Introduction to Unix, DTDM, GrADS. AOSC115/

Transcription

1 Introduction to Unix, DTDM, GrADS AOSC115/

2 Some Unix basics (basis of Linux and Mac OS X) The command prompt is $ (do not type it) Unix commands presented in Courier font $ ls [lists your visible files] $ ls -a [lists all files, including invisible] $ ls -al! [lists all files, includes size & other info] $ pwd [print working directory - shows your location]

3 Some Unix basics (continued) $ mkdir TEST [makes a directory called TEST ] $ cd TEST [changes directory to TEST ] $ cd..! [moves UP in directory hierarchy] $ cd TeST [command should FAIL Unix is usually CASE SENSITIVE though it isn t on Mac]

4 Some Unix basics (continued) $ touch crap.txt [makes an empty file] $ gedit crap.txt!! [invoked Notepad-like text editor on Synoptic Lab machines] [add some text, save file and exit] $ ls -al crap.txt! [see it s there] $ cp crap.txt crap.txt.backup! [make a copy with cp] $ rm crap.txt [the remove command. Asks for confirmation. Don t type y ] $ \rm crap.txt! [remove without confirmation. Think before hitting ENTER!]

5 Some Unix basics (continued) $ mkdir BACKUP [makes a new directory] $ cp crap.txt.backup BACKUP/. [type exactly as written - there is NO space before the period] [the period means keep the same name ] $ ls -al BACKUP/! [see a copy is in the new location] $ mkdir BACKUP/more_backup! [a new subdirectory in a directory] $ cd BACKUP/more_backup [move to new subdirectory] $ cd! $ pwd [cd by itself always takes you to your home directory]

6 Some Unix basics (continued) $ cp /home/fovell/part*. [asterisk is wild card character. There IS a space before the period] [copies all files matching text pattern to your directory] $ ls part* [lists files matching pattern] $ cat part1 part2 > both_parts! [concatenates files] [greater-than sign is output redirect] $ more both_parts! [more lists contents, one screen at a time] [hit space bar for next screenfull, type q to quit]

7 Your Unix PATH $ cp /home/fovell/execute_me. $ execute_me - if you receive execute_me: command not found your PATH needs changing - The PATH is an environment variable that tells Unix where to find stuff, and the order in which to look $./execute_me - this forces Unix to look in the current directory for the program to run

8 Fortran compiler Try this command $ which ifort If you get this we definitely need to alter your Unix environment $ ifort: Command not found!

9 Preparation for new users [for users with bash shell ONLY] $ cd $ mv.bash_profile.bash_profile_old! [mv is move command]![.bash_profile is script file of commands, paths, etc., executed for every new terminal window] $ cat.bash_profile_old /home/fovell/addon2014.sh >.bash_profile [type exactly as shown] [greater-than sign is output redirect] $ source.bash_profile! [changes to script file in present window do not take effect until sourced ] $ which ifort! [see: /opt/intel/composer_xe_ /bin/intel64/ifort ] $ which grads! [see /usr/bin/grads]

10 DTDM on our Synoptic Lab Linux computers Synoptic Lab computers open during business hours ONLY and printing is difficult $ cp /home/fovell/dtdm_package_linux.tar. [note space and period!] $ tar xvf DTDM_package_linux.tar! $ cd DTDM! $ make! [makes the dtdm executable file]

11 Using DTDM $ dtdm < input_thermal.txt! [runs model, makes output] [less-than sign provides contents of txt file to the dtdm executable] $ grads l!! [starts up GrADS; ga-> is GrADS prompt] ga-> open thermal.anelastic! ga-> query file

12 Getting to know GrADS Important commands open [file]!!!open my_experiment! q or query!!!q file, q dims! d or display!!!d theta, d qvapor! c or clear!!!c! set gxout!!!contour, shaded, print, scatter! d u;v!!!![plots vectors! set t 13!!![sets to 13 th time! set cint 1.5!!![contour interval! set ccolor 4!!![contour color blue! printim out.gif gif![makes a GIF plot! set display color white![makes white background**! quit!!!![quits GrADS!! **GrADS 2.1 and later ignores color, so set display white suffices

13 Using DTDM (cont.) File 1 : DTDM demo simulation Descriptor: thermal.anelastic.ctl Binary: thermal.anelastic.dat Type = Gridded Xsize = 99 Ysize = 1 Zsize = 82 Tsize = 11 Number of Variables = 17 u 82 0 horizontal velocity up 82 0 pert horizontal velocity w 82 0 vertical velocity th 82 0 potential temperature thp 82 0 pert potential temperature pi 82 0 ndim pressure pip 82 0 pert ndim pressure ppmb 82 0 pert pressure in millibars pbyc 82 0 buoyancy pressure in millibars pdyn 82 0 dynamic pressure in millibars ptot 82 0 total pressure in millibars dudtd 82 0 U acceleration - dynamic dudtb 82 0 U acceleration - buoyancy dudtt 82 0 U acceleration - total dwdtd 82 0 W acceleration - dynamic dwdtb 82 0 W acceleration - buoyancy dwdtt 82 0 W acceleration - total running dtdm model created two new GrADS files: thermal.anelastic.ctl! thermal.anelastic.dat contents of thermal.anelastic.ctl shown at left!

14 ga-> set t 6 ga-> start.gs ga-> d thp

15 ga-> c ga-> set black 0 0 ga-> d thp

16 ga-> d ppmb [Note zero contour is back ]

17 ga-> c ga-> set ccolor 1 ga-> d pbyc

18 ga-> c ga-> set ccolor 4 ga-> d pdyn

19 GrADS default color sequence

20 ga-> c ga-> set ccolor 2 ga-> d w*100

21 ga-> c ga-> set gxout shaded ga-> d w ga-> scripts/cbarn.gs ga-> set gxout contour ga-> set ccolor 1 ga-> d dwdtt dwdtt is Lagrangian dw/dt, not Eulerian w/ t

22 ga-> set t 9 ga-> c ga-> d u;w

23 ga-> c ga-> d skip(u,2,3);w Control vector length with set arrscl ! [standard length set to 20 m/s]

24 ga-> c ga-> q dims ga-> set x ga-> set xaxis ga-> d skip(u,2,3);w Zoom in

25 ga-> draw xlab x (km) ga-> draw ylab height (km) ga-> draw title EXP01 uw t=9 ga-> printim example01.gif gif Outside of GrADS, can display images using display!

26 scripts/thermal.gs 'set mproj off' 'set display color white' 'clear' 'set grads off' 'scripts/rgbset.gs' * plot w 'set x 30 70' 'set gxout shaded' 'set clevs ' 'set ccols ' 'd w' 'scripts/cbarn.gs' 'set gxout contour'

27 ga-> set t 6 ga-> scripts/thermal.gs

28 Three important commands ga-> reset! resets GrADS environment to starting conditions Time dimension set to 1 st time, gxout to contour, etc.. Does not close open files. ga-> reinit! resets AND closes all open files. All but quit. ga-> quit!

29 Running another case $ gedit! [edit input_thermal.txt] [change casename, ianelastic, csnd]! &experiment! casename = 'thermal.nonanelastic.30',! $!! &framework! ipressure = 1,! ianelastic = 0,! csnd = 30.,! $!!! $ dtdm < input_thermal.txt!

30 Multiple files with GrADS $ grads l!! ga-> open thermal.anelastic! ga-> open thermal.nonanelastic.30 When multiple files are open, append file number to variable name: e.g., d thp.2!

31 ga-> start.gs ga-> set t 11 ga-> scripts/thermal.gs ga-> set gxout contour ga-> set ccolor 1 ga-> set cthick 8 ga-> set cint 0.1 ga-> d ppmb.1-ppmb.2

32 Animations made painless ga-> step.gs thp Plots field thp! for steps through times 1 through 11, inclusive with contour interval 1.0 hit return to proceed to the next time

33 ga-> c ga-> set x 50 ga-> set z 1 ga-> set t 1 11 ga-> d max(w,z=1,z=82) ga-> set ccolor 4 ga-> d max(w.2,z=1,z=82) Time series plots

34 ga-> c ga-> set x 50 ga-> set z 1 82 ga-> set t 1 11 ga-> d thp Hovmoller plots

35 More on GrADS image output ga-> printim image01.png ga-> printim image01.jpg jpg! ga-> enable print image01.m! ga-> print! ga-> disable print GrADS 2.1 simplifies all of this Once a *.m file is created, it can be converted (outside of GrADS) to a postscript or eps file! $ gxps c i image01.m o image01.ps! $ gxeps c i image01.m o image01.eps!!

36 Final cautions Make backups This command runs the model $ dtdm < input_thermal.txt This command destroys the input file! $ dtdm > input_thermal.txt!!

37 Advice Don t ask what s the least you can do for me. Instead, ask what s the most you can do for yourself.