Delft3d-FLOW Quick Start Manual

Transcription

1 Delft3d-FLOW Quick Start Manual Michael Kliphuis April 2, Introduction Delft3D-FLOW is a multi-dimensional (2D or 3D) hydrodynamic (and transport) simulation program which calculates non-steady flow and transport phenomena that result from tidal and meteorological forcing on a rectilinear or a curvilinear, boundary fitted grid. Chapter two describes how to start a parallel Delft3d-FLOW run on a cluster like Cartesius and chapter three how to plot the results of a run with Matlab. We discuss specific scripts and a handy application called QUICKPLOT. 2. Start a Delft3d-FLOW run This chapter describes how to quickly setup and start a Delft3d-FLOW run. As an example we take a low resolution (approximately 200m) run that simulates the Lake Garda in Italy on the dijkbio login on Cartesius. 2.1 Log in to Cartesius ssh X dijkbio@cartesius.surfsara.nl with password: ****** you know it, I better not mention it because this document will be on my website All the needed files to start a run are on Cartesius* on the dijkbio login in the directory: /projects/0/samoc/henk/delft3d/garda/f2004/200m/scripts/run_template If you want to start a new run to test parameters, e.g. let s call it lg_run1 then type: cd /projects/0/samoc/henk/delft3d/garda/f2004/200m/scripts cp r run_template lg_run1 cd lg_run1 then in run.sh change the line * If you want to run it on another login on Cartesius or on another machine please contact Michael Kliphuis (m.kliphuis@uu.nl)

2 cd /projects/0/samoc/henk/delft3d/garda/f2004/200m/scripts/run_template into cd /projects/0/samoc/henk/delft3d/garda/f2004/200m/scripts/lg_run1 If needed change any of the parameters in the file g2004.mdf check the meaning of the parameters via the manual After that you are ready to start the run. 2.2 Start run (in the batch queue) 1. cd /projects/0/samoc/henk/delft3d/garda/f2004/200m/scripts/lg_run1 2. Open the MDF file g2004.mdf Determine the reference start date of the run. e.g. set it to: Itdate = # # Set the restart file from which you want to restart from. We did a spinup run of 5 modelyears and we want to start from its last restart file trim-y2008_21jun-31dec_f2004.dat containing all modeldays from 21 jun dec2008. Restid = #trim-y2008_21jun-31dec_f2004# Suppose you want to run for 1 extra modelyear. Then set the start time 'Tstart' of your run as follows. Since the value of 'Tunit' is #M# which means minutes, set it to: Tstart = In this example we want to start on the last day of the spinup run so at the last day of the restart file Restid = trim-y2008_21jun-31dec_f2004. The name is a bit misleading but this is actually 1 jan 2009 = day 1827 with respect to Itdate = 1 jan 2004 (366*2 + 3*365 = 1827). So the start minute Tstart = 1827*60*24= Set the stop time 'Tstop' of your run 1 modelyear later. Since the value of 'Tunit' is #M# which means minutes, set it to: Tstop = Tstop is the last day of year 2009 =( )*60*24= Note that year 2004 and 2008 are leap years Set the frequency of writing 3D output like temperature and velocities to a so called map file (in this case trim-g2004.dat) e.g. set it to:

3 Flmap = which means start writing at minute 0 and stop at minute (Tstop) with a time interval of every 1440 minutes. In other words write to the trim file every model day. Set the frequency of writing 2D output like temperature and velocities in certain observation points (set in file obspoints_unitn_62x222.obs in table 1 above) to a so called history file (in this case trih-g2004.dat) e.g. set it to: Flhis = which means start writing at minute 0 and stop at minute with a time interval of every 60 minutes. In other words write to the trim file every model hour. Set the frequency of writing a restart file (in this case for instance trirst.g ) e.g. set it to: Flrst = Open the file run.sh which means write every minutes (30 model days). In fact these restart files are not used, we use the trim*dat files (also possible). Perhaps we can just leave this empty then??? These were the main keyword settings but there are many more keywords you can set in the MDF file. For a complete list go to section A.1.2 on page 417 of the user manual at FLOW_User_Manual.pdf Set the number of cores you want to run on, e.g. set it to 32: #SBATCH -n 32 Set the name of the job, e.g. set it to 200m_garda: #SBATCH -J 200m_garda Reserve time for running this job in the batch, e.g. reserve 30 hours. #SBATCH -t 30:00:00 Make sure this is long enough for the job to finish. If it finishes sooner then this is no problem. The higher you set this value the longer it can take for a job to get picked up. 4. Start the job by submitting it to the batch queue by typing: sbatch run.sh

4 5. Check the status of the job by typing: mysqueue (this is an alias for squeue -u dijkbio -u to denote the login you work on is dijkbio) you then see for instance: JOBID PARTITION NAME USER TIME_LIMIT START_TIME ST TIME NODES NODELIST(REASON) broadwell 200m_g dijkbio 4-00:00: T14:28:34 R 10:50 1 tcn921 which means that the job has jobid , it is running on a broadwell node and has name 200m_g. It is reserved to run for 96 wallclock hours (4 wallclock days), it started on 22 May 2017 at 14:28:34, it has status (ST) running (R) and it is already running for 10m 50s on 1 node namely node tcn921. If you want to stop the run then type: scancel Check how far the run is by opening the file slurm out. I usually type: tail -f slurm out 2. Finally AND THIS IS VERY IMPORTANT! When the run is finished rename the outputfiles: trih-g2004.dat trih-g2004.def trim-g2004.dat trim-g2004.def If you do not do this then starting the run again or restarting it from another restartfile will overwrite these files and you lost all data. I usually run for 1 modelyear e.g. year 2009 and when the run is done I type: mv trih-g2004.dat trih-y2009_f2004.dat mv trih-g2004.def trih-y2009_f2004.def mv trim-g2004.def trim-y2009_f2004.def mv trim-g2004.dat trim-y2009_f2004.dat cp g2004.mdf g2004.mdf_y2009 After that you can restart the run to simulate year 2010 by setting in g2004.mdf Tstart = Tstop = Restid = #trim-y2009_f2004# The next section describes all the files in the run directory that are needed for the run

5 2.3 More info on the needed files The table below shows all the files (and information about them) in directory run_template (and pm_run1) These files are needed in order to run this/a Delft3d-FLOW run: g2004.mdf Gardagrid_unitn.grd Gardagrid_unitn.enc benaco_ dep drypoints_unitn.dry obspoints_unitn_62x222.obs _interp.amc _interp.amp _interp.amr _interp.amt _interp.amu _interp.amv _interp.ams 2004_interp.grd config_d_hydro.xml run.sh the so called Master Definition Flow file (MDF-file) which contains all information to execute a flow simulation. It is the main input file in which a user sets the time step, the start and stop time, used parametrizations etc. but also the name of the grid file (.grd), bathymetry file (.dep), the forcing files containing the atmospheric wind forcing (.amu and.amv) and all other files in this table. Here it is called g2004.mdf because it starts a run that is forced with a year 2004 atmospheric forcing grid file grid enclosure file bathymetry file indices of dry points file observation points file air cloudiness forcing file 7 years all containing forcing of year 2004 atmospheric pressure forcing file 7 years all containing forcing of year 2004 relative air humidity forcing file 7 years all containing forcing of year 2004 air temperature forcing file 7 years all containing forcing of year 2004 wind speed in East direction forcing file 7 years all containing forcing of year 2004 wind speed in North direction forcing file 7 years all containing forcing of year 2004 Solar radiation forcing file 7 years all containing forcing of year 2004 forcing grid file (set in the 7 forcing files above) config file expected as argument for Delft3d-FLOW executable d_hydro.exe. It contains the name of the MDF file (in this case g2004.mdf) script to start the run in the batch on Cartesius Making the grid (.grd) and enclosure (.enc) files is done with the Delft3d application RGFGRID. The bathymetry (.dep) file is made with Delft3d application QUICKIN. The way to do this is not in the scope of this document. The following manuals show how:

6 3. Analyse and plot the results Running Delft3d-FLOW with the.mdf file above will generate 3D map files: and 2D history files: trim-g2004.dat trim-g2004.def trih-g2004.dat trih-g2004.def The.dat files contain the actual data, the.def files contain metadata info like size and description of the variables which are in specific format and can be read with MATLAB. 3.1 with QUICKPLOT The easiest way to check the variables is with a MATLAB application called QUICKPLOT. You do this as follows: 1. cd /projects/0/samoc/henk/delft3d/garda/f2004/200m/matlab 2. type: module load matlab 3. type: matlab 4. In the Matlab command window type: d3d_qp Don t worry about all the WARNINGS you will get! You will soon see the following window:

7 5. Then select an input file by clicking on File followed by Open File and select for instance the map output file one directory up in../scripts/lg_run1 called trim-g2004.dat as shown in the figure below: 6. Standard the selected variable is 'morphological grid'. Select one of the many other variables for instance 'temperature'

8 7. This variable is valid for all 100 depth values. If you only want to see the temperature flux in the highest level (100) then deselect the 'all' box and set value 100 as shown in the figure below: 8. Then plot the 'temperature' by clicking the button 'Quick View' righ below. You then get a new window showing the plot.

9 You can loop to other time frames by clicking on the < or > of the slide left below in the figure above. For more information about the use of QUICKPLOT check its manual at: with myscripts Another way to check the results is with some MATLAB scripts written by Marina, Sebastiano and Michael to plot basic things like: 1. Timeseries of for instance the mean SST or mean volume temperature 2. X-Y grid plots of variables like the temperature anomaly with respect to the mean with in the background arrows showing the value and direction of the wind or water flow. 3. X-Z (or Y-Z) grid transect plots of variables like temperature, zonal velocity U (meridional velocity V) etc along a transect going from the West to the East (or South to North) side of the lake. Below we will analyse a 10 year long 200m resolution lake Garda run with a realistic atmospheric forcing for years Usually a delft3d run generates multiple output files. This particular run generated the following three so called trim files in the directory: /projects/0/samoc/henk/delft3d/garda/f /200m/scripts/lg_run - trim-1jan mar2008_f dat - trim-13mar2008-1jan2011_f dat - trim-1jan dec2013_f dat

10 For postprocessing it is not handy to have the data in multiple files. We decided to make a script data_extractor.m that extracts layers and transects from multiple outputfiles like the three above and puts it in one file Extract layers and/or transects 1. type: module load matlab 2. type: cd /projects/0/samoc/henk/delft3d/garda/f /200m/matlab/myscripts Before you decide to extract a certain transect make sure that the transect is a continuous line without interuptions going from the east to the west side or from the south to the north side of the lake. Remember that this 200m resolution run is defined on M x N = 64 x 224 gridpoints. The south to north transects are so called M transects (M Î [0,64]) The east to west transects are so called N transects (N Î [0,224]) 3. With the script show_transect.m you can check if a transect is continuous. Open this script and set for instance: IDtransect = 'n13'; plotid = 'transect_n13_long_lg_run_y2013'; Then type: matlab -nosplash -noawt show_transect.m This generates an image file: transect_n13_long_lg_run_y2013_position.png (open with command: display)

11 As you can see the line N=13 is not continuous. But for instance N=100 is OK! Also transect M=23 is OK 4. Ok suppose we are interested in: layers 99 and 100 and transects M=23 and N=100 Then open script data_extractor.m and set:

12 flag_grid=1; flag_transect = 1; transectsm = [23]; transectsn = [100]; flag_layer = 1; layer = [ ]; 5. Then type: Plot timeseries matlab -nosplash -noawt < data_extractor.m This will extract the variables u,v,w,t,nuz and windu and windv on the requested layers and transects. The data will be extracted for all modeldays of the simulation, in this case 3653 days and put in underlying directory extracted/. The script also extracts the used grid (X, Y, Z, bathymetry) that was used for this run. Most of the plot scripts mentioned below need this grid file. Extracting the grid and layers does not take so long but extracting just one transect can take up to 45 minutes! Fortunately many of the layers and transects are already extracted, just check in directory extracted/ which ones you can use. If more or other variables are needed the user can change the scripts f_extract_layer.m f_extrac_transectm.m f_extract_transectn.m that are being called by data_extractor.m 6. Now plot the timeseries of the mean SST of the lake for all the generated years For this purpose we need file layer100_long_lg_run_y _days mat which was generated in previous step 5. Then type: matlab -nosplash -noawt < plot_tseries_sst.m This generates an image file: tseries_mean_sst_long_lg_run_y png (open with command: display)

13 3.2.3 Plot layers 7. Now let us plot data on layer 100. More specific, make an X-Y grid plot of the mean year 2013 (last year of the simulation) ) temperature anomaly with respect to the Lake mean temperature on the surface layer 100 with in the background arrows showing the value and direction of the wind or water flow. For this purpose we (again) need file layer100_long_lg_run_y _days mat which was generated in step 5. Then open script: plot_layer.m And set: file = 'layer100_long_lg_run_y _days mat' grid = 'grid_long_lg_run_y mat' plotid = 'wind_and_flow_layer100_long_lg_run_y2013' Also in order to average over year 365 set: % define the time window to average the data over % order in datenum below = datenum(y,m,d) date1=datenum([ ]); date2=datenum([ ]); % for some reason last day does not work It is ofcourse also possible to average over other years or for instance the month March or September of a specific year. 8. Then type: matlab -nosplash -noawt < plot_layer.m

14 This generates an image file: wind_and_flow_layer100_long_lg_run_y2013.png (open with command: display) Plot transects 9. Now let us make some X-Z (and Y-Z) grid transect plots of variables like temperature and zonal velocity U (meridional velocity V) along a transect going from the West to the East (or South to North) side of the lake. Again we want to plot mean values of year 2013 (last year of the simulation). We first plot it for transect N=100 discussed in step 3. For this purpose we need file n100_long_lg_run_y _days mat which was generated in step 5. Then open script: plot_transectn.m And set: file = 'n100_long_lg_run_y _days mat' IDtransect = 'n100';

15 plotid = 'transect_n100_long_lg_run_y2013'; % define the time window to average the data over % order in datenum below = datenum(y,m,d) date1=datenum([ ]); date2=datenum([ ]); % for some reason last day does not work 10. Then type: matlab -nosplash -noawt < plot_transectn.m This generates 5 image files: transect_n100_long_lg_run_y2013_position.png transect_n100_long_lg_run_y2013_v.png transect_n100_long_lg_run_y2013_t.png transect_n100_long_lg_run_y2013_dt.png transect_n100_long_lg_run_y2013_dtnorm.png (open with command: display) The first one is the same plot as can be made by show_transect.m discussed in step 3 and it shows the position of the transect. The plots are shown below:

16 And below the anomaly with respect to the mean

17 Next is the anomaly above normalized relative to Tmean

18 11. Finally let us make the same plots for transect M=23 discussed in step 3. For this purpose we need file m23_long_lg_run_y _days mat which was generated in step 5. Then open script: plot_transectm.m And set: file = 'm23_long_lg_run_y _days mat' IDtransect = 'm23'; plotid = 'transect_m23_long_lg_run_y2013'; % define the time window to average the data over % order in datenum below = datenum(y,m,d) date1=datenum([ ]); date2=datenum([ ]); % for some reason last day does not work 12. Then type: matlab -nosplash -noawt < plot_transectm.m This generates 5 image files: transect_m23_long_lg_run_y2013_position.png transect_m23_long_lg_run_y2013_v.png transect_m23_long_lg_run_y2013_t.png transect_m23_long_lg_run_y2013_dt.png transect_m23_long_lg_run_y2013_dtnorm.png (open with command: display) The first one is the same plot as can be made by show_transect.m discussed in step 3 and it shows the position of the transect. The plots are shown below:

19

20 And below the anomaly with respect to the mean Next is the anomaly above normalized relative to Tmean