Mercurial > repos > climate > ctsm_fates
changeset 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 |
| parents | |
| children | 74b675f9d7c8 |
| files | config config_compilers.xml config_machines.xml ctsm-fates.xml ctsm-fates.xml.SLEEP ctsm-fates.xml.TRIC ctsm-fates.xml.binutils ctsm-fates.xml_detail test-data/atm.log test-data/cesm.log test-data/cpl.log test-data/history_file.netcdf test-data/inputdata_test.tar test-data/lnd.log test-data/restart.tar test-data/restart_info.txt test-data/rof.log test-data/workdir.tar |
| diffstat | 16 files changed, 4326 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/config Wed Oct 21 20:30:35 2020 +0000 @@ -0,0 +1,2 @@ +[main] +CIME_MODEL=cesm
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/config_compilers.xml Wed Oct 21 20:30:35 2020 +0000 @@ -0,0 +1,25 @@ +<?xml version="1.0"?> + +<config_compilers version="2.0"> + + <compiler COMPILER="gnu" MACH="espresso"> + <LD>mpifort</LD> + <AR>x86_64-conda_cos6-linux-gnu-ar</AR> + <SFC>x86_64-conda_cos6-linux-gnu-gfortran</SFC> + <SCC>x86_64-conda_cos6-linux-gnu-cc</SCC> + <SCXX>x86_64-conda_cos6-linux-gnu-c++</SCXX> + <MPIFC>mpifort</MPIFC> + <MPICC>mpicc</MPICC> + <MPICXX>mpicxx</MPICXX> + <NETCDF_PATH>$ENV{CONDA_PREFIX}</NETCDF_PATH> + <FFLAGS> + <append DEBUG="FALSE"> -O2 </append> + <append MODEL="micom"> -fdefault-real-8 </append> + <append MODEL="cam"> -finit-local-zero </append> + </FFLAGS> + <SLIBS> + <append> -L$(NETCDF_PATH)/lib -lnetcdff -lnetcdf -ldl </append> + <append> -lmkl_gf_lp64 -lmkl_gnu_thread -lmkl_core -lgomp -lpthread -lm -fopenmp </append> + </SLIBS> + </compiler> +</config_compilers>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/config_machines.xml Wed Oct 21 20:30:35 2020 +0000 @@ -0,0 +1,42 @@ +<?xml version="1.0"?> +<config_machines> + <machine MACH="espresso"> + <DESC> + VM + x4 CPUs + Gold Centos 7 + </DESC> + <NODENAME_REGEX>UNSET</NODENAME_REGEX> + <OS>LINUX</OS> + <PROXY>UNSET</PROXY> + <COMPILERS>gnu</COMPILERS> + <MPILIBS>mpich</MPILIBS> + <SAVE_TIMING_DIR>UNSET</SAVE_TIMING_DIR> + <CIME_OUTPUT_ROOT>$ENV{HOME}/work</CIME_OUTPUT_ROOT> + <DIN_LOC_ROOT>$ENV{HOME}/inputdata</DIN_LOC_ROOT> + <DIN_LOC_ROOT_CLMFORC>$ENV{HOME}/inputdata/atm/datm7</DIN_LOC_ROOT_CLMFORC> + <DOUT_S_ROOT>$ENV{HOME}/archive/$CASE</DOUT_S_ROOT> + <BASELINE_ROOT>UNSET</BASELINE_ROOT> + <CCSM_CPRNC>UNSET</CCSM_CPRNC> + <GMAKE>make</GMAKE> + <GMAKE_J>1</GMAKE_J> + <BATCH_SYSTEM>none</BATCH_SYSTEM> + <SUPPORTED_BY>nobody</SUPPORTED_BY> + <MAX_TASKS_PER_NODE>1</MAX_TASKS_PER_NODE> + <MAX_MPITASKS_PER_NODE>1</MAX_MPITASKS_PER_NODE> + <PROJECT_REQUIRED>FALSE</PROJECT_REQUIRED> + <mpirun mpilib="default"> + <executable>nohup mpiexec</executable> + <arguments> + <arg name="anum_tasks"> -np $TOTALPES</arg> + </arguments> + </mpirun> + <module_system type="none"/> + <environment_variables> + <env name="KMP_STACKSIZE">64M</env> + </environment_variables> + <resource_limits> + <resource name="RLIMIT_STACK">-1</resource> + </resource_limits> + </machine> +</config_machines>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ctsm-fates.xml Wed Oct 21 20:30:35 2020 +0000 @@ -0,0 +1,325 @@ +<tool id="ctsm-fates" name="CTSM/FATES-EMERALD" version="2.0.1"> + <description>Functionally Assembled Terrestrial Ecosystem Simulator</description> + <requirements> + <requirement type="package" version="2.0.1">fates-emerald</requirement> + <requirement type="package" version="1.32">tar</requirement> + <requirement type="package" version="2.35">binutils</requirement> + <requirement type="package" version="3">python</requirement> + <requirement type="package" version="2.0132">perl-xml-libxml</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + ( export HOME=`pwd` && + export USER='jovyan' && + mkdir -p .cime && + cp '$__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> + <collection name="history_files" type="list" label="${tool.name} on ${inputdata.name} (history file)"> + <discover_datasets pattern="__designation_and_ext__" directory="output_dir" visible="true" format="netcdf"/> + </collection> + <data name="atm_log" format="txt" label="${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" compare="sim_size" delta="1000"> + <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" compare="sim_size" delta="1000"> + <assert_contents> + <has_text text="pes participating in computation for CLM" /> + </assert_contents> + </output> + <output name="cpl_log" ftype="txt" file="cpl.log" compare="sim_size" delta="1000"> + <assert_contents> + <has_text text="SUCCESSFUL TERMINATION" /> + </assert_contents> + </output> + <output name="lnd_log" ftype="txt" file="lnd.log" compare="sim_size" delta="1000"> + <assert_contents> + <has_text text="Successfully" /> + </assert_contents> + </output> + <output name="rof_log" ftype="txt" file="rof.log" compare="sim_size" delta="1000"> + <assert_contents> + <has_text text="MOSART model initialization" /> + </assert_contents> + </output> + <output name="work" ftype="tar" file="workdir.tar" compare="sim_size" delta="1000"> + <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" compare="sim_size" delta="1000"> + <assert_contents> + <has_text text="datm.r.2000-01-01-01800.nc" /> + <has_text text="datm.rs1.2000-01-01-01800.bin" /> + <has_text text="cpl.r.2000-01-01-01800.nc" /> + <has_text text="clm2.r.2000-01-01-01800.nc" /> + </assert_contents> + </output> + <output_collection name="history_files" count="0"> + </output_collection> + </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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ctsm-fates.xml.SLEEP Wed Oct 21 20:30:35 2020 +0000 @@ -0,0 +1,332 @@ +<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 && + sleep 1000 ) || + (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> + <collection name="history_files" type="list" label="${tool.name} on ${inputdata.name} (history file)"> + <discover_datasets pattern="__designation_and_ext__" directory="output_dir" visible="true" format="netcdf"/> + </collection> + <data name="atm_log" format="txt" label="${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_collection name="history_files" count="0"> + </output_collection> + </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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ctsm-fates.xml.TRIC Wed Oct 21 20:30:35 2020 +0000 @@ -0,0 +1,338 @@ +<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="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' && + export AR=/usr/local/bin/x86_64-conda_cos6-linux-gnu-ar && + mkdir bin && + cd bin && ln -s /usr/local/bin/x86_64-conda_cos6-linux-gnu-ar ar && + cd .. && + export PATH=\$HOME/bin:\$PATH && + 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>
--- /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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ctsm-fates.xml_detail Wed Oct 21 20:30:35 2020 +0000 @@ -0,0 +1,331 @@ +<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> + <collection name="history_files" type="list" label="${tool.name} on ${inputdata.name} (history file)"> + <discover_datasets pattern="__designation_and_ext__" directory="output_dir" visible="true" format="netcdf"/> + </collection> + <data name="atm_log" format="txt" label="${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_text text="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_text text="datm.r.2000-01-01-01800.nc" /> + <has_text text="datm.rs1.2000-01-01-01800.bin" /> + <has_text text="cpl.r.2000-01-01-01800.nc" /> + <has_text text="clm2.r.2000-01-01-01800.nc" /> + </assert_contents> + </output> + <output_collection name="history_files" count="0"> + </output_collection> + </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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/atm.log Wed Oct 21 20:30:35 2020 +0000 @@ -0,0 +1,240 @@ +(datm_comp_init) decomp = 1d +(datm_comp_init) iradsw = 1 +(datm_comp_init) factorFn = null +(datm_comp_init) restfilm = undefined +(datm_comp_init) restfils = undefined +(datm_comp_init) presaero = T +(datm_comp_init) force_prognostic_true = F +(datm_comp_init) wiso_datm = F +(datm_comp_init) inst_index = 1 +(datm_comp_init) inst_name = ATM +(datm_comp_init) inst_suffix = +(shr_strdata_readnml) reading input namelist file: datm_in +(shr_stream_init) Reading file datm.streams.txt.CLM1PT.1x1_ALP1.Solar +(shr_file_freeUnit) unit 97 was not in use +(shr_stream_init) Reading file datm.streams.txt.CLM1PT.1x1_ALP1.Precip +(shr_file_freeUnit) unit 97 was not in use +(shr_stream_init) Reading file datm.streams.txt.CLM1PT.1x1_ALP1.TPQW +(shr_file_freeUnit) unit 97 was not in use +(shr_stream_init) Reading file datm.streams.txt.presaero.clim_2000 +(shr_file_freeUnit) unit 97 was not in use +(shr_stream_init) Reading file datm.streams.txt.topo.observed +(shr_file_freeUnit) unit 97 was not in use +(datm_comp_init) datm datamode = CLMNCEP + (shr_strdata_init_streams) stream 1 + (shr_strdata_init_streams) filePath = 1 /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/share/domains/ALP1/ + (shr_strdata_init_streams) fileName = 1 /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/share/domains/ALP1/domain.lnd.ALP1.200422.nc + (shr_strdata_init_streams) timeName = 1 time + (shr_strdata_init_streams) lonName = 1 xc + (shr_strdata_init_streams) latName = 1 yc + (shr_strdata_init_streams) hgtName = 1 unknownname + (shr_strdata_init_streams) maskName = 1 mask + (shr_strdata_init_streams) areaName = 1 area + (shr_strdata_init_streams) stream 2 + (shr_strdata_init_streams) filePath = 2 /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/share/domains/ALP1/ + (shr_strdata_init_streams) fileName = 2 /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/share/domains/ALP1/domain.lnd.ALP1.200422.nc + (shr_strdata_init_streams) timeName = 2 time + (shr_strdata_init_streams) lonName = 2 xc + (shr_strdata_init_streams) latName = 2 yc + (shr_strdata_init_streams) hgtName = 2 unknownname + (shr_strdata_init_streams) maskName = 2 mask + (shr_strdata_init_streams) areaName = 2 area + (shr_strdata_init_streams) stream 3 + (shr_strdata_init_streams) filePath = 3 /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/share/domains/ALP1/ + (shr_strdata_init_streams) fileName = 3 /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/share/domains/ALP1/domain.lnd.ALP1.200422.nc + (shr_strdata_init_streams) timeName = 3 time + (shr_strdata_init_streams) lonName = 3 xc + (shr_strdata_init_streams) latName = 3 yc + (shr_strdata_init_streams) hgtName = 3 unknownname + (shr_strdata_init_streams) maskName = 3 mask + (shr_strdata_init_streams) areaName = 3 area + (shr_strdata_init_streams) stream 4 + (shr_strdata_init_streams) filePath = 4 /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/atm/cam/chem/trop_mozart_aero/aero/ + (shr_strdata_init_streams) fileName = 4 /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/atm/cam/chem/trop_mozart_aero/aero/ALP1/aerosoldep_WACCM.ensmean_monthly_hist_1849-2015_0.9x1.25_CMIP6_c180926_ALP1.nc + (shr_strdata_init_streams) timeName = 4 time + (shr_strdata_init_streams) lonName = 4 lon + (shr_strdata_init_streams) latName = 4 lat + (shr_strdata_init_streams) hgtName = 4 unknownname + (shr_strdata_init_streams) maskName = 4 mask + (shr_strdata_init_streams) areaName = 4 area + (shr_strdata_init_streams) stream 5 + (shr_strdata_init_streams) filePath = 5 /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/atm/datm7/topo_forcing/ + (shr_strdata_init_streams) fileName = 5 /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/atm/datm7/topo_forcing/ALP1/topodata_ALP1.nc + (shr_strdata_init_streams) timeName = 5 time + (shr_strdata_init_streams) lonName = 5 LONGXY + (shr_strdata_init_streams) latName = 5 LATIXY + (shr_strdata_init_streams) hgtName = 5 unknownname + (shr_strdata_init_streams) maskName = 5 mask + (shr_strdata_init_streams) areaName = 5 area +(shr_strdata_print) ---------------------------------------------------------- +(shr_strdata_print) name = ATM data +(shr_strdata_print) dataMode = CLMNCEP +(shr_strdata_print) domainFile = /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/share/domains/ALP1/domain.lnd.ALP1.200422.nc +(shr_strdata_print) nxg = 1 +(shr_strdata_print) nyg = 1 +(shr_strdata_print) nzg = -1 +(shr_strdata_print) calendar = NO_LEAP +(shr_strdata_print) io_type = 6 +(shr_strdata_print) eccen = 1.000000E+36 +(shr_strdata_print) mvelpp = 1.000000E+36 +(shr_strdata_print) lambm0 = 1.000000E+36 +(shr_strdata_print) obliqr = 1.000000E+36 +(shr_strdata_print) nstreams = 5 +(shr_strdata_print) pio_iotype = 6 +(shr_strdata_print) streams ( 1) = datm.streams.txt.CLM1PT.1x1_ALP1.Solar 1901 1901 1950 +(shr_strdata_print) taxMode ( 1) = cycle +(shr_strdata_print) dtlimit ( 1) = 1.500000E+00 +(shr_strdata_print) strnxg ( 1) = 1 +(shr_strdata_print) strnyg ( 1) = 1 +(shr_strdata_print) strnzg ( 1) = -1 +(shr_strdata_print) dofill ( 1) = F +(shr_strdata_print) fillalgo( 1) = nn +(shr_strdata_print) fillmask( 1) = nomask +(shr_strdata_print) fillread( 1) = NOT_SET +(shr_strdata_print) fillwrit( 1) = NOT_SET +(shr_strdata_print) domaps ( 1) = F +(shr_strdata_print) mapalgo ( 1) = nn +(shr_strdata_print) mapmask ( 1) = nomask +(shr_strdata_print) mapread ( 1) = NOT_SET +(shr_strdata_print) mapwrit ( 1) = NOT_SET +(shr_strdata_print) tintalgo( 1) = coszen +(shr_strdata_print) readmode( 1) = single +(shr_strdata_print) +(shr_strdata_print) streams ( 2) = datm.streams.txt.CLM1PT.1x1_ALP1.Precip 1901 1901 1950 +(shr_strdata_print) taxMode ( 2) = cycle +(shr_strdata_print) dtlimit ( 2) = 1.500000E+00 +(shr_strdata_print) strnxg ( 2) = 1 +(shr_strdata_print) strnyg ( 2) = 1 +(shr_strdata_print) strnzg ( 2) = -1 +(shr_strdata_print) dofill ( 2) = F +(shr_strdata_print) fillalgo( 2) = nn +(shr_strdata_print) fillmask( 2) = nomask +(shr_strdata_print) fillread( 2) = NOT_SET +(shr_strdata_print) fillwrit( 2) = NOT_SET +(shr_strdata_print) domaps ( 2) = F +(shr_strdata_print) mapalgo ( 2) = nn +(shr_strdata_print) mapmask ( 2) = nomask +(shr_strdata_print) mapread ( 2) = NOT_SET +(shr_strdata_print) mapwrit ( 2) = NOT_SET +(shr_strdata_print) tintalgo( 2) = nearest +(shr_strdata_print) readmode( 2) = single +(shr_strdata_print) +(shr_strdata_print) streams ( 3) = datm.streams.txt.CLM1PT.1x1_ALP1.TPQW 1901 1901 1950 +(shr_strdata_print) taxMode ( 3) = cycle +(shr_strdata_print) dtlimit ( 3) = 1.500000E+00 +(shr_strdata_print) strnxg ( 3) = 1 +(shr_strdata_print) strnyg ( 3) = 1 +(shr_strdata_print) strnzg ( 3) = -1 +(shr_strdata_print) dofill ( 3) = F +(shr_strdata_print) fillalgo( 3) = nn +(shr_strdata_print) fillmask( 3) = nomask +(shr_strdata_print) fillread( 3) = NOT_SET +(shr_strdata_print) fillwrit( 3) = NOT_SET +(shr_strdata_print) domaps ( 3) = F +(shr_strdata_print) mapalgo ( 3) = nn +(shr_strdata_print) mapmask ( 3) = nomask +(shr_strdata_print) mapread ( 3) = NOT_SET +(shr_strdata_print) mapwrit ( 3) = NOT_SET +(shr_strdata_print) tintalgo( 3) = linear +(shr_strdata_print) readmode( 3) = single +(shr_strdata_print) +(shr_strdata_print) streams ( 4) = datm.streams.txt.presaero.clim_2000 1 2000 2000 +(shr_strdata_print) taxMode ( 4) = cycle +(shr_strdata_print) dtlimit ( 4) = 1.500000E+00 +(shr_strdata_print) strnxg ( 4) = 1 +(shr_strdata_print) strnyg ( 4) = 1 +(shr_strdata_print) strnzg ( 4) = -1 +(shr_strdata_print) dofill ( 4) = F +(shr_strdata_print) fillalgo( 4) = nn +(shr_strdata_print) fillmask( 4) = nomask +(shr_strdata_print) fillread( 4) = NOT_SET +(shr_strdata_print) fillwrit( 4) = NOT_SET +(shr_strdata_print) domaps ( 4) = F +(shr_strdata_print) mapalgo ( 4) = nn +(shr_strdata_print) mapmask ( 4) = nomask +(shr_strdata_print) mapread ( 4) = NOT_SET +(shr_strdata_print) mapwrit ( 4) = NOT_SET +(shr_strdata_print) tintalgo( 4) = linear +(shr_strdata_print) readmode( 4) = single +(shr_strdata_print) +(shr_strdata_print) streams ( 5) = datm.streams.txt.topo.observed 1 1 1 +(shr_strdata_print) taxMode ( 5) = cycle +(shr_strdata_print) dtlimit ( 5) = 1.500000E+00 +(shr_strdata_print) strnxg ( 5) = 1 +(shr_strdata_print) strnyg ( 5) = 1 +(shr_strdata_print) strnzg ( 5) = -1 +(shr_strdata_print) dofill ( 5) = F +(shr_strdata_print) fillalgo( 5) = nn +(shr_strdata_print) fillmask( 5) = nomask +(shr_strdata_print) fillread( 5) = NOT_SET +(shr_strdata_print) fillwrit( 5) = NOT_SET +(shr_strdata_print) domaps ( 5) = F +(shr_strdata_print) mapalgo ( 5) = nn +(shr_strdata_print) mapmask ( 5) = nomask +(shr_strdata_print) mapread ( 5) = NOT_SET +(shr_strdata_print) mapwrit ( 5) = NOT_SET +(shr_strdata_print) tintalgo( 5) = lower +(shr_strdata_print) readmode( 5) = single +(shr_strdata_print) +(shr_strdata_print) nvectors = 0 +(shr_strdata_print) ---------------------------------------------------------- +(datm_comp_init) initialize gsmaps +(datm_comp_init) copy domains +(datm_comp_init) allocate AVs +(datm_comp_init) flds_strm = strm_swdn:strm_precn:strm_tbot:strm_wind:strm_pbot:strm_shum:strm_lwdn +(shr_dmodel_readstrm) open : /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/atm/datm7/ALP1/clm1pt_ALP1_1950-01.nc +(shr_dmodel_readstrm) file lb: /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/atm/datm7/ALP1/clm1pt_ALP1_1950-01.nc 1 +(shr_dmodel_readstrm) file ub: /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/atm/datm7/ALP1/clm1pt_ALP1_1950-01.nc 2 +(shr_dmodel_readstrm) open : /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/atm/datm7/ALP1/clm1pt_ALP1_1949-12.nc +(shr_dmodel_readstrm) file lb: /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/atm/datm7/ALP1/clm1pt_ALP1_1949-12.nc 248 +(shr_dmodel_readstrm) close : /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/atm/datm7/ALP1/clm1pt_ALP1_1949-12.nc +(shr_dmodel_readstrm) open : /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/atm/datm7/ALP1/clm1pt_ALP1_1950-01.nc +(shr_dmodel_readstrm) file ub: /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/atm/datm7/ALP1/clm1pt_ALP1_1950-01.nc 1 +(shr_dmodel_readstrm) open : /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/atm/datm7/ALP1/clm1pt_ALP1_1949-12.nc +(shr_dmodel_readstrm) file lb: /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/atm/datm7/ALP1/clm1pt_ALP1_1949-12.nc 248 +(shr_dmodel_readstrm) close : /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/atm/datm7/ALP1/clm1pt_ALP1_1949-12.nc +(shr_dmodel_readstrm) open : /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/atm/datm7/ALP1/clm1pt_ALP1_1950-01.nc +(shr_dmodel_readstrm) file ub: /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/atm/datm7/ALP1/clm1pt_ALP1_1950-01.nc 1 +(shr_dmodel_readstrm) open : /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/atm/cam/chem/trop_mozart_aero/aero/ALP1/aerosoldep_WACCM.ensmean_monthly_hist_1849-2015_0.9x1.25_CMIP6_c180926_ALP1.nc +(shr_dmodel_readstrm) file lb: /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/atm/cam/chem/trop_mozart_aero/aero/ALP1/aerosoldep_WACCM.ensmean_monthly_hist_1849-2015_0.9x1.25_CMIP6_c180926_ALP1.nc 1824 +(shr_dmodel_readstrm) file ub: /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/atm/cam/chem/trop_mozart_aero/aero/ALP1/aerosoldep_WACCM.ensmean_monthly_hist_1849-2015_0.9x1.25_CMIP6_c180926_ALP1.nc 1813 +(shr_dmodel_readstrm) open : /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/atm/datm7/topo_forcing/ALP1/topodata_ALP1.nc +(shr_dmodel_readstrm) file lb: /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/atm/datm7/topo_forcing/ALP1/topodata_ALP1.nc 1 +(shr_dmodel_readstrm) file ub: /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/atm/datm7/topo_forcing/ALP1/topodata_ALP1.nc 1 + (datm_comp_run) max values = 266.23443603515625 0.0000000000000000 0.0000000000000000 +(datm_comp_run) atm: model date 20000101 0s +(datm_comp_init) datm_comp_init done +(datm_comp_run) writing test.datm.rs1.2000-01-01-01800.bin20000101 1800s +(shr_stream_restWrite) case name : test +(shr_stream_restWrite) case description : SDATM strdata +(shr_stream_restWrite) File created : 2020-10-20 14:24:33 +(shr_stream_restWrite) Number of streams 5 +(shr_stream_restWrite) * stream 1 first file name = clm1pt_ALP1_1901-01.nc +(shr_stream_restWrite) * stream 1 first have data = T +(shr_stream_restWrite) * stream 1 first nt = 248 +(shr_stream_restWrite) * stream 1 first date secs = 19010101 0 +(shr_stream_restWrite) * stream 1 last date secs = 19010131 75600 +(shr_stream_restWrite) * stream 2 first file name = clm1pt_ALP1_1901-01.nc +(shr_stream_restWrite) * stream 2 first have data = T +(shr_stream_restWrite) * stream 2 first nt = 248 +(shr_stream_restWrite) * stream 2 first date secs = 19010101 5400 +(shr_stream_restWrite) * stream 2 last date secs = 19010131 81000 +(shr_stream_restWrite) * stream 3 first file name = clm1pt_ALP1_1901-01.nc +(shr_stream_restWrite) * stream 3 first have data = T +(shr_stream_restWrite) * stream 3 first nt = 248 +(shr_stream_restWrite) * stream 3 first date secs = 19010101 5400 +(shr_stream_restWrite) * stream 3 last date secs = 19010131 81000 +(shr_stream_restWrite) * stream 4 first file name = ALP1/aerosoldep_WACCM.ensmean_monthly_hist_1849-2015_0.9x1.25_CMIP6_c180926_ALP1.nc +(shr_stream_restWrite) * stream 4 first have data = T +(shr_stream_restWrite) * stream 4 first nt = 2004 +(shr_stream_restWrite) * stream 4 first date secs = 18490116 43200 +(shr_stream_restWrite) * stream 4 last date secs = 20151216 43200 +(shr_stream_restWrite) * stream 5 first file name = ALP1/topodata_ALP1.nc +(shr_stream_restWrite) * stream 5 first have data = T +(shr_stream_restWrite) * stream 5 first nt = 1 +(shr_stream_restWrite) * stream 5 first date secs = 10101 0 +(shr_stream_restWrite) * stream 5 last date secs = 10101 0 +(datm_comp_run) atm: model date 20000101 1800s +(datm_comp_final) ------------------------------------------------------------------------- +(datm_comp_final) atm: end of main integration loop +(datm_comp_final) -------------------------------------------------------------------------
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cesm.log Wed Oct 21 20:30:35 2020 +0000 @@ -0,0 +1,233 @@ +nohup: ignoring input + PIO rearranger options: + comm type =p2p + comm fcd =2denable + max pend req (comp2io) = 0 + enable_hs (comp2io) = T + enable_isend (comp2io) = F + max pend req (io2comp) = 0 + enable_hs (io2comp) = F + enable_isend (io2comp) = T +(seq_comm_setcomm) init ID ( 1 GLOBAL ) pelist = 0 0 1 ( npes = 1) ( nthreads = 1)( suffix =) +(seq_comm_setcomm) init ID ( 2 CPL ) pelist = 0 0 1 ( npes = 1) ( nthreads = 1)( suffix =) +(seq_comm_setcomm) init ID ( 5 ATM ) pelist = 0 0 1 ( npes = 1) ( nthreads = 1)( suffix =) +(seq_comm_joincomm) init ID ( 6 CPLATM ) join IDs = 2 5 ( npes = 1) ( nthreads = 1) +(seq_comm_jcommarr) init ID ( 3 ALLATMID ) join multiple comp IDs ( npes = 1) ( nthreads = 1) +(seq_comm_joincomm) init ID ( 4 CPLALLATMID ) join IDs = 2 3 ( npes = 1) ( nthreads = 1) +(seq_comm_setcomm) init ID ( 9 LND ) pelist = 0 0 1 ( npes = 1) ( nthreads = 1)( suffix =) +(seq_comm_joincomm) init ID ( 10 CPLLND ) join IDs = 2 9 ( npes = 1) ( nthreads = 1) +(seq_comm_jcommarr) init ID ( 7 ALLLNDID ) join multiple comp IDs ( npes = 1) ( nthreads = 1) +(seq_comm_joincomm) init ID ( 8 CPLALLLNDID ) join IDs = 2 7 ( npes = 1) ( nthreads = 1) +(seq_comm_setcomm) init ID ( 13 ICE ) pelist = 0 0 1 ( npes = 1) ( nthreads = 1)( suffix =) +(seq_comm_joincomm) init ID ( 14 CPLICE ) join IDs = 2 13 ( npes = 1) ( nthreads = 1) +(seq_comm_jcommarr) init ID ( 11 ALLICEID ) join multiple comp IDs ( npes = 1) ( nthreads = 1) +(seq_comm_joincomm) init ID ( 12 CPLALLICEID ) join IDs = 2 11 ( npes = 1) ( nthreads = 1) +(seq_comm_setcomm) init ID ( 17 OCN ) pelist = 0 0 1 ( npes = 1) ( nthreads = 1)( suffix =) +(seq_comm_joincomm) init ID ( 18 CPLOCN ) join IDs = 2 17 ( npes = 1) ( nthreads = 1) +(seq_comm_jcommarr) init ID ( 15 ALLOCNID ) join multiple comp IDs ( npes = 1) ( nthreads = 1) +(seq_comm_joincomm) init ID ( 16 CPLALLOCNID ) join IDs = 2 15 ( npes = 1) ( nthreads = 1) +(seq_comm_setcomm) init ID ( 21 ROF ) pelist = 0 0 1 ( npes = 1) ( nthreads = 1)( suffix =) +(seq_comm_joincomm) init ID ( 22 CPLROF ) join IDs = 2 21 ( npes = 1) ( nthreads = 1) +(seq_comm_jcommarr) init ID ( 19 ALLROFID ) join multiple comp IDs ( npes = 1) ( nthreads = 1) +(seq_comm_joincomm) init ID ( 20 CPLALLROFID ) join IDs = 2 19 ( npes = 1) ( nthreads = 1) +(seq_comm_setcomm) init ID ( 25 GLC ) pelist = 0 0 1 ( npes = 1) ( nthreads = 1)( suffix =) +(seq_comm_joincomm) init ID ( 26 CPLGLC ) join IDs = 2 25 ( npes = 1) ( nthreads = 1) +(seq_comm_jcommarr) init ID ( 23 ALLGLCID ) join multiple comp IDs ( npes = 1) ( nthreads = 1) +(seq_comm_joincomm) init ID ( 24 CPLALLGLCID ) join IDs = 2 23 ( npes = 1) ( nthreads = 1) +(seq_comm_setcomm) init ID ( 29 WAV ) pelist = 0 0 1 ( npes = 1) ( nthreads = 1)( suffix =) +(seq_comm_joincomm) init ID ( 30 CPLWAV ) join IDs = 2 29 ( npes = 1) ( nthreads = 1) +(seq_comm_jcommarr) init ID ( 27 ALLWAVID ) join multiple comp IDs ( npes = 1) ( nthreads = 1) +(seq_comm_joincomm) init ID ( 28 CPLALLWAVID ) join IDs = 2 27 ( npes = 1) ( nthreads = 1) +(seq_comm_setcomm) init ID ( 33 ESP ) pelist = 0 0 1 ( npes = 1) ( nthreads = 1)( suffix =) +(seq_comm_joincomm) init ID ( 34 CPLESP ) join IDs = 2 33 ( npes = 1) ( nthreads = 1) +(seq_comm_jcommarr) init ID ( 31 ALLESPID ) join multiple comp IDs ( npes = 1) ( nthreads = 1) +(seq_comm_joincomm) init ID ( 32 CPLALLESPID ) join IDs = 2 31 ( npes = 1) ( nthreads = 1) +(seq_comm_setcomm) init ID ( 37 IAC ) pelist = 0 0 1 ( npes = 1) ( nthreads = 1)( suffix =) +(seq_comm_joincomm) init ID ( 38 CPLIAC ) join IDs = 2 37 ( npes = 1) ( nthreads = 1) +(seq_comm_jcommarr) init ID ( 35 ALLIACID ) join multiple comp IDs ( npes = 1) ( nthreads = 1) +(seq_comm_joincomm) init ID ( 36 CPLALLIACID ) join IDs = 2 35 ( npes = 1) ( nthreads = 1) +(seq_comm_printcomms) 1 0 1 1 GLOBAL: +(seq_comm_printcomms) 2 0 1 1 CPL: +(seq_comm_printcomms) 3 0 1 1 ALLATMID: +(seq_comm_printcomms) 4 0 1 1 CPLALLATMID: +(seq_comm_printcomms) 5 0 1 1 ATM: +(seq_comm_printcomms) 6 0 1 1 CPLATM: +(seq_comm_printcomms) 7 0 1 1 ALLLNDID: +(seq_comm_printcomms) 8 0 1 1 CPLALLLNDID: +(seq_comm_printcomms) 9 0 1 1 LND: +(seq_comm_printcomms) 10 0 1 1 CPLLND: +(seq_comm_printcomms) 11 0 1 1 ALLICEID: +(seq_comm_printcomms) 12 0 1 1 CPLALLICEID: +(seq_comm_printcomms) 13 0 1 1 ICE: +(seq_comm_printcomms) 14 0 1 1 CPLICE: +(seq_comm_printcomms) 15 0 1 1 ALLOCNID: +(seq_comm_printcomms) 16 0 1 1 CPLALLOCNID: +(seq_comm_printcomms) 17 0 1 1 OCN: +(seq_comm_printcomms) 18 0 1 1 CPLOCN: +(seq_comm_printcomms) 19 0 1 1 ALLROFID: +(seq_comm_printcomms) 20 0 1 1 CPLALLROFID: +(seq_comm_printcomms) 21 0 1 1 ROF: +(seq_comm_printcomms) 22 0 1 1 CPLROF: +(seq_comm_printcomms) 23 0 1 1 ALLGLCID: +(seq_comm_printcomms) 24 0 1 1 CPLALLGLCID: +(seq_comm_printcomms) 25 0 1 1 GLC: +(seq_comm_printcomms) 26 0 1 1 CPLGLC: +(seq_comm_printcomms) 27 0 1 1 ALLWAVID: +(seq_comm_printcomms) 28 0 1 1 CPLALLWAVID: +(seq_comm_printcomms) 29 0 1 1 WAV: +(seq_comm_printcomms) 30 0 1 1 CPLWAV: +(seq_comm_printcomms) 31 0 1 1 ALLESPID: +(seq_comm_printcomms) 32 0 1 1 CPLALLESPID: +(seq_comm_printcomms) 33 0 1 1 ESP: +(seq_comm_printcomms) 34 0 1 1 CPLESP: +(seq_comm_printcomms) 35 0 1 1 ALLIACID: +(seq_comm_printcomms) 36 0 1 1 CPLALLIACID: +(seq_comm_printcomms) 37 0 1 1 IAC: +(seq_comm_printcomms) 38 0 1 1 CPLIAC: + (t_initf) Read in prof_inparm namelist from: drv_in + (t_initf) Using profile_disable= F + (t_initf) profile_timer= 4 + (t_initf) profile_depth_limit= 4 + (t_initf) profile_detail_limit= 2 + (t_initf) profile_barrier= F + (t_initf) profile_outpe_num= 1 + (t_initf) profile_outpe_stride= 0 + (t_initf) profile_single_file= F + (t_initf) profile_global_stats= T + (t_initf) profile_ovhd_measurement= F + (t_initf) profile_add_detail= F + (t_initf) profile_papi_enable= F + + + 1 pes participating in computation for CLM + +----------------------------------- + +NODE# NAME +( 0) galaxy-tools.novalocal + NetCDF: Invalid dimension ID or name + NetCDF: Invalid dimension ID or name + NetCDF: Invalid dimension ID or name + NetCDF: Invalid dimension ID or name + NetCDF: Invalid dimension ID or name + NetCDF: Variable not found + NetCDF: Invalid dimension ID or name + NetCDF: Invalid dimension ID or name + NetCDF: Invalid dimension ID or name + NetCDF: Invalid dimension ID or name + NetCDF: Invalid dimension ID or name + NetCDF: Invalid dimension ID or name + NetCDF: Invalid dimension ID or name + NetCDF: Invalid dimension ID or name + NetCDF: Invalid dimension ID or name + NetCDF: Invalid dimension ID or name + clmfates_interfaceMod.F90::FatesReadPFTs :: CLM reading ED/FATES PFTs + clmfates_interfaceMod.F90:: reading fates_mort_freezetol + clmfates_interfaceMod.F90:: reading fates_recruit_hgt_min + clmfates_interfaceMod.F90:: reading fates_fire_crown_depth_frac + clmfates_interfaceMod.F90:: reading fates_fire_bark_scaler + clmfates_interfaceMod.F90:: reading fates_fire_crown_kill + clmfates_interfaceMod.F90:: reading fates_recruit_initd + clmfates_interfaceMod.F90:: reading fates_seed_suppl + clmfates_interfaceMod.F90:: reading fates_leaf_stomatal_slope_ballberry + clmfates_interfaceMod.F90:: reading fates_leaf_stomatal_slope_medlyn + clmfates_interfaceMod.F90:: reading fates_leaf_stomatal_intercept + clmfates_interfaceMod.F90:: reading fates_lf_flab + clmfates_interfaceMod.F90:: reading fates_lf_fcel + clmfates_interfaceMod.F90:: reading fates_lf_flig + clmfates_interfaceMod.F90:: reading fates_fr_flab + clmfates_interfaceMod.F90:: reading fates_fr_fcel + clmfates_interfaceMod.F90:: reading fates_fr_flig + clmfates_interfaceMod.F90:: reading fates_leaf_xl + clmfates_interfaceMod.F90:: reading fates_leaf_clumping_index + clmfates_interfaceMod.F90:: reading fates_leaf_c3psn + clmfates_interfaceMod.F90:: reading fates_smpso + clmfates_interfaceMod.F90:: reading fates_smpsc + clmfates_interfaceMod.F90:: reading fates_maintresp_reduction_curvature + clmfates_interfaceMod.F90:: reading fates_maintresp_reduction_intercept + clmfates_interfaceMod.F90:: reading fates_prescribed_npp_canopy + clmfates_interfaceMod.F90:: reading fates_prescribed_npp_understory + clmfates_interfaceMod.F90:: reading fates_prescribed_mortality_canopy + clmfates_interfaceMod.F90:: reading fates_prescribed_mortality_understory + clmfates_interfaceMod.F90:: reading fates_prescribed_recruitment + clmfates_interfaceMod.F90:: reading fates_fire_alpha_SH + clmfates_interfaceMod.F90:: reading fates_allom_frbstor_repro + clmfates_interfaceMod.F90:: reading fates_hydr_p_taper + clmfates_interfaceMod.F90:: reading fates_hydr_rs2 + clmfates_interfaceMod.F90:: reading fates_hydr_srl + clmfates_interfaceMod.F90:: reading fates_hydr_rfrac_stem + clmfates_interfaceMod.F90:: reading fates_hydr_avuln_gs + clmfates_interfaceMod.F90:: reading fates_hydr_p50_gs + clmfates_interfaceMod.F90:: reading fates_mort_bmort + clmfates_interfaceMod.F90:: reading fates_mort_r_size_senescence + clmfates_interfaceMod.F90:: reading fates_mort_ip_size_senescence + clmfates_interfaceMod.F90:: reading fates_mort_r_age_senescence + clmfates_interfaceMod.F90:: reading fates_mort_ip_age_senescence + clmfates_interfaceMod.F90:: reading fates_mort_scalar_coldstress + clmfates_interfaceMod.F90:: reading fates_mort_scalar_cstarvation + clmfates_interfaceMod.F90:: reading fates_mort_scalar_hydrfailure + clmfates_interfaceMod.F90:: reading fates_mort_hf_sm_threshold + clmfates_interfaceMod.F90:: reading fates_mort_hf_flc_threshold + clmfates_interfaceMod.F90:: reading fates_leaf_vcmaxha + clmfates_interfaceMod.F90:: reading fates_leaf_jmaxha + clmfates_interfaceMod.F90:: reading fates_leaf_tpuha + clmfates_interfaceMod.F90:: reading fates_leaf_vcmaxhd + clmfates_interfaceMod.F90:: reading fates_leaf_jmaxhd + clmfates_interfaceMod.F90:: reading fates_leaf_tpuhd + clmfates_interfaceMod.F90:: reading fates_leaf_vcmaxse + clmfates_interfaceMod.F90:: reading fates_leaf_jmaxse + clmfates_interfaceMod.F90:: reading fates_leaf_tpuse + clmfates_interfaceMod.F90:: reading fates_seed_germination_rate + clmfates_interfaceMod.F90:: reading fates_seed_decay_rate + clmfates_interfaceMod.F90:: reading fates_trim_limit + clmfates_interfaceMod.F90:: reading fates_trim_inc + clmfates_interfaceMod.F90:: reading fates_leaf_diameter + clmfates_interfaceMod.F90:: reading fates_z0mr + clmfates_interfaceMod.F90:: reading fates_displar + clmfates_interfaceMod.F90:: reading fates_phenflush_fraction + clmfates_interfaceMod.F90:: reading fates_phen_cold_size_threshold + clmfates_interfaceMod.F90:: reading fates_phen_stem_drop_fraction + clmfates_interfaceMod.F90:: reading fates_eca_decompmicc + clmfates_interfaceMod.F90:: reading fates_eca_km_nh4 + clmfates_interfaceMod.F90:: reading fates_eca_vmax_nh4 + clmfates_interfaceMod.F90:: reading fates_eca_km_no3 + clmfates_interfaceMod.F90:: reading fates_eca_vmax_no3 + clmfates_interfaceMod.F90:: reading fates_eca_km_p + clmfates_interfaceMod.F90:: reading fates_eca_vmax_p + clmfates_interfaceMod.F90:: reading fates_eca_km_ptase + clmfates_interfaceMod.F90:: reading fates_eca_vmax_ptase + clmfates_interfaceMod.F90:: reading fates_eca_alpha_ptase + clmfates_interfaceMod.F90:: reading fates_eca_lambda_ptase + clmfates_interfaceMod.F90:: reading fates_prescribed_nuptake + clmfates_interfaceMod.F90:: reading fates_prescribed_puptake + clmfates_interfaceMod.F90:: reading fates_rholvis + clmfates_interfaceMod.F90:: reading fates_rholnir + clmfates_interfaceMod.F90:: reading fates_rhosvis + clmfates_interfaceMod.F90:: reading fates_rhosnir + clmfates_interfaceMod.F90:: reading fates_taulvis + clmfates_interfaceMod.F90:: reading fates_taulnir + clmfates_interfaceMod.F90:: reading fates_tausvis + clmfates_interfaceMod.F90:: reading fates_tausnir + clmfates_interfaceMod.F90:: reading fates_hydr_avuln_node + clmfates_interfaceMod.F90:: reading fates_hydr_p50_node + clmfates_interfaceMod.F90:: reading fates_hydr_thetas_node + clmfates_interfaceMod.F90:: reading fates_hydr_epsil_node + clmfates_interfaceMod.F90:: reading fates_hydr_pitlp_node + clmfates_interfaceMod.F90:: reading fates_hydr_resid_node + clmfates_interfaceMod.F90:: reading fates_hydr_fcap_node + clmfates_interfaceMod.F90:: reading fates_hydr_pinot_node + clmfates_interfaceMod.F90:: reading fates_hydr_kmax_node + clmfates_interfaceMod.F90:: reading fates_leaf_vcmax25top + NetCDF: Variable not found + NetCDF: Invalid dimension ID or name + NetCDF: Invalid dimension ID or name + NetCDF: Invalid dimension ID or name + NetCDF: Invalid dimension ID or name + NetCDF: Invalid dimension ID or name + NetCDF: Invalid dimension ID or name + NetCDF: Invalid dimension ID or name + NetCDF: Invalid dimension ID or name + NetCDF: Invalid dimension ID or name + NetCDF: Invalid dimension ID or name + NetCDF: Variable not found + NetCDF: Variable not found
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/lnd.log Wed Oct 21 20:30:35 2020 +0000 @@ -0,0 +1,2106 @@ +(lnd_init_mct) :CLM land model initialization + unknown + + Attempting to initialize the land model ..... + + Attempting to initialize run control settings ..... + Read in clm_inparm namelist from: lnd_in + + rooting_profile settings: + rooting_profile_method_water = 1 + (rooting_profile_varindex_water = 1 ) + rooting_profile_method_carbon = 1 + (rooting_profile_varindex_carbon = 2 ) + + soilwater_movement settings: + soilwater_movement_method = 1 + upper_boundary_condition = 1 + lower_boundary_condition = 2 + use_bedrock = F + dtmin = 60.000000000000000 + verySmall = 1.0000000000000000E-008 + xTolerUpper = 0.10000000000000001 + xTolerLower = 1.0000000000000000E-002 + expensive = 42 + inexpensive = 1 + flux_calculation = 1 + + soil_resis settings: + soil_resis_method = 1 + Read in canopyfluxes_inparm namelist + (OPNFIL): Successfully opened file lnd_in on unit= 96 + + canopyfluxes_inparm settings: +&CANOPYFLUXES_INPARM + USE_UNDERCANOPY_STABILITY=F, + ITMAX_CANOPY_FLUXES= 40, + / + + Read in clm_CanopyHydrology_inparm namelist + (OPNFIL): Successfully opened file lnd_in on unit= 96 + + canopyhydrology settings: + interception_fraction = 1.0000000000000000 + maximum_leaf_wetted_fraction = 5.0000000000000003E-002 + use_clm5_fpi = T + Read in surfacealbedo_inparm namelist + (OPNFIL): Successfully opened file lnd_in on unit= 96 + + surfacealbedo_inparm settings +&SURFACEALBEDO_INPARM + SNOWVEG_AFFECTS_RADIATION=T, + / + + Read in clm_SnowHydrology_inparm namelist + (OPNFIL): Successfully opened file lnd_in on unit= 96 + + SnowHydrology settings: +&CLM_SNOWHYDROLOGY_INPARM + WIND_DEPENDENT_SNOW_DENSITY=T, + SNOW_OVERBURDEN_COMPACTION_METHOD="Vionnet2012 ", + LOTMP_SNOWDENSITY_METHOD="Slater2017 ", + UPPLIM_DESTRUCT_METAMORPH= 175.00000000000000 , + OVERBURDEN_COMPRESS_TFACTOR= 8.0000000000000002E-002, + MIN_WIND_SNOWCOMPACT= 5.0000000000000000 , + RESET_SNOW=F, + RESET_SNOW_GLC=F, + RESET_SNOW_GLC_ELA= 1000000000.0000000 , + SNOW_DZMIN_1= 1.0000000000000000E-002, + SNOW_DZMAX_L_1= 2.9999999999999999E-002, + SNOW_DZMAX_U_1= 2.0000000000000000E-002, + SNOW_DZMIN_2= 1.4999999999999999E-002, + SNOW_DZMAX_L_2= 7.0000000000000007E-002, + SNOW_DZMAX_U_2= 5.0000000000000003E-002, + / + + Read in clmu_inparm namelist + (OPNFIL): Successfully opened file lnd_in on unit= 96 + urban air conditioning/heating and wasteheat = ON_WASTEHEAT + urban traffic flux = F + Read in clm_humanindex_inparm namelist + (OPNFIL): Successfully opened file lnd_in on unit= 96 + Read in luna namelist + (OPNFIL): Successfully opened file lnd_in on unit= 96 + + luna settings: +&LUNA + JMAXB1= 0.10000000000000001 , + / + + Read in soilhydrology_inparm namelist + (OPNFIL): Successfully opened file lnd_in on unit= 96 + + soilhydrology_inparm settings: +&SOILHYDROLOGY_INPARM + BASEFLOW_SCALAR= 1.0000000000000000E-003, + / + + Read in CENTURY_soilBGCDecompCascade namelist + (OPNFIL): Successfully opened file lnd_in on unit= 96 + + CENTURY_soilBGCDecompCascade settings: +&CENTURY_SOILBGCDECOMPCASCADE + INITIAL_CSTOCKS= 3*200.00000000000000 , + INITIAL_CSTOCKS_DEPTH= 1.5000000000000000 , + / + + Successfully initialized run control settings + + Attempting to read maxsoil_patches and numcft from the surface data ..... + (GETFIL): attempting to find local file surfdata_ALP1_simyr2000.nc + (GETFIL): using /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/lnd/clm2/surfdata_map/ALP1/surfdata_ALP1_simyr2000.nc + Opened existing file /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/lnd/clm2/surfdata_map/ALP1/surfdata_ALP1_simyr2000.nc 393216 + Successfully read maxsoil_patches and numcft from the surface data + + soil_layerstruct_predefined varpar 20SL_8.5m + soil_layerstruct_userdefined varpar -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 + nlevsoi, nlevgrnd varpar 20 25 + CLM varpar subsurface discretization levels + nlevsoi = 20 + nlevgrnd = 25 + nlevdecomp = 20 + nlevdecomp_full = 25 + nlevlak = 10 + + define run: + source = Community Terrestrial Systems Model + model_version = unknown + run type = initial + case title = UNSET + username = jovyan + hostname = espresso + process control parameters: + use_lch4 = F + use_nitrif_denitrif = F + use_vertsoilc = T + use_extralakelayers = F + use_vichydro = F + use_century_decomp = T + use_cn = F + use_cndv = F + use_crop = F + use_fertilizer = F + use_grainproduct = F + use_ozone = F + use_snicar_frc = F + use_vancouver = F + use_mexicocity = F + use_noio = F + use_SSRE = F + input data files: + PFT physiology and parameters file = /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/lnd/clm2/paramdata/clm5_params.c200402.nc + surface data = /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/lnd/clm2/surfdata_map/ALP1/surfdata_ALP1_simyr2000.nc + land frac data = /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/share/domains/ALP1/domain.lnd.ALP1.200422.nc + Number of ACTIVE PFTS (0 means input pft data NOT collapsed to n_dom_pfts) = 0 + Number of ACTIVE LANDUNITS (0 means input landunit data NOT collapsed to n_dom_landunits) = 0 + Collapse urban landunits; done before collapsing all landunits to n_dom_landunits; .false. means do nothing i.e. keep all the urban landunits, though n_dom_landunits may still remove them = F + Threshold above which the model keeps the soil landunit = 0.0000000000000000 + Threshold above which the model keeps the crop landunit = 0.0000000000000000 + Threshold above which the model keeps the glacier landunit = 0.0000000000000000 + Threshold above which the model keeps the lake landunit = 0.0000000000000000 + Threshold above which the model keeps the wetland landunit = 0.0000000000000000 + Threshold above which the model keeps the urban landunits = 0.0000000000000000 + snow optical properties file = /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/lnd/clm2/snicardata/snicar_optics_5bnd_c090915.nc + snow aging parameters file = /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/lnd/clm2/snicardata/snicar_drdt_bst_fit_60_c070416.nc + Number of snow layers = 12 + Max snow depth (mm) = 10000.000000000000 + glc number of elevation classes = 10 + glc CLM glacier areas and topography will NOT evolve dynamically + glc snow persistence max days = 0 + initial data created by model (cold start) + atmospheric forcing data is from cesm atm model + Restart parameters: + restart pointer file directory = . + restart pointer file name = rpointer.lnd + model physics parameters: + CO2 volume mixing ratio (umol/mol) = 367.00000000000000 + land-ice albedos (unitless 0-1) = 0.50000000000000000 0.29999999999999999 + pre-defined soil layer structure = 20SL_8.5m + user-defined soil layer structure = -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 -9999999.0000000000 + user-defined number of soil layers = -9999999 + plant hydraulic stress = F + dynamic roots = F + nsegspc = 35 + perchroot (plant water stress based on unfrozen layers only) = F + perchroot (plant water stress based on time-integrated active layer only) = F + + Lake Model Namelists: + Increased mixing relative to Hostetler wind-driven eddy expression will be used for deep lakes exceeding depth 25.000000000000000 by a factor of 10.000000000000000 . + Albedo over melting lakes will approach values (visible, NIR): 0.10000000000000001 0.10000000000000001 as compared with 0.60, 0.40 for cold frozen lakes with no snow. + plant nitrogen model namelists: + use_flexibleCN = F + use_luna = F + ED/FATES: + use_fates = T + fates_spitfire_mode = 0 + use_fates_logging = F + fates_paramfile = /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/lnd/clm2/paramdata/fates_params_api.14.0.0_12pft_c200921.nc + fates_parteh_mode = 1 + use_fates_planthydro = F + use_fates_cohort_age_tracking = F + use_fates_ed_st3 = F + use_fates_ed_prescribed_phys = F + use_fates_inventory_init = F + use_fates_fixed_biogeog = F + fates_inventory_ctrl_filename = + + dynamic_subgrid settings: +&DYNAMIC_SUBGRID + FLANDUSE_TIMESERIES=" ", + DO_TRANSIENT_PFTS=F, + DO_TRANSIENT_CROPS=F, + DO_HARVEST=F, + RESET_DYNBAL_BASELINES=F, + FOR_TESTING_ALLOW_NON_ANNUAL_CHANGES=F, + FOR_TESTING_ZERO_DYNBAL_FLUXES=F, + / + + Attempting to read global land mask from /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/share/domains/ALP1/domain.lnd.ALP1.200422.nc + (GETFIL): attempting to find local file domain.lnd.ALP1.200422.nc + (GETFIL): using /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/share/domains/ALP1/domain.lnd.ALP1.200422.nc + Opened existing file /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/share/domains/ALP1/domain.lnd.ALP1.200422.nc 458752 + lat/lon grid flag (isgrid2d) is F + ncd_inqvid: variable LANDMASK is not on dataset + decomp precompute numg,nclumps,seglen1,avg_seglen,nsegspc= 1 1 T 1.00000000 1.00000000 + Surface Grid Characteristics + longitude points = 1 + latitude points = 1 + total number of land gridcells = 1 + Decomposition Characteristics + clumps per process = 1 + gsMap Characteristics + lnd gsmap glo num of segs = 1 + + Attempting to read ldomain from /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/share/domains/ALP1/domain.lnd.ALP1.200422.nc + (GETFIL): attempting to find local file domain.lnd.ALP1.200422.nc + (GETFIL): using /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/share/domains/ALP1/domain.lnd.ALP1.200422.nc + Opened existing file /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/share/domains/ALP1/domain.lnd.ALP1.200422.nc 458752 + domain_check set = domain_set + domain_check decomped = F + domain_check ns = 1 + domain_check ni,nj = 1 1 + domain_check nbeg,nend = 1 1 + domain_check lonc = 8.1234299999999990 8.1234299999999990 + domain_check latc = 61.024299999999997 61.024299999999997 + domain_check mask = 1 1 + domain_check frac = 1.0000000000000000 1.0000000000000000 + domain_check area = 0.59903950391113359 0.59903950391113359 + domain_check pftm = -9999 -9999 + + Attempting to read GLACIER_REGION... + (GETFIL): attempting to find local file surfdata_ALP1_simyr2000.nc + (GETFIL): using /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/lnd/clm2/surfdata_map/ALP1/surfdata_ALP1_simyr2000.nc + Opened existing file /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/lnd/clm2/surfdata_map/ALP1/surfdata_ALP1_simyr2000.nc 458752 + (OPNFIL): Successfully opened file lnd_in on unit= 96 + + clm_glacier_behavior settings: +&CLM_GLACIER_BEHAVIOR + GLACIER_REGION_BEHAVIOR="single_at_atm_topo ", 2*"virtual ","multiple ", 7*"UNSET ", + GLACIER_REGION_MELT_BEHAVIOR="remains_in_place ", 3*"replaced_by_ice ", 7*"UNSET ", + GLACIER_REGION_ICE_RUNOFF_BEHAVIOR= 2*"melted ", 2*"remains_ice ", 7*"UNSET ", + / + + Reading in urban input data from fsurdat file ... + (GETFIL): attempting to find local file surfdata_ALP1_simyr2000.nc + (GETFIL): using /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/lnd/clm2/surfdata_map/ALP1/surfdata_ALP1_simyr2000.nc + Opened existing file /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/lnd/clm2/surfdata_map/ALP1/surfdata_ALP1_simyr2000.nc 458752 + UrbanInput /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/lnd/clm2/surfdata_map/ALP1/surfdata_ALP1_simyr2000.nc + Sucessfully read urban input data + + Attempting to read PFT physiological data ..... + (GETFIL): attempting to find local file clm5_params.c200402.nc + (GETFIL): using /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/lnd/clm2/paramdata/clm5_params.c200402.nc + Opened existing file /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/lnd/clm2/paramdata/clm5_params.c200402.nc 458752 + (GETFIL): attempting to find local file fates_params_api.14.0.0_12pft_c200921.nc + (GETFIL): using /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/lnd/clm2/paramdata/fates_params_api.14.0.0_12pft_c200921.nc + Opened existing file /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/lnd/clm2/paramdata/fates_params_api.14.0.0_12pft_c200921.nc 458752 + (GETFIL): attempting to find local file clm5_params.c200402.nc + (GETFIL): using /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/lnd/clm2/paramdata/clm5_params.c200402.nc + Opened existing file /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/lnd/clm2/paramdata/clm5_params.c200402.nc 458752 + Successfully read PFT physiological data + + Attempting to read surface boundary data ..... + (GETFIL): attempting to find local file surfdata_ALP1_simyr2000.nc + (GETFIL): using /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/lnd/clm2/surfdata_map/ALP1/surfdata_ALP1_simyr2000.nc + Opened existing file /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/lnd/clm2/surfdata_map/ALP1/surfdata_ALP1_simyr2000.nc 458752 + check_var: variable xc is not on dataset + surfrd_get_data lon_var = LONGXY lat_var =LATIXY + WARNING: New CFT-based format surface datasets should be run with create_crop_landunit=T + WARNING: When fates is on we allow new CFT based surface datasets to be used with create_crop_land FALSE + Successfully read surface boundary data + + clmfates_interfaceMod.F90::FatesReadParameters :: CLM reading ED/FATES parameters + (GETFIL): attempting to find local file fates_params_api.14.0.0_12pft_c200921.nc + (GETFIL): using /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/lnd/clm2/paramdata/fates_params_api.14.0.0_12pft_c200921.nc + Opened existing file /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/lnd/clm2/paramdata/fates_params_api.14.0.0_12pft_c200921.nc 458752 + clmfates_interfaceMod.F90:: reading fates_mort_disturb_frac + clmfates_interfaceMod.F90:: reading fates_comp_excln + clmfates_interfaceMod.F90:: reading fates_init_litter + clmfates_interfaceMod.F90:: reading fates_fire_nignitions + clmfates_interfaceMod.F90:: reading fates_mort_understorey_death + clmfates_interfaceMod.F90:: reading fates_cwd_fcel + clmfates_interfaceMod.F90:: reading fates_cwd_flig + clmfates_interfaceMod.F90:: reading fates_base_mr_20 + clmfates_interfaceMod.F90:: reading fates_phen_drought_threshold + clmfates_interfaceMod.F90:: reading fates_phen_doff_time + clmfates_interfaceMod.F90:: reading fates_phen_a + clmfates_interfaceMod.F90:: reading fates_phen_b + clmfates_interfaceMod.F90:: reading fates_phen_c + clmfates_interfaceMod.F90:: reading fates_phen_chiltemp + clmfates_interfaceMod.F90:: reading fates_phen_mindayson + clmfates_interfaceMod.F90:: reading fates_phen_ncolddayslim + clmfates_interfaceMod.F90:: reading fates_phen_coldtemp + clmfates_interfaceMod.F90:: reading fates_cohort_size_fusion_tol + clmfates_interfaceMod.F90:: reading fates_cohort_age_fusion_tol + clmfates_interfaceMod.F90:: reading fates_patch_fusion_tol + clmfates_interfaceMod.F90:: reading fates_canopy_closure_thresh + clmfates_interfaceMod.F90:: reading fates_leaf_stomatal_model + clmfates_interfaceMod.F90:: reading fates_hydr_kmax_rsurf1 + clmfates_interfaceMod.F90:: reading fates_hydr_kmax_rsurf2 + clmfates_interfaceMod.F90:: reading fates_hydr_psi0 + clmfates_interfaceMod.F90:: reading fates_hydr_psicap + clmfates_interfaceMod.F90:: reading fates_soil_salinity + clmfates_interfaceMod.F90:: reading fates_logging_dbhmin + clmfates_interfaceMod.F90:: reading fates_logging_dbhmax + clmfates_interfaceMod.F90:: reading fates_logging_collateral_frac + clmfates_interfaceMod.F90:: reading fates_logging_coll_under_frac + clmfates_interfaceMod.F90:: reading fates_logging_direct_frac + clmfates_interfaceMod.F90:: reading fates_logging_mechanical_frac + clmfates_interfaceMod.F90:: reading fates_logging_event_code + clmfates_interfaceMod.F90:: reading fates_logging_dbhmax_infra + clmfates_interfaceMod.F90:: reading fates_logging_export_frac + clmfates_interfaceMod.F90:: reading fates_eca_plant_escalar + clmfates_interfaceMod.F90:: reading fates_q10_mr + clmfates_interfaceMod.F90:: reading fates_q10_froz + clmfates_interfaceMod.F90:: reading fates_history_sizeclass_bin_edges + clmfates_interfaceMod.F90:: reading fates_history_ageclass_bin_edges + clmfates_interfaceMod.F90:: reading fates_history_height_bin_edges + clmfates_interfaceMod.F90:: reading fates_fire_active_crown_fire + clmfates_interfaceMod.F90:: reading fates_fire_cg_strikes + clmfates_interfaceMod.F90:: reading fates_history_coageclass_bin_edges + clmfates_interfaceMod.F90:: reading fates_fire_fdi_a + clmfates_interfaceMod.F90:: reading fates_fire_fdi_b + clmfates_interfaceMod.F90:: reading fates_fire_fdi_alpha + clmfates_interfaceMod.F90:: reading fates_fire_miner_total + clmfates_interfaceMod.F90:: reading fates_fire_fuel_energy + clmfates_interfaceMod.F90:: reading fates_fire_part_dens + clmfates_interfaceMod.F90:: reading fates_fire_miner_damp + clmfates_interfaceMod.F90:: reading fates_fire_max_durat + clmfates_interfaceMod.F90:: reading fates_fire_durat_slope + clmfates_interfaceMod.F90:: reading fates_fire_drying_ratio + clmfates_interfaceMod.F90:: reading fates_fire_threshold + clmfates_interfaceMod.F90:: reading fates_CWD_frac + clmfates_interfaceMod.F90:: reading fates_fire_SAV + clmfates_interfaceMod.F90:: reading fates_fire_FBD + clmfates_interfaceMod.F90:: reading fates_fire_min_moisture + clmfates_interfaceMod.F90:: reading fates_fire_mid_moisture + clmfates_interfaceMod.F90:: reading fates_fire_low_moisture_Coeff + clmfates_interfaceMod.F90:: reading fates_fire_low_moisture_Slope + clmfates_interfaceMod.F90:: reading fates_fire_mid_moisture_Coeff + clmfates_interfaceMod.F90:: reading fates_fire_mid_moisture_Slope + clmfates_interfaceMod.F90:: reading fates_max_decomp + clmfates_interfaceMod.F90:: reading fates_phen_stress_decid + clmfates_interfaceMod.F90:: reading fates_phen_season_decid + clmfates_interfaceMod.F90:: reading fates_phen_evergreen + clmfates_interfaceMod.F90:: reading fates_fnrt_prof_a + clmfates_interfaceMod.F90:: reading fates_fnrt_prof_b + clmfates_interfaceMod.F90:: reading fates_fnrt_prof_mode + clmfates_interfaceMod.F90:: reading fates_woody + clmfates_interfaceMod.F90:: reading fates_wood_density + clmfates_interfaceMod.F90:: reading fates_leaf_slamax + clmfates_interfaceMod.F90:: reading fates_leaf_slatop + clmfates_interfaceMod.F90:: reading fates_allom_sai_scaler + clmfates_interfaceMod.F90:: reading fates_seed_dbh_repro_threshold + clmfates_interfaceMod.F90:: reading fates_alloc_storage_cushion + clmfates_interfaceMod.F90:: reading fates_leaf_stor_priority + clmfates_interfaceMod.F90:: reading fates_senleaf_long_fdrought + clmfates_interfaceMod.F90:: reading fates_root_long + clmfates_interfaceMod.F90:: reading fates_seed_alloc_mature + clmfates_interfaceMod.F90:: reading fates_seed_alloc + clmfates_interfaceMod.F90:: reading fates_c2b + clmfates_interfaceMod.F90:: reading fates_allom_l2fr + clmfates_interfaceMod.F90:: reading fates_grperc + clmfates_interfaceMod.F90:: reading fates_allom_dbh_maxheight + clmfates_interfaceMod.F90:: reading fates_allom_hmode + clmfates_interfaceMod.F90:: reading fates_allom_lmode + clmfates_interfaceMod.F90:: reading fates_allom_fmode + clmfates_interfaceMod.F90:: reading fates_allom_amode + clmfates_interfaceMod.F90:: reading fates_allom_stmode + clmfates_interfaceMod.F90:: reading fates_allom_cmode + clmfates_interfaceMod.F90:: reading fates_allom_smode + clmfates_interfaceMod.F90:: reading fates_allom_la_per_sa_int + clmfates_interfaceMod.F90:: reading fates_allom_la_per_sa_slp + clmfates_interfaceMod.F90:: reading fates_allom_agb_frac + clmfates_interfaceMod.F90:: reading fates_allom_d2h1 + clmfates_interfaceMod.F90:: reading fates_allom_d2h2 + clmfates_interfaceMod.F90:: reading fates_allom_d2h3 + clmfates_interfaceMod.F90:: reading fates_allom_d2bl1 + clmfates_interfaceMod.F90:: reading fates_allom_d2bl2 + clmfates_interfaceMod.F90:: reading fates_allom_d2bl3 + clmfates_interfaceMod.F90:: reading fates_allom_blca_expnt_diff + clmfates_interfaceMod.F90:: reading fates_allom_d2ca_coefficient_max + clmfates_interfaceMod.F90:: reading fates_allom_d2ca_coefficient_min + clmfates_interfaceMod.F90:: reading fates_allom_agb1 + clmfates_interfaceMod.F90:: reading fates_allom_agb2 + clmfates_interfaceMod.F90:: reading fates_allom_agb3 + clmfates_interfaceMod.F90:: reading fates_allom_agb4 + clmfates_interfaceMod.F90:: reading fates_turnover_retrans_mode + clmfates_interfaceMod.F90:: reading fates_branch_turnover + clmfates_interfaceMod.F90:: reading fates_prt_nitr_stoich_p1 + clmfates_interfaceMod.F90:: reading fates_prt_nitr_stoich_p2 + clmfates_interfaceMod.F90:: reading fates_prt_phos_stoich_p1 + clmfates_interfaceMod.F90:: reading fates_prt_phos_stoich_p2 + clmfates_interfaceMod.F90:: reading fates_prt_alloc_priority + clmfates_interfaceMod.F90:: reading fates_turnover_carb_retrans + clmfates_interfaceMod.F90:: reading fates_turnover_nitr_retrans + clmfates_interfaceMod.F90:: reading fates_turnover_phos_retrans + clmfates_interfaceMod.F90:: reading fates_leaf_long + (GETFIL): attempting to find local file clm5_params.c200402.nc + (GETFIL): using /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/lnd/clm2/paramdata/clm5_params.c200402.nc + Opened existing file /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/lnd/clm2/paramdata/clm5_params.c200402.nc 458752 + + ---clm_ptrs_check: + clm_ptrs_check: g index ranges - OK + clm_ptrs_check: l index ranges - OK + clm_ptrs_check: c index ranges - OK + clm_ptrs_check: p index ranges - OK + clm_ptrs_check: l mono increasing - OK + clm_ptrs_check: c mono increasing - OK + clm_ptrs_check: p mono increasing - OK + clm_ptrs_check: tree consistent - OK + + Surface Grid Characteristics + longitude points = 1 + latitude points = 1 + total number of gridcells = 1 + total number of landunits = 2 + total number of columns = 2 + total number of patches = 18 + total number of cohorts = 1680 + Decomposition Characteristics + clumps per process = 1 + gsMap Characteristics + lnd gsmap glo num of segs = 1 + gce gsmap glo num of segs = 1 + lun gsmap glo num of segs = 1 + col gsmap glo num of segs = 1 + patch gsmap glo num of segs = 1 + coh gsmap glo num of segs = 1 + + + proc= 0 beg gridcell= 1 end gridcell= 1 total gridcells per proc= 1 + proc= 0 beg landunit= 1 end landunit= 2 total landunits per proc= 2 + proc= 0 beg column = 1 end column = 2 total columns per proc = 2 + proc= 0 beg patch = 1 end patch = 18 total patches per proc = 18 + proc= 0 beg coh = 1 end coh = 1680 total coh per proc = 1680 + proc= 0 lnd ngseg = 1 lnd nlseg = 1 + proc= 0 gce ngseg = 1 gce nlseg = 1 + proc= 0 lun ngseg = 1 lun nlseg = 1 + proc= 0 col ngseg = 1 col nlseg = 1 + proc= 0 patch ngseg = 1 patch nlseg = 1 + proc= 0 coh ngseg = 1 coh nlseg = 1 + proc= 0 nclumps = 1 + proc= 0 clump no = 1 clump id= 1 beg gridcell= 1 end gridcell= 1 total gridcells per clump= 1 + proc= 0 clump no = 1 clump id= 1 beg landunit= 1 end landunit= 2 total landunits per clump = 2 + proc= 0 clump no = 1 clump id= 1 beg column = 1 end column = 2 total columns per clump = 2 + proc= 0 clump no = 1 clump id= 1 beg patch = 1 end patch = 18 total patches per clump = 18 + proc= 0 clump no = 1 clump id= 1 beg cohort = 1 end cohort = 1680 total cohorts per clump = 1680 + Read in clm_canopy_inparm namelist + (OPNFIL): Successfully opened file lnd_in on unit= 96 + Read in photosyns_inparm namelist + (OPNFIL): Successfully opened file lnd_in on unit= 96 + + photosyns_inparm settings: +&PHOTOSYNS_INPARM + LEAFRESP_METHOD= 0, + LIGHT_INHIBIT=T, + ROOTSTEM_ACC=F, + STOMATALCOND_METHOD="Ball-Berry1987 ", + MODIFYPHOTO_AND_LMR_FORCROP=T, + / + + Read in crop namelist + (OPNFIL): Successfully opened file lnd_in on unit= 96 + baset mapping for ALL crops are constant + + crop settings: +&CROP + BASET_MAPPING="constant ", + BASET_LATVARY_INTERCEPT= 12.000000000000000 , + BASET_LATVARY_SLOPE= 0.40000000000000002 , + / + + paramMod.F90::readParameters :: reading CLM parameters + (GETFIL): attempting to find local file clm5_params.c200402.nc + (GETFIL): using /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/lnd/clm2/paramdata/clm5_params.c200402.nc + Opened existing file /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/lnd/clm2/paramdata/clm5_params.c200402.nc 458752 + Attempting to read CN/BGC shared namelist parameters ..... + Read in bgc_shared namelist from: lnd_in + CN/BGC shared namelist parameters: + + decomp_depth_efolding = 10.000000000000000 + constrain_stress_deciduous_onset = T + + ******** CLM Time Manager Configuration ******** + Calendar type: NO_LEAP + Timestep size (seconds): 1800 + Start date (yr mon day tod): 2000 1 1 0 + Stop date (yr mon day tod): 2000 1 1 1800 + Reference date (yr mon day tod): 2000 1 1 0 + Current step number: 0 + Ending step number: -999999999 + Current date (yr mon day tod): 2000 1 1 0 + ************************************************ + Skip balance checking for the first 2 time steps + (GETFIL): attempting to find local file clm5_params.c200402.nc + (GETFIL): using /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/lnd/clm2/paramdata/clm5_params.c200402.nc + Opened existing file /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/lnd/clm2/paramdata/clm5_params.c200402.nc 458752 + + urbantv_streams settings: + stream_year_first_urbantv = 2000 + stream_year_last_urbantv = 2000 + model_year_align_urbantv = 1 + stream_fldFileName_urbantv = /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/lnd/clm2/urbandata/ALP1/CLM50_tbuildmax_Oleson_2016_0.9x1.25_simyr1849-2106_c160923_ALP1.nc + urbantv_tintalgo = linear + + (shr_strdata_init_streams) stream 1 + (shr_strdata_init_streams) filePath = 1 + (shr_strdata_init_streams) fileName = 1 /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/lnd/clm2/urbandata/ALP1/CLM50_tbuildmax_Oleson_2016_0.9x1.25_simyr1849-2106_c160923_ALP1.nc + (shr_strdata_init_streams) timeName = 1 time + (shr_strdata_init_streams) lonName = 1 lon + (shr_strdata_init_streams) latName = 1 lat + (shr_strdata_init_streams) hgtName = 1 undefined + (shr_strdata_init_streams) maskName = 1 LANDMASK + (shr_strdata_init_streams) areaName = 1 area +(shr_strdata_print) ---------------------------------------------------------- +(shr_strdata_print) name = urban time varying data +(shr_strdata_print) dataMode = NULL +(shr_strdata_print) domainFile = null +(shr_strdata_print) nxg = 1 +(shr_strdata_print) nyg = 1 +(shr_strdata_print) nzg = 1 +(shr_strdata_print) calendar = NO_LEAP +(shr_strdata_print) io_type = 6 +(shr_strdata_print) eccen = 1.000000E+36 +(shr_strdata_print) mvelpp = 1.000000E+36 +(shr_strdata_print) lambm0 = 1.000000E+36 +(shr_strdata_print) obliqr = 1.000000E+36 +(shr_strdata_print) nstreams = 1 +(shr_strdata_print) pio_iotype = 6 +(shr_strdata_print) streams ( 1) = null +(shr_strdata_print) taxMode ( 1) = extend +(shr_strdata_print) dtlimit ( 1) = 1.000000E+30 +(shr_strdata_print) strnxg ( 1) = 1 +(shr_strdata_print) strnyg ( 1) = 1 +(shr_strdata_print) strnzg ( 1) = -1 +(shr_strdata_print) dofill ( 1) = F +(shr_strdata_print) fillalgo( 1) = none +(shr_strdata_print) fillmask( 1) = nomask +(shr_strdata_print) fillread( 1) = NOT_SET +(shr_strdata_print) fillwrit( 1) = NOT_SET +(shr_strdata_print) domaps ( 1) = F +(shr_strdata_print) mapalgo ( 1) = nn +(shr_strdata_print) mapmask ( 1) = dstmask +(shr_strdata_print) mapread ( 1) = NOT_SET +(shr_strdata_print) mapwrit ( 1) = NOT_SET +(shr_strdata_print) tintalgo( 1) = linear +(shr_strdata_print) readmode( 1) = single +(shr_strdata_print) +(shr_strdata_print) nvectors = 0 +(shr_strdata_print) ---------------------------------------------------------- +(shr_dmodel_readstrm) open : /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/lnd/clm2/urbandata/ALP1/CLM50_tbuildmax_Oleson_2016_0.9x1.25_simyr1849-2106_c160923_ALP1.nc +(shr_dmodel_readstrm) file lb: /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/lnd/clm2/urbandata/ALP1/CLM50_tbuildmax_Oleson_2016_0.9x1.25_simyr1849-2106_c160923_ALP1.nc 152 +(shr_dmodel_readstrm) file ub: /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/lnd/clm2/urbandata/ALP1/CLM50_tbuildmax_Oleson_2016_0.9x1.25_simyr1849-2106_c160923_ALP1.nc 152 + (GETFIL): attempting to find local file surfdata_ALP1_simyr2000.nc + (GETFIL): using /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/lnd/clm2/surfdata_map/ALP1/surfdata_ALP1_simyr2000.nc + Opened existing file /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/lnd/clm2/surfdata_map/ALP1/surfdata_ALP1_simyr2000.nc 589824 + zsoi 1.0000000000000000E-002 4.0000000000000001E-002 8.9999999999999997E-002 0.16000000000000000 0.26000000000000001 0.40000000000000002 0.57999999999999996 0.79999999999999993 1.0600000000000001 1.3599999999999999 1.7000000000000002 2.0800000000000001 2.5000000000000000 2.9900000000000002 3.5800000000000001 4.2700000000000005 5.0600000000000005 5.9500000000000002 6.9399999999999995 8.0299999999999994 9.7949999999999999 13.327766952966369 19.483129170124386 28.870724434316031 41.998436864002869 + zisoi: 0.0000000000000000 2.0000000000000000E-002 5.9999999999999998E-002 0.12000000000000000 0.20000000000000001 0.32000000000000001 0.47999999999999998 0.67999999999999994 0.91999999999999993 1.2000000000000000 1.5200000000000000 1.8800000000000001 2.2800000000000002 2.7200000000000002 3.2600000000000002 3.9000000000000004 4.6400000000000006 5.4800000000000004 6.4199999999999999 7.4600000000000000 8.5999999999999996 10.990000000000000 15.665533905932739 23.300724434316031 34.440724434316031 49.556149293689714 + dzsoi: 2.0000000000000000E-002 4.0000000000000001E-002 5.9999999999999998E-002 8.0000000000000002E-002 0.12000000000000000 0.16000000000000000 0.20000000000000001 0.23999999999999999 0.28000000000000003 0.32000000000000001 0.36000000000000004 0.40000000000000002 0.44000000000000000 0.54000000000000004 0.64000000000000001 0.73999999999999999 0.84000000000000008 0.93999999999999995 1.0400000000000000 1.1400000000000001 2.3900000000000001 4.6755339059327383 7.6351905283832906 11.140000000000001 15.115424859373686 + dzsoi_decomp: 2.0000000000000000E-002 4.0000000000000001E-002 5.9999999999999998E-002 8.0000000000000002E-002 0.12000000000000000 0.16000000000000000 0.20000000000000001 0.23999999999999999 0.28000000000000003 0.32000000000000001 0.36000000000000004 0.40000000000000002 0.44000000000000000 0.54000000000000004 0.64000000000000001 0.73999999999999999 0.84000000000000008 0.93999999999999995 1.0400000000000000 1.1400000000000001 2.3900000000000001 4.6755339059327383 7.6351905283832906 11.140000000000001 15.115424859373686 + not using use_bedrock!! + jmin_bedrock: 6 + dzmin = 1.0000000000000000E-002 1.4999999999999999E-002 2.5000000000000001E-002 5.5000000000000000E-002 0.11500000000000000 0.23500000000000001 0.47500000000000003 0.95500000000000007 1.9150000000000000 3.8350000000000000 7.6749999999999998 15.355000000000000 + dzmax_l = 2.9999999999999999E-002 7.0000000000000007E-002 0.17999999999999999 0.41000000000000003 0.88000000000000012 1.8300000000000001 3.7400000000000002 7.5700000000000003 15.240000000000000 30.590000000000000 61.299999999999997 1.7976931348623157E+308 + dzmax_u = 2.0000000000000000E-002 5.0000000000000003E-002 0.11000000000000000 0.23000000000000001 0.47000000000000003 0.95000000000000007 1.9100000000000001 3.8300000000000001 7.6699999999999999 15.350000000000000 30.710000000000001 1.7976931348623157E+308 + (OPNFIL): Successfully opened file lnd_in on unit= 96 + + atm2lnd_inparm settings: + repartition_rain_snow = T + glcmec_downscale_longwave = T + lapse_rate = 6.0000000000000001E-003 + lapse_rate_longwave = 3.2000000000000001E-002 + longwave_downscaling_limit = 0.50000000000000000 + precip_repartition_glc_all_snow_t = -2.0000000000000000 + precip_repartition_glc_all_rain_t = 0.0000000000000000 + precip_repartition_nonglc_all_snow_t = 0.0000000000000000 + precip_repartition_nonglc_all_rain_t = 2.0000000000000000 + + Read in lnd2atm_inparm namelist + (OPNFIL): Successfully opened file lnd_in on unit= 96 + + lnd2atm_inparm settings: +&LND2ATM_INPARM + MELT_NON_ICESHEET_ICE_RUNOFF=T, + / + + Read in clm_soilstate_inparm namelist + (OPNFIL): Successfully opened file lnd_in on unit= 96 + (GETFIL): attempting to find local file clm5_params.c200402.nc + (GETFIL): using /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/lnd/clm2/paramdata/clm5_params.c200402.nc + Opened existing file /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/lnd/clm2/paramdata/clm5_params.c200402.nc 589824 + Attempting to read soil color, sand and clay boundary data ..... + (GETFIL): attempting to find local file surfdata_ALP1_simyr2000.nc + (GETFIL): using /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/lnd/clm2/surfdata_map/ALP1/surfdata_ALP1_simyr2000.nc + Opened existing file /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/lnd/clm2/surfdata_map/ALP1/surfdata_ALP1_simyr2000.nc 589824 + Attempting to read organic matter data ..... + organicrd /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/lnd/clm2/surfdata_map/ALP1/surfdata_ALP1_simyr2000.nc + (GETFIL): attempting to find local file surfdata_ALP1_simyr2000.nc + (GETFIL): using /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/lnd/clm2/surfdata_map/ALP1/surfdata_ALP1_simyr2000.nc + Opened existing file /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/lnd/clm2/surfdata_map/ALP1/surfdata_ALP1_simyr2000.nc 655360 + Successfully read organic matter data + + Read in water_tracers namelist + (OPNFIL): Successfully opened file lnd_in on unit= 96 + + water_tracers settings +&WATER_TRACERS_INPARM + ENABLE_WATER_TRACER_CONSISTENCY_CHECKS=F, + ENABLE_WATER_ISOTOPES=F, + / + + Read in aerosol namelist + (OPNFIL): Successfully opened file lnd_in on unit= 96 + + aerosol settings: +&AEROSOL + FRESH_SNW_RDS_MAX= 204.52600000000001 , + / + + Read in friction_velocity namelist + (OPNFIL): Successfully opened file lnd_in on unit= 96 + + friction_velocity settings: +&FRICTION_VELOCITY + ZETAMAXSTABLE= 0.50000000000000000 , + / + + (GETFIL): attempting to find local file surfdata_ALP1_simyr2000.nc + (GETFIL): using /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/lnd/clm2/surfdata_map/ALP1/surfdata_ALP1_simyr2000.nc + Opened existing file /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/lnd/clm2/surfdata_map/ALP1/surfdata_ALP1_simyr2000.nc 589824 + ncd_inqvid: variable ETALAKE is not on dataset + WARNING:: ETALAKE not found on surface data set. All lake columns will have eta set equal to default value as a function of depth. + ncd_inqvid: variable LAKEFETCH is not on dataset + WARNING:: LAKEFETCH not found on surface data set. All lake columns will have fetch set equal to default value as a function of depth. + Attempting to initialize time invariant variables for lakes + Successfully initialized time invariant variables for lakes + Read in clm_soilhydrology_inparm namelist + (OPNFIL): Successfully opened file lnd_in on unit= 96 + (GETFIL): attempting to find local file surfdata_ALP1_simyr2000.nc + (GETFIL): using /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/lnd/clm2/surfdata_map/ALP1/surfdata_ALP1_simyr2000.nc + Opened existing file /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/lnd/clm2/surfdata_map/ALP1/surfdata_ALP1_simyr2000.nc 589824 + Attempting to read soil colo data ..... + Read in scf_swenson_lawrence_2012_inparm namelist + (OPNFIL): Successfully opened file lnd_in on unit= 96 + + scf_swenson_lawrence_2012_inparm settings: +&SCF_SWENSON_LAWRENCE_2012_INPARM + INT_SNOW_MAX= 2000.0000000000000 , + N_MELT_GLCMEC= 10.000000000000000 , + / + + Read in irrigation_inparm namelist + (OPNFIL): Successfully opened file lnd_in on unit= 96 + + irrigation_inparm settings: + irrig_min_lai = 0.0000000000000000 + irrig_start_time = 21600 + irrig_length = 14400 + irrig_target_smp = -3400.0000000000000 + irrig_depth = 0.59999999999999998 + irrig_threshold_fraction = 1.0000000000000000 + limit_irrigation_if_rof_enabled = F + use_groundwater_irrigation = F + irrig_method_default = drip + + Spinup_state 0 + Spinup factors 1.0000000000000000 1.0000000000000000 1.0000000000000000 1.0000000000000000 5.0000000000000000 222.22222900390625 + (GETFIL): attempting to find local file surfdata_ALP1_simyr2000.nc + (GETFIL): using /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/lnd/clm2/surfdata_map/ALP1/surfdata_ALP1_simyr2000.nc + Opened existing file /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/lnd/clm2/surfdata_map/ALP1/surfdata_ALP1_simyr2000.nc 589824 + Successfully read fmax, soil color, sand and clay boundary data + + Read in lifire_inparm namelist + (OPNFIL): Successfully opened file lnd_in on unit= 96 + + lifire_inparm settings: +&LIFIRE_INPARM + CLI_SCALE= 3.5000000000000003E-002, + BOREAL_PEATFIRE_C= 4.1999999999999998E-005, + POT_HMN_IGN_COUNTS_ALPHA= 3.5000000000000001E-003, + NON_BOREAL_PEATFIRE_C= 1.0000000000000000E-003, + CROPFIRE_A1= 0.29999999999999999 , + RH_LOW= 30.000000000000000 , + RH_HGH= 80.000000000000000 , + BT_MIN= 0.29999999999999999 , + BT_MAX= 0.69999999999999996 , + OCCUR_HI_GDP_TREE= 0.39000000000000001 , + LFUEL= 75.000000000000000 , + UFUEL= 650.00000000000000 , + CMB_CMPLT_FACT= 0.50000000000000000 , 0.25000000000000000 , + / + + + Initializing variables for time accumulation ..... +------------------------------------------------------------ + Accumulated fields + No Name Units Type Period Inival Description +_______________________________________________________________________ + 1 FSD24 W/m2 runmean 48 0. 24hr average of direct solar radiation + 2 FSD240 W/m2 runmean 480 0. 240hr average of direct solar radiation + 3 FSI24 W/m2 runmean 48 0. 24hr average of diffuse solar radiation + 4 FSI240 W/m2 runmean 480 0. 240hr average of diffuse solar radiation + 5 WIND24 m runmean 48 0. 24hr average of wind + 6 T_VEG24 K runmean 48 0. 24hr average of vegetation temperature + 7 T_VEG240 K runmean 480 0. 240hr average of vegetation temperature + 8 TREFAV K timeavg 2 0. average over an hour of 2-m temperature + 9 TREFAV_U K timeavg 2 0. average over an hour of urban 2-m temper + 10 TREFAV_R K timeavg 2 0. average over an hour of rural 2-m temper + 11 T10 K runmean 480 293. 10-day running mean of 2-m temperature + 12 PREC24 m runmean 48 0. 24hr sum of precipitation + 13 RH24 m runmean 48 100. 24hr average of RH + 14 BTRANAV - timeavg 2 0. average over an hour of btran + 15 FSUN24 fraction runmean 48 0. 24hr average of diffuse solar radiation + 16 FSUN240 fraction runmean 480 0. 240hr average of diffuse solar radiation + 17 LAI240 m2/m2 runmean 480 0. 240hr average of leaf area index +_______________________________________________________________________ + +------------------------------------------------------------ + Successfully initialized variables for accumulation + + Attempting to read snow optical properties ..... + (GETFIL): attempting to find local file snicar_optics_5bnd_c090915.nc + (GETFIL): using /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/lnd/clm2/snicardata/snicar_optics_5bnd_c090915.nc + Opened existing file /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/lnd/clm2/snicardata/snicar_optics_5bnd_c090915.nc 458752 + SnowOptics_init /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/lnd/clm2/snicardata/snicar_optics_5bnd_c090915.nc + Successfully read snow optical properties + SNICAR: Mie single scatter albedos for direct-beam ice, rds=100um: 0.99998855464297542 0.99968103719886303 0.99760760567597084 0.98649793425058974 0.86362501115905810 + SNICAR: Mie single scatter albedos for diffuse ice, rds=100um: 0.99998868830564358 0.99969570486702131 0.99764126147987453 0.98842452132814818 0.87409591319270097 + SNICAR: Excluding OC aerosols from snow radiative transfer calculations + SNICAR: Mie single scatter albedos for hydrophillic BC: 0.51594530551280438 0.43431362653642447 0.34610376599263543 0.27552292633055464 0.13857609644281504 + SNICAR: Mie single scatter albedos for hydrophobic BC: 0.28768531597618147 0.18657727712522390 0.12315223708920099 8.8346288590554295E-002 4.0342156226937813E-002 + SNICAR: Mie single scatter albedos for dust species 1: 0.97891105715304971 0.99417591604245092 0.99335758076220670 0.99254575131626566 0.95329155004677202 + SNICAR: Mie single scatter albedos for dust species 2: 0.94375224880279296 0.98419166859941920 0.98930906391702478 0.99179394683626376 0.98299959066891252 + SNICAR: Mie single scatter albedos for dust species 3: 0.90404453064604895 0.96465162969455487 0.96827580955152159 0.97259841987410656 0.97761241832987633 + SNICAR: Mie single scatter albedos for dust species 4: 0.84981819535541647 0.94046032504434285 0.94831630553416912 0.95284117511780686 0.95537952819380212 + + Attempting to read snow aging parameters ..... + (GETFIL): attempting to find local file snicar_drdt_bst_fit_60_c070416.nc + (GETFIL): using /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/lnd/clm2/snicardata/snicar_drdt_bst_fit_60_c070416.nc + Opened existing file /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/lnd/clm2/snicardata/snicar_drdt_bst_fit_60_c070416.nc 458752 + SnowOptics_init /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/lnd/clm2/snicardata/snicar_drdt_bst_fit_60_c070416.nc + Successfully read snow aging properties + SNICAR: snowage tau for T=263K, dTdz = 100 K/m, rhos = 150 kg/m3: 6.3205800298267860 + SNICAR: snowage kappa for T=263K, dTdz = 100 K/m, rhos = 150 kg/m3: 1.5669689418953008 + SNICAR: snowage dr/dt_0 for T=263K, dTdz = 100 K/m, rhos = 150 kg/m3: 5.4872755027422642 + CLM_hist_printflds : number of master fields = 882 + ******* MASTER FIELD LIST ******* + 1 SNO_Z m + 2 SNO_Z_ICE m + 3 ZII m + 4 SWBGT C + 5 SWBGT_U C + 6 SWBGT_R C + 7 HUMIDEX C + 8 HUMIDEX_U C + 9 HUMIDEX_R C + 10 WBT C + 11 WBT_U C + 12 WBT_R C + 13 HIA C + 14 HIA_U C + 15 HIA_R C + 16 TBUILD_MAX K + 17 WIND m/s + 18 Wind m/s + 19 ZBOT m + 20 ATM_TOPO m + 21 FSDS W/m^2 + 22 PCO2 Pa + 23 SWdown W/m^2 + 24 Tair_from_atm K + 25 TBOT K + 26 Tair K + 27 PBOT Pa + 28 PSurf Pa + 29 FLDS W/m^2 + 30 LWdown W/m^2 + 31 FLDS_ICE W/m^2 + 32 THBOT K + 33 FSI24 K + 34 FSI240 K + 35 FSD24 K + 36 FSD240 K + 37 FSH_TO_COUPLER W/m^2 + 38 FSH_RUNOFF_ICE_TO_LIQ W/m^2 + 39 FCO2 kgCO2/m2/s + 40 ICE_MODEL_FRACTION unitless + 41 QICE_FORC mm/s + 42 TSRF_FORC K + 43 TOPO_FORC m + 44 TH2OSFC K + 45 TG_U K + 46 TLAKE K + 47 SNO_T K + 48 SNO_T_ICE K + 49 TSA K + 50 TSA_ICE K + 51 TSA_R K + 52 TREFMNAV K + 53 TREFMXAV K + 54 TREFMNAV_R K + 55 TREFMXAV_R K + 56 TSA_U K + 57 TREFMNAV_U K + 58 TREFMXAV_U K + 59 TV K + 60 TSKIN K + 61 TG K + 62 TG_ICE K + 63 TG_R K + 64 TSOI K + 65 TSOI_ICE K + 66 TSOI_10CM K + 67 TSL K + 68 SNOTXMASS K kg/m2 + 69 SNOTXMASS_ICE K kg/m2 + 70 T10 K + 71 TBUILD K + 72 TROOF_INNER K + 73 TSUNW_INNER K + 74 TSHDW_INNER K + 75 TFLOOR K + 76 HEAT_CONTENT1 J/m^2 + 77 HEAT_CONTENT1_VEG J/m^2 + 78 HEAT_CONTENT2 J/m^2 + 79 LIQUID_WATER_TEMP1 K + 80 SNOTTOPL K + 81 SNOTTOPL_ICE K + 82 SNOdTdzL K/m + 83 TV24 K + 84 TV240 K + 85 ALT m + 86 ALTMAX m + 87 ALTMAX_LASTYEAR m + 88 ELAI m^2/m^2 + 89 ESAI m^2/m^2 + 90 TLAI m^2/m^2 + 91 TSAI m^2/m^2 + 92 LAISUN m^2/m^2 + 93 LAISHA m^2/m^2 + 94 FSUN proportion + 95 HTOP m + 96 HBOT m + 97 DISPLA m + 98 Z0M m + 99 FSUN24 K + 100 FSUN240 K + 101 LAI240 m^2/m^2 + 102 RSCANOPY s m-1 + 103 SMP mm + 104 KROOT 1/s + 105 KSOIL 1/s + 106 SOILPSI MPa + 107 SNO_TK W/m-K + 108 SNO_TK_ICE W/m-K + 109 HK mm/s + 110 SoilAlpha unitless + 111 SoilAlpha_U unitless + 112 SOILRESIS s/m + 113 DSL mm + 114 SNO_LIQH2O kg/m2 + 115 SNO_ICE kg/m2 + 116 H2OSOI mm3/mm3 + 117 SOILLIQ kg/m2 + 118 SOILICE kg/m2 + 119 SNOCAN mm + 120 LIQCAN mm + 121 H2OSFC mm + 122 WA mm + 123 INT_SNOW mm + 124 INT_SNOW_ICE mm + 125 SNOW_PERSISTENCE seconds + 126 H2OCAN mm + 127 SOILWATER_10CM kg/m2 + 128 TWS mm + 129 Q2M kg/kg + 130 SNOWLIQ kg/m2 + 131 SNOWLIQ_ICE kg/m2 + 132 SNOWICE kg/m2 + 133 SNOWICE_ICE kg/m2 + 134 H2OSNO mm + 135 H2OSNO_ICE mm + 136 TOTSOILLIQ kg/m2 + 137 TOTSOILICE kg/m2 + 138 RH2M % + 139 RH2M_R % + 140 RH2M_U % + 141 RHAF fraction + 142 FH2OSFC unitless + 143 FH2OSFC_NOSNOW unitless + 144 FSNO unitless + 145 FSNO_ICE unitless + 146 FSNO_EFF unitless + 147 SNOW_DEPTH m + 148 SNOW_DEPTH_ICE m + 149 SNOWDP m + 150 H2OSNO_TOP kg/m2 + 151 SNORDSL m^-6 + 152 SNOLIQFL fraction + 153 SNO_EXISTENCE unitless + 154 SNO_BW kg/m3 + 155 SNO_BW_ICE kg/m3 + 156 SNO_GS Microns + 157 SNO_GS_ICE Microns + 158 QINTR mm/s + 159 SNOW_SOURCES mm/s + 160 SNOW_SINKS mm/s + 161 LIQUID_CONTENT1 mm + 162 LIQUID_CONTENT2 mm + 163 ICE_CONTENT1 mm + 164 ICE_CONTENT2 mm + 165 ERRH2O mm + 166 ERRH2OSNO mm + 167 QDIRECT_THROUGHFALL mm/s + 168 QDIRECT_THROUGHFALL_SNOW mm/s + 169 QDRIP mm/s + 170 QDRIP_SNOW mm/s + 171 QSNOUNLOAD mm/s + 172 QTOPSOIL mm/s + 173 QINFL mm/s + 174 QOVER mm/s + 175 QRGWL mm/s + 176 QDRAI mm/s + 177 QDRAI_PERCH mm/s + 178 QFLX_LIQ_DYNBAL mm/s + 179 QFLX_ICE_DYNBAL mm/s + 180 QRUNOFF mm/s + 181 QRUNOFF_ICE mm/s + 182 QRUNOFF_U mm/s + 183 QRUNOFF_R mm/s + 184 QSNOMELT mm/s + 185 QSNOMELT_ICE mm/s + 186 QSNOFRZ kg/m2/s + 187 QSNOFRZ_ICE mm/s + 188 SNO_FRZ kg/m2/s + 189 SNO_FRZ_ICE mm/s + 190 QFLX_SNOW_DRAIN mm/s + 191 QFLX_SNOW_DRAIN_ICE mm/s + 192 QSOIL mm/s + 193 QSOIL_ICE mm/s + 194 QVEGE mm/s + 195 QVEGT mm/s + 196 QSNOCPLIQ mm H2O/s + 197 QSNWCPICE mm H2O/s + 198 QICE mm/s + 199 QICE_FRZ mm/s + 200 QICE_MELT mm/s + 201 QFLX_LIQ_GRND mm H2O/s + 202 QFLX_SNOW_GRND mm H2O/s + 203 QFLX_LIQEVAP_FROM_TOP_LAYER mm H2O/s + 204 QFLX_EVAP_VEG mm H2O/s + 205 QFLX_EVAP_TOT kg m-2 s-1 + 206 QFLX_LIQDEW_TO_TOP_LAYER mm H2O/s + 207 QFLX_SOLIDEVAP_FROM_TOP_LAYER mm H2O/s + 208 QFLX_SOLIDEVAP_FROM_TOP_LAYER_IC mm H2O/s + 209 QFLX_SOLIDDEW_TO_TOP_LAYER mm H2O/s + 210 QDRAI_XS mm/s + 211 QH2OSFC_TO_ICE mm/s + 212 QIRRIG_FROM_SURFACE mm/s + 213 QIRRIG_FROM_GW_UNCONFINED mm/s + 214 QIRRIG_FROM_GW_CONFINED mm/s + 215 QIRRIG_DRIP mm/s + 216 QIRRIG_SPRINKLER mm/s + 217 SNO_MELT mm/s + 218 SNO_MELT_ICE mm/s + 219 QROOTSINK mm/s + 220 QSNO_WINDUNLOAD mm/s + 221 QSNO_TEMPUNLOAD mm/s + 222 QSNOEVAP mm/s + 223 QH2OSFC mm/s + 224 QPHSNEG mm/s + 225 AnnET mm/s + 226 QRUNOFF_TO_COUPLER mm/s + 227 QRUNOFF_ICE_TO_COUPLER mm/s + 228 QRUNOFF_ICE_TO_LIQ mm/s + 229 RAIN_FROM_ATM mm/s + 230 SNOW_FROM_ATM mm/s + 231 QBOT kg/kg + 232 Qair kg/kg + 233 QFLOOD mm/s + 234 RAIN mm/s + 235 Rainf mm/s + 236 RAIN_ICE mm/s + 237 SNOW mm/s + 238 SNOW_ICE mm/s + 239 VOLR m3 + 240 VOLRMCH m3 + 241 RH % + 242 EFLX_DYNBAL W/m^2 + 243 FSM W/m^2 + 244 FSM_ICE W/m^2 + 245 FSM_R W/m^2 + 246 FSM_U W/m^2 + 247 FIRA W/m^2 + 248 FIRA_ICE W/m^2 + 249 FIRA_R W/m^2 + 250 FIRE W/m^2 + 251 LWup W/m^2 + 252 FIRE_ICE W/m^2 + 253 FIRE_R W/m^2 + 254 FCTR W/m^2 + 255 FCEV W/m^2 + 256 FGEV W/m^2 + 257 FSH W/m^2 + 258 FSH_ICE W/m^2 + 259 FSH_R W/m^2 + 260 Qh W/m^2 + 261 Qle W/m^2 + 262 EFLX_LH_TOT W/m^2 + 263 EFLX_LH_TOT_ICE W/m^2 + 264 EFLX_LH_TOT_R W/m^2 + 265 Qstor W/m^2 + 266 FSH_V W/m^2 + 267 FSH_G W/m^2 + 268 FGR W/m^2 + 269 FGR_ICE W/m^2 + 270 FGR_R W/m^2 + 271 FIRA_U W/m^2 + 272 EFLX_SOIL_GRND W/m^2 + 273 FIRE_U W/m^2 + 274 FSH_U W/m^2 + 275 FSH_PRECIP_CONVERSION W/m^2 + 276 EFLX_LH_TOT_U W/m^2 + 277 FGR_U W/m^2 + 278 Rnet W/m^2 + 279 EFLX_GRND_LAKE W/m^2 + 280 EFLXBUILD W/m^2 + 281 URBAN_AC W/m^2 + 282 URBAN_HEAT W/m^2 + 283 DGNETDT W/m^2/K + 284 FGR12 W/m^2 + 285 FGR_SOIL_R watt/m^2 + 286 TRAFFICFLUX W/m^2 + 287 WASTEHEAT W/m^2 + 288 HEAT_FROM_AC W/m^2 + 289 TAUX kg/m/s^2 + 290 Qtau kg/m/s^2 + 291 TAUY kg/m/s^2 + 292 BTRAN unitless + 293 BTRANMN unitless + 294 BTRAN2 unitless + 295 ERRSOI W/m^2 + 296 ERRSEB W/m^2 + 297 ERRSOL W/m^2 + 298 DSTDEP kg/m^2/s + 299 BCDEP kg/m^2/s + 300 OCDEP kg/m^2/s + 301 SNOBCMCL kg/m2 + 302 SNOBCMSL kg/m2 + 303 SNOOCMCL kg/m2 + 304 SNOOCMSL kg/m2 + 305 SNODSTMCL kg/m2 + 306 SNODSTMSL kg/m2 + 307 Z0MG m + 308 Z0HG m + 309 Z0QG m + 310 VA m/s + 311 U10 m/s + 312 U10_ICE m/s + 313 U10_DUST m/s + 314 LAKEICEFRAC unitless + 315 LAKEICEFRAC_SURF unitless + 316 LAKEICETHICK m + 317 TKE1 W/(mK) + 318 RAM_LAKE s/m + 319 UST_LAKE m/s + 320 RH_LEAF fraction + 321 LNC gN leaf/m^2 + 322 RSSUN s/m + 323 RSSHA s/m + 324 GSSUN umol H20/m2/s + 325 GSSHA umol H20/m2/s + 326 GSSUNLN umol H20/m2/s + 327 GSSHALN umol H20/m2/s + 328 QCHARGE mm/s + 329 NSUBSTEPS unitless + 330 FROST_TABLE m + 331 ZWT m + 332 ZWT_PERCH m + 333 FCOV unitless + 334 FSAT unitless + 335 FSA W/m^2 + 336 FSA_ICE W/m^2 + 337 FSA_R W/m^2 + 338 FSA_U W/m^2 + 339 FSR W/m^2 + 340 SWup W/m^2 + 341 FSR_ICE W/m^2 + 342 SNO_ABS W/m^2 + 343 SNO_ABS_ICE W/m^2 + 344 SABV W/m^2 + 345 SABG W/m^2 + 346 SABG_PEN watt/m^2 + 347 FSDSND W/m^2 + 348 FSDSNI W/m^2 + 349 FSDSNDLN W/m^2 + 350 FSRND W/m^2 + 351 FSRNI W/m^2 + 352 FSRNDLN W/m^2 + 353 SNOINTABS - + 354 COSZEN none + 355 ALBGRD proportion + 356 ALBGRI proportion + 357 ALBD proportion + 358 ALBI proportion + 359 FSDSVD W/m^2 + 360 FSDSVI W/m^2 + 361 FSRVD W/m^2 + 362 FSRVI W/m^2 + 363 FSDSVDLN W/m^2 + 364 FSDSVILN W/m^2 + 365 PARVEGLN W/m^2 + 366 FSRVDLN W/m^2 + 367 SNOFSDSVD W/m^2 + 368 SNOFSDSND W/m^2 + 369 SNOFSDSVI W/m^2 + 370 SNOFSDSNI W/m^2 + 371 SNOFSRVD W/m^2 + 372 SNOFSRND W/m^2 + 373 SNOFSRVI W/m^2 + 374 SNOFSRNI W/m^2 + 375 DSTFLXT kg/m2/s + 376 DPVLTRB1 m/s + 377 DPVLTRB2 m/s + 378 DPVLTRB3 m/s + 379 DPVLTRB4 m/s + 380 QIRRIG_DEMAND mm/s + 381 TOPO_COL m + 382 TOPO_COL_ICE m + 383 SOILC_vr gC/m^3 + 384 LITR1C_vr gC/m^3 + 385 LITR1C gC/m^2 + 386 LITR1C_1m gC/m^2 + 387 LITR2C_vr gC/m^3 + 388 LITR2C gC/m^2 + 389 LITR2C_1m gC/m^2 + 390 LITR3C_vr gC/m^3 + 391 LITR3C gC/m^2 + 392 LITR3C_1m gC/m^2 + 393 SOIL1C_vr gC/m^3 + 394 SOIL1C gC/m^2 + 395 SOIL1C_1m gC/m^2 + 396 SOIL2C_vr gC/m^3 + 397 SOIL2C gC/m^2 + 398 SOIL2C_1m gC/m^2 + 399 SOIL3C_vr gC/m^3 + 400 SOIL3C gC/m^2 + 401 SOIL3C_1m gC/m^2 + 402 TOTLITC gC/m^2 + 403 TOTSOMC gC/m^2 + 404 TOTLITC_1m gC/m^2 + 405 TOTSOMC_1m gC/m^2 + 406 COL_CTRUNC gC/m^2 + 407 DYN_COL_SOIL_ADJUSTMENTS_C gC/m^2 + 408 HR gC/m^2/s + 409 LITTERC_HR gC/m^2/s + 410 SOILC_HR gC/m^2/s + 411 SOMC_FIRE gC/m^2/s + 412 K_LITR1 1/s + 413 K_LITR2 1/s + 414 K_LITR3 1/s + 415 K_SOIL1 1/s + 416 K_SOIL2 1/s + 417 K_SOIL3 1/s + 418 LITR1_HR gC/m^2/s + 419 LITR1C_TO_SOIL1C gC/m^2/s + 420 LITR1_HR_vr gC/m^3/s + 421 LITR1C_TO_SOIL1C_vr gC/m^3/s + 422 LITR2_HR gC/m^2/s + 423 LITR2C_TO_SOIL1C gC/m^2/s + 424 LITR2_HR_vr gC/m^3/s + 425 LITR2C_TO_SOIL1C_vr gC/m^3/s + 426 LITR3_HR gC/m^2/s + 427 LITR3C_TO_SOIL2C gC/m^2/s + 428 LITR3_HR_vr gC/m^3/s + 429 LITR3C_TO_SOIL2C_vr gC/m^3/s + 430 SOIL1_HR_S2 gC/m^2/s + 431 SOIL1C_TO_SOIL2C gC/m^2/s + 432 SOIL1_HR_S2_vr gC/m^3/s + 433 SOIL1C_TO_SOIL2C_vr gC/m^3/s + 434 SOIL1_HR_S3 gC/m^2/s + 435 SOIL1C_TO_SOIL3C gC/m^2/s + 436 SOIL1_HR_S3_vr gC/m^3/s + 437 SOIL1C_TO_SOIL3C_vr gC/m^3/s + 438 SOIL2_HR_S1 gC/m^2/s + 439 SOIL2C_TO_SOIL1C gC/m^2/s + 440 SOIL2_HR_S1_vr gC/m^3/s + 441 SOIL2C_TO_SOIL1C_vr gC/m^3/s + 442 SOIL2_HR_S3 gC/m^2/s + 443 SOIL2C_TO_SOIL3C gC/m^2/s + 444 SOIL2_HR_S3_vr gC/m^3/s + 445 SOIL2C_TO_SOIL3C_vr gC/m^3/s + 446 SOIL3_HR gC/m^2/s + 447 SOIL3C_TO_SOIL1C gC/m^2/s + 448 SOIL3_HR_vr gC/m^3/s + 449 SOIL3C_TO_SOIL1C_vr gC/m^3/s + 450 T_SCALAR unitless + 451 W_SCALAR unitless + 452 O_SCALAR unitless + 453 SOM_C_LEACHED gC/m^2/s + 454 M_LITR1C_TO_LEACHING gC/m^2/s + 455 LITR1C_TNDNCY_VERT_TRANS gC/m^3/s + 456 M_LITR2C_TO_LEACHING gC/m^2/s + 457 LITR2C_TNDNCY_VERT_TRANS gC/m^3/s + 458 M_LITR3C_TO_LEACHING gC/m^2/s + 459 LITR3C_TNDNCY_VERT_TRANS gC/m^3/s + 460 M_SOIL1C_TO_LEACHING gC/m^2/s + 461 SOIL1C_TNDNCY_VERT_TRANS gC/m^3/s + 462 M_SOIL2C_TO_LEACHING gC/m^2/s + 463 SOIL2C_TNDNCY_VERT_TRANS gC/m^3/s + 464 M_SOIL3C_TO_LEACHING gC/m^2/s + 465 SOIL3C_TNDNCY_VERT_TRANS gC/m^3/s + 466 HR_vr gC/m^3/s + 467 FATES_c_to_litr_lab_c gC/m^3/s + 468 FATES_c_to_litr_cel_c gC/m^3/s + 469 FATES_c_to_litr_lig_c gC/m^3/s + 470 SOILN_vr gN/m^3 + 471 LITR1N_vr gN/m^3 + 472 LITR1N gN/m^2 + 473 LITR1N_1m gN/m^2 + 474 LITR2N_vr gN/m^3 + 475 LITR2N gN/m^2 + 476 LITR2N_1m gN/m^2 + 477 LITR3N_vr gN/m^3 + 478 LITR3N gN/m^2 + 479 LITR3N_1m gN/m^2 + 480 SOIL1N_vr gN/m^3 + 481 SOIL1N gN/m^2 + 482 SOIL1N_1m gN/m^2 + 483 SOIL2N_vr gN/m^3 + 484 SOIL2N gN/m^2 + 485 SOIL2N_1m gN/m^2 + 486 SOIL3N_vr gN/m^3 + 487 SOIL3N gN/m^2 + 488 SOIL3N_1m gN/m^2 + 489 SMINN gN/m^2 + 490 TOTLITN_1m gN/m^2 + 491 TOTSOMN_1m gN/m^2 + 492 COL_NTRUNC gN/m^2 + 493 SMINN_vr gN/m^3 + 494 TOTLITN gN/m^2 + 495 TOTSOMN gN/m^2 + 496 DYN_COL_SOIL_ADJUSTMENTS_N gN/m^2 + 497 NDEP_TO_SMINN gN/m^2/s + 498 NFIX_TO_SMINN gN/m^2/s + 499 SMINN_TO_SOIL1N_L1 gN/m^2 + 500 LITR1N_TO_SOIL1N gN/m^2 + 501 SMINN_TO_SOIL1N_L1_vr gN/m^3 + 502 LITR1N_TO_SOIL1N_vr gN/m^3 + 503 SMINN_TO_SOIL1N_L2 gN/m^2 + 504 LITR2N_TO_SOIL1N gN/m^2 + 505 SMINN_TO_SOIL1N_L2_vr gN/m^3 + 506 LITR2N_TO_SOIL1N_vr gN/m^3 + 507 SMINN_TO_SOIL2N_L3 gN/m^2 + 508 LITR3N_TO_SOIL2N gN/m^2 + 509 SMINN_TO_SOIL2N_L3_vr gN/m^3 + 510 LITR3N_TO_SOIL2N_vr gN/m^3 + 511 SMINN_TO_SOIL2N_S1 gN/m^2 + 512 SOIL1N_TO_SOIL2N gN/m^2 + 513 SMINN_TO_SOIL2N_S1_vr gN/m^3 + 514 SOIL1N_TO_SOIL2N_vr gN/m^3 + 515 SMINN_TO_SOIL3N_S1 gN/m^2 + 516 SOIL1N_TO_SOIL3N gN/m^2 + 517 SMINN_TO_SOIL3N_S1_vr gN/m^3 + 518 SOIL1N_TO_SOIL3N_vr gN/m^3 + 519 SMINN_TO_SOIL1N_S2 gN/m^2 + 520 SOIL2N_TO_SOIL1N gN/m^2 + 521 SMINN_TO_SOIL1N_S2_vr gN/m^3 + 522 SOIL2N_TO_SOIL1N_vr gN/m^3 + 523 SMINN_TO_SOIL3N_S2 gN/m^2 + 524 SOIL2N_TO_SOIL3N gN/m^2 + 525 SMINN_TO_SOIL3N_S2_vr gN/m^3 + 526 SOIL2N_TO_SOIL3N_vr gN/m^3 + 527 SMINN_TO_SOIL1N_S3 gN/m^2 + 528 SOIL3N_TO_SOIL1N gN/m^2 + 529 SMINN_TO_SOIL1N_S3_vr gN/m^3 + 530 SOIL3N_TO_SOIL1N_vr gN/m^3 + 531 DENIT gN/m^2/s + 532 SOM_N_LEACHED gN/m^2/s + 533 M_LITR1N_TO_LEACHING gN/m^2/s + 534 LITR1N_TNDNCY_VERT_TRANS gN/m^3/s + 535 M_LITR2N_TO_LEACHING gN/m^2/s + 536 LITR2N_TNDNCY_VERT_TRANS gN/m^3/s + 537 M_LITR3N_TO_LEACHING gN/m^2/s + 538 LITR3N_TNDNCY_VERT_TRANS gN/m^3/s + 539 M_SOIL1N_TO_LEACHING gN/m^2/s + 540 SOIL1N_TNDNCY_VERT_TRANS gN/m^3/s + 541 M_SOIL2N_TO_LEACHING gN/m^2/s + 542 SOIL2N_TNDNCY_VERT_TRANS gN/m^3/s + 543 M_SOIL3N_TO_LEACHING gN/m^2/s + 544 SOIL3N_TNDNCY_VERT_TRANS gN/m^3/s + 545 SMINN_TO_DENIT_L1S1 gN/m^2 + 546 SMINN_TO_DENIT_L1S1_vr gN/m^3 + 547 SMINN_TO_DENIT_L2S1 gN/m^2 + 548 SMINN_TO_DENIT_L2S1_vr gN/m^3 + 549 SMINN_TO_DENIT_L3S2 gN/m^2 + 550 SMINN_TO_DENIT_L3S2_vr gN/m^3 + 551 SMINN_TO_DENIT_S1S2 gN/m^2 + 552 SMINN_TO_DENIT_S1S2_vr gN/m^3 + 553 SMINN_TO_DENIT_S1S3 gN/m^2 + 554 SMINN_TO_DENIT_S1S3_vr gN/m^3 + 555 SMINN_TO_DENIT_S2S1 gN/m^2 + 556 SMINN_TO_DENIT_S2S1_vr gN/m^3 + 557 SMINN_TO_DENIT_S2S3 gN/m^2 + 558 SMINN_TO_DENIT_S2S3_vr gN/m^3 + 559 SMINN_TO_DENIT_S3S1 gN/m^2 + 560 SMINN_TO_DENIT_S3S1_vr gN/m^3 + 561 SMINN_TO_DENIT_EXCESS gN/m^2/s + 562 SMINN_LEACHED gN/m^2/s + 563 SMINN_TO_DENIT_EXCESS_vr gN/m^3/s + 564 SMINN_LEACHED_vr gN/m^3/s + 565 POTENTIAL_IMMOB gN/m^2/s + 566 ACTUAL_IMMOB gN/m^2/s + 567 SMINN_TO_PLANT gN/m^2/s + 568 SUPPLEMENT_TO_SMINN gN/m^2/s + 569 GROSS_NMIN gN/m^2/s + 570 NET_NMIN gN/m^2/s + 571 ED_NPATCHES none + 572 ED_NCOHORTS none + 573 TRIMMING none + 574 AREA_PLANT m2 + 575 AREA_TREES m2 + 576 SITE_COLD_STATUS 0,1,2 + 577 SITE_DROUGHT_STATUS 0,1,2,3 + 578 SITE_GDD degC + 579 SITE_NCHILLDAYS days + 580 SITE_NCOLDDAYS days + 581 SITE_DAYSINCE_COLDLEAFOFF days + 582 SITE_DAYSINCE_COLDLEAFON days + 583 SITE_DAYSINCE_DROUGHTLEAFOFF days + 584 SITE_DAYSINCE_DROUGHTLEAFON days + 585 SITE_MEANLIQVOL_DROUGHTPHEN m3/m3 + 586 CANOPY_SPREAD 0-1 + 587 PFTbiomass gC/m2 + 588 PFTleafbiomass gC/m2 + 589 PFTstorebiomass gC/m2 + 590 PFTcrownarea m2/ha + 591 PFTcanopycrownarea m2/ha + 592 PFTnindivs indiv / m2 + 593 RECRUITMENT indiv/ha/yr + 594 MORTALITY indiv/ha/yr + 595 PATCH_AREA_BY_AGE m2/m2 + 596 LAI_BY_AGE m2/m2 + 597 CANOPY_AREA_BY_AGE m2/m2 + 598 NCL_BY_AGE -- + 599 NPATCH_BY_AGE -- + 600 ZSTAR_BY_AGE m + 601 CANOPY_HEIGHT_DIST m2/m2 + 602 LEAF_HEIGHT_DIST m2/m2 + 603 BIOMASS_BY_AGE kgC/m2 + 604 SECONDARY_FOREST_FRACTION m2/m2 + 605 WOOD_PRODUCT gC/m2 + 606 SECONDARY_FOREST_BIOMASS kgC/m2 + 607 SECONDARY_AREA_AGE_ANTHRO_DIST m2/m2 + 608 SECONDARY_AREA_PATCH_AGE_DIST m2/m2 + 609 FIRE_NESTEROV_INDEX none + 610 FIRE_ROS m/min + 611 FIRE_ROS_AREA_PRODUCT m/min + 612 EFFECT_WSPEED none + 613 FIRE_TFC_ROS kgC/m2 + 614 FIRE_TFC_ROS_AREA_PRODUCT kgC/m2 + 615 FIRE_INTENSITY kJ/m/s + 616 FIRE_INTENSITY_AREA_PRODUCT kJ/m/s + 617 FIRE_AREA fraction + 618 FIRE_FUEL_MEF m + 619 FIRE_FUEL_BULKD kg biomass/m3 + 620 FIRE_FUEL_EFF_MOIST m + 621 FIRE_FUEL_SAV per m + 622 SUM_FUEL gC m-2 + 623 FUEL_MOISTURE_NFSC - + 624 AREA_BURNT_BY_PATCH_AGE m2/m2 + 625 FIRE_INTENSITY_BY_PATCH_AGE kJ/m/2 + 626 SUM_FUEL_BY_PATCH_AGE gC / m2 of site + 627 BURNT_LITTER_FRAC_AREA_PRODUCT fraction + 628 LITTER_IN gC m-2 s-1 + 629 LITTER_OUT gC m-2 s-1 + 630 SEED_BANK gC m-2 + 631 SEEDS_IN gC m-2 s-1 + 632 LITTER_IN_ELEM kg ha-1 d-1 + 633 LITTER_OUT_ELEM kg ha-1 d-1 + 634 SEED_BANK_ELEM kg ha-1 + 635 SEEDS_IN_LOCAL_ELEM kg ha-1 d-1 + 636 SEEDS_IN_EXTERN_ELEM kg ha-1 d-1 + 637 SEED_GERM_ELEM kg ha-1 d-1 + 638 SEED_DECAY_ELEM kg ha-1 d-1 + 639 STOREC kgC ha-1 + 640 TOTVEGC kgC ha-1 + 641 SAPWC kgC ha-1 + 642 LEAFC kgC ha-1 + 643 FNRTC kgC ha-1 + 644 REPROC kgC ha-1 + 645 CEFFLUX kgC/ha/day + 646 ED_bstore gC m-2 + 647 ED_bdead gC m-2 + 648 ED_balive gC m-2 + 649 ED_bleaf gC m-2 + 650 ED_bsapwood gC m-2 + 651 ED_bfineroot gC m-2 + 652 ED_biomass gC m-2 + 653 AGB gC m-2 + 654 BIOMASS_CANOPY gC m-2 + 655 BIOMASS_UNDERSTORY gC m-2 + 656 PRIMARYLAND_PATCHFUSION_ERROR m2 m-2 d-1 + 657 DISTURBANCE_RATE_P2P m2 m-2 d-1 + 658 DISTURBANCE_RATE_P2S m2 m-2 d-1 + 659 DISTURBANCE_RATE_S2S m2 m-2 d-1 + 660 DISTURBANCE_RATE_FIRE m2 m-2 d-1 + 661 DISTURBANCE_RATE_LOGGING m2 m-2 d-1 + 662 DISTURBANCE_RATE_TREEFALL m2 m-2 d-1 + 663 DISTURBANCE_RATE_POTENTIAL m2 m-2 d-1 + 664 HARVEST_CARBON_FLUX kg C m-2 d-1 + 665 C_STOMATA umol m-2 s-1 + 666 C_LBLAYER umol m-2 s-1 + 667 NPP gC/m^2/s + 668 GPP gC/m^2/s + 669 AR gC/m^2/s + 670 GROWTH_RESP gC/m^2/s + 671 MAINT_RESP gC/m^2/s + 672 C_STOMATA_BY_AGE umol m-2 s-1 + 673 C_LBLAYER_BY_AGE umol m-2 s-1 + 674 NPP_BY_AGE gC/m^2/s + 675 GPP_BY_AGE gC/m^2/s + 676 GPP_CANOPY gC/m^2/s + 677 AR_CANOPY gC/m^2/s + 678 GPP_UNDERSTORY gC/m^2/s + 679 AR_UNDERSTORY gC/m^2/s + 680 PARSUN_Z_CNLF W/m2 + 681 PARSHA_Z_CNLF W/m2 + 682 PARSUN_Z_CNLFPFT W/m2 + 683 PARSHA_Z_CNLFPFT W/m2 + 684 PARSUN_Z_CAN W/m2 + 685 PARSHA_Z_CAN W/m2 + 686 LAISUN_Z_CNLF m2/m2 + 687 LAISHA_Z_CNLF m2/m2 + 688 LAISUN_Z_CNLFPFT m2/m2 + 689 LAISHA_Z_CNLFPFT m2/m2 + 690 LAISUN_TOP_CAN m2/m2 + 691 LAISHA_TOP_CAN m2/m2 + 692 FABD_SUN_CNLFPFT fraction + 693 FABD_SHA_CNLFPFT fraction + 694 FABI_SUN_CNLFPFT fraction + 695 FABI_SHA_CNLFPFT fraction + 696 FABD_SUN_CNLF fraction + 697 FABD_SHA_CNLF fraction + 698 FABI_SUN_CNLF fraction + 699 FABI_SHA_CNLF fraction + 700 PARPROF_DIR_CNLFPFT W/m2 + 701 PARPROF_DIF_CNLFPFT W/m2 + 702 PARPROF_DIR_CNLF W/m2 + 703 PARPROF_DIF_CNLF W/m2 + 704 FABD_SUN_TOPLF_BYCANLAYER fraction + 705 FABD_SHA_TOPLF_BYCANLAYER fraction + 706 FABI_SUN_TOPLF_BYCANLAYER fraction + 707 FABI_SHA_TOPLF_BYCANLAYER fraction + 708 NET_C_UPTAKE_CNLF gC/m2/s + 709 CROWNAREA_CNLF m2/m2 + 710 CROWNAREA_CAN m2/m2 + 711 DEMOTION_CARBONFLUX gC/m2/s + 712 PROMOTION_CARBONFLUX gC/m2/s + 713 MORTALITY_CARBONFLUX_CANOPY gC/m2/s + 714 MORTALITY_CARBONFLUX_UNDERSTORY gC/m2/s + 715 NPLANT_SCAG plants/ha + 716 NPLANT_CANOPY_SCAG plants/ha + 717 NPLANT_UNDERSTORY_SCAG plants/ha + 718 DDBH_CANOPY_SCAG cm/yr/ha + 719 DDBH_UNDERSTORY_SCAG cm/yr/ha + 720 MORTALITY_CANOPY_SCAG plants/ha/yr + 721 MORTALITY_UNDERSTORY_SCAG plants/ha/yr + 722 NPLANT_SCAGPFT plants/ha + 723 NPP_AGEPFT kgC/m2/yr + 724 BIOMASS_AGEPFT kg C / m2 + 725 SCORCH_HEIGHT m + 726 GPP_SCPF kgC/m2/yr + 727 GPP_CANOPY_SCPF kgC/m2/yr + 728 AR_CANOPY_SCPF kgC/m2/yr + 729 GPP_UNDERSTORY_SCPF kgC/m2/yr + 730 AR_UNDERSTORY_SCPF kgC/m2/yr + 731 NPP_SCPF kgC/m2/yr + 732 NPP_LEAF_SCPF kgC/m2/yr + 733 NPP_SEED_SCPF kgC/m2/yr + 734 NPP_FNRT_SCPF kgC/m2/yr + 735 NPP_BGSW_SCPF kgC/m2/yr + 736 NPP_BGDW_SCPF kgC/m2/yr + 737 NPP_AGSW_SCPF kgC/m2/yr + 738 NPP_AGDW_SCPF kgC/m2/yr + 739 NPP_STOR_SCPF kgC/m2/yr + 740 DDBH_SCPF cm/yr/ha + 741 GROWTHFLUX_SCPF n/yr/ha + 742 GROWTHFLUX_FUSION_SCPF n/yr/ha + 743 DDBH_CANOPY_SCPF cm/yr/ha + 744 DDBH_UNDERSTORY_SCPF cm/yr/ha + 745 BA_SCPF m2/ha + 746 AGB_SCPF kgC/m2 + 747 NPLANT_SCPF N/ha + 748 NPLANT_CAPF N/ha + 749 M1_SCPF N/ha/yr + 750 M2_SCPF N/ha/yr + 751 M3_SCPF N/ha/yr + 752 M4_SCPF N/ha/yr + 753 M5_SCPF N/ha/yr + 754 CROWNFIREMORT_SCPF N/ha/yr + 755 CAMBIALFIREMORT_SCPF N/ha/yr + 756 M6_SCPF N/ha/yr + 757 M7_SCPF N/ha/event + 758 M8_SCPF N/ha/yr + 759 M9_SCPF N/ha/yr + 760 M10_SCPF N/ha/yr + 761 M10_CAPF N/ha/yr + 762 MORTALITY_CANOPY_SCPF N/ha/yr + 763 C13disc_SCPF per mil + 764 BSTOR_CANOPY_SCPF kgC/ha + 765 BLEAF_CANOPY_SCPF kgC/ha + 766 NPLANT_CANOPY_SCPF N/ha + 767 MORTALITY_UNDERSTORY_SCPF N/ha/yr + 768 BSTOR_UNDERSTORY_SCPF kgC/ha + 769 BLEAF_UNDERSTORY_SCPF kgC/ha + 770 NPLANT_UNDERSTORY_SCPF N/ha + 771 CWD_AG_CWDSC gC/m^2 + 772 CWD_BG_CWDSC gC/m^2 + 773 CWD_AG_IN_CWDSC gC/m^2/y + 774 CWD_BG_IN_CWDSC gC/m^2/y + 775 CWD_AG_OUT_CWDSC gC/m^2/y + 776 CWD_BG_OUT_CWDSC gC/m^2/y + 777 AR_SCPF kgC/m2/yr + 778 AR_GROW_SCPF kgC/m2/yr + 779 AR_MAINT_SCPF kgC/m2/yr + 780 AR_DARKM_SCPF kgC/m2/yr + 781 AR_AGSAPM_SCPF kgC/m2/yr + 782 AR_CROOTM_SCPF kgC/m2/yr + 783 AR_FROOTM_SCPF kgC/m2/yr + 784 DDBH_CANOPY_SCLS cm/yr/ha + 785 DDBH_UNDERSTORY_SCLS cm/yr/ha + 786 YESTERDAYCANLEV_CANOPY_SCLS indiv/ha + 787 YESTERDAYCANLEV_UNDERSTORY_SCLS indiv/ha + 788 BA_SCLS m2/ha + 789 AGB_SCLS kgC/m2 + 790 BIOMASS_SCLS kgC/m2 + 791 DEMOTION_RATE_SCLS indiv/ha/yr + 792 PROMOTION_RATE_SCLS indiv/ha/yr + 793 NPLANT_CANOPY_SCLS indiv/ha + 794 LAI_CANOPY_SCLS m2/m2 + 795 SAI_CANOPY_SCLS m2/m2 + 796 MORTALITY_CANOPY_SCLS indiv/ha/yr + 797 NPLANT_UNDERSTORY_SCLS indiv/ha + 798 LAI_UNDERSTORY_SCLS indiv/ha + 799 SAI_UNDERSTORY_SCLS indiv/ha + 800 NPLANT_SCLS indiv/ha + 801 NPLANT_CACLS indiv/ha + 802 M1_SCLS N/ha/yr + 803 M2_SCLS N/ha/yr + 804 M3_SCLS N/ha/yr + 805 M4_SCLS N/ha/yr + 806 M5_SCLS N/ha/yr + 807 M6_SCLS N/ha/yr + 808 M7_SCLS N/ha/event + 809 M8_SCLS N/ha/event + 810 M9_SCLS N/ha/yr + 811 M10_SCLS N/ha/yr + 812 M10_CACLS N/ha/yr + 813 CARBON_BALANCE_CANOPY_SCLS kg C / ha / yr + 814 CARBON_BALANCE_UNDERSTORY_SCLS kg C / ha / yr + 815 MORTALITY_UNDERSTORY_SCLS indiv/ha/yr + 816 TRIMMING_CANOPY_SCLS indiv/ha + 817 TRIMMING_UNDERSTORY_SCLS indiv/ha + 818 CROWN_AREA_CANOPY_SCLS m2/ha + 819 CROWN_AREA_UNDERSTORY_SCLS m2/ha + 820 LEAF_MD_CANOPY_SCLS kg C / ha / yr + 821 ROOT_MD_CANOPY_SCLS kg C / ha / yr + 822 BSTORE_MD_CANOPY_SCLS kg C / ha / yr + 823 BDEAD_MD_CANOPY_SCLS kg C / ha / yr + 824 BSW_MD_CANOPY_SCLS kg C / ha / yr + 825 SEED_PROD_CANOPY_SCLS kg C / ha / yr + 826 NPP_LEAF_CANOPY_SCLS kg C / ha / yr + 827 NPP_FROOT_CANOPY_SCLS kg C / ha / yr + 828 NPP_BSW_CANOPY_SCLS kg C / ha / yr + 829 NPP_BDEAD_CANOPY_SCLS kg C / ha / yr + 830 NPP_BSEED_CANOPY_SCLS kg C / ha / yr + 831 NPP_STORE_CANOPY_SCLS kg C / ha / yr + 832 LEAF_MR kg C / m2 / yr + 833 FROOT_MR kg C / m2 / yr + 834 LIVECROOT_MR kg C / m2 / yr + 835 LIVESTEM_MR kg C / m2 / yr + 836 RDARK_CANOPY_SCLS kg C / ha / yr + 837 LIVESTEM_MR_CANOPY_SCLS kg C / ha / yr + 838 LIVECROOT_MR_CANOPY_SCLS kg C / ha / yr + 839 FROOT_MR_CANOPY_SCLS kg C / ha / yr + 840 RESP_G_CANOPY_SCLS kg C / ha / yr + 841 RESP_M_CANOPY_SCLS kg C / ha / yr + 842 LEAF_MD_UNDERSTORY_SCLS kg C / ha / yr + 843 ROOT_MD_UNDERSTORY_SCLS kg C / ha / yr + 844 BSTORE_MD_UNDERSTORY_SCLS kg C / ha / yr + 845 BDEAD_MD_UNDERSTORY_SCLS kg C / ha / yr + 846 BSW_MD_UNDERSTORY_SCLS kg C / ha / yr + 847 SEED_PROD_UNDERSTORY_SCLS kg C / ha / yr + 848 NPP_LEAF_UNDERSTORY_SCLS kg C / ha / yr + 849 NPP_FROOT_UNDERSTORY_SCLS kg C / ha / yr + 850 NPP_BSW_UNDERSTORY_SCLS kg C / ha / yr + 851 NPP_BDEAD_UNDERSTORY_SCLS kg C / ha / yr + 852 NPP_BSEED_UNDERSTORY_SCLS kg C / ha / yr + 853 NPP_STORE_UNDERSTORY_SCLS kg C / ha / yr + 854 RDARK_UNDERSTORY_SCLS kg C / ha / yr + 855 LIVESTEM_MR_UNDERSTORY_SCLS kg C / ha / yr + 856 LIVECROOT_MR_UNDERSTORY_SCLS kg C / ha / yr + 857 FROOT_MR_UNDERSTORY_SCLS kg C / ha / yr + 858 RESP_G_UNDERSTORY_SCLS kg C / ha / yr + 859 RESP_M_UNDERSTORY_SCLS kg C / ha / yr + 860 NEP gC/m^2/s + 861 Fire_Closs gC/m^2/s + 862 FIRE_FLUX g/m^2/s + 863 CBALANCE_ERROR_FATES mgC/day + 864 ERROR_FATES mg/day + 865 LITTER_FINES_AG_ELEM kg ha-1 + 866 LITTER_FINES_BG_ELEM kg ha-1 + 867 LITTER_CWD_BG_ELEM kg ha-1 + 868 LITTER_CWD_AG_ELEM kg ha-1 + 869 LITTER_CWD kg ha-1 + 870 TOTVEGC_SCPF kgC/ha + 871 LEAFC_SCPF kgC/ha + 872 FNRTC_SCPF kgC/ha + 873 SAPWC_SCPF kgC/ha + 874 STOREC_SCPF kgC/ha + 875 REPROC_SCPF kgC/ha + 876 CEFFLUX_SCPF kg/ha/day + 877 NPP_LEAF kgC/m2/yr + 878 NPP_SEED kgC/m2/yr + 879 NPP_STEM kgC/m2/yr + 880 NPP_FROOT kgC/m2/yr + 881 NPP_CROOT kgC/m2/yr + 882 NPP_STOR kgC/m2/yr + Using cold start initial conditions + hist_htapes_build Initializing clm2 history files +------------------------------------------------------------ + htapes_fieldlist : Included fields tape 1 = 415 + 1 ACTUAL_IMMOB 1 A + 2 AGB 1 A + 3 AGB_SCLS 13 A + 4 AR 1 A + 5 AREA_BURNT_BY_PATCH_AGE 7 A + 6 AREA_PLANT 1 A + 7 AREA_TREES 1 A + 8 AR_CANOPY 1 A + 9 AR_UNDERSTORY 1 A + 10 ATM_TOPO 1 A + 11 BA_SCLS 13 A + 12 BCDEP 1 A + 13 BIOMASS_CANOPY 1 A + 14 BIOMASS_UNDERSTORY 1 A + 15 BTRAN 1 A + 16 BTRAN2 1 A + 17 BTRANMN 1 A + 18 BURNT_LITTER_FRAC_AREA_PRODUCT 6 A + 19 CANOPY_AREA_BY_AGE 7 A + 20 CANOPY_HEIGHT_DIST 6 A + 21 CANOPY_SPREAD 1 A + 22 CBALANCE_ERROR_FATES 1 A + 23 CEFFLUX 1 A + 24 CROWNAREA_CAN 2 A + 25 C_LBLAYER 1 A + 26 C_STOMATA 1 A + 27 DDBH_CANOPY_SCLS 13 A + 28 DDBH_UNDERSTORY_SCLS 13 A + 29 DEMOTION_CARBONFLUX 1 A + 30 DENIT 1 A + 31 DISTURBANCE_RATE_FIRE 1 A + 32 DISTURBANCE_RATE_LOGGING 1 A + 33 DISTURBANCE_RATE_P2P 1 A + 34 DISTURBANCE_RATE_P2S 1 A + 35 DISTURBANCE_RATE_POTENTIAL 1 A + 36 DISTURBANCE_RATE_S2S 1 A + 37 DISTURBANCE_RATE_TREEFALL 1 A + 38 DSL 1 A + 39 DSTDEP 1 A + 40 DSTFLXT 1 A + 41 ED_NCOHORTS 1 A + 42 ED_NPATCHES 1 A + 43 ED_balive 1 A + 44 ED_bdead 1 A + 45 ED_bfineroot 1 A + 46 ED_biomass 1 A + 47 ED_bleaf 1 A + 48 ED_bsapwood 1 A + 49 ED_bstore 1 A + 50 EFFECT_WSPEED 1 A + 51 EFLXBUILD 1 A + 52 EFLX_DYNBAL 1 A + 53 EFLX_GRND_LAKE 1 A + 54 EFLX_LH_TOT 1 A + 55 EFLX_LH_TOT_R 1 A + 56 ELAI 1 A + 57 ERRH2O 1 A + 58 ERRH2OSNO 1 A + 59 ERROR_FATES 1 A + 60 ERRSEB 1 A + 61 ERRSOI 1 A + 62 ERRSOL 1 A + 63 ESAI 1 A + 64 FATES_c_to_litr_cel_c 25 A + 65 FATES_c_to_litr_lab_c 25 A + 66 FATES_c_to_litr_lig_c 25 A + 67 FCEV 1 A + 68 FCOV 1 A + 69 FCTR 1 A + 70 FGEV 1 A + 71 FGR 1 A + 72 FGR12 1 A + 73 FH2OSFC 1 A + 74 FIRA 1 A + 75 FIRA_R 1 A + 76 FIRE 1 A + 77 FIRE_AREA 1 A + 78 FIRE_FLUX 1 A + 79 FIRE_FUEL_BULKD 1 A + 80 FIRE_FUEL_EFF_MOIST 1 A + 81 FIRE_FUEL_MEF 1 A + 82 FIRE_FUEL_SAV 1 A + 83 FIRE_INTENSITY 1 A + 84 FIRE_INTENSITY_AREA_PRODUCT 1 A + 85 FIRE_INTENSITY_BY_PATCH_AGE 7 A + 86 FIRE_NESTEROV_INDEX 1 A + 87 FIRE_R 1 A + 88 FIRE_ROS 1 A + 89 FIRE_ROS_AREA_PRODUCT 1 A + 90 FIRE_TFC_ROS 1 A + 91 FIRE_TFC_ROS_AREA_PRODUCT 1 A + 92 FLDS 1 A + 93 FNRTC 1 A + 94 FROOT_MR 1 A + 95 FSA 1 A + 96 FSAT 1 A + 97 FSDS 1 A + 98 FSDSND 1 A + 99 FSDSNDLN 1 A + 100 FSDSNI 1 A + 101 FSDSVD 1 A + 102 FSDSVDLN 1 A + 103 FSDSVI 1 A + 104 FSDSVILN 1 A + 105 FSH 1 A + 106 FSH_G 1 A + 107 FSH_PRECIP_CONVERSION 1 A + 108 FSH_R 1 A + 109 FSH_RUNOFF_ICE_TO_LIQ 1 A + 110 FSH_TO_COUPLER 1 A + 111 FSH_V 1 A + 112 FSM 1 A + 113 FSNO 1 A + 114 FSNO_EFF 1 A + 115 FSR 1 A + 116 FSRND 1 A + 117 FSRNDLN 1 A + 118 FSRNI 1 A + 119 FSRVD 1 A + 120 FSRVDLN 1 A + 121 FSRVI 1 A + 122 FUEL_MOISTURE_NFSC 6 A + 123 Fire_Closs 1 A + 124 GPP 1 A + 125 GPP_CANOPY 1 A + 126 GPP_UNDERSTORY 1 A + 127 GROSS_NMIN 1 A + 128 GROWTH_RESP 1 A + 129 GSSHA 1 A + 130 GSSHALN 1 A + 131 GSSUN 1 A + 132 GSSUNLN 1 A + 133 H2OCAN 1 A + 134 H2OSFC 1 A + 135 H2OSNO 1 A + 136 H2OSNO_TOP 1 A + 137 H2OSOI 20 A + 138 HARVEST_CARBON_FLUX 1 A + 139 HEAT_CONTENT1 1 A + 140 HEAT_FROM_AC 1 A + 141 HIA 1 A + 142 HIA_R 1 A + 143 HIA_U 1 A + 144 HR 1 A + 145 HR_vr 20 A + 146 HTOP 1 A + 147 HUMIDEX 1 A + 148 HUMIDEX_R 1 A + 149 HUMIDEX_U 1 A + 150 ICE_CONTENT1 1 A + 151 LAISHA 1 A + 152 LAISUN 1 A + 153 LAI_BY_AGE 7 A + 154 LAI_CANOPY_SCLS 13 A + 155 LAI_UNDERSTORY_SCLS 13 A + 156 LAKEICEFRAC_SURF 1 A + 157 LAKEICETHICK 1 A + 158 LEAFC 1 A + 159 LEAF_HEIGHT_DIST 6 A + 160 LEAF_MR 1 A + 161 LIQCAN 1 A + 162 LIQUID_CONTENT1 1 A + 163 LITR1C 1 A + 164 LITR1C_vr 20 A + 165 LITR1N 1 A + 166 LITR1N_vr 25 A + 167 LITR2C 1 A + 168 LITR2C_vr 20 A + 169 LITR2N 1 A + 170 LITR2N_vr 25 A + 171 LITR3C 1 A + 172 LITR3C_vr 20 A + 173 LITR3N 1 A + 174 LITR3N_vr 25 A + 175 LITTERC_HR 1 A + 176 LITTER_CWD 4 A + 177 LITTER_CWD_AG_ELEM 1 A + 178 LITTER_CWD_BG_ELEM 1 A + 179 LITTER_FINES_AG_ELEM 1 A + 180 LITTER_FINES_BG_ELEM 1 A + 181 LITTER_IN 1 A + 182 LITTER_IN_ELEM 1 A + 183 LITTER_OUT 1 A + 184 LITTER_OUT_ELEM 1 A + 185 LIVECROOT_MR 1 A + 186 LIVESTEM_MR 1 A + 187 LNC 1 A + 188 M10_CACLS 2 A + 189 M10_SCLS 13 A + 190 M1_SCLS 13 A + 191 M2_SCLS 13 A + 192 M3_SCLS 13 A + 193 M4_SCLS 13 A + 194 M5_SCLS 13 A + 195 M6_SCLS 13 A + 196 M7_SCLS 13 A + 197 M8_SCLS 13 A + 198 M9_SCLS 13 A + 199 MAINT_RESP 1 A + 200 MORTALITY 12 A + 201 MORTALITY_CANOPY_SCLS 13 A + 202 MORTALITY_CARBONFLUX_CANOPY 1 A + 203 MORTALITY_CARBONFLUX_UNDERSTORY 1 A + 204 MORTALITY_UNDERSTORY_SCLS 13 A + 205 NDEP_TO_SMINN 1 A + 206 NEP 1 A + 207 NET_NMIN 1 A + 208 NFIX_TO_SMINN 1 A + 209 NPLANT_CACLS 2 A + 210 NPLANT_CANOPY_SCLS 13 A + 211 NPLANT_SCAG 91 A + 212 NPLANT_SCLS 13 A + 213 NPLANT_UNDERSTORY_SCLS 13 A + 214 NPP 1 A + 215 NPP_CROOT 1 A + 216 NPP_FROOT 1 A + 217 NPP_LEAF 1 A + 218 NPP_SEED 1 A + 219 NPP_STEM 1 A + 220 NPP_STOR 1 A + 221 OCDEP 1 A + 222 O_SCALAR 20 A + 223 PARVEGLN 1 A + 224 PATCH_AREA_BY_AGE 7 A + 225 PBOT 1 A + 226 PCO2 1 A + 227 PCT_GLC_MEC 10 A + 228 PCT_LANDUNIT 9 A + 229 PFTbiomass 12 A + 230 PFTleafbiomass 12 A + 231 PFTnindivs 12 A + 232 PFTstorebiomass 12 A + 233 POTENTIAL_IMMOB 1 A + 234 PRIMARYLAND_PATCHFUSION_ERROR 1 A + 235 PROMOTION_CARBONFLUX 1 A + 236 Q2M 1 A + 237 QBOT 1 A + 238 QCHARGE 1 A + 239 QDRAI 1 A + 240 QDRAI_PERCH 1 A + 241 QDRAI_XS 1 A + 242 QFLOOD 1 A + 243 QFLX_EVAP_TOT 1 A + 244 QFLX_ICE_DYNBAL 1 A + 245 QFLX_LIQDEW_TO_TOP_LAYER 1 A + 246 QFLX_LIQEVAP_FROM_TOP_LAYER 1 A + 247 QFLX_LIQ_DYNBAL 1 A + 248 QFLX_SNOW_DRAIN 1 A + 249 QFLX_SNOW_DRAIN_ICE 1 A + 250 QFLX_SOLIDDEW_TO_TOP_LAYER 1 A + 251 QFLX_SOLIDEVAP_FROM_TOP_LAYER 1 A + 252 QH2OSFC 1 A + 253 QICE 1 A + 254 QICE_FRZ 1 A + 255 QICE_MELT 1 A + 256 QINFL 1 A + 257 QINTR 1 A + 258 QIRRIG_FROM_GW_CONFINED 1 A + 259 QIRRIG_FROM_GW_UNCONFINED 1 A + 260 QIRRIG_FROM_SURFACE 1 A + 261 QOVER 1 A + 262 QRGWL 1 A + 263 QRUNOFF 1 A + 264 QRUNOFF_ICE 1 A + 265 QRUNOFF_ICE_TO_COUPLER 1 A + 266 QRUNOFF_TO_COUPLER 1 A + 267 QSNOCPLIQ 1 A + 268 QSNOEVAP 1 A + 269 QSNOFRZ 1 A + 270 QSNOFRZ_ICE 1 A + 271 QSNOMELT 1 A + 272 QSNOMELT_ICE 1 A + 273 QSNOUNLOAD 1 A + 274 QSNO_TEMPUNLOAD 1 A + 275 QSNO_WINDUNLOAD 1 A + 276 QSNWCPICE 1 A + 277 QSOIL 1 A + 278 QSOIL_ICE 1 A + 279 QVEGE 1 A + 280 QVEGT 1 A + 281 RAIN 1 A + 282 RAIN_FROM_ATM 1 A + 283 RECRUITMENT 12 A + 284 REPROC 1 A + 285 RH2M 1 A + 286 RSCANOPY 1 A + 287 RSSHA 1 M + 288 RSSUN 1 M + 289 SABG 1 A + 290 SABG_PEN 1 A + 291 SABV 1 A + 292 SAPWC 1 A + 293 SCORCH_HEIGHT 84 A + 294 SEEDS_IN 1 A + 295 SEEDS_IN_EXTERN_ELEM 1 A + 296 SEEDS_IN_LOCAL_ELEM 1 A + 297 SEED_BANK 1 A + 298 SEED_BANK_ELEM 1 A + 299 SEED_DECAY_ELEM 1 A + 300 SEED_GERM_ELEM 1 A + 301 SITE_COLD_STATUS 1 A + 302 SITE_DAYSINCE_COLDLEAFOFF 1 A + 303 SITE_DAYSINCE_COLDLEAFON 1 A + 304 SITE_DAYSINCE_DROUGHTLEAFOFF 1 A + 305 SITE_DAYSINCE_DROUGHTLEAFON 1 A + 306 SITE_DROUGHT_STATUS 1 A + 307 SITE_GDD 1 A + 308 SITE_MEANLIQVOL_DROUGHTPHEN 1 A + 309 SITE_NCHILLDAYS 1 A + 310 SITE_NCOLDDAYS 1 A + 311 SMINN 1 A + 312 SMINN_LEACHED 1 A + 313 SMINN_TO_PLANT 1 A + 314 SMINN_vr 20 A + 315 SMP 25 A + 316 SNOBCMCL 1 A + 317 SNOBCMSL 1 A + 318 SNOCAN 1 A + 319 SNODSTMCL 1 A + 320 SNODSTMSL 1 A + 321 SNOFSRND 1 A + 322 SNOFSRNI 1 A + 323 SNOFSRVD 1 A + 324 SNOFSRVI 1 A + 325 SNOINTABS 1 A + 326 SNOOCMCL 1 A + 327 SNOOCMSL 1 A + 328 SNOTXMASS 1 A + 329 SNOW 1 A + 330 SNOWDP 1 A + 331 SNOWICE 1 A + 332 SNOWLIQ 1 A + 333 SNOW_DEPTH 1 A + 334 SNOW_FROM_ATM 1 A + 335 SNOW_PERSISTENCE 1 I + 336 SNOW_SINKS 1 A + 337 SNOW_SOURCES 1 A + 338 SOIL1C 1 A + 339 SOIL1C_vr 20 A + 340 SOIL1N 1 A + 341 SOIL1N_vr 25 A + 342 SOIL2C 1 A + 343 SOIL2C_vr 20 A + 344 SOIL2N 1 A + 345 SOIL2N_vr 25 A + 346 SOIL3C 1 A + 347 SOIL3C_vr 20 A + 348 SOIL3N 1 A + 349 SOIL3N_vr 25 A + 350 SOILC_HR 1 A + 351 SOILC_vr 20 A + 352 SOILICE 20 A + 353 SOILLIQ 20 A + 354 SOILN_vr 25 A + 355 SOILRESIS 1 A + 356 SOILWATER_10CM 1 A + 357 SOMC_FIRE 1 A + 358 SOM_C_LEACHED 1 A + 359 STOREC 1 A + 360 SUM_FUEL 1 A + 361 SUM_FUEL_BY_PATCH_AGE 7 A + 362 SUPPLEMENT_TO_SMINN 1 A + 363 SWBGT 1 A + 364 SWBGT_R 1 A + 365 SWBGT_U 1 A + 366 TAUX 1 A + 367 TAUY 1 A + 368 TBOT 1 A + 369 TBUILD 1 A + 370 TG 1 A + 371 TH2OSFC 1 A + 372 THBOT 1 A + 373 TKE1 1 A + 374 TLAI 1 A + 375 TLAKE 10 A + 376 TOTLITC 1 A + 377 TOTLITC_1m 1 A + 378 TOTLITN 1 A + 379 TOTLITN_1m 1 A + 380 TOTSOILICE 1 A + 381 TOTSOILLIQ 1 A + 382 TOTSOMC 1 A + 383 TOTSOMC_1m 1 A + 384 TOTSOMN 1 A + 385 TOTSOMN_1m 1 A + 386 TOTVEGC 1 A + 387 TREFMNAV 1 A + 388 TREFMXAV 1 A + 389 TRIMMING 1 A + 390 TSA 1 A + 391 TSAI 1 A + 392 TSKIN 1 A + 393 TSL 1 A + 394 TSOI 25 A + 395 TSOI_10CM 1 A + 396 TSOI_ICE 25 A + 397 TV 1 A + 398 TWS 1 A + 399 T_SCALAR 20 A + 400 U10 1 A + 401 U10_DUST 1 A + 402 URBAN_AC 1 A + 403 URBAN_HEAT 1 A + 404 VOLR 1 A + 405 VOLRMCH 1 A + 406 WA 1 A + 407 WASTEHEAT 1 A + 408 WBT 1 A + 409 WBT_R 1 A + 410 WBT_U 1 A + 411 WIND 1 A + 412 W_SCALAR 20 A + 413 ZBOT 1 A + 414 ZWT 1 A + 415 ZWT_PERCH 1 A + There will be a total of 1 history tapes + + History tape 1 write frequency is MONTHLY + All fields on history tape 1 are grid averaged + Number of time samples on history tape 1 is 120 + Output precision on history tape 1 = 2 + + hist_htapes_build hist tape = 1 written with dov2xy= T + hist_htapes_build Successfully initialized clm2 history files +------------------------------------------------------------ + Successfully initialized the land model + begin initial run at: + nstep= 0 year= 2000 month= 1 day= 1 seconds= 0 + +************************************************************ + + dtime_sync= 1800 dtime_clm= 1800 mod = 0 + clm: completed timestep 0 + clm: calling FATES model 1 +FATES Dynamics: 2000-01-01 + clm: leaving fates model 1 1 + clm: completed timestep 1 + hist_htapes_wrapup : history tape 1 : no open file to close + writing restart file ./test.clm2.r.2000-01-01-01800.nc for model date = 2000-01-01-01800 + + restFile_open: writing restart dataset at ./test.clm2.r.2000-01-01-01800.nc at nstep = 1 + + Opened file ./test.clm2.r.2000-01-01-01800.nc to write 458752 + htape_create : Opening netcdf rhtape ./test.clm2.rh0.2000-01-01-01800.nc + Opened file ./test.clm2.rh0.2000-01-01-01800.nc to write 589824 + htape_create : Successfully defined netcdf restart history file 1 + Successfully wrote local restart file ./test.clm2.r.2000-01-01-01800.nc +------------------------------------------------------------ + + (OPNFIL): Successfully opened file ./rpointer.lnd on unit= 95 + Successfully wrote local restart pointer file + Successfully wrote out restart data at nstep = 1 +------------------------------------------------------------
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/restart_info.txt Wed Oct 21 20:30:35 2020 +0000 @@ -0,0 +1,4 @@ +test.datm.r.2000-01-01-01800.nc +test.datm.rs1.2000-01-01-01800.bin +test.cpl.r.2000-01-01-01800.nc +./test.clm2.r.2000-01-01-01800.nc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rof.log Wed Oct 21 20:30:35 2020 +0000 @@ -0,0 +1,14 @@ +(rof_init_mct) :MOSART model initialization + mosart npes = 1 + mosart iam = 0 + inst_name = ROF + Read in mosart_inparm namelist from: mosart_in + define run: + run type = initial + coupling_period = 10800 + delt_mosart = 3600 + decomp option = roundrobin + bypass_routing option = direct_in_place + qgwl runoff option = threshold + smat option = Xonly + MOSART will not be active