Model was compiled at least once If this is not the case please compile the model with the makemeso command see section 2 2 The compilation process created an installation directo
7. please type the following commands replacing the g95_32_single directory with its corresponding value on your system cp LMD_MM_MARS_TESTCASE tar gz LMDMOD LMD_MM_MARS tar xzvf LMD_MM_MARS_TESTCASE tar gz cd TESTCASE In sf g95 32 single real x61 y61 z61 di t1 pi exe wrf exe tar xzvf wrfinput tar gz nohup wrf exe gt log wrf amp t f you compiled the model using MPICH2 the command to launch a simulation is slightly different simulation on 2 processors on 1 machine amp first time only or after a reboot NB may request the creation of a file mpd conf mpirun np 8 wrf exe lt dev null amp NB mpirun is only a link to mpiexec tail 20 rsl out 000 to check the outputs simulation on 16 processors in 4 connected machines echo barry lmd jussieu fr gt mpd hosts echo white lmd jussieu fr gt gt mpd hosts echo loves lmd jussieu fr gt gt mpd hosts echo tapas lmd jussieu fr gt gt mpd hosts ssh barry lmd jussieu fr make sure that ssh to other machines is possible without authentification mpdboot f mpd hosts n 4 mpdtrace mpirun l np 16 wrf exe lt dev null amp NB mpirun is only a link to mpiexec tail 20 rsl out 00 to check the outputs CHAPTER III SETTING THE SIMULATION PARAMETERS In this chapter we describe how to set the various parameters defining a given simulation As could be inferred from the content of the TESTCASE directory two parameter fil
8. position of the bottom left nest corner n p2 Ratio of horizontal resolution parent nest n Ratio of time step parent nest User Manual for the LMD Martian Mesoscale Model 11 amp physics 1 OPTIONAL 1 radt mars 1 0 init TI 0 init_AL init_U init V init WX init WY init MU init MV aa init_LES F uo uo 1 t 0 04 0 0 amp dynamics 1 OPTIONAL n time step sound non hydrostatic pd scalar F 1 diff_opt 1 km_opt 4 diff_6th_factor diff_6th_opt smdiv 0 1 0 01 epssm 0 1 h_mom_adv_order v_mom_adv_order emdiv h_sca_adv_order v_sca_adv_order amp bdy control 11 OPTIONAL 1 specified T nested F periodic_x periodic_y open_xs Hy 9 _ ao 5 open_ys F open ye Spec bdy vidth relax zone 4 1 0 2 o M 5 Ratio between physical and dynamical time step p2 Configuration of tracers 0 no tracers 1 water vapor ice 2 dust p3 Define constant thermal inertia value p3 Define constant albedo value p3 Define constant ini bdy zonal wind value p3 Define constant ini bdy meridional wind value p3 Ini bdy wind profile is everywhere equal to p3 the wind profile grid pt init_WX init_WY p3 Multiply ini amp bdy zonal wind by init_U p3 Multiply ini amp bdy meridional wind by init_V p3 Uniform domain initia
9. the program writes the results in met em files and also collects the static fields and domain parameters included in the geo em file s Please type the following commands cd LMDMOD LMD MM MARS your install dir WPS metgrid exe If every went well the directory LMDMOD TMPDIR WRFFEED should contain the met em files IV 2 2 3 STEP 3 VERTICAL INTERPOLATION ON MESOSCALE LEVELS The last step is to execute real exe to perform the interpolation from the vertical levels of the GCM to the vertical levels defined in the mesoscale model This program also prepares the final initial state for the simulation in files called wrfinput and the boundary conditions in files called wrfbdy To successfully execute real exe you need the met em files and the namelist input file to be in the same directory as real exe Parameters in namelist input controlling the behavior of the vertical interpolation are those labelled with p3 in the detailed list introduced in the previous chapter Please type the following commands to prepare files for the Arsia Mons test case or your personal test case if you changed the parameters in namelist wps cd LMDMOD TESTCASE ln sf LMDMOD WRFFEED met em real exe The final message of the real exe should claim the success of the processes and you are now ready to launch the integrations of the LMD Martian Mesoscale Model again with the wrf exe command as in section t When you modify either namel
10. tsurf title Surface temperature tsurf units K float ps Time latitude longitude ps title surface pressure ps units K float co2ice Time latitude longitude co2ice title co2 ice thickness co2ice units kg m 2 float temp Time altitude latitude longitude temp title temperature temp units float u Time altitude latitude longitude u title Zonal wind u units m s 1 float v Time altitude latitude longitude v title Meridional wind v units m s 1 float tsoil Time altitude latitude longitude tsoil title soil temperature tsoil units float qOi Time altitude latitude longitude q0i title ice q0i units kg kg float q02 Time altitude latitude longitude q02 title h2o q02 units kg kg ws Ifthe fields emis co2ice 401 402 tsoil are missing in the diagfi nc file they are replaced by respective default values 0 95 0 0 0 tsurf An example of input meteorological file diagfi nc file can be downloaded at jussieu fr aslmd LMD MM MARS diagfi nc tar gz Please deflate the archive and copy the diagfi nc file in LMDMOD TMPDIR GCMINI Such a file can then be used to define the initial and boundary conditions and we will go through the three preprocessing steps IV 2 2 PREPROCESSING STEPS IV 2 2 1 STEP 1 CONVERTING GCM DATA The programs in the PREP MARS directory convert the data from the NETC
11. 1 0 8 tar gz LMDMOD MPI cd LMDMOD MPI tar xzvf mpich2 1 0 8 tar gz cd mpich2 1 0 8 configure prefix PWD with device ch3 nemesis gt conf log 2 gt conferr log amp please wait make gt mk log 2 gt mkerr log amp declare x WHERE MPI LMDMOD MPI mpich2 1 0 8 bin t Even if you add the LMDMOD MPI mpich2 1 0 8 bin directory to your PATH variable defin ing the environment variable _ is still required to ensure a successful compilation of the model 1 3 COMPILING THE TERRESTRIAL WRF MODEL The LMD Martian Mesoscale Model is based on the terrestrial NCEP NCAR ARW WRF Mesoscale Model As a first step towards the compilation of the Martian version we advise you to check that the terrestrial model compiles on your computer with either g95 or pgf90 On the ARW WRF website http www mmm ucar edu wrf users download get source html you will be allowed to freely download the model after a quick registration process click on New users Make sure to download the version 2 2 of the WRF model and copy the WRFV2 2 TAR gz archive to the LMDMOD folder Then please extract the model sources and configure the compilation process cd LMDMOD tar xzvf WRFV2 2 TAR gz cd WRFV2 configure The configure script analyzes your architecture and proposes you several possible compilation options Make sure to choose the single threaded no nesting option related to either g95 should be option 13 o
12. DF diagfi nc file into separated binary datafiles for each date contained in diagfi nc according to the formatting needed by the preprocessing programs at step 2 These programs can be executed by the following commands LMDMOD LMD MM MARS your install dir PREPN MARS echo 1 create readmeteo exe drop the echo 1 if you want control readmeteo exe lt readmeteo def If every went well with the conversion the directory LMDMOD TMPDIR WPSFEED should contain files named LMD IV 2 2 2 2 INTERPOLATION ON THE REGIONAL DOMAIN In the WPS directory the geogrid exe program allows you to define the mesoscale simulation domain to horizontally interpolate the topography thermal inertia and albedo fields at the domain resolution and to calculate useful fields such as topographical slopes 22 User Manual for the LMD Martian Mesoscale Model Please execute the commands cd LMDMOD LMD MM MARS your install dir WPS In sf TESTCASE namelist wps test case geogrid exe The result of geogrid exe and thus the definition of the mesoscale domain can be checked in the NETCDF file geo em d01 nc A quick check can be performed using the command line ncview geo em dO1 nc if ncview is installed or the IDL script out geo pro idl IDL out geo fieldi TOPO IDL gt out geo fieldi TI IDL gt SPAWN ghostview geo em dO1 HGT M ps amp IDL gt SPAWN ghostview geo em d0O1 THERMAL INERTIA ps amp
13. ESA CNES contracts Mars Environment Models WP11 1 Deliverable Report Ref ESA 11369 95 NL JG SC CNES Base de donn es atmosph riques martiennes DRAFT User Manual for the LMD Martian Mesoscale Model A Spiga Laboratoire de M t orologie Dynamique Institut Pierre Simon Laplace Universit Pierre et Marie Curie Paris France Contact spiga 1lmd jussieu fr forget lmd jussieu fr December 13 2008 CONTENTS I Introducing the model I I First steps toward running the model ILI Prerequisites x9 9o Oe 4e 1 1 1 General requirements 1 1 2 Parallel computations 1 1 3 Compiling the terrestrial WRF model 1 2 Compiling the Martian model 1 2 1 Extracting and preparing the sources 1 2 2 Main compilation step 1 3 Running a simple test casel Setting the simulation parameters 11 1 Dynamical settings e 11 2 Physical settings be b REERUUPI dd IV 2 2 3 Step 3 Vertical interpolation on mesoscale levels Starting simulations from scratch V 1 Running your own GCM simulations V 2 Complete simulations with runmeso VI 1 Postprocessing utilities and graphics VI 2 Modify the outputs VIIFrequently Asked Questions iii COR amp Co 17 17 18 18 18 20 21 21 23 25 25 25 27 27 27 29
14. IDL gt exit if the demo version of IDL is installed Of course if your favorite graphical tool supports the NETCDF standard you might use it to check the domain definition in geo em d01 nc If you are unhappy with the results or you want to change the location of the mesoscale domain on the planet the horizontal resolution the number of grid points please modify the parameter file namelist wps and execute again geogrid exe Here are the contents of namelist wps amp share wrf core ARW do not modify choice of dynamical core number of simulation domains YYYY MM DD HH mm ss start date YYYY MM DD HH mm ss end date frequency of GCM updates 1 Mars hour 3700 s do not modify choice of NETCDF outputs verbose level of the programs location of the geogrid outputs max dom 1 start date 2024 01 04 02 00 00 end date 2024 01 04 12 00 00 interval seconds 3700 io form geogrid 2 debug level 0 opt output from geogrid path 0 truelat2 0 stand lon 0 geog_data_path do not modify lambert or polar lon position of projection cone do not modify symbolic link in the WPS folder gt gt amp geogrid parent_id 1 number identifying the related parent domain parent grid ratio 1 ratio between parent and nested domains i parent start 1 x position of the southwest corner of nest j parent start y position of the southwest corner of nest e we 61
15. MARTIAN MODEL IL2 1 EXTRACTING AND PREPARING THE SOURCES To start the installation of the Martian mesoscale model download the archive LMD MM MARS tar gz click on http www 1md jussieu fr aslmd LMD MM MARS LMD MM MARS tar gz or use the wget command Copy the sources in the LMDMOD directory and extract the files LMD MM MARS tar gz LMDMOD cd LMDMOD tar xzvf LMD MM MARS tar gz Execute the prepare script that would do some necessary preparatory tasks for you deflate the various compressed archives contained into LMD MM MARS download the ARW WREF sources from the web apply a quite significant Martian patch to these sources and build the final structure of your LMD MM MARS directory cd LMDMOD LMD MM MARS prepare Please check the contents of the LMD MM MARS directory o seven bash scripts build static copy model makemeso prepare prepare ini prepare post save all o the sources directory SRC o the static data directory WPS GEOG o the simulation utilities directory SIMU and check that the LMD MM MARS SRC directory contains o the model main sources in WRFV2 o the preprocessing sources in WPS and PREP MARS o the postprocessing sources in ARWpost o three tar gz archives and two information text files User Manual for the LMD Martian Mesoscale Model 2 2 MAIN COMPILATION STEP In order to compile the model execute the makemeso compilation script in the LMD MM MARS direct
16. callthermos call thermosphere 7 F thermoswater WATER included without cycle only if water F F callconduct call thermal conduction matter only if callthermos T calleuv call EUV heating matter only if callthermos T F callmolvis call molecular viscosity matter only if callthermos T F User Manual for the LMD Martian Mesoscale Model 15 callmoldiff call molecular diffusion matter only if callthermos T F thermochem call thermospheric photochemistry matter only if callthermos T F solarcondate date for solar flux calculation 1985 lt date lt 2002 1993 4 Solar min 1996 4 ave 1993 4 max 1990 6 end file callphys def t Note that in the given example the convective adjustment the gravity wave parameterization and the NLTE schemes are turned off as is usually the case in typical Martian tropospheric mesoscale simulations gt iradia sets the frequency in dynamical timesteps at which the radiative computations are performed t Modifying callphys def only implies to recompile the model if the number of tracers is different ts f you run a simulation with say domains please ensure that you defined three files callphys def callphys_d2 def and callphys_d3 def 16 User Manual for the LMD Martian Mesoscale Model CHAPTER IV PREPROCESSING UTILITIES In the previous chapter we decribed the simulation settings in the namelist input file We saw that any modification
17. d T nested F F F TT III 2 PHYSICAL SETTINGS callphys def controls the behavior of the physical parameterizations in the LMD Martian Mesoscale Model The organization of this file is exactly similar to the corresponding file in the LMD Martian GCM which user manual can be found at http web 1md jussieu fr forget datagcm user manual pdf Please find in what follows the contents of callphys def file callphys def General options tracer Run with or without tracer transport F diurnal Diurnal cycle if diurnal F diurnal averaged solar heating T Season Seasonal cycle if season F Ls stays constant like in start T lwrite want some more output on the screen F stats Saving statistics in file cumul 7 F calleofdump Saving EOF profiles in file profiles for Climate Database F Dust scenario Used if the dust is prescribed i e if tracer F or active F iaervar 1 Dust opt deph read in startfi 2 Viking scenario 3 MGS scenario 4 4 Mars Year 24 from TES assimilation iddist Dust vertical distribution 0 old distrib Pollack90 3 21 top set by topdustref 2 Viking scenario 3 MGS scenario topdustref Dust top altitude km Matter only if iddist 1 55 Physical Parameterizations callrad call radiative transfer 7 T callnlte call NLTE radiative schemes matter only if callrad T F callnirco2 call C02 NIR absorption matter only if callrad T T 14
18. d scripts to install finer resolution datasets 32 and or 64 pixel per degree ppd MOLA topography Smith et al 2001 8 ppd MGS Thermal Emission Spectrometer TES albedo Christensen et al 2001 20 ppd TES thermal inertia Putzig and Mellon 2007 1 Corresponding to the fields stored in the file surface nc known by LMD MGCM users jussieu fr forget datagcm datafile surface nc Preprocessing Step 1 Preprocessing Step 2a input_diagfi nc WPS GEOG gt time series of winds temperature tracers gt global domain gt GCM vertical levels gt topography thermal inertia albedo gt global domain create_readmeteo exe readmeteo exe geogrid exe LMD 2024 07 01 06 00 00 7 winds temperature tracers at a given date 7 global domain gt GCM vertical levels geo em dO1 nc 7 topography thermal inertia albedo 7 regional projected domain Preprocessing Step 2b metgrid exe Ev met em d01 2024 07 01 06 00 00 nc 7 topography thermal inertia albedo 7 winds temperature tracers at a given date gt regional projected domain gt GCM vertical levels wrfbdy d01 wrfinput 7 topography thermal inertia albedo gt topography thermal inertia albedo 7 winds temperature tracers at all simulation steps 7 winds temperature tracers at starting time 7 boundaries only gt regional projected domain g
19. diting your personal namelist input file to avoid reading error t To modify the default values or even add personal parameters in the namelist input file edit the SRC WRFV2 Registry Registry EM file You will then have to recompile the model with makemeso answer y to the last question In case you run simulations with max dom nested domains you have to set max dom parameters wherever there is a 56 in the above list Here is an example of the resulting syntax of the time control domains and bdy control categories in namelist input amp time control Start year 2024 2024 2024 start month 01 01 01 start day 49 49 49 start hour 06 06 06 end year 2024 2024 2024 end month 01 01 01 end day 54 54 54 end hour 06 06 06 history interval 74 74 74 frames_per_outfile 12 12 12 restart false restart_interval 8880 io_form_history io_form_restart io_form_input io_form_boundary debug_level Il H N NN MI input from file T T T amp domains time step 40 dx 36000 9000 2250 36000 9000 2250 _ 153 157 157 e_sn 153 157 157 e_vert 61 61 61 p_top_requested 3 User Manual for the LMD Martian Mesoscale Model 13 max_dom 3 grid_id 1 2 3 parent_id 0 1 25 i parent start 0 5T BT j parent start 0 57 57 parent_grid_ratio 1 4 4 parent time step ratio 1 2 25 amp bdy control Specifie
20. es are needed to run the model 1 The parameters related to the dynamical part of the model can be set in the file namelist input according to the ARW WRF namelist formatting 2 The parameters related to the physical part of the model can be set in the file callphys def according to the LMD MGOM formatting III 1 DYNAMICAL SETTINGS namelist input controls the behavior of the dynamical core in the LMD Martian Mesoscale Model Compared to the file the ARW WRF users are familiar with the namelist input in the LMD Martian Mesoscale Model is much shorter The only mandatory parameters in this file are information on time control and domain definition The minimal version of the namelist input file corresponds to standard simulations with the model It is however possible to modify optional parameters if needed as is the case in the namelist input associated to the Arsia Mons test case e g the parameter non_hydrostatic is set to false to assume hydrostatic equilibrium whereas standard simulations are non hydrostatic A detailed description of the namelist input file is given below Comments on each of the parameters are provided with the following labels o denotes parameters not to be modified o r indicates parameters which modification implies a new recompilation of the model o n describes parameters involved when nested domains are defined o p1 p2 p3 mention parameters which modification implies a new processing o
21. f initial and boundary conditions see next chapter o d denotes dynamical parameters which modification implies non standard simulations please read SRC WRFV2 run README namelist and use with caution If omitted the optional parameters would be set to their default values indicated below 1 A description of this file can be found in SRC WRFV2 run README namelist 2 More information on the adopted Martian calendar http www mars lmd jussieu fr mars time solar longitude html You may find the corresponding file in SIMU namelist input full 10 User Manual for the LMD Martian Mesoscale Model file amp time_control start_year start_month start_day start_hour end_year end_month end_day end_hour history_interval frames_per_outfile restart false 2024 2024 restart_interval io_form_history io_form_restart io_form_input io_form_boundary debug_level Il ONNNN OPTIONAL 1 3700 T interval_ seconds input_from_file amp domains time_step dx 20000 dy 20000 51 51 e_vert 61 p_top_requested 5 11 50 e we e_sn OPTIONAL 1 time_step_fract_num 0 time_step_fract_den 1 num_metgrid_levels 26 force_sfc_in_vinterp 8 1500 max_dz eta_levels max_dom 1 grid_id parent_id i_parent_start j parent start parent grid ratio parent time step ratio namelist i
22. from the diagfi nc outputs of LMD MGOM simulations If you would like to run a mesoscale simulation at a given season you need to first run a GCM simulation and output the meteorological fields at the considered season For optimal forcing at the boundaries we advise you to write the meteorological fields to the diagfi nc file at least each two hours Please also make sure that the following fields are stored in the NETCDF diagfi nc file netcdf diagfi dimensions Time UNLIMITED 72 currently index 100 latitude 49 longitude 65 altitude 32 variables float Time Time Time long_name Time Time units days since 0000 00 0 00 00 00 float controle index controle title Control parameters float latitude latitude latitude units degrees_north latitude long_name North latitude float longitude longitude longitude long_name East longitude longitude units degrees_east float aps altitude aps title hybrid pressure at midlayers aps units Pa float bps altitude bps title hybrid sigma at midlayers bps units 2 Available at http www gnu org software octave User Manual for the LMD Martian Mesoscale Model 21 float phisinit latitude longitude phisinit title Geopotential at the surface float emis Time latitude longitude emis title Surface emissivity emis units w m 1 float tsurf Time latitude longitude
23. ist wps or namelist input make sure that the common parameters are exactly similar in both files especially when running nested simulations otherwise either real exe or wrf exe command will exit with an error message 24 User Manual for the LMD Martian Mesoscale Model CHAPTER V STARTING SIMULATIONS FROM SCRATCH V 1 RUNNING YOUR OWN GCM SIMULATIONS To be completed V 2 COMPLETE SIMULATIONS WITH RUNMESO be completed 25 26 User Manual for the LMD Martian Mesoscale Model CHAPTER VI OUTPUTS VI 1 POSTPROCESSING UTILITIES AND GRAPHICS To be completed Do it all idl scripts would be described here VI 2 MODIFY THE OUTPUTS be completed Though the method is different we kept all the convenient aspects of writediagfi 27 28 User Manual for the LMD Martian Mesoscale Model FREQUENTLY ASKED QUESTIONS Which timestep should I choose to avoid crashes of the model In the Martian simulations why can t I define boundaries each 6 hours as on Earth Help I get strange assembler errors or ILM errors while compiling Is it possible to run the model on a specific configuration that is not supported Why do I have to define four less rows in the parent domain when performing nested runs I am kind of nostalgic of early middle Mars How could I run mesoscale simulations at low high obliquity Why real exe is crashing when the model top pressure is lower than
24. lization for LES Ratio of time step dynamic acoustic integration NB an increase could help solve instabilities Integrate in non hydrostatic hydrostatic mode Positive definite advection scheme for tracers xd Diffusion option set to 0 if LES or GCM d Eddy coefficient option d Knievel numerical diffusion set to 0 if LES d Knievel numerical coeff set to 0 5 if GCM d Divergence damping External mode filter for mass coord model d Time off centering for vertical sound waves d Horizontal momentum advection order Vertical momentum advection order Horizontal scalar advection order d Vertical scalar advection order n p3 Boundary conditions specified by GCM n p3 Boundary conditions from parent domain p3 Periodic boundary conditions over x p3 Periodic boundary conditions over y p3 Open boundary conditions western boundary p3 Open boundary conditions eastern boundary p3 Open boundary conditions southern boundary p3 Open boundary conditions northern boundary p3 Width of transition zone with specified T NB spec bdy width must equal relax zone p3 Width of relaxation zone with specified T 12 User Manual for the LMD Martian Mesoscale Model amp grib2 amp fdda amp namelist quilt 1 x nio tasks per group 0 1 nio groups 1 11 1 end file namelist input full t Please pay attention to rigorous syntax while e
25. n a 32 bits Linux PC or pgf90 should be option 1 on a 32 bits Linux PC The next step is to compile the WRF model by choosing the kind of simulations you would like to run A simple and direct test consists in trying to compile the idealized case of a 2D flow impinging on a small hill compile em hill2d x gt log compile 2 log error amp t n case you encounter problems compiling the ARW WRF model please read documentation on the website http www mmm ucar edu wrf users contact the WRF helpdesk or search the web for your error message User Manual for the LMD Martian Mesoscale Model 5 If the compilation was successful the file log error should be empty or only reporting few warn ings you should find in the main folder two executables ideal exe and run exe that would allow you to run the test simulation cd test em_hill2d_x ideal exe wrf exe During the simulation the time taken by the computer to perform integrations at each dynamical timestep is displayed in the standard output The simulation should end with a message SUCCESS COMPLETE WRF T he model results are stored in a wrfout data file you might like to browse with a NETCDF compliant software such as ncview t fyou compiled the model with g95 ideal exe will probably complain about an error reading the namelist Please move the line non hydrostatic below the line v sca adv order in the namelist input file to solve the problem 2 COMPILING THE
26. nput full Start Martian Year 20XX for MY XX Month Day Start Martian Hour at longitude 0 End Martian Year 20XX for MY XX End Martian Month pi End Martian Day 1 End Martian Hour at longitude 0 Frequency of outputs 37 gt 3700s 1 Martian hour Size of time dimension in files Output restart files Frequency of output restart files Choice of NETCDF for ouputs Choice of NETCDF for ouputs Choice of NETCDF for ouputs Choice of NETCDF for ouputs Verbose level p1 p1 p1 p1 p1 p1 Start Martian Start Martian p2 Frequency of large scale fields update s n p2 Initialize a given domain with an input file Dynamical timestep p2 Horizontal resolution p2 Horizontal resolution should be equal to dx r p2 Number of longitude grid points r p2 Number of latitude grid points r p2 Number of vertical levels p3 Chosen value of pressure at the top of the model Additional fraction to time step numerator Additional fraction to time step denominator p1 number of vertical levels in GCM inputs 1 p3 Number of levels hardwired in the PBL NB decrease this parameter when low model top p3 Maximal interval m between vertical levels p3 Specify a list of e vert eta levels 2 Total number of domains n p2 Identification of the domain n p2 Associated parent domain p2 x position of the bottom left nest corner n p2 x
27. ool to visualize the contents of a NETCDF file o the IDL demo version which is used by the plot utilities provided with the model Three environment variables associated with the NETCDF libraries must be defined declare x NETCDF disk user netcdf declare x NCDFLIB NETCDF lib declare x NCDFINC NETCDF inc t command lines in the document are proposed in bash You also need the environment variable LMDMOD to point at the directory where you will install the model e g disk user MODELS declare x LMDMOD disk user MODELS ts Please check that 200 Mo free disk space is available in disk 1 The model was also successfully compiled on MacOSX howto information is available upon request 2 Sources and binaries available on http www g95 org http meteora ucsd edu pi i 4 http www ittvis com ProductServices IDL aspx 4 User Manual for the LMD Martian Mesoscale Model 11 1 2 PARALLEL COMPUTATIONS Parallel computations with the Message Passing Interface MPI standard are supported by the ARW WRF mesoscale model If you want to use this capability in the LMD Martian Mesoscale Model you would have the installation of MPICH2 as a additional prerequisite Please download the current stable version of the sources e g mpich2 1 0 8 tar gz on the MPICH2 website http www mcs anl gov research projects mpich2 and install the MPICH2 utilities by the following commands mkdir LMDMOD MPI mv mpich2
28. ory cd LMDMOD LMD_MM_MARS makemeso and answer to the questions about D o um como compiler choice and number of processors if using MPI number of grid points in longitude 61 number of grid points in latitude 61 number of vertical levels 61 number of tracers 1 number of domains 1 On the first time you compile the model you will probably wonder what to reply to questions 2 to 6 type the answers given in brackets to compile an executable suitable for the test case given below Suppose you compiled a version of the model for a given set of parameters 1 to 6 to run a specific compilation If you would like to run another simulation with at least one of parameters 1 to 6 subject to change the model needs to be recompiled with makemeso When you use parallel computations please bear in mind that with 2 resp 4 6 8 16 processors the whole domain would be separated into 2 resp 2 3 4 4 tiles over the latitude direction and 1 resp 2 2 2 4 tile over the longitude direction Thus make sure that the number of grid points minus 1 in each direction could be divided by the aforementioned number of tiles over the considered direction If you use grid nesting note that no more than 4 processors can be used The makemeso is an automated script which performs the following serie of tasks oO determine if the machine is 32 64 bits ask the user about the compilation settings create
29. piled objects in the library 1iblmd a t During this step that could be a bit long especially if you defined more than one domain the makemeso script provides you with the full path towards the text file log_compile_phys in which you can check for compilation progress and possible errors In the end of the process you will find an error message associated to the generation of the final executable Please do not pay attention to this as the compilation of the LMD sources is meant to generate a library of compiled objects called liblmd a instead of a program o compile the modified Martian ARW WREF solver including the 1iblmd a library When it is the first time the model is compiled this step could be quite long The makemeso script provides you with a log compile text file where the progress of the compilation can be checked and a 1og error text file listing errors and warnings during compilation list of warnings related to grib utilities not used in the Martian model may appear and have no impact on the final executables t The compilation with 595 might be unsuccessful due to some problems with files related to terrestrial microphysics Please type the following commands cd LMDMOD LMD MM MARS SRC tar xzvf g95 tar gz f g95 WRFV2 g95 fix WRFV2 phys cd LMDMOD LMD MM MARS then recompile the model with the makemeso command o change the name of the executables in agreements with the settings provided by the use
30. r t f you choose to answer to the makemeso questions using the aforementioned parameters in brackets you should have in the DIRCOMP directory two executables real x61 y61 z61 di t1 pl exe wrf x61 y61 z61 d1 ti pl exe The directory also contains a text file in which the answers to the questions are stored which allows you to re run the script without the questions to the user step makemeso lt makemeso x61 y61 z61 di t p1 RUNNING A SIMPLE TEST CASE We suppose that you had successfully compiled the model at the end of the previous section and you had used the answers in brackets to the makemeso questions In order to test the compiled executables a ready to use test case with pre generated initial and boundary conditions is proposed in the LMD MM MARS TESTCASE tar gz archive you can download at http www lmd jussieu fr aslmd LMD MM MARS LMD MM MARS TESTCASE tar This test case simulates the hydrostatic atmospheric flow around Arsia Mons during half a sol with constant thermal inertia albedo and dust opacity t Though the simulation reproduces some reasonable features of the mesoscale circulation around Arsia Mons e g slope winds it should not be used for scientific purpose for the number of grid points is unsufficient for single domain simulation and the integration time is below the necessary spin up time 8 User Manual for the LMD Martian Mesoscale Model To launch the test simulation
31. ry adapted to your particular choice of compiler machine The preprocessing tools will also be installed in this directory Please type the following commands cd LMDMOD LMD MM MARS g95 32 single or any install directory ln sf prepare ini prepare ini The script prepare_ini plays with the preprocessing tools an equivalent role as the copy model with the model sources files are simply linked to their actual location in the SRC folder Once you have executed prepare ini please check that two folders were generated PREP MARS and WPS In the PREP MARS directory please compile the programs create readmeteo exe and readmeteo exe using the compiler mentionned in the name of the current installation directory 17 18 User Manual for the LMD Martian Mesoscale Model echo PWD cd PREP_MARS compile or compile_g95 ls lt create_readmeteo exe readmeteo exe cd In the WPS directory please compile the programs geogrid exe and metgrid exe cd WPS configure select your compiler NO GRIB2 option compile ls lt geogrid exe metgrid exe Apart from the executables you just compiled the preprocessing utilities include real exe which was compiled by the makemeso script along with the mesoscale model executable wrf exe real exe should be copied or linked in the simulation directory e g TESTCASE for the Arsia Mons test case to be at the same level than namelist input t Even though the name of the e
32. t mesoscale vertical levels gt mesoscale vertical levels 20 User Manual for the LMD Martian Mesoscale Model The role of the build static script is to automatically download these datasets from the web namely archives and convert them to an acceptable format for a future use by the prepro cessing utilities cd LMDMOD LMD MM MARS build static gt Please install the octave free softward on your system to be able to use the build_static script Another solution is to browse into each of the directories contained within WPS_GEOG download the data with the shell scripts and execute the m scripts with either octave or the commercial software matlab just replace by If you do not manage to execute the build_static script converted ready to use datafiles are available upon request The building of the MOLA 64ppd topographical database can be quite long Thus such a process is not performed by default by the build_static script If the user would like to build this database please remove the exit command in the script just above the commands related to the MOLA 64ppd The resulting WPS_GEOG can reach a size of several hundreds of Mo You might move such a folder in a place with more disk space available but then be sure to create in LMDMOD LMD_MM_MARS a link to the new location of the directory IV 2 1 2 METEOROLOGICAL DATA The preprocessing tools generate initial and boundary conditions
33. xecutable writes e g real x61 y61 z61 di ti pi exe such program is not related to the specific makemeso parameters contrary to the wrf exe ex ecutable We just found that renaming the possibly similar if the model sources were not modified real exe was a practical way not to confuse between executables compiled at different moments IV 2 RUNNING THE PREPROCESSING UTILITIES When you run a simulation with wrf exe the program attempts to read the initial state in the files wrfinput d01 wrfinput d02 one file per domain and the parent domain boundary conditions in wrfbdy 401 The whole chain of data conversion and interpolation needed to generate those files is summarized in the diagram next page Three distinct preprocessing steps are necessary to generate the final files As is described in the previous section some modifications in the namelist input file e g start end dates labelled with p1 requires a complete reprocessing from step 1 to step 3 to successfully launch the simulation whereas other changes e g model top labelled with p3 only requires a quick reprocessing at step 3 keeping the files generated at the end of step 2 the same IV 2 1 INPUT DATA IV 2 1 1 STATIC DATA All the static data topography thermal inertia albedo needed to initialize the model are included in the LMDMOD LMD MM MARS WPS_GEOG directory By default only coarse resolution datasetd are available but the directory also contains sources an
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