Embed Size (px)
Citation preview
CESM1.2Tutorial:BasicModifica7ons
SusanBatesMaterialfrom:Chris4neA.Shields
August9,2016
CESM1Tutorial:BasicModifica7ons:Review
1. WewillusetheCESMcodelocatedlocallyonyellowstone,noneedtocheckoutordownloadanyinputdata.
2.Wewillrunwithresolu4onT31_gx3v7.3. Defaultscriptswillautoma7callybeconfiguredforyouusingthecode/script
baseprepareduniquelyforthistutorial.
4. Pleaselogintoyourassignedyellowstone(orcaldera/geyser)nodeanddoNOTcompileunlessyouhaveacompilecard.Tomakethetutorialrunsmoothlyforall,weneedtocontrolanddistributeallworkevenlyacrossyellowstone.
TutorialCodeandscriptbase:
/glade/p/cesm/tutorial/cesm1_2_2.tutorial
Thistutorialcontainsstepbystepinstruc7onsapplicabletothecurrentrelease(cesm1.2)only.
Forolderreleases,pleaseseepasttutorials.Forinforma7onournextrelease,pleaseaHendtoJimEdwardspresenta7onWednesdayat1:05pm:“CESM2:Whattoexpect”
create_newcase requires 4 arguments
create_newcase –case case01 –res T31_g37 -compset B_1850_CN -mach yellowstone
case01 yellowstone B_1850_CN T31_gx3v7
What is the casename ?
Which resolution?
Which model configuration ? Which set of components ?
Which machine are you running on?
CESM1Tutorial:BasicModifica7ons:Review:Crea7nganewcase
courtesy: c.hannay
Grid naming convention Each model resolution can be specified by its alias, short name and long name. Example of equivalent alias, short name and long name: - alias: T31_g37 (atm/lnd_ocn/ice) - short name: T31_gx3v7 - long name = a%T31_l%T31_oi%gx3v7_r%r05_m%gx3v7_g%null_w%null
atm lnd ocn/ice river lnd mask
lnd-ice wave
Compset naming convention Each model compset can be specified by its alias, short name and long name. Example of equivalent alias, short name and long name: - alias: B1850CN - short name: B_1850_CN - long name = 1850_CAM4_CLM40%CN_CICE_POP2_RTM_SGLC_SWAV
Time Period Model Physics submode “S”=stub/inactive
courtesy: c.hannay
CESM1Tutorial:BasicModifica7ons:Review:Crea7nganewcase
EXERCISE.0:Logintoyourassignednode.(Haveyoucopiedthegeyser.csh/caldera.cshscripttoyourhomedirectory)?Createandconfigureanout-of-the-boxsetofscriptscalled“b.day2.0”onyellowstoneusingT31_gx3v7andcompsetB_1850_CN.Buildandrunthemodel.
Explana4onofsteps:1. Changedirectories,(“cd”)totutorialcodebasescriptsdirectory.2. Viewcompsetandgridchoices.(hint:use–listop4on)3. Createini4alscripts.(Wewillusethesame“cases”subdirectoryasday1).4. “cd”toyourcasedir.5. Invokecesm_setup.6. Buildthemodel.7. Submita5-daytest.8. “cd”toyourrun4medirectoryandexplore
CESM1Tutorial:BasicModifica7ons:Review:Crea7nganewcase
EXERCISE.0:Createandconfigureanout-of-the-boxsetofscriptscalled“b.day2.0”onyellowstoneusingT31_gx3v7andcompsetB_1850_CN.Buildthemodel.
1. cd/glade/p/cesm/tutorial/cesm1_2_2.tutorial/scripts2. ./create_newcase–listcompsets(and–listgrids)3. ./create_newcase-case~/cases/b.day2.0-resT31_gx3v7-mach
yellowstone-compsetB_1850_CN4.cd~/cases/b.day2.05../cesm_setup6. ./b.day2.0.build7../b.day2.0.submit8.cd/glade/scratch/$LOGNAME/b.day2.09.Aberthejobcompletes,explorethe“4ming”subdirectoriesinbothyour
scratchspaceandinyourcasedirectory.Explorethe“logs”subdirectoryinyourcasedirectory.
CESM1Tutorial:BasicModifica7ons:Review:QueuesandJobs
1. Submidngjobs:Type$CASE.submiti.e.b.day2.0.submit
2. Checkingjobs:a.Typebjobsorb.Typebjobs-ualltoseeeveryone’sjobs,or
3.Killingjobs:a.FindyourJOBIDabertypingbjobsb.Typebkill<JOBID>
Yellowstone
CESM1Tutorial:BasicModifica7ons:Review:README
Inyourcasedirectory,inaddi4ontoyourscripts,youwillfindautoma4callygenerateddocumenta4onfiles.
1. README.science_support:refersyoutotheon-line
documenta4on.2. README.casefile:detailedinforma4ononyourcompsetand
grid,includingwhetheryourconfigura4onhassciencesupport.
SCIENCE_SUPPORT:NO
README.case, we highly recommend YOU document any changes you make to the default scripts. It is YOUR paper trail and opportunity to list modifications.
1. Thecreate_cloneu4litycreatesanEXACTcopyofapreviouslycreatedcase.
2. Thecreate_cloneu4lityisveryhandywhentheuserwishestorunaslightlymodifiedversionofapreviousexperiment.
a.Invokecreate_clonetocreateanexactcopyofanoldcasebytypingthefollowingonthecommandline:
create_clone-case<newcase>-clone<casetoclone>
b.Implementdesiredmodifica4onsbeforebuildingandrunning.(Wewilllearnnumerouswaytomodifythescriptsduringthispresenta4on).
c.EditandDOCUMENTchangesinREADME.case
CESM1Tutorial:BasicModifica7ons:Review:create_clone
EditandDOCUMENTchangesinREADME.case.
OtherwiseyourREADME.casefilewilllookexactlylikeyouroriginalcaseanditwillbemuchhardertobacktrackyourmethodswhentroubleshoo4ng.
CAVEATSforCREATE_CLONE:youneedtouse….1)samemodeltag2)samemachine3)samecompset4)sameresolu7on5)samerun-type(slide20)
CESM1Tutorial:BasicModifica7ons:Review:create_clone
CESM1Tutorial:BasicModifica7ons:Pre“cesm-setup”files-rwxr-xr-x1shieldsncar15789Jun717:33archive_metadata.shdrwxr-xr-x2shieldsncar16384Jun2516:11Buildconf-rw-r--r--1shieldsncar162Jun2516:11CaseStatus-rwxr-xr-x1shieldsncar14495Jun717:33cesm_setup-rwxr-xr-x1shieldsncar837Jun717:33check_case-rwxr-xr-x1shieldsncar10126Jun717:33check_input_data-rwxr-xr-x1shieldsncar3672Jun717:33create_produc4on_test-rw-r--r--1shieldsncar10841Jun2516:11env_build.xml-rw-r--r--1shieldsncar4441Jun2516:11env_case.xml-rw-r--r--1shieldsncar6992Jun2516:11env_mach_pes.xml-rwxr-xr-x1shieldsncar2678Jun2516:11env_mach_specific-rw-r--r--1shieldsncar23069Jun2516:11env_run.xmldrwxr-xr-x2shieldsncar16384Jun2516:11LockedFiles-rwxr-xr-x1shieldsncar2127Jun2516:11preview_namelists-rw-r--r--1shieldsncar1630Jun2516:11README.case-rw-r--r--1shieldsncar380Jun2516:11README.science_supportdrwxr-xr-x11shieldsncar16384Jun2516:11SourceMods-rwxr-xr-x1shieldsncar13233Jun2516:11b.day2.1.build-rwxr-xr-x1shieldsncar1048Jun2516:11b.day2.1.clean_build-rwxrwxr-x1shieldsncar947Jun2516:11b.day2.1.l_archive-rwxr-xr-x1shieldsncar608Jun2516:11b.day2.1.submitdrwxr-xr-x3shieldsncar16384Jun2516:11Tools-rwxr-xr-x1shieldsncar12569Jun717:33xmlchange-rwxr-xr-x1shieldsncar10503Jun717:33xmlquery
ENV Files Tools Case Scripts Documentation Buildconf scripts (do not modify) SourceMods (day 4 of tutorial)
drwxr-xr-x2shieldsncar16384Jun2516:18CaseDocs-rw-r--r--1shieldsncar9Jun2516:18hosaile-rw-r--r--1shieldsncar949Jun2516:18Macros-rwxr-xr-x1shieldsncar10287Jun2516:18b.day0.1.run
-rw-r--r--1shieldsncar115Jun2516:18user_nl_cam -rw-r--r--1shieldsncar367Jun2516:18user_nl_cice -rw-r--r--1shieldsncar1257Jun2516:18user_nl_clm -rw-r--r--1shieldsncar2284Jun2516:18user_nl_cpl -rw-r--r--1shieldsncar2949Jun2516:18user_nl_pop2 -rw-r--r--1shieldsncar573Jun2516:18user_nl_rtm
CESM1Tutorial:BasicModifica7ons:Post“cesm-setup”files
ENV Files Tools Case Scripts Documentation Buildconf scripts (do not modify) SourceMods (day 4 of tutorial) Namelist modifications
All case modifications are applied in env_run.xml or user_nl_<model>
CESM1Tutorial:BasicModifica7ons:Edi7ngMethods/Tools
Whenmodifyingfiles,theuserisfreetouseher/hiseditorofchoice,i.e. vi emacs
Whenmodifying“xml”files,theusermayalsousethetool,xmlchange.1. Forhelp,typexmlchange-help2. Example:Singlevariablemodifica7on,original(long)method:
Youwanttomanuallyresubmitanini4alcasethatpreviouslyhadaRESUBMITvalueof0,(i.e.youdidnotini4allyresubmittherun).
Editenv_run.xmlviathexmlchangetool,type./xmlchange-fileenv_run.xml-idCONTINUE_RUN-valTRUE
CESM1Tutorial:BasicModifica7ons:Edi7ngMethods/Tools
Forhelp,typexmlchange-help
3. Example:Mul7ple(orlist)variablemodifica7onmethod:*:
Youmaywanttochangemorethanoneitemata4me,ortousethisabbreviated“list”methodforasinglemodifica4on.Tomanuallyresubmitthemodel,plustellthescriptstoautoma4callydothistwicemore…
a.Editenv_run.xmlviathexmlchangetool,type
./xmlchangeCONTINUE_RUN=TRUE,RESUBMIT=2*Noteformostcomponentnamelistvariables,thesinglemodifica4onmethodis
necessary.(moreonthislater).
CESM1Tutorial:BasicModifica7ons:Run7mevariables:env_run.xml
Run4mevariablescanbechangedinenv_run.xmlatanypointduringtherunandcontrolthemechanicsoftherun,i.elength,resubmits,andarchiving.
Commonvariablestochangeinclude
1.RESUBMITàsetsthenumberof4mestoresubmittherun
2.STOP_OPTIONàsetstherunlength4meintervaltype,i.e.nmonths,ndays,nyearsoraspecificdate
3.STOP_Nàsetsthenumberofintervals(setbySTOP_OPTION)torunthemodelduringthespecifiedwallclock4me.Wallclock4meissetinyour*.runfileandisameasureoftheactual4me.
STOP_OPTIONandSTOP_Ncontrolthelengthoftherunpercomputerjobsubmission.Atypicalsimula4oniscomprisedofmanyjobsubmissions.(Youcanonlystayinthecomputerqueueforaspecified4me.Thisqueue4melimitisobenshorterthanthedesiredsimula4onlength.
CESM1Tutorial:BasicModifica7ons:Run7mevariables:env_run.xml
1.RESUBMITàsetsthenumberof4mestoresubmittherun2.STOP_OPTIONànmonths,ndays,nyearsoraspecificdate3.STOP_Nàsetsthenumberofintervals(setbySTOP_OPTION)torun
Ques4on:ThespecialtutorialversionofT31_gx3v7CESMonyellowstone(runsonmul4plenodes)simulates~44modelyearsperwallclockday.
Maximumwallclockrequestsis12hours.
Ifyouwanttorun100years,whatvaluesshouldbesetforSTOP_OPTION,STOP_N,andRESUBMIT?
CESM1Tutorial:BasicModifica7ons:Run7mevariablesenv_run.xml
Ques4on:Ifyouwanttorun100years,whatvaluesshouldbesetforSTOP_OPTION,STOP_N,andRESUBMIT?Answer:Assume2jobssubmissionsperday,(212-hrjobs).Modelruns44yrs/day,so44/2=22modelyearsperjobsubmission.Ifwerounddownto20modelyrs/submissiontogiveourselvesabufferandhave
evennumbers….
STOP_OPTION=nyears,STOP_N=20,RESUBMIT=4Ini7alrunof20yrs+(4resubmits*20yearsperjob)=100years
CESM1Tutorial:BasicModifica7ons:Run7mevariablesenv_run.xml
env_run.xmlcon4nued…morecommonrun4mevariablestochangeinclude
4.CONTINUE_RUNàifTRUE,impliesaCONTINUErun.Note:ifRESUBMITis>0anditisanini4alrun(i.e.CONTINUE_RUN=FALSE),
CONTINUE_RUNwillautoma4callyupdatetoTRUEuponcomple4onofini4alrun.
5.INFO_DBUGàsetslevelofstdout(standardout)printstatements.Ifdebugging,ahighervaluemaybeset.
6.DOUT_Sàturnsonshort-termarchiving.DOUT_SisTRUEbydefault.
7.HIST_OPTIONàcouplerhistoryfilespecifica4on.Note:Allothermodelcomponentsspecifyhistoryfileinforma4onwithinthemodelcomponentnamelists!(Moreonnamelistsinafewslides).
Takesome4metoreviewallotherenv_run.xmlsedngs….
CESM1Tutorial:BasicModifica7ons:Run-typevariables:env_run.xml
Run-typevariablesdefinetypeofrun(startup,hybrid)andphysicalcontrols(namelistparameters).Samplevariablesspecifiedinthisfileinclude:
1.RUN_TYPEàstartup,hybrid,branch2.RUN_REFCASEàifbranch/hybrid,casenameyouarestar4ngfrom3.RUN_REFDATEàif““,datestampofreferencecaseyouarestar4ngfrom4. GET_REFCASEàdefault=TRUE;automa4callyretrievesrefcaserestartdata;
assumesrefcaseisonHPSS
5.CCSM_CO2_PPMàCO2valuetobepropagatedtoCAMandCLM
6.CAM_NAMELIST_OPTSàCAMnamelistop4onsthatdifferfromdefaultvalues7.CLM_NAMELIST_OPTSàCLMnamelistop4onsthatdifferfromdefaultvalues8.CICE_NAMELIST_OPTSàCICEnamelistop4onsthatdifferfromdefaultvalues9.RTM_NAMELIST_OPTSàRTMnamelistop4onsthatdifferfromdefaultvalues
CESM1Tutorial:BasicModifica7ons:Run-typevariablesenv_run.xml
CESMhasfour“types”ofruns:
STARTUP: Allmodelcomponentsareini4alizedfrombasicdefaultini4al condi4ons.
HYBRID: -Theatmosphereandlandareini4alizedfromini4alcondi4on filesgeneratedbyauser-specifiedCESMsimula4on.
-Theoceanandiceareini4alizedfromrestartfilesgeneratedbya user-specifiedCESMsimula4on.
-Ini4alcondi4onsandrestartfilesusethesamereferencecase andreferencedate.
BRANCH: Allmodelcomponentsareini4alizedfromrestartfilesgenerated byauser-specifiedCESMsimula4on.
CONTINUE: Con4nua4onrunsforallruntypes.
DefaultT31_gx3v7casesusingcompsetB_1850_CN(INCLUDINGOURTUTORIAL)areHYBRIDrunsthatareini7alizedfromtheCESM1T31x31850Control.
CESM1Tutorial:BasicModifica7ons:Run-typevariables:BranchvsHybrid
Branchandhybridrunsareusefulifyouhaveanexperimentwhichonlyslightlydiffersfromyourcontrol,butyouwanttomakeaslightmodifica4on,addhistoryoutput,orstartyoursimula4onfromaCESMspun-upini4alstate.
YourdefaulttutorialexercisesstartasahybridrunfromtheCCSM4T31_gx3v7control1850simula4on.
Useahybridrun:formostapplica4onswhereyoudoNOTneedbitforbitrestart.YouCANspecifyanewstartdateforyourmodelrun.Usebranchrun:onlyforapplica4onswhichrequireexactrestart.YouCANNOTspecifyanewstartdateforyourmodelrun.Itwillbeassignedbythereferencecase(RUN_REFDATE).
Namelistvariablescanbechangedusing:env_run.xmloruser_nl_<model>(e.g.user_nl_cam,user_nl_pop2,etc)
CAM,CLM,CICE,RTMnamelistvariablescanbechangedusingbothmethods.POP,CPLcanbeonlychangedusingtheuser_nl_<model>method.Foracompletelistofnamelists,pleaseseetheon-linedocumenta4onforeach
componentmodel.hxp://www.cesm.ucar.edu/models/cesm1.2/cesm/doc/modelnl/modelnl.html
CESM1Tutorial:BasicModifica7ons:Namelistvariables
CESM1Tutorial:BasicModifica7ons:env_run.xml
EXERCISE.1:Createanewfullycoupled(withCN)hybridcasefrom1850condi4ons,butdoubletheCO2valuesandturnontheicerunoffintheRTMmodel.Increasetheamountofstandardoutproducedbythemodelandchangethedefaultloca4onforthelogfilestoadirectoryon/glade/scratch.Run2months.
1. fromscriptsdirectory,createyourcasescripts:./create_newcase-case~/cases/b.day2.1-resT31_gx3v7-machyellowstone-compsetB_1850_CN
2. fromcasedirectory,changeyourrun4mevariables:./xmlchangeINFO_DBUG=2,STOP_N=2,STOP_OPTION=nmonths
3. vi(oremacs)env_run.xmltochangeLOGDIRto/glade/scratch/$CCSMUSER/logs/$CASE,or
./xmlchange-fileenv_run.xml-idLOGDIR-val‘/glade/scratch/$CCSMUSER/logs/$CASE‘(notethatsinglequotespreventevalua4onofenvironmentvariables)
Con4nuednextpage
CESM1Tutorial:BasicModifica7ons:env_run.xml
EXERCISE.1con7nued:
4. Makeyourphysicsnamelistchanges:a.Usethelistmethod:./xmlchangeCCSM_CO2_PPMV=569.4b.Usetheoriginalmethod:./xmlchange-fileenv_run.xml-idRTM_NAMELIST_OPTS-valice_runoff=.true.
5. ./cesm_setup
6. ManuallyupdateyourREADME.casefiletodocumentyourchanges
7../b.day2.1.build
8. Reviewb.day2.1.run:a)#BSUB–PUESM0004yourprojectnumber
b)#BSUB–qsmallrequestedqueueNotethisisfortutorialpurposesONLY.
9../b.day2.1.submitReview logfiles to familiarizeyourselfwithstandardout.Start lookingatyourhistoryfiles.CheckyourCaseDocs/*_infiles.Wereyournamelistchangesapplied?
CESM1Tutorial:BasicModifica7ons:Ex1:ExampleREADME.case
.
CESM1Tutorial:BasicModifica7ons:HOMEWORK
Beforeyouleavefortheday:Resubmitandcon7nuetorunExercise1for36moremonths.Thiswillrun
overnightintheyellowstonequeues.YourdatawillbeusedforthePrac4calSessiontomorrowonDiagnoshcsandOutput.Assumingyourb.day2.1exerciseransuccessfullyinclass….Inenv_run.xml: 1. SetCONTINUE_RUNto“TRUE” 2.KeepSTOP_OPTIONsetto“nmonths” 3. SetSTOP_Nto“36” 4. SetINFO_DBUGto15. Commentout“#BSUB–UCESM_WS”lineinyourrunscript(b.day2.1.run).
(shouldlooklike“##BSUB-UCESM_WS”)Trytogetasmanyexercisesinthispresenta7oncompletedinclassBEFOREyougobackandsetupthiscon7nuerun.Note:Thereservednodesareforday-4meuseonly.Overnightjobscaneitherberunintheworkshopqueueorregularqueue.
• Not all changes can be made in env_run.xml.
• user_nl_<model> files appear in the case directory after ./cesm_setup has been invoked), i.e.
user_nl_cam atmosphere
user_nl_clm land
user_nl_cice ice
user_nl_pop2 ocean
user_nl_cpl coupler (driver) user_nl_rtm river transport
CESM1Tutorial:BasicModifica7ons:Namelistvariables/tool:user_nl_<model>
CESM1Tutorial:BasicModifica7ons:Namelistvariables:user_nl_<model>
CESM1Tutorial:BasicModifica7ons:Namelisttool:preview_namelist
• Insert namelist syntax for desired variable change into the appropriate file. To find the proper syntax and see all default namelist values, use preview_namelist to create the resolved namelists the model will use at runtime in your run directory (i.e. /glade/scratch/<user>/<case>/run/ ). Note that cesm_setup automatically runs preview_namelist so if you have already run ./cesm_setup, you don’t need to do this again.
• In your case directory, type ./preview_namelists
• cd to your run directory and view *_in files:
user_nl_cam modifies atm_in user_nl_clm modifies lnd_in user_nl_cice modifies ice_in user_nl_pop2 modifies pop2_in user_nl_cpl modifies drv_in user_nl_rtm modifies rof_in
• Default namelist can also be reviewed in your CaseDocs subdirectory (found in your case directory after cesm_setup has been invoked).
CESM1Tutorial:BasicModifica7ons:Namelisttool:preview_namelist
Example: Decrease timestep in the ocean model by increasing dt_count from 12 steps per day to 23 steps per day. 1. Edit (vi or emacs) user_nl_pop2 2. Insert correct syntax as a new line at the end of the comment section in the form
of: namelist_var = new_namelist_value
i.e., dt_count = 23
3. Invoke preview_namelists again to verify change in your run directory and update
the documentation pop2_in file in CaseDocs.
http://www.cesm.ucar.edu/models/cesm1.2/pop2/doc/faq/#nml_general_change_dt
CESM1Tutorial:BasicModifica7ons:Exercise2
EXERCISE.2:BRANCHfromtheend(ofthesecondmonth)inExercise.1(nottheendofthehomework).TurnofficerunoffintheRTM(runoff)model,quadrupleCO2anddoublemethane.Run1month.Restartfor1month.Checkyourresolvednamelistsinyourrundirectory.
1../create_newcase-case~/cases/b.day2.2-resT31_gx3v7-machyellowstone-compsetB_1850_CN
2.cd~/cases/b.day2.2
3../xmlchangeRUN_TYPE=branch,RUN_REFCASE=b.day2.1,RUN_REFDATE=0001-03-01,GET_REFCASE=FALSE,STOP_OPTION=nmonths,STOP_N=1,RESUBMIT=1,CCSM_CO2_PPMV=1138.8(nospacesbetweenarguments).
WhydoweneedtosetGET_REFCASE=FALSE?
Con4nuednextpage
CESM1Tutorial:BasicModifica7ons:Exercise2
EXERCISE.2:con7nued
4../xmlchange-fileenv_run.xml-idCAM_NAMELIST_OPTS-valch4vmr=1583.2e-95. ./xmlchange-fileenv_run.xml-idRTM_NAMELIST_OPTS-valice_runoff=.false.
Whydoweusethesingle./xmlchangemethodhere?
6. ./cesm_setup
7. Copyyourrestartfilesfromyourbday2.1shorttermarchivespacetoyourbday2.2$RUNDIR:
cp/glade/scratch/<user>/archive/b.day2.1/rest/0001-03-01-00000/*/glade/scratch/<user>/b.day2.2/run/.
8../b.day2.2.build
9../b.day2.2.submit
10.Reviewqueuesandlogfiles.Howfastdoesthefirstmonthrun?Wasthesecondmonthresubmixed?
CESM1Tutorial:BasicModifica7ons:env_run.xmlvs.user_nl_<model>
Whatmethodisbestfornamelistchanges?env_run.xml:• Run_typespecifica4on(startup,hybrid,branch,con4nue)• Run4mevariables(stop_op4on,resubmits,etc.)• NamelistchangesforCAM,CLM,CICE,RTMbeforecesm_setupisinvoked
user_nl_<model>:• Swappingoutadefaultinputdatasetforahome-growndataset• NamelistchangesforPOPorCPL• Namelistchangesappliedtoclonedscripts.
CESM1Tutorial:BasicModifica7ons:env_run.xmlvs.user_nl_<model>
Atrun4me,thescriptswillautoma4callyre-populateyourresolvednamelists
basedonenv_runandtheuser_nl_<model>files,however,itisalwaysgoodtodocumentandcheckyourchangesBEFORErun4me.
Alwayscheckyourresolved*_infiles(rundirectory,i.e./glade/scratch)tomakesureyourchangeshavebeenapplied.
CESM1Tutorial:BasicModifica7ons:TimeStepChanges
WhereandWhentoChangeTimeSteps
Whenthemodelcrashesduetolarge,temporaryinstabili4es,onemethodtoovercometheproblemistochangethe4mestep.
Thisistypicallydoneineithertheatmosphereoroceancomponents.
CAM/CLM:ATM_NCPLinenv_run.xml.
POP:dt_countinPOPnamelist.Editandchangetheuser_nl_popfile.
CESM1Tutorial:BasicModifica7ons:TimeStepChanges
1.ATM_NCPLinenv_run.xmlspecifiesthenumberofcouplingintervalsperdaybetweentheatmosphere/landandthecoupledsystem.BasedonATM_NCPL,thescriptswillautoma4callycomputethe4mestepfortheatmosphereandland(DTIME)andpopulatethenamelistfilesaccordingly.
2. CLM7mestep=CAM4mestep;thisisautoma4callysetwiththeCAM4mestepviaATM_NCPL.Youcannotsetthisseparately.
3. RTM7mestep,4mestepisexplicitlydefinedandisnotrela4vetotheCLM4mestep.(DefaultRTM4mestepis3hours).
CESM1Tutorial:BasicModifica7ons:MoreExercises
Exercise.3:Createnewcase,hybridstart,fullycoupledforPre-Industrialcondi4ons(withCN).Quadruplethespecifiedmethanetracegasvalueintheatmosphere,butdecreasethesolarconstantby0.1%,andsettheorbitalparametersto1600.(Note:thisisanexerciseanddoesnotrepresentanyhistoricalperiod).Run5days(default).Resubmitforanother5days.WhathappenstoCONTINUE_RUNinenv_run.xmlabercomple4onoftheini4al5dayrun(assumingyousetRESUBMIT=1)?
1../create_newcase-case~/cases/b.day2.3-resT31_gx3v7-machyellowstone-compsetB_1850_CN
2.cd~/cases/b.day2.33../xmlchangeRESUBMIT=14../xmlchange-fileenv_run.xml-idCAM_NAMELIST_OPTS
-valsolar_const=1359.53,ch4vmr=3166.40e-95../cesm_setup
Con4nuednextpage
CESM1Tutorial:BasicModifica7ons:MoreExercises
Exercise.3:Con7nued:6. Edituser_nl_cpl,abercomments,addline:orb_iyear=16007. UpdateREADME.case8. Op4onal:./preview_namelists9../b.day2.3.build
Checkyour$RUNDIRandreviewyournamelistchangesinatm_inanddrv_in
10.Reviewb.day2.3.run: Notequeue(small)andprojectnumber(UESM0004)arefortutorial
purposesONLY.Normally,youwillrunwithyourownprojectnumberintheregularqueue.
11. ./b.day2.3.submit
Aberthejobcompletes,gototheshorttermarchivespaceandexplore.
CESM1Tutorial:BasicModifica7ons:MoreExercises
Exercise.4:ClonecasefromExercise.3.Includeallmodifica4onsfromExercise.3exceptinsteadofspecifyingorbitalyear,assignindividualparameters(eccentricity=0,obliquity=23.,andprecession=0.)Includenewmodifica4ontouseadifferentshortwaveabsorp4onparameteriza4oninPOPcalled“jerlov”.(Thedefaultswabsorp4onparameteriza4onisgeography-specificandcalled“chlorophyll”.“Jerlov”istypicallyusedforpaleoclimatesimula4onswherethegeographyisdifferentfrompresentday).TurnofftheUrbanparamteriza4oninCLM.Run5days(default).
1../create_clone-case~/cases/b.day2.4-clone~/cases/b.day2.32.Cleanupstderrandstdoutthatdon’tbelongtoyournewcase.3.Edituser_nl_cplandchangethefollowing:
a.Removeorb_iyearb.Addorb_mode=‘fixed_parameters’
c.Addorb_eccen=0.d.Addorb_mvelp=0.e.Addorb_obliq=23.
Con4nuednextpage
CESM1Tutorial:BasicModifica7ons:MoreExercises
Exercise.4:con4nued
4.Edituser_nl_pop2andadd:sw_absorphon_type='jerlov‘
5. Edituser_nl_clmandadd:urban_hac=‘OFF’
6. Notethatinenv_run.xml,create_clonehasautoma4callysetCONTINUE_RUNbacktoFALSE,thisisanini4alrun.
7.UpdateyourREADME.casefile.Documentyourchanges
8../cesm_setupBecauseyouclonedthiscaseyoualreadyhadyouruser_nl_<model>fileinyourcase
casedirectory,butyouhavechangedthemandthereforeneedtoinvokecesm_setuporpreview_namelisttoupdateyourCaseDocs,createtheresolvednamelistsinyourrundirectory,andcreateyourrunscript.
Con4nuednextpage
CESM1Tutorial:BasicModifica7ons:MoreExercises
Exercise.4:con4nued9../b.day2.4.build
10../b.day2.4.submit
11. Gooveralllogfilesand4mingfiles.Ifyouwant,youcanstarttolookatthehistoryoutput.Onlytheatm/ocnwillhavedailyoutputtoview.(ncview).Whereistheshorttermhistoryoutputlocated?Tousencview,youwillneedtotype“moduleloadncview”onyourcommandline.
12.Compareb.day2.4historydatatob.day2.3historydata.(ncdiff).Tousencdiff,youwillneedtotype“moduleloadnco”onyourcommandline.
13.Op7onal:ResubmitExercise.3andExercise.4for1monthtoobtainmonthlyhistoryfilesforallmodelcomponents.Whatwillyouneedtochange?
CESM1Tutorial:BasicModifica7ons:MoreExercisesExercise.5:Onyourown…Doa“startup”run.Changetheatm/lnd4mestepto900seconds.(Defaultvalueis1800secondswithATM_NCPL=48).Run1month.Besureall4mestepsarecompa4ble.BesuretoupdateyourREADME.casefiletokeeptrackofyourchanges.Reviewlogstoverify4mestepchanges.
Exercise.6:Onyourown…BranchstartusingExercise.5restartfiles.IncludeallExercise5modifica4ons.ReducethesnowalbedoesoverseaiceinCICEbyhalf.Run1month.
Knowwhatyouarechanging.Lookupinforma4ononnamelistvariablesinthedocumenta4on.(hxp://www.cesm.ucar.edu/models/cesm1.2/cice/doc/index.html).BesuretoupdateyourREADME.casefiletokeeptrackofyourchanges.Themodelwillrunregardlessofwhetherornotyourremembertoincludeallofyourchanges.Checkyourresolved/processednamelistfiles($RUNDIR/<model>_infiles)tomakesureallchangesareincluded.Ifyoulike,resubmitandcon4nuetherunfor1moremonth.
CESM1Tutorial:BasicModifica7ons:BoHomLine
Whatuser-modifiedfilesareactuallyusedatrun7me?./cesm_setup(or./preview_namelists) $RUNDIR/atm_in
$RUNDIR/lnd_in $RUNDIR/pop2_in $RUNDIR/ice_in $RUNDIR/drv_in
BoHomLine:Usermodifica7onsshouldbeimplementedintheenv_run.xmlortheuser_nl_<model>files.
Whatfilesarefordocumenta7onpurposes?Buildconf/*.input_data_listCaseDocs,CaseStatus,LockedFiles,README.*
Note:Buildconf/*confdirectoriesarecreatedabercesm_setup.TheuserdoesNOTneedtotouchthesefiles.
CESM1Tutorial:BasicModifica7ons:RunScripts
Reviewrunscript:b.day2.x.runCommonBSUBcommandtochange:
#BSUB-qsmallqueuetype*#BSUB-ocesm.stdout.%J machinestandardout#BSUB-ecesm.stderr.%J machinestandarderror#BSUB–Jb.day2.x jobname#BSUB-W2:00 wallclock4merequested#BSUB-PUESM0004 projectnumber
Note:Maximumallowablewallclock4meperjobsubmissionvariesfrommachinetomachineandqueuetoqueue.Yellowstone(NCAR’sIBM)regularqueueis12hours.Submissionsreques4ngunderanhourtypicallyhaveshorterwait4mesinthequeue.
CESM1Tutorial:BasicModifica7ons:LogFiles
LogFiles:Duringmodelexecu4on: Abermodelcomple4on: atm.log.yyddmm-nnnnnn.gzlnd.log.yyddmm-nnnnnn.gzocn.log.yyddmm-nnnnnn.gzice.log.yyddmm-nnnnnn.gzcpl.log.yyddmm-nnnnnn.gzrof.log.yyddmm-nnnnnn.gzcesm.log.yyddmm-nnnnnn.gz
Modelrun7mestandardoutput$RUNDIR/*$LOGDIR/*Filesaregzippedabermodelcomple4on.Restorebytypinggunzip<logfile>.yyddmm=year,month,daynnnnnn=4meidstamp
CESM1Tutorial:BasicModifica7ons:OtherTips
CHECKyourresolvednamelists!• Beforeyousubmityourjob,itisalwaysgoodtodoublecheckyour
$RUNDIR/<model>_innamelistfiles.Thesearethefilesthemodelwillactuallyuseatrun4meandarebasedonyourenv_run.xmlanduser_nl_<model>files.
• Verifythatthemodelisusingwhatyouthinkitisusing!
DOCUMENTeverythingyoudo!• Apapertrailofyourproceduresandthoughtsisgoodscien4ficprac4ce.
TheREADME.casefileistheperfectplacetowritenotes.Youwillthankyourselfmonths(years)later,whenyouaretryingtofigureoutwhatyoudidoh-so-longago!
CESM1Tutorial:BasicModifica7ons:PostRunTips
Checklogs• Checkyourlogfilestomakesuretherearenohiddenproblemsandtoverifythemodelis
runningsmoothlyandasyouexpect.Thelogfilesmayalsohelpyouverifyyourmodifica4onswereincludedinyourrun.
Checkoutput• Checkyourhistoryfiles.Itisagoodideatorunasmalltestsampleofyourexperiment
beforelaunchingyourfullproduc4onrun.Forexample,ifyouwanttoruna500yearcontrolwithvariousmodifica4ons,firstrun10years.Checkthehistoryoutputfilesandverifythemodelisrunningasyoudesignedbeforecon4nuingwiththefull500years.Itisalwaysbesttofinderrorsearly,ratherthanlater,intherun.
Check7mings• Checkyour4mings.Abermodelcomple4on,a4mingsubdirectorywillbeplacedinyour
scriptsdirectory.Checkthe4mingsaberseveraljobcomple4onstoverifythatthemodelisrunningefficientlyandasexpected.Doublecheckyour4mingswiththeCESMdefault4mingsforyourspecificmodelresolu4onandmachine.Default4mingsforCESM1.2canbefoundat:hxp://www.cesm.ucar.edu/models/cesm1.2/4ming/
CESM1Tutorial:BasicModifica7ons:HELP!
FindingHelp…1. Documenta4on:hxp://www.cesm.ucar.edu/models/cesm1.2/
2. DiscussCESM:hxp://bb.cgd.ucar.edu
CESM1Tutorial:BasicModifica7ons
HaveFun!!!
