Mercurial > repos > climate > ctsm_fates
diff ctsm-fates.xml.binutils @ 0:8c7414c07367 draft
"planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/fates-emerald commit f282701cadbb0c90c2c77a52579f18b44a357e24"
| author | climate |
|---|---|
| date | Wed, 21 Oct 2020 20:30:35 +0000 |
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| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ctsm-fates.xml.binutils Wed Oct 21 20:30:35 2020 +0000 @@ -0,0 +1,334 @@ +<tool id="ctsm-fates" name="CTSM/FATES-EMERALD" version="2.0.1"> + <description>Functionally Assembled Terrestrial Ecosystem Simulator</description> + <requirements> + <requirement type="package" version="2.0.1">fates-emerald</requirement> + <requirement type="package" version="1.32">tar</requirement> + <requirement type="package" version="2.35">binutils</requirement> + <requirement type="package" version="3">python</requirement> + <requirement type="package" version="2.0132">perl-xml-libxml</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + ( export HOME=`pwd` && + export USER='jovyan' && + mkdir -p .cime && + cp '$__tool_directory__/config' .cime/config && + cp '$__tool_directory__/config_compilers.xml' '.cime/config_compilers.xml' && + cp '$__tool_directory__/config_machines.xml' '.cime/config_machines.xml' && + mkdir inputdata && + tar -xf '$inputdata' -C 'inputdata/' && + mkdir output_dir && + mkdir usermods_dirs && + #if str($adv.condi_user_mods).strip() == 'yes' + # should create a new type user_mods.tar + cd usermods_dirs && + tar xf '$user_mods' && + cd .. && + #end if + create_newcase --case '$casename' --compset 2000_DATM%1PTGSWP3_CLM50%FATES_SICE_SOCN_MOSART_SGLC_SWAV --machine espresso --run-unsupported + #if str($adv.condi_user_mods).strip() == 'yes' + --user-mods-dir usermods_dirs + #end if + --res '$resolution' && + cd '$casename' && + ./case.setup > $case_info 2>&1 && + #if (str($adv_period.condi_type_run.run_type) == 'hybrid' or str($adv_period.condi_type_run.run_type) == 'branch') + ./xmlchange RUN_TYPE=$adv_period.condi_type_run.run_type && + ./xmlchange RUN_REFDATE=$adv_period.condi_type_run.run_refdate && + ./xmlchange RUN_REFCASE=$adv_period.condi_type_run.run_refcase && + #end if + #if ((str($adv_period.condi_type_run.run_type) == 'hybrid' or str($adv_period.condi_type_run.run_type) == 'startup') and ($adv_period.condi_type_run.run_startdate != '')) + ./xmlchange RUN_STARTDATE=$adv_period.condi_type_run.run_startdate && + #end if + ./xmlchange STOP_N=$adv_period.stopn && + ./xmlchange STOP_OPTION=$adv_period.stop_option && + ./xmlchange CCSM_CO2_PPMV=$adv.co2 && + ./xmlchange DOUT_S=FALSE && + cp '$user_nl_clm_customization' user_nl_clm && + ./case.build >> $case_info 2>&1 && + #if (str($adv_period.condi_type_run.run_type) == 'hybrid' or str($adv_period.condi_type_run.run_type) == 'branch') + tar -xf '$adv_period.condi_type_run.restart' -C '../work/$casename/run/' && + + #end if + ./case.submit >> $case_info 2>&1 && + mkdir -p restart && + (cat '../work/$casename/run/rpointer'.* > $rinfo || printf "No restarts\n") && + (cp '../work/$casename/run/$casename'.*.r*.*.nc restart/ || printf "No netCDF restarts\n") && + (cp '../work/$casename/run/$casename'.*.r*.*.bin restart/ || printf "No bin restarts\n") && + (cp '../work/$casename/run/rpointer'.* restart/ || printf "no rpointer\n") && + cd restart && + tar cvf $restart . && + cd .. && + (cp '../work/$casename/run/$casename'.*.h*.*.nc ../output_dir/ || printf "no netCDF outputs\n") && + (gunzip '../work/$casename/run/'*.log.* || printf "no compressed logs") && + cat '../work/$casename/run/'atm.log.* >> $atm_log && + cat '../work/$casename/run/'cesm.log.* >> $cesm_log && + cat '../work/$casename/run/'cpl.log.* >> $cpl_log && + cat '../work/$casename/run/'lnd.log.* >> $lnd_log && + cat '../work/$casename/run/'rof.log.* >> $rof_log ) || + (printf "Case failed" && tar cf $work \${HOME}/work) + ]]></command> + <configfiles> + <configfile name="user_nl_clm_customization"><![CDATA[ +&clm_inparm + hist_mfilt = 120, + use_fates = .true., + fates_spitfire_mode = $adv_clm.fates_spitfire_mode, + use_fates_planthydro = $adv_clm.use_fates_planthydro, + use_fates_cohort_age_tracking = $adv_clm.use_fates_cohort_age_tracking, + use_fates_ed_st3 = $adv_clm.use_fates_ed_st3, + use_fates_ed_prescribed_phys = $adv_clm.use_fates_ed_prescribed_phys, + use_fates_logging = $adv_clm.use_fates_logging, + use_fates_fixed_biogeog = $adv_clm.use_fates_fixed_biogeog, + #if (str($adv_clm.fates_parteh_mode).strip() != '') + fates_parteh_mode = $adv_clm.fates_parteh_mode + #end if +/ + ]]> + </configfile> + </configfiles> + <inputs> + <param name="inputdata" type="data" format='tar' label="inputdata for running FATES EMERALD"></param> + <param name="casename" type="text" value="usecase" label="Name of your case"> + <validator type="regex" message="start with a letter and no blanks">^[A-Za-z][A-Za-z0-9]*</validator> + </param> + <param name="resolution" type="select" label="Model resolution"> + <option value="1x1_ALP1">ALP1</option> + <option value="1x1_ALP2">ALP2</option> + <option value="1x1_ALP3">ALP3</option> + <option value="1x1_ALP4">ALP4</option> + <option value="1x1_SUB1">SUB1</option> + <option value="1x1_SUB2">SUB2</option> + <option value="1x1_SUB3">SUB3</option> + <option value="1x1_SUB4">SUB4</option> + <option value="1x1_BOR1">BOR1</option> + <option value="1x1_BOR2">BOR2</option> + <option value="1x1_BOR3">BOR3</option> + <option value="1x1_BOR4">BOR4</option> + <option value="1x1_LYG">LYG</option> + <option value="1x1_BUO">BUO</option> + <option value="1x1_HAV">HAV</option> + <option value="1x1_SKO">SKO</option> + <option value="1x1_VIKE">VIKE</option> + <option value="1x1_LIAH">LIAH</option> + <option value="1x1_FINN">FINN</option> + </param> + <section name="adv_period" title="Customize the model run period" expanded="false"> + + <conditional name="condi_type_run"> + <param name="run_type" type="select" label="Determines the model run initialization type."> + <option value="startup" selected="true">startup</option> + <option value="hybrid">hybrid</option> + <option value="branch">branch</option> + </param> + <when value="startup"> + <param name="run_startdate" type="text" value="" label="Run start date (yyyy-mm-dd). Only used for startup or hybrid runs."> + <validator type="regex" message="YYYY-MM-DD">(^$|(\d{4}-(0[1-9]|1[0-2])-(0[1-9]|[12]\d|3[01])))</validator> + </param> + </when> + <when value="branch"> + <param name="run_refcase" type="text" value="" label="Reference case for hybrid or branch runs"></param> + <param name="run_refdate" type="text" value="" label="Reference date for hybrid or branch runs (yyyy-mm-dd)"> + <validator type="regex" message="YYYY-MM-DD">(^$|(\d{4}-(0[1-9]|1[0-2])-(0[1-9]|[12]\d|3[01])))</validator> + </param> + <param name="restart" type="data" format='tar' label="restart for running FATES EMERALD"></param> + </when> + <when value="hybrid"> + <param name="run_refcase" type="text" value="" label="Reference case for hybrid or branch runs"></param> + <param name="run_refdate" type="text" value="" label="Reference date for hybrid or branch runs (yyyy-mm-dd)"> + <validator type="regex" message="YYYY-MM-DD">(^$|(\d{4}-(0[1-9]|1[0-2])-(0[1-9]|[12]\d|3[01])))</validator> + </param> + <param name="run_startdate" type="text" value="" label="Run start date (yyyy-mm-dd). Only used for startup or hybrid runs."> + <validator type="regex" message="YYYY-MM-DD">(^$|(\d{4}-(0[1-9]|1[0-2])-(0[1-9]|[12]\d|3[01])))</validator> + </param> + <param name="restart" type="data" format='tar' label="restart for running FATES EMERALD"></param> + </when> + </conditional> + <param name="stopn" type="integer" value="5" label="Provides a numerical count for STOP_OPTION."></param> + <param name="stop_option" type="select" label=" Sets the run length along with STOP_N and STOP_DATE"> + <option value="ndays" selected="true">ndays</option> + <option value="none">none</option> + <option value="never">never</option> + <option value="nsteps">nsteps</option> + <option value="nseconds">nseconds</option> + <option value="nminutes">nminutes</option> + <option value="nhours">nhours</option> + <option value="nday">ndays</option> + <option value="nmonths">nmonths</option> + <option value="nyears">nyears</option> + <option value="date">date</option> + <option value="ifdays0">ifday0</option> + <option value="end">end</option> + </param> + </section> + <section name="adv_clm" title="CLM namelist customization" expanded="false"> + <param name="use_fates_planthydro" type="boolean" label="Toggle to turn on plant hydraulics" truevalue=".true." falsevalue=".false." checked="false"/> + <param name="use_fates_cohort_age_tracking" type="boolean" label="Toggle to turn on cohort age tracking" truevalue=".true." falsevalue=".false." checked="false"/> + <param name="use_fates_ed_st3" type="boolean" label="Toggle to turn on Static Stand Structure Mode" truevalue=".true." falsevalue=".false." checked="false"/> + <param name="use_fates_ed_prescribed_phys" type="boolean" label="Toggle to turn on prescribed physiology" truevalue=".true." falsevalue=".false." checked="false"/> + <param name="use_fates_logging" type="boolean" label="Toggle to turn on the logging module" truevalue=".true." falsevalue=".false." checked="false"/> + <param name="use_fates_fixed_biogeog" type="boolean" label="Toggle to turn on fixed biogeography mode" truevalue=".true." falsevalue=".false." checked="false"/> + <param name="fates_spitfire_mode" type="select" label="Spitfire module to simulate fire"> + <option value="0" selected="true">None</option> + <option value="1">Use a global constant lightning rate found in fates_params</option> + <option value="2">Use an external lightning dataset</option> + <option value="3">Use an external confirmed ignitions dataset</option> + <option value="4">Use external lightning and population datasets to simulate both natural and anthropogenic ignitions</option> + </param> + <param name="fates_parteh_mode" type="select" label="Switch deciding which nutrient model to use in FATES"> + <option value="" selected="true">None</option> + <option value="1">1</option> + <option value="2">2</option> + </param> + </section> + <section name="adv" title="Advanced customization" expanded="false"> + <param name="co2" type="float" value="367.0" label="Atmospheric CO2 molar ratio (by volume) only used when co2_type==constant (umol/mol)"></param> + <conditional name="condi_user_mods"> + <param name="add_changes" type="select" label="user-modified source code"> + <option value="no" selected="true">no</option> + <option value="yes">yes</option> + </param> + <when value="yes"> + <param name="usermods" type="data" format="tar" label="SourceMods"></param> + </when> + <when value="no"/> + </conditional> + </section> + </inputs> + <outputs> + <data name="history_files" format="netcdf" label="${tool.name} on ${inputdata.name} (history file)"> + <discover_datasets pattern="__designation_and_ext__" directory="output_dir" visible="true" /> + </data> + <data name="atm_log" format="txt" label="${tool.name} on ${inputdata.name} (atm.log)"/> + <data name="cesm_log" format="txt" label="${tool.name} on ${inputdata.name} (cesm.log)"/> + <data name="cpl_log" format="txt" label="${tool.name} on ${inputdata.name} (cpl.log)"/> + <data name="lnd_log" format="txt" label="${tool.name} on ${inputdata.name} (lnd.log)"/> + <data name="rof_log" format="txt" label="${tool.name} on ${inputdata.name} (rof.log)"/> + <data name="restart" format="tar" label="${tool.name} on ${inputdata.name} (restart)"></data> + <data name="case_info" format="txt" label="${tool.name} on ${inputdata.name} (case info)"></data> + <data name="rinfo" format="txt" label="${tool.name} on ${inputdata.name} (restart info)"></data> + <data name="work" format="tar" label="${tool.name} on ${inputdata.name} (workdir)"> + </data> + </outputs> + <tests> + <test> + <param name="inputdata" value="inputdata_test.tar" /> + <param name="casename" value="test" /> + <param name="resolution" value="1x1_ALP1" /> + <param name="run_startdate" value="2000-01-01" /> + <param name="stop_option" value="nsteps" /> + <param name="stopn" value="1" /> + <output name="atm_log" ftype="txt" file="atm.log"> + <assert_contents> + <has_text text="(datm_comp_final) atm: end of main integration loop" /> + </assert_contents> + </output> + <output name="cesm_log" ftype="txt" file="cesm.log"> + <assert_contents> + <has_text text="pes participating in computation for CLM" /> + </assert_contents> + </output> + <output name="cpl_log" ftype="txt" file="cpl.log"> + <assert_contents> + <has_text text="SUCCESSFUL TERMINATION" /> + </assert_contents> + </output> + <output name="lnd_log" ftype="txt" file="lnd.log"> + <assert_contents> + <has_text text="Successfully" /> + </assert_contents> + </output> + <output name="rof_log" ftype="txt" file="rof.log"> + <assert_contents> + <has_text text="MOSART model initialization" /> + </assert_contents> + </output> + <output name="case_info" ftype="txt" file="case_info.txt"> + <assert_contents> + <has_text text="MODEL BUILD HAS FINISHED SUCCESSFULLY" /> + <has_line_matching expression="Submitted job" /> + </assert_contents> + </output> + <output name="work" ftype="tar" file="workdir.tar"> + <assert_contents> + <has_size value="0"/> + </assert_contents> + </output> + <output name="restart" ftype="tar" file="restart.tar" compare="sim_size" delta="100" /> + <output name="rinfo" ftype="txt" file="restart_info.txt"> + <assert_contents> + <has_line_matching expression="*datm.r.2000-01-01-01800.nc*" /> + <has_line_matching expression="*datm.rs1.2000-01-01-01800.bin*" /> + <has_line_matching expression="*cpl.r.2000-01-01-01800.nc*" /> + <has_line_matching expression="*clm2.r.2000-01-01-01800.nc*" /> + </assert_contents> + </output> + <output name="history_files" ftype="netcdf" file="history_file.netcdf"> + <assert_contents> + <has_size value="0"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ + +**The Functionally Assembled Terrestrial Ecosystem Simulator (FATES)** +========================================================================== + +This tool create and run CTSM-FATES EMERALD experiments from fates-emerald release. + +This version of FATES is maintained by the University of Oslo. + +Currently available resolution are as following: + +SeedClim Sites: +~~~~~~~~~~~~~~~ + +- ALP1,61.0243N,8.12343E +- ALP2,60.8231N,7.27596E +- ALP3,60.8328N,7.17561E +- ALP4,60.9335N,6.41504E +- SUB1,60.8203N,8.70466E +- SUB2,60.8760N,7.17666E +- SUB3,61.0866N,6.63028E +- SUB4,60.5445N,6.51468E +- BOR1,61.0355N,9.07876E +- BOR2,60.8803N,7.16982E +- BOR3,60.6652N,6.33738E +- BOR4,60.6901N,5.96487E + +LandPress Sites: +~~~~~~~~~~~~~~~~ + +- LYG,60.70084N,5.092566E +- BUO,65.83677N,12.224506E +- HAV,64.779N,11.2193E +- SKO,65.79602N,12.219299E + +Three-D Sites: +~~~~~~~~~~~~~~ + +- VIKE,60.88019N,7.16990E +- JOAS,60.86183N,7.16800E +- LIAH,60.85994N,7.19504E + + +Finnmark Site: +~~~~~~~~~~~~~~ + +- FINN,69.341088N,25.293524E + + ]]></help> + <citations> + + </citations> + <edam_topics> + <edam_topic>topic_3855</edam_topic> + <edam_topic>topic_3318</edam_topic> + <edam_topic>topic_3050</edam_topic> + <edam_topic>topic_0610</edam_topic> + </edam_topics> + <edam_operations> + <edam_operation>operation_3946</edam_operation> + <edam_operation>operation_2426</edam_operation> + </edam_operations> +</tool>