| Next changeset 1:74b675f9d7c8 (2020-10-21) |
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Commit message:
"planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/fates-emerald commit f282701cadbb0c90c2c77a52579f18b44a357e24" |
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added:
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 |
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| diff -r 000000000000 -r 8c7414c07367 config --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/config Wed Oct 21 20:30:35 2020 +0000 |
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| @@ -0,0 +1,2 @@ +[main] +CIME_MODEL=cesm |
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| diff -r 000000000000 -r 8c7414c07367 config_compilers.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/config_compilers.xml Wed Oct 21 20:30:35 2020 +0000 |
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| @@ -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> |
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| diff -r 000000000000 -r 8c7414c07367 config_machines.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/config_machines.xml Wed Oct 21 20:30:35 2020 +0000 |
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| @@ -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 $TOTALPES</arg> + </arguments> + </mpirun> + <module_system type="none"/> + <environment_variables> + <env name="KMP_STACKSIZE">64M</env> + </environment_variables> + <resource_limits> + <resource name="RLIMIT_STACK">-1</resource> + </resource_limits> + </machine> +</config_machines> |
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| diff -r 000000000000 -r 8c7414c07367 ctsm-fates.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ctsm-fates.xml Wed Oct 21 20:30:35 2020 +0000 |
| [ |
| b'@@ -0,0 +1,325 @@\n+<tool id="ctsm-fates" name="CTSM/FATES-EMERALD" version="2.0.1">\n+ <description>Functionally Assembled Terrestrial Ecosystem Simulator</description>\n+ <requirements>\n+ <requirement type="package" version="2.0.1">fates-emerald</requirement>\n+ <requirement type="package" version="1.32">tar</requirement>\n+ <requirement type="package" version="2.35">binutils</requirement>\n+ <requirement type="package" version="3">python</requirement>\n+ <requirement type="package" version="2.0132">perl-xml-libxml</requirement>\n+ </requirements>\n+ <command detect_errors="exit_code"><![CDATA[\n+ ( export HOME=`pwd` &&\n+ export USER=\'jovyan\' &&\n+ mkdir -p .cime &&\n+ cp \'$__tool_directory__/config\' .cime/config &&\n+ cp \'$__tool_directory__/config_compilers.xml\' \'.cime/config_compilers.xml\' &&\n+ cp \'$__tool_directory__/config_machines.xml\' \'.cime/config_machines.xml\' &&\n+ mkdir inputdata &&\n+ tar -xf \'$inputdata\' -C \'inputdata/\' && \n+ mkdir output_dir &&\n+ mkdir usermods_dirs &&\n+ #if str($adv.condi_user_mods).strip() == \'yes\'\n+ # should create a new type user_mods.tar\n+ cd usermods_dirs &&\n+ tar xf \'$user_mods\' &&\n+ cd .. &&\n+ #end if\n+ create_newcase --case \'$casename\' --compset 2000_DATM%1PTGSWP3_CLM50%FATES_SICE_SOCN_MOSART_SGLC_SWAV --machine espresso --run-unsupported \n+ #if str($adv.condi_user_mods).strip() == \'yes\'\n+ --user-mods-dir usermods_dirs\n+ #end if\n+ --res \'$resolution\' && \n+ cd \'$casename\' &&\n+ ./case.setup > $case_info 2>&1 &&\n+ #if (str($adv_period.condi_type_run.run_type) == \'hybrid\' or str($adv_period.condi_type_run.run_type) == \'branch\')\n+ ./xmlchange RUN_TYPE=$adv_period.condi_type_run.run_type &&\n+ ./xmlchange RUN_REFDATE=$adv_period.condi_type_run.run_refdate &&\n+ ./xmlchange RUN_REFCASE=$adv_period.condi_type_run.run_refcase &&\n+ #end if\n+ #if ((str($adv_period.condi_type_run.run_type) == \'hybrid\' or str($adv_period.condi_type_run.run_type) == \'startup\') and ($adv_period.condi_type_run.run_startdate != \'\'))\n+ ./xmlchange RUN_STARTDATE=$adv_period.condi_type_run.run_startdate &&\n+ #end if\n+ ./xmlchange STOP_N=$adv_period.stopn &&\n+ ./xmlchange STOP_OPTION=$adv_period.stop_option &&\n+ ./xmlchange CCSM_CO2_PPMV=$adv.co2 &&\n+ ./xmlchange DOUT_S=FALSE &&\n+ cp \'$user_nl_clm_customization\' user_nl_clm &&\n+ ./case.build >> $case_info 2>&1 &&\n+ #if (str($adv_period.condi_type_run.run_type) == \'hybrid\' or str($adv_period.condi_type_run.run_type) == \'branch\')\n+ tar -xf \'$adv_period.condi_type_run.restart\' -C \'../work/$casename/run/\' && \n+ \n+ #end if\n+ ./case.submit >> $case_info 2>&1 &&\n+ mkdir -p restart &&\n+ (cat \'../work/$casename/run/rpointer\'.* > $rinfo || printf "No restarts\\n") &&\n+ (cp \'../work/$casename/run/$casename\'.*.r*.*.nc restart/ || printf "No netCDF restarts\\n") &&\n+ (cp \'../work/$casename/run/$casename\'.*.r*.*.bin restart/ || printf "No bin restarts\\n") &&\n+ (cp \'../work/$casename/run/rpointer\'.* restart/ || printf "no rpointer\\n") &&\n+ cd restart && \n+ tar cvf $restart . &&\n+ cd .. && \n+ (cp \'../work/$casename/run/$casename\'.*.h*.*.nc ../output_dir/ || printf "no netCDF outputs\\n") &&\n+ (gunzip \'../work/$casename/run/\'*.log.* || printf "no compressed logs") && \n+ cat \'../work/$casename/run/\'atm.log.* >> $atm_log &&\n+ cat \'../work/$casename/run/\'cesm.log.* >> $cesm_log &&\n+ cat \'../work/$casename/run/\'cpl.log.* >> $cpl_log &&\n+ cat \'../work/$casename/run/\'lnd.log.* >> $lnd_log &&\n+ cat \'..'..b'="inputdata_test.tar" />\n+ <param name="casename" value="test" />\n+ <param name="resolution" value="1x1_ALP1" />\n+ <param name="run_startdate" value="2000-01-01" />\n+ <param name="stop_option" value="nsteps" />\n+ <param name="stopn" value="1" />\n+ <output name="atm_log" ftype="txt" file="atm.log" compare="sim_size" delta="1000">\n+ <assert_contents>\n+ <has_text text="(datm_comp_final) atm: end of main integration loop" />\n+ </assert_contents>\n+ </output>\n+ <output name="cesm_log" ftype="txt" file="cesm.log" compare="sim_size" delta="1000">\n+ <assert_contents>\n+ <has_text text="pes participating in computation for CLM" />\n+ </assert_contents>\n+ </output>\n+ <output name="cpl_log" ftype="txt" file="cpl.log" compare="sim_size" delta="1000">\n+ <assert_contents>\n+ <has_text text="SUCCESSFUL TERMINATION" />\n+ </assert_contents>\n+ </output>\n+ <output name="lnd_log" ftype="txt" file="lnd.log" compare="sim_size" delta="1000">\n+ <assert_contents>\n+ <has_text text="Successfully" />\n+ </assert_contents>\n+ </output>\n+ <output name="rof_log" ftype="txt" file="rof.log" compare="sim_size" delta="1000">\n+ <assert_contents>\n+ <has_text text="MOSART model initialization" />\n+ </assert_contents>\n+ </output>\n+ <output name="work" ftype="tar" file="workdir.tar" compare="sim_size" delta="1000">\n+ <assert_contents>\n+ <has_size value="0"/>\n+ </assert_contents>\n+ </output>\n+ <output name="restart" ftype="tar" file="restart.tar" compare="sim_size" delta="100" />\n+ <output name="rinfo" ftype="txt" file="restart_info.txt" compare="sim_size" delta="1000">\n+ <assert_contents>\n+ <has_text text="datm.r.2000-01-01-01800.nc" />\n+ <has_text text="datm.rs1.2000-01-01-01800.bin" />\n+ <has_text text="cpl.r.2000-01-01-01800.nc" />\n+ <has_text text="clm2.r.2000-01-01-01800.nc" />\n+ </assert_contents>\n+ </output>\n+ <output_collection name="history_files" count="0">\n+ </output_collection>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+\n+**The Functionally Assembled Terrestrial Ecosystem Simulator (FATES)**\n+==========================================================================\n+\n+This tool create and run CTSM-FATES EMERALD experiments from fates-emerald release.\n+\n+This version of FATES is maintained by the University of Oslo.\n+\n+Currently available resolution are as following:\n+\n+SeedClim Sites:\n+~~~~~~~~~~~~~~~\n+\n+- ALP1,61.0243N,8.12343E\n+- ALP2,60.8231N,7.27596E\n+- ALP3,60.8328N,7.17561E\n+- ALP4,60.9335N,6.41504E\n+- SUB1,60.8203N,8.70466E\n+- SUB2,60.8760N,7.17666E\n+- SUB3,61.0866N,6.63028E\n+- SUB4,60.5445N,6.51468E\n+- BOR1,61.0355N,9.07876E\n+- BOR2,60.8803N,7.16982E\n+- BOR3,60.6652N,6.33738E\n+- BOR4,60.6901N,5.96487E\n+\n+LandPress Sites:\n+~~~~~~~~~~~~~~~~\n+\n+- LYG,60.70084N,5.092566E \n+- BUO,65.83677N,12.224506E\n+- HAV,64.779N,11.2193E\n+- SKO,65.79602N,12.219299E\n+\n+Three-D Sites:\n+~~~~~~~~~~~~~~\n+\n+- VIKE,60.88019N,7.16990E\n+- JOAS,60.86183N,7.16800E\n+- LIAH,60.85994N,7.19504E\n+\n+\n+Finnmark Site:\n+~~~~~~~~~~~~~~\n+\n+- FINN,69.341088N,25.293524E\n+\n+ ]]></help>\n+ <citations>\n+\n+ </citations>\n+ <edam_topics>\n+ <edam_topic>topic_3855</edam_topic>\n+ <edam_topic>topic_3318</edam_topic>\n+ <edam_topic>topic_3050</edam_topic>\n+ <edam_topic>topic_0610</edam_topic>\n+ </edam_topics>\n+ <edam_operations>\n+ <edam_operation>operation_3946</edam_operation>\n+ <edam_operation>operation_2426</edam_operation>\n+ </edam_operations>\n+</tool>\n' |
| b |
| diff -r 000000000000 -r 8c7414c07367 ctsm-fates.xml.SLEEP --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ctsm-fates.xml.SLEEP Wed Oct 21 20:30:35 2020 +0000 |
| [ |
| b'@@ -0,0 +1,332 @@\n+<tool id="ctsm-fates" name="CTSM/FATES-EMERALD" version="2.0.1">\n+ <description>Functionally Assembled Terrestrial Ecosystem Simulator</description>\n+ <requirements>\n+ <requirement type="package" version="2.0.1">fates-emerald</requirement>\n+ <requirement type="package" version="1.32">tar</requirement>\n+ <requirement type="package" version="2.35">binutils</requirement>\n+ <requirement type="package" version="3">python</requirement>\n+ <requirement type="package" version="2.0132">perl-xml-libxml</requirement>\n+ </requirements>\n+ <command detect_errors="exit_code"><![CDATA[\n+ ( export HOME=`pwd` &&\n+ export USER=\'jovyan\' &&\n+ mkdir -p .cime &&\n+ cp \'$__tool_directory__/config\' .cime/config &&\n+ cp \'$__tool_directory__/config_compilers.xml\' \'.cime/config_compilers.xml\' &&\n+ cp \'$__tool_directory__/config_machines.xml\' \'.cime/config_machines.xml\' &&\n+ mkdir inputdata &&\n+ tar -xf \'$inputdata\' -C \'inputdata/\' && \n+ mkdir output_dir &&\n+ mkdir usermods_dirs &&\n+ #if str($adv.condi_user_mods).strip() == \'yes\'\n+ # should create a new type user_mods.tar\n+ cd usermods_dirs &&\n+ tar xf \'$user_mods\' &&\n+ cd .. &&\n+ #end if\n+ create_newcase --case \'$casename\' --compset 2000_DATM%1PTGSWP3_CLM50%FATES_SICE_SOCN_MOSART_SGLC_SWAV --machine espresso --run-unsupported \n+ #if str($adv.condi_user_mods).strip() == \'yes\'\n+ --user-mods-dir usermods_dirs\n+ #end if\n+ --res \'$resolution\' && \n+ cd \'$casename\' &&\n+ ./case.setup > $case_info 2>&1 &&\n+ #if (str($adv_period.condi_type_run.run_type) == \'hybrid\' or str($adv_period.condi_type_run.run_type) == \'branch\')\n+ ./xmlchange RUN_TYPE=$adv_period.condi_type_run.run_type &&\n+ ./xmlchange RUN_REFDATE=$adv_period.condi_type_run.run_refdate &&\n+ ./xmlchange RUN_REFCASE=$adv_period.condi_type_run.run_refcase &&\n+ #end if\n+ #if ((str($adv_period.condi_type_run.run_type) == \'hybrid\' or str($adv_period.condi_type_run.run_type) == \'startup\') and ($adv_period.condi_type_run.run_startdate != \'\'))\n+ ./xmlchange RUN_STARTDATE=$adv_period.condi_type_run.run_startdate &&\n+ #end if\n+ ./xmlchange STOP_N=$adv_period.stopn &&\n+ ./xmlchange STOP_OPTION=$adv_period.stop_option &&\n+ ./xmlchange CCSM_CO2_PPMV=$adv.co2 &&\n+ ./xmlchange DOUT_S=FALSE &&\n+ cp \'$user_nl_clm_customization\' user_nl_clm &&\n+ ./case.build >> $case_info 2>&1 &&\n+ #if (str($adv_period.condi_type_run.run_type) == \'hybrid\' or str($adv_period.condi_type_run.run_type) == \'branch\')\n+ tar -xf \'$adv_period.condi_type_run.restart\' -C \'../work/$casename/run/\' && \n+ \n+ #end if\n+ ./case.submit >> $case_info 2>&1 &&\n+ mkdir -p restart &&\n+ (cat \'../work/$casename/run/rpointer\'.* > $rinfo || printf "No restarts\\n") &&\n+ (cp \'../work/$casename/run/$casename\'.*.r*.*.nc restart/ || printf "No netCDF restarts\\n") &&\n+ (cp \'../work/$casename/run/$casename\'.*.r*.*.bin restart/ || printf "No bin restarts\\n") &&\n+ (cp \'../work/$casename/run/rpointer\'.* restart/ || printf "no rpointer\\n") &&\n+ cd restart && \n+ tar cvf $restart . &&\n+ cd .. && \n+ (cp \'../work/$casename/run/$casename\'.*.h*.*.nc ../output_dir/ || printf "no netCDF outputs\\n") &&\n+ (gunzip \'../work/$casename/run/\'*.log.* || printf "no compressed logs") && \n+ cat \'../work/$casename/run/\'atm.log.* >> $atm_log &&\n+ cat \'../work/$casename/run/\'cesm.log.* >> $cesm_log &&\n+ cat \'../work/$casename/run/\'cpl.log.* >> $cpl_log &&\n+ cat \'../work/$casename/run/\'lnd.log.* >> $lnd_log &&\n+ cat \'..'..b'ram name="run_startdate" value="2000-01-01" />\n+ <param name="stop_option" value="nsteps" />\n+ <param name="stopn" value="1" />\n+ <output name="atm_log" ftype="txt" file="atm.log">\n+ <assert_contents>\n+ <has_text text="(datm_comp_final) atm: end of main integration loop" />\n+ </assert_contents>\n+ </output>\n+ <output name="cesm_log" ftype="txt" file="cesm.log">\n+ <assert_contents>\n+ <has_text text="pes participating in computation for CLM" />\n+ </assert_contents>\n+ </output>\n+ <output name="cpl_log" ftype="txt" file="cpl.log">\n+ <assert_contents>\n+ <has_text text="SUCCESSFUL TERMINATION" />\n+ </assert_contents>\n+ </output>\n+ <output name="lnd_log" ftype="txt" file="lnd.log">\n+ <assert_contents>\n+ <has_text text="Successfully" />\n+ </assert_contents>\n+ </output>\n+ <output name="rof_log" ftype="txt" file="rof.log">\n+ <assert_contents>\n+ <has_text text="MOSART model initialization" />\n+ </assert_contents>\n+ </output>\n+ <output name="case_info" ftype="txt" file="case_info.txt">\n+ <assert_contents>\n+ <has_text text="MODEL BUILD HAS FINISHED SUCCESSFULLY" />\n+ <has_line_matching expression="Submitted job" />\n+ </assert_contents>\n+ </output>\n+ <output name="work" ftype="tar" file="workdir.tar">\n+ <assert_contents>\n+ <has_size value="0"/>\n+ </assert_contents>\n+ </output>\n+ <output name="restart" ftype="tar" file="restart.tar" compare="sim_size" delta="100" />\n+ <output name="rinfo" ftype="txt" file="restart_info.txt">\n+ <assert_contents>\n+ <has_line_matching expression="*datm.r.2000-01-01-01800.nc*" />\n+ <has_line_matching expression="*datm.rs1.2000-01-01-01800.bin*" />\n+ <has_line_matching expression="*cpl.r.2000-01-01-01800.nc*" />\n+ <has_line_matching expression="*clm2.r.2000-01-01-01800.nc*" />\n+ </assert_contents>\n+ </output>\n+ <output_collection name="history_files" count="0">\n+ </output_collection>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+\n+**The Functionally Assembled Terrestrial Ecosystem Simulator (FATES)**\n+==========================================================================\n+\n+This tool create and run CTSM-FATES EMERALD experiments from fates-emerald release.\n+\n+This version of FATES is maintained by the University of Oslo.\n+\n+Currently available resolution are as following:\n+\n+SeedClim Sites:\n+~~~~~~~~~~~~~~~\n+\n+- ALP1,61.0243N,8.12343E\n+- ALP2,60.8231N,7.27596E\n+- ALP3,60.8328N,7.17561E\n+- ALP4,60.9335N,6.41504E\n+- SUB1,60.8203N,8.70466E\n+- SUB2,60.8760N,7.17666E\n+- SUB3,61.0866N,6.63028E\n+- SUB4,60.5445N,6.51468E\n+- BOR1,61.0355N,9.07876E\n+- BOR2,60.8803N,7.16982E\n+- BOR3,60.6652N,6.33738E\n+- BOR4,60.6901N,5.96487E\n+\n+LandPress Sites:\n+~~~~~~~~~~~~~~~~\n+\n+- LYG,60.70084N,5.092566E \n+- BUO,65.83677N,12.224506E\n+- HAV,64.779N,11.2193E\n+- SKO,65.79602N,12.219299E\n+\n+Three-D Sites:\n+~~~~~~~~~~~~~~\n+\n+- VIKE,60.88019N,7.16990E\n+- JOAS,60.86183N,7.16800E\n+- LIAH,60.85994N,7.19504E\n+\n+\n+Finnmark Site:\n+~~~~~~~~~~~~~~\n+\n+- FINN,69.341088N,25.293524E\n+\n+ ]]></help>\n+ <citations>\n+\n+ </citations>\n+ <edam_topics>\n+ <edam_topic>topic_3855</edam_topic>\n+ <edam_topic>topic_3318</edam_topic>\n+ <edam_topic>topic_3050</edam_topic>\n+ <edam_topic>topic_0610</edam_topic>\n+ </edam_topics>\n+ <edam_operations>\n+ <edam_operation>operation_3946</edam_operation>\n+ <edam_operation>operation_2426</edam_operation>\n+ </edam_operations>\n+</tool>\n' |
| b |
| diff -r 000000000000 -r 8c7414c07367 ctsm-fates.xml.TRIC --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ctsm-fates.xml.TRIC Wed Oct 21 20:30:35 2020 +0000 |
| [ |
| b'@@ -0,0 +1,338 @@\n+<tool id="ctsm-fates" name="CTSM/FATES-EMERALD" version="2.0.1">\n+ <description>Functionally Assembled Terrestrial Ecosystem Simulator</description>\n+ <requirements>\n+ <requirement type="package" version="2.0.1">fates-emerald</requirement>\n+ <requirement type="package" version="1.32">tar</requirement>\n+ <requirement type="package" version="3">python</requirement>\n+ <requirement type="package" version="2.0132">perl-xml-libxml</requirement>\n+ </requirements>\n+ <command detect_errors="exit_code"><![CDATA[\n+ ( export HOME=`pwd` &&\n+ export USER=\'jovyan\' &&\n+ export AR=/usr/local/bin/x86_64-conda_cos6-linux-gnu-ar &&\n+ mkdir bin && \n+ cd bin && ln -s /usr/local/bin/x86_64-conda_cos6-linux-gnu-ar ar &&\n+ cd .. &&\n+ export PATH=\\$HOME/bin:\\$PATH &&\n+ mkdir -p .cime &&\n+ cp \'$__tool_directory__/config\' .cime/config &&\n+ cp \'$__tool_directory__/config_compilers.xml\' \'.cime/config_compilers.xml\' &&\n+ cp \'$__tool_directory__/config_machines.xml\' \'.cime/config_machines.xml\' &&\n+ mkdir inputdata &&\n+ tar -xf \'$inputdata\' -C \'inputdata/\' && \n+ mkdir output_dir &&\n+ mkdir usermods_dirs &&\n+ #if str($adv.condi_user_mods).strip() == \'yes\'\n+ # should create a new type user_mods.tar\n+ cd usermods_dirs &&\n+ tar xf \'$user_mods\' &&\n+ cd .. &&\n+ #end if\n+ create_newcase --case \'$casename\' --compset 2000_DATM%1PTGSWP3_CLM50%FATES_SICE_SOCN_MOSART_SGLC_SWAV --machine espresso --run-unsupported \n+ #if str($adv.condi_user_mods).strip() == \'yes\'\n+ --user-mods-dir usermods_dirs\n+ #end if\n+ --res \'$resolution\' && \n+ cd \'$casename\' &&\n+ ./case.setup > $case_info 2>&1 &&\n+ #if (str($adv_period.condi_type_run.run_type) == \'hybrid\' or str($adv_period.condi_type_run.run_type) == \'branch\')\n+ ./xmlchange RUN_TYPE=$adv_period.condi_type_run.run_type &&\n+ ./xmlchange RUN_REFDATE=$adv_period.condi_type_run.run_refdate &&\n+ ./xmlchange RUN_REFCASE=$adv_period.condi_type_run.run_refcase &&\n+ #end if\n+ #if ((str($adv_period.condi_type_run.run_type) == \'hybrid\' or str($adv_period.condi_type_run.run_type) == \'startup\') and ($adv_period.condi_type_run.run_startdate != \'\'))\n+ ./xmlchange RUN_STARTDATE=$adv_period.condi_type_run.run_startdate &&\n+ #end if\n+ ./xmlchange STOP_N=$adv_period.stopn &&\n+ ./xmlchange STOP_OPTION=$adv_period.stop_option &&\n+ ./xmlchange CCSM_CO2_PPMV=$adv.co2 &&\n+ ./xmlchange DOUT_S=FALSE &&\n+ cp \'$user_nl_clm_customization\' user_nl_clm &&\n+ ./case.build >> $case_info 2>&1 &&\n+ #if (str($adv_period.condi_type_run.run_type) == \'hybrid\' or str($adv_period.condi_type_run.run_type) == \'branch\')\n+ tar -xf \'$adv_period.condi_type_run.restart\' -C \'../work/$casename/run/\' && \n+ \n+ #end if\n+ ./case.submit >> $case_info 2>&1 &&\n+ mkdir -p restart &&\n+ (cat \'../work/$casename/run/rpointer\'.* > $rinfo || printf "No restarts\\n") &&\n+ (cp \'../work/$casename/run/$casename\'.*.r*.*.nc restart/ || printf "No netCDF restarts\\n") &&\n+ (cp \'../work/$casename/run/$casename\'.*.r*.*.bin restart/ || printf "No bin restarts\\n") &&\n+ (cp \'../work/$casename/run/rpointer\'.* restart/ || printf "no rpointer\\n") &&\n+ cd restart && \n+ tar cvf $restart . &&\n+ cd .. && \n+ (cp \'../work/$casename/run/$casename\'.*.h*.*.nc ../output_dir/ || printf "no netCDF outputs\\n") &&\n+ (gunzip \'../work/$casename/run/\'*.log.* || printf "no compressed logs") && \n+ cat \'../work/$casename/run/\'atm.log.* >> $atm_log &&\n+ cat \'../work/$casename/run/\'cesm.lo'..b' name="stopn" value="1" />\n+ <output name="atm_log" ftype="txt" file="atm.log">\n+ <assert_contents>\n+ <has_text text="(datm_comp_final) atm: end of main integration loop" />\n+ </assert_contents>\n+ </output>\n+ <output name="cesm_log" ftype="txt" file="cesm.log">\n+ <assert_contents>\n+ <has_text text="pes participating in computation for CLM" />\n+ </assert_contents>\n+ </output>\n+ <output name="cpl_log" ftype="txt" file="cpl.log">\n+ <assert_contents>\n+ <has_text text="SUCCESSFUL TERMINATION" />\n+ </assert_contents>\n+ </output>\n+ <output name="lnd_log" ftype="txt" file="lnd.log">\n+ <assert_contents>\n+ <has_text text="Successfully" />\n+ </assert_contents>\n+ </output>\n+ <output name="rof_log" ftype="txt" file="rof.log">\n+ <assert_contents>\n+ <has_text text="MOSART model initialization" />\n+ </assert_contents>\n+ </output>\n+ <output name="case_info" ftype="txt" file="case_info.txt">\n+ <assert_contents>\n+ <has_text text="MODEL BUILD HAS FINISHED SUCCESSFULLY" />\n+ <has_line_matching expression="Submitted job" />\n+ </assert_contents>\n+ </output>\n+ <output name="work" ftype="tar" file="workdir.tar">\n+ <assert_contents>\n+ <has_size value="0"/>\n+ </assert_contents>\n+ </output>\n+ <output name="restart" ftype="tar" file="restart.tar" compare="sim_size" delta="100" />\n+ <output name="rinfo" ftype="txt" file="restart_info.txt">\n+ <assert_contents>\n+ <has_line_matching expression="*datm.r.2000-01-01-01800.nc*" />\n+ <has_line_matching expression="*datm.rs1.2000-01-01-01800.bin*" />\n+ <has_line_matching expression="*cpl.r.2000-01-01-01800.nc*" />\n+ <has_line_matching expression="*clm2.r.2000-01-01-01800.nc*" />\n+ </assert_contents>\n+ </output>\n+ <output name="history_files" ftype="netcdf" file="history_file.netcdf">\n+ <assert_contents>\n+ <has_size value="0"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+\n+**The Functionally Assembled Terrestrial Ecosystem Simulator (FATES)**\n+==========================================================================\n+\n+This tool create and run CTSM-FATES EMERALD experiments from fates-emerald release.\n+\n+This version of FATES is maintained by the University of Oslo.\n+\n+Currently available resolution are as following:\n+\n+SeedClim Sites:\n+~~~~~~~~~~~~~~~\n+\n+- ALP1,61.0243N,8.12343E\n+- ALP2,60.8231N,7.27596E\n+- ALP3,60.8328N,7.17561E\n+- ALP4,60.9335N,6.41504E\n+- SUB1,60.8203N,8.70466E\n+- SUB2,60.8760N,7.17666E\n+- SUB3,61.0866N,6.63028E\n+- SUB4,60.5445N,6.51468E\n+- BOR1,61.0355N,9.07876E\n+- BOR2,60.8803N,7.16982E\n+- BOR3,60.6652N,6.33738E\n+- BOR4,60.6901N,5.96487E\n+\n+LandPress Sites:\n+~~~~~~~~~~~~~~~~\n+\n+- LYG,60.70084N,5.092566E \n+- BUO,65.83677N,12.224506E\n+- HAV,64.779N,11.2193E\n+- SKO,65.79602N,12.219299E\n+\n+Three-D Sites:\n+~~~~~~~~~~~~~~\n+\n+- VIKE,60.88019N,7.16990E\n+- JOAS,60.86183N,7.16800E\n+- LIAH,60.85994N,7.19504E\n+\n+\n+Finnmark Site:\n+~~~~~~~~~~~~~~\n+\n+- FINN,69.341088N,25.293524E\n+\n+ ]]></help>\n+ <citations>\n+\n+ </citations>\n+ <edam_topics>\n+ <edam_topic>topic_3855</edam_topic>\n+ <edam_topic>topic_3318</edam_topic>\n+ <edam_topic>topic_3050</edam_topic>\n+ <edam_topic>topic_0610</edam_topic>\n+ </edam_topics>\n+ <edam_operations>\n+ <edam_operation>operation_3946</edam_operation>\n+ <edam_operation>operation_2426</edam_operation>\n+ </edam_operations>\n+</tool>\n' |
| b |
| diff -r 000000000000 -r 8c7414c07367 ctsm-fates.xml.binutils --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ctsm-fates.xml.binutils Wed Oct 21 20:30:35 2020 +0000 |
| [ |
| b'@@ -0,0 +1,334 @@\n+<tool id="ctsm-fates" name="CTSM/FATES-EMERALD" version="2.0.1">\n+ <description>Functionally Assembled Terrestrial Ecosystem Simulator</description>\n+ <requirements>\n+ <requirement type="package" version="2.0.1">fates-emerald</requirement>\n+ <requirement type="package" version="1.32">tar</requirement>\n+ <requirement type="package" version="2.35">binutils</requirement>\n+ <requirement type="package" version="3">python</requirement>\n+ <requirement type="package" version="2.0132">perl-xml-libxml</requirement>\n+ </requirements>\n+ <command detect_errors="exit_code"><![CDATA[\n+ ( export HOME=`pwd` &&\n+ export USER=\'jovyan\' &&\n+ mkdir -p .cime &&\n+ cp \'$__tool_directory__/config\' .cime/config &&\n+ cp \'$__tool_directory__/config_compilers.xml\' \'.cime/config_compilers.xml\' &&\n+ cp \'$__tool_directory__/config_machines.xml\' \'.cime/config_machines.xml\' &&\n+ mkdir inputdata &&\n+ tar -xf \'$inputdata\' -C \'inputdata/\' && \n+ mkdir output_dir &&\n+ mkdir usermods_dirs &&\n+ #if str($adv.condi_user_mods).strip() == \'yes\'\n+ # should create a new type user_mods.tar\n+ cd usermods_dirs &&\n+ tar xf \'$user_mods\' &&\n+ cd .. &&\n+ #end if\n+ create_newcase --case \'$casename\' --compset 2000_DATM%1PTGSWP3_CLM50%FATES_SICE_SOCN_MOSART_SGLC_SWAV --machine espresso --run-unsupported \n+ #if str($adv.condi_user_mods).strip() == \'yes\'\n+ --user-mods-dir usermods_dirs\n+ #end if\n+ --res \'$resolution\' && \n+ cd \'$casename\' &&\n+ ./case.setup > $case_info 2>&1 &&\n+ #if (str($adv_period.condi_type_run.run_type) == \'hybrid\' or str($adv_period.condi_type_run.run_type) == \'branch\')\n+ ./xmlchange RUN_TYPE=$adv_period.condi_type_run.run_type &&\n+ ./xmlchange RUN_REFDATE=$adv_period.condi_type_run.run_refdate &&\n+ ./xmlchange RUN_REFCASE=$adv_period.condi_type_run.run_refcase &&\n+ #end if\n+ #if ((str($adv_period.condi_type_run.run_type) == \'hybrid\' or str($adv_period.condi_type_run.run_type) == \'startup\') and ($adv_period.condi_type_run.run_startdate != \'\'))\n+ ./xmlchange RUN_STARTDATE=$adv_period.condi_type_run.run_startdate &&\n+ #end if\n+ ./xmlchange STOP_N=$adv_period.stopn &&\n+ ./xmlchange STOP_OPTION=$adv_period.stop_option &&\n+ ./xmlchange CCSM_CO2_PPMV=$adv.co2 &&\n+ ./xmlchange DOUT_S=FALSE &&\n+ cp \'$user_nl_clm_customization\' user_nl_clm &&\n+ ./case.build >> $case_info 2>&1 &&\n+ #if (str($adv_period.condi_type_run.run_type) == \'hybrid\' or str($adv_period.condi_type_run.run_type) == \'branch\')\n+ tar -xf \'$adv_period.condi_type_run.restart\' -C \'../work/$casename/run/\' && \n+ \n+ #end if\n+ ./case.submit >> $case_info 2>&1 &&\n+ mkdir -p restart &&\n+ (cat \'../work/$casename/run/rpointer\'.* > $rinfo || printf "No restarts\\n") &&\n+ (cp \'../work/$casename/run/$casename\'.*.r*.*.nc restart/ || printf "No netCDF restarts\\n") &&\n+ (cp \'../work/$casename/run/$casename\'.*.r*.*.bin restart/ || printf "No bin restarts\\n") &&\n+ (cp \'../work/$casename/run/rpointer\'.* restart/ || printf "no rpointer\\n") &&\n+ cd restart && \n+ tar cvf $restart . &&\n+ cd .. && \n+ (cp \'../work/$casename/run/$casename\'.*.h*.*.nc ../output_dir/ || printf "no netCDF outputs\\n") &&\n+ (gunzip \'../work/$casename/run/\'*.log.* || printf "no compressed logs") && \n+ cat \'../work/$casename/run/\'atm.log.* >> $atm_log &&\n+ cat \'../work/$casename/run/\'cesm.log.* >> $cesm_log &&\n+ cat \'../work/$casename/run/\'cpl.log.* >> $cpl_log &&\n+ cat \'../work/$casename/run/\'lnd.log.* >> $lnd_log &&\n+ cat \'..'..b' name="stopn" value="1" />\n+ <output name="atm_log" ftype="txt" file="atm.log">\n+ <assert_contents>\n+ <has_text text="(datm_comp_final) atm: end of main integration loop" />\n+ </assert_contents>\n+ </output>\n+ <output name="cesm_log" ftype="txt" file="cesm.log">\n+ <assert_contents>\n+ <has_text text="pes participating in computation for CLM" />\n+ </assert_contents>\n+ </output>\n+ <output name="cpl_log" ftype="txt" file="cpl.log">\n+ <assert_contents>\n+ <has_text text="SUCCESSFUL TERMINATION" />\n+ </assert_contents>\n+ </output>\n+ <output name="lnd_log" ftype="txt" file="lnd.log">\n+ <assert_contents>\n+ <has_text text="Successfully" />\n+ </assert_contents>\n+ </output>\n+ <output name="rof_log" ftype="txt" file="rof.log">\n+ <assert_contents>\n+ <has_text text="MOSART model initialization" />\n+ </assert_contents>\n+ </output>\n+ <output name="case_info" ftype="txt" file="case_info.txt">\n+ <assert_contents>\n+ <has_text text="MODEL BUILD HAS FINISHED SUCCESSFULLY" />\n+ <has_line_matching expression="Submitted job" />\n+ </assert_contents>\n+ </output>\n+ <output name="work" ftype="tar" file="workdir.tar">\n+ <assert_contents>\n+ <has_size value="0"/>\n+ </assert_contents>\n+ </output>\n+ <output name="restart" ftype="tar" file="restart.tar" compare="sim_size" delta="100" />\n+ <output name="rinfo" ftype="txt" file="restart_info.txt">\n+ <assert_contents>\n+ <has_line_matching expression="*datm.r.2000-01-01-01800.nc*" />\n+ <has_line_matching expression="*datm.rs1.2000-01-01-01800.bin*" />\n+ <has_line_matching expression="*cpl.r.2000-01-01-01800.nc*" />\n+ <has_line_matching expression="*clm2.r.2000-01-01-01800.nc*" />\n+ </assert_contents>\n+ </output>\n+ <output name="history_files" ftype="netcdf" file="history_file.netcdf">\n+ <assert_contents>\n+ <has_size value="0"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+\n+**The Functionally Assembled Terrestrial Ecosystem Simulator (FATES)**\n+==========================================================================\n+\n+This tool create and run CTSM-FATES EMERALD experiments from fates-emerald release.\n+\n+This version of FATES is maintained by the University of Oslo.\n+\n+Currently available resolution are as following:\n+\n+SeedClim Sites:\n+~~~~~~~~~~~~~~~\n+\n+- ALP1,61.0243N,8.12343E\n+- ALP2,60.8231N,7.27596E\n+- ALP3,60.8328N,7.17561E\n+- ALP4,60.9335N,6.41504E\n+- SUB1,60.8203N,8.70466E\n+- SUB2,60.8760N,7.17666E\n+- SUB3,61.0866N,6.63028E\n+- SUB4,60.5445N,6.51468E\n+- BOR1,61.0355N,9.07876E\n+- BOR2,60.8803N,7.16982E\n+- BOR3,60.6652N,6.33738E\n+- BOR4,60.6901N,5.96487E\n+\n+LandPress Sites:\n+~~~~~~~~~~~~~~~~\n+\n+- LYG,60.70084N,5.092566E \n+- BUO,65.83677N,12.224506E\n+- HAV,64.779N,11.2193E\n+- SKO,65.79602N,12.219299E\n+\n+Three-D Sites:\n+~~~~~~~~~~~~~~\n+\n+- VIKE,60.88019N,7.16990E\n+- JOAS,60.86183N,7.16800E\n+- LIAH,60.85994N,7.19504E\n+\n+\n+Finnmark Site:\n+~~~~~~~~~~~~~~\n+\n+- FINN,69.341088N,25.293524E\n+\n+ ]]></help>\n+ <citations>\n+\n+ </citations>\n+ <edam_topics>\n+ <edam_topic>topic_3855</edam_topic>\n+ <edam_topic>topic_3318</edam_topic>\n+ <edam_topic>topic_3050</edam_topic>\n+ <edam_topic>topic_0610</edam_topic>\n+ </edam_topics>\n+ <edam_operations>\n+ <edam_operation>operation_3946</edam_operation>\n+ <edam_operation>operation_2426</edam_operation>\n+ </edam_operations>\n+</tool>\n' |
| b |
| diff -r 000000000000 -r 8c7414c07367 ctsm-fates.xml_detail --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ctsm-fates.xml_detail Wed Oct 21 20:30:35 2020 +0000 |
| [ |
| b'@@ -0,0 +1,331 @@\n+<tool id="ctsm-fates" name="CTSM/FATES-EMERALD" version="2.0.1">\n+ <description>Functionally Assembled Terrestrial Ecosystem Simulator</description>\n+ <requirements>\n+ <requirement type="package" version="2.0.1">fates-emerald</requirement>\n+ <requirement type="package" version="1.32">tar</requirement>\n+ <requirement type="package" version="2.35">binutils</requirement>\n+ <requirement type="package" version="3">python</requirement>\n+ <requirement type="package" version="2.0132">perl-xml-libxml</requirement>\n+ </requirements>\n+ <command detect_errors="exit_code"><![CDATA[\n+ ( export HOME=`pwd` &&\n+ export USER=\'jovyan\' &&\n+ mkdir -p .cime &&\n+ cp \'$__tool_directory__/config\' .cime/config &&\n+ cp \'$__tool_directory__/config_compilers.xml\' \'.cime/config_compilers.xml\' &&\n+ cp \'$__tool_directory__/config_machines.xml\' \'.cime/config_machines.xml\' &&\n+ mkdir inputdata &&\n+ tar -xf \'$inputdata\' -C \'inputdata/\' && \n+ mkdir output_dir &&\n+ mkdir usermods_dirs &&\n+ #if str($adv.condi_user_mods).strip() == \'yes\'\n+ # should create a new type user_mods.tar\n+ cd usermods_dirs &&\n+ tar xf \'$user_mods\' &&\n+ cd .. &&\n+ #end if\n+ create_newcase --case \'$casename\' --compset 2000_DATM%1PTGSWP3_CLM50%FATES_SICE_SOCN_MOSART_SGLC_SWAV --machine espresso --run-unsupported \n+ #if str($adv.condi_user_mods).strip() == \'yes\'\n+ --user-mods-dir usermods_dirs\n+ #end if\n+ --res \'$resolution\' && \n+ cd \'$casename\' &&\n+ ./case.setup > $case_info 2>&1 &&\n+ #if (str($adv_period.condi_type_run.run_type) == \'hybrid\' or str($adv_period.condi_type_run.run_type) == \'branch\')\n+ ./xmlchange RUN_TYPE=$adv_period.condi_type_run.run_type &&\n+ ./xmlchange RUN_REFDATE=$adv_period.condi_type_run.run_refdate &&\n+ ./xmlchange RUN_REFCASE=$adv_period.condi_type_run.run_refcase &&\n+ #end if\n+ #if ((str($adv_period.condi_type_run.run_type) == \'hybrid\' or str($adv_period.condi_type_run.run_type) == \'startup\') and ($adv_period.condi_type_run.run_startdate != \'\'))\n+ ./xmlchange RUN_STARTDATE=$adv_period.condi_type_run.run_startdate &&\n+ #end if\n+ ./xmlchange STOP_N=$adv_period.stopn &&\n+ ./xmlchange STOP_OPTION=$adv_period.stop_option &&\n+ ./xmlchange CCSM_CO2_PPMV=$adv.co2 &&\n+ ./xmlchange DOUT_S=FALSE &&\n+ cp \'$user_nl_clm_customization\' user_nl_clm &&\n+ ./case.build >> $case_info 2>&1 &&\n+ #if (str($adv_period.condi_type_run.run_type) == \'hybrid\' or str($adv_period.condi_type_run.run_type) == \'branch\')\n+ tar -xf \'$adv_period.condi_type_run.restart\' -C \'../work/$casename/run/\' && \n+ \n+ #end if\n+ ./case.submit >> $case_info 2>&1 &&\n+ mkdir -p restart &&\n+ (cat \'../work/$casename/run/rpointer\'.* > $rinfo || printf "No restarts\\n") &&\n+ (cp \'../work/$casename/run/$casename\'.*.r*.*.nc restart/ || printf "No netCDF restarts\\n") &&\n+ (cp \'../work/$casename/run/$casename\'.*.r*.*.bin restart/ || printf "No bin restarts\\n") &&\n+ (cp \'../work/$casename/run/rpointer\'.* restart/ || printf "no rpointer\\n") &&\n+ cd restart && \n+ tar cvf $restart . &&\n+ cd .. && \n+ (cp \'../work/$casename/run/$casename\'.*.h*.*.nc ../output_dir/ || printf "no netCDF outputs\\n") &&\n+ (gunzip \'../work/$casename/run/\'*.log.* || printf "no compressed logs") && \n+ cat \'../work/$casename/run/\'atm.log.* >> $atm_log &&\n+ cat \'../work/$casename/run/\'cesm.log.* >> $cesm_log &&\n+ cat \'../work/$casename/run/\'cpl.log.* >> $cpl_log &&\n+ cat \'../work/$casename/run/\'lnd.log.* >> $lnd_log &&\n+ cat \'..'..b'test" />\n+ <param name="resolution" value="1x1_ALP1" />\n+ <param name="run_startdate" value="2000-01-01" />\n+ <param name="stop_option" value="nsteps" />\n+ <param name="stopn" value="1" />\n+ <output name="atm_log" ftype="txt" file="atm.log">\n+ <assert_contents>\n+ <has_text text="(datm_comp_final) atm: end of main integration loop" />\n+ </assert_contents>\n+ </output>\n+ <output name="cesm_log" ftype="txt" file="cesm.log">\n+ <assert_contents>\n+ <has_text text="pes participating in computation for CLM" />\n+ </assert_contents>\n+ </output>\n+ <output name="cpl_log" ftype="txt" file="cpl.log">\n+ <assert_contents>\n+ <has_text text="SUCCESSFUL TERMINATION" />\n+ </assert_contents>\n+ </output>\n+ <output name="lnd_log" ftype="txt" file="lnd.log">\n+ <assert_contents>\n+ <has_text text="Successfully" />\n+ </assert_contents>\n+ </output>\n+ <output name="rof_log" ftype="txt" file="rof.log">\n+ <assert_contents>\n+ <has_text text="MOSART model initialization" />\n+ </assert_contents>\n+ </output>\n+ <output name="case_info" ftype="txt" file="case_info.txt">\n+ <assert_contents>\n+ <has_text text="MODEL BUILD HAS FINISHED SUCCESSFULLY" />\n+ <has_text text="Submitted job" />\n+ </assert_contents>\n+ </output>\n+ <output name="work" ftype="tar" file="workdir.tar">\n+ <assert_contents>\n+ <has_size value="0"/>\n+ </assert_contents>\n+ </output>\n+ <output name="restart" ftype="tar" file="restart.tar" compare="sim_size" delta="100" />\n+ <output name="rinfo" ftype="txt" file="restart_info.txt">\n+ <assert_contents>\n+ <has_text text="datm.r.2000-01-01-01800.nc" />\n+ <has_text text="datm.rs1.2000-01-01-01800.bin" />\n+ <has_text text="cpl.r.2000-01-01-01800.nc" />\n+ <has_text text="clm2.r.2000-01-01-01800.nc" />\n+ </assert_contents>\n+ </output>\n+ <output_collection name="history_files" count="0">\n+ </output_collection>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+\n+**The Functionally Assembled Terrestrial Ecosystem Simulator (FATES)**\n+==========================================================================\n+\n+This tool create and run CTSM-FATES EMERALD experiments from fates-emerald release.\n+\n+This version of FATES is maintained by the University of Oslo.\n+\n+Currently available resolution are as following:\n+\n+SeedClim Sites:\n+~~~~~~~~~~~~~~~\n+\n+- ALP1,61.0243N,8.12343E\n+- ALP2,60.8231N,7.27596E\n+- ALP3,60.8328N,7.17561E\n+- ALP4,60.9335N,6.41504E\n+- SUB1,60.8203N,8.70466E\n+- SUB2,60.8760N,7.17666E\n+- SUB3,61.0866N,6.63028E\n+- SUB4,60.5445N,6.51468E\n+- BOR1,61.0355N,9.07876E\n+- BOR2,60.8803N,7.16982E\n+- BOR3,60.6652N,6.33738E\n+- BOR4,60.6901N,5.96487E\n+\n+LandPress Sites:\n+~~~~~~~~~~~~~~~~\n+\n+- LYG,60.70084N,5.092566E \n+- BUO,65.83677N,12.224506E\n+- HAV,64.779N,11.2193E\n+- SKO,65.79602N,12.219299E\n+\n+Three-D Sites:\n+~~~~~~~~~~~~~~\n+\n+- VIKE,60.88019N,7.16990E\n+- JOAS,60.86183N,7.16800E\n+- LIAH,60.85994N,7.19504E\n+\n+\n+Finnmark Site:\n+~~~~~~~~~~~~~~\n+\n+- FINN,69.341088N,25.293524E\n+\n+ ]]></help>\n+ <citations>\n+\n+ </citations>\n+ <edam_topics>\n+ <edam_topic>topic_3855</edam_topic>\n+ <edam_topic>topic_3318</edam_topic>\n+ <edam_topic>topic_3050</edam_topic>\n+ <edam_topic>topic_0610</edam_topic>\n+ </edam_topics>\n+ <edam_operations>\n+ <edam_operation>operation_3946</edam_operation>\n+ <edam_operation>operation_2426</edam_operation>\n+ </edam_operations>\n+</tool>\n' |
| b |
| diff -r 000000000000 -r 8c7414c07367 test-data/atm.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/atm.log Wed Oct 21 20:30:35 2020 +0000 |
| b |
| b'@@ -0,0 +1,240 @@\n+(datm_comp_init) decomp = 1d\n+(datm_comp_init) iradsw = 1\n+(datm_comp_init) factorFn = null\n+(datm_comp_init) restfilm = undefined\n+(datm_comp_init) restfils = undefined\n+(datm_comp_init) presaero = T\n+(datm_comp_init) force_prognostic_true = F\n+(datm_comp_init) wiso_datm = F\n+(datm_comp_init) inst_index = 1\n+(datm_comp_init) inst_name = ATM\n+(datm_comp_init) inst_suffix = \n+(shr_strdata_readnml) reading input namelist file: datm_in\n+(shr_stream_init) Reading file datm.streams.txt.CLM1PT.1x1_ALP1.Solar\n+(shr_file_freeUnit) unit 97 was not in use\n+(shr_stream_init) Reading file datm.streams.txt.CLM1PT.1x1_ALP1.Precip\n+(shr_file_freeUnit) unit 97 was not in use\n+(shr_stream_init) Reading file datm.streams.txt.CLM1PT.1x1_ALP1.TPQW\n+(shr_file_freeUnit) unit 97 was not in use\n+(shr_stream_init) Reading file datm.streams.txt.presaero.clim_2000\n+(shr_file_freeUnit) unit 97 was not in use\n+(shr_stream_init) Reading file datm.streams.txt.topo.observed\n+(shr_file_freeUnit) unit 97 was not in use\n+(datm_comp_init) datm datamode = CLMNCEP\n+ (shr_strdata_init_streams) stream 1\n+ (shr_strdata_init_streams) filePath = 1 /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/share/domains/ALP1/\n+ (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\n+ (shr_strdata_init_streams) timeName = 1 time\n+ (shr_strdata_init_streams) lonName = 1 xc\n+ (shr_strdata_init_streams) latName = 1 yc\n+ (shr_strdata_init_streams) hgtName = 1 unknownname\n+ (shr_strdata_init_streams) maskName = 1 mask\n+ (shr_strdata_init_streams) areaName = 1 area\n+ (shr_strdata_init_streams) stream 2\n+ (shr_strdata_init_streams) filePath = 2 /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/share/domains/ALP1/\n+ (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\n+ (shr_strdata_init_streams) timeName = 2 time\n+ (shr_strdata_init_streams) lonName = 2 xc\n+ (shr_strdata_init_streams) latName = 2 yc\n+ (shr_strdata_init_streams) hgtName = 2 unknownname\n+ (shr_strdata_init_streams) maskName = 2 mask\n+ (shr_strdata_init_streams) areaName = 2 area\n+ (shr_strdata_init_streams) stream 3\n+ (shr_strdata_init_streams) filePath = 3 /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/share/domains/ALP1/\n+ (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\n+ (shr_strdata_init_streams) timeName = 3 time\n+ (shr_strdata_init_streams) lonName = 3 xc\n+ (shr_strdata_init_streams) latName = 3 yc\n+ (shr_strdata_init_streams) hgtName = 3 unknownname\n+ (shr_strdata_init_streams) maskName = 3 mask\n+ (shr_strdata_init_streams) areaName = 3 area\n+ (shr_strdata_init_streams) stream 4\n+ (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/\n+ (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\n+ (shr_strdata_init_streams) timeName = 4 time\n+ (shr_strdata_init_streams) lonName = 4 lon\n+ (shr_strdata_init_streams) latName = 4 lat\n+ (shr_strdata_init_streams) hgtName = 4 unknownname\n+ (shr_strdata_init_streams'..b'q__51/job_working_directory/000/2/working/inputdata/atm/datm7/ALP1/clm1pt_ALP1_1950-01.nc\n+(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\n+(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\n+(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\n+(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\n+(shr_dmodel_readstrm) open : /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working/inputdata/atm/datm7/topo_forcing/ALP1/topodata_ALP1.nc\n+(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\n+(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\n+ (datm_comp_run) max values = 266.23443603515625 0.0000000000000000 0.0000000000000000 \n+(datm_comp_run) atm: model date 20000101 0s\n+(datm_comp_init) datm_comp_init done\n+(datm_comp_run) writing test.datm.rs1.2000-01-01-01800.bin20000101 1800s\n+(shr_stream_restWrite) case name : test\n+(shr_stream_restWrite) case description : SDATM strdata\n+(shr_stream_restWrite) File created : 2020-10-20 14:24:33\n+(shr_stream_restWrite) Number of streams 5\n+(shr_stream_restWrite) * stream 1 first file name = clm1pt_ALP1_1901-01.nc\n+(shr_stream_restWrite) * stream 1 first have data = T\n+(shr_stream_restWrite) * stream 1 first nt = 248\n+(shr_stream_restWrite) * stream 1 first date secs = 19010101 0\n+(shr_stream_restWrite) * stream 1 last date secs = 19010131 75600\n+(shr_stream_restWrite) * stream 2 first file name = clm1pt_ALP1_1901-01.nc\n+(shr_stream_restWrite) * stream 2 first have data = T\n+(shr_stream_restWrite) * stream 2 first nt = 248\n+(shr_stream_restWrite) * stream 2 first date secs = 19010101 5400\n+(shr_stream_restWrite) * stream 2 last date secs = 19010131 81000\n+(shr_stream_restWrite) * stream 3 first file name = clm1pt_ALP1_1901-01.nc\n+(shr_stream_restWrite) * stream 3 first have data = T\n+(shr_stream_restWrite) * stream 3 first nt = 248\n+(shr_stream_restWrite) * stream 3 first date secs = 19010101 5400\n+(shr_stream_restWrite) * stream 3 last date secs = 19010131 81000\n+(shr_stream_restWrite) * stream 4 first file name = ALP1/aerosoldep_WACCM.ensmean_monthly_hist_1849-2015_0.9x1.25_CMIP6_c180926_ALP1.nc\n+(shr_stream_restWrite) * stream 4 first have data = T\n+(shr_stream_restWrite) * stream 4 first nt = 2004\n+(shr_stream_restWrite) * stream 4 first date secs = 18490116 43200\n+(shr_stream_restWrite) * stream 4 last date secs = 20151216 43200\n+(shr_stream_restWrite) * stream 5 first file name = ALP1/topodata_ALP1.nc\n+(shr_stream_restWrite) * stream 5 first have data = T\n+(shr_stream_restWrite) * stream 5 first nt = 1\n+(shr_stream_restWrite) * stream 5 first date secs = 10101 0\n+(shr_stream_restWrite) * stream 5 last date secs = 10101 0\n+(datm_comp_run) atm: model date 20000101 1800s\n+(datm_comp_final) -------------------------------------------------------------------------\n+(datm_comp_final) atm: end of main integration loop\n+(datm_comp_final) -------------------------------------------------------------------------\n' |
| b |
| diff -r 000000000000 -r 8c7414c07367 test-data/cesm.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cesm.log Wed Oct 21 20:30:35 2020 +0000 |
| b |
| b'@@ -0,0 +1,233 @@\n+nohup: ignoring input\n+ PIO rearranger options:\n+ comm type =p2p \n+ comm fcd =2denable \n+ max pend req (comp2io) = 0\n+ enable_hs (comp2io) = T\n+ enable_isend (comp2io) = F\n+ max pend req (io2comp) = 0\n+ enable_hs (io2comp) = F\n+ enable_isend (io2comp) = T\n+(seq_comm_setcomm) init ID ( 1 GLOBAL ) pelist = 0 0 1 ( npes = 1) ( nthreads = 1)( suffix =)\n+(seq_comm_setcomm) init ID ( 2 CPL ) pelist = 0 0 1 ( npes = 1) ( nthreads = 1)( suffix =)\n+(seq_comm_setcomm) init ID ( 5 ATM ) pelist = 0 0 1 ( npes = 1) ( nthreads = 1)( suffix =)\n+(seq_comm_joincomm) init ID ( 6 CPLATM ) join IDs = 2 5 ( npes = 1) ( nthreads = 1)\n+(seq_comm_jcommarr) init ID ( 3 ALLATMID ) join multiple comp IDs ( npes = 1) ( nthreads = 1)\n+(seq_comm_joincomm) init ID ( 4 CPLALLATMID ) join IDs = 2 3 ( npes = 1) ( nthreads = 1)\n+(seq_comm_setcomm) init ID ( 9 LND ) pelist = 0 0 1 ( npes = 1) ( nthreads = 1)( suffix =)\n+(seq_comm_joincomm) init ID ( 10 CPLLND ) join IDs = 2 9 ( npes = 1) ( nthreads = 1)\n+(seq_comm_jcommarr) init ID ( 7 ALLLNDID ) join multiple comp IDs ( npes = 1) ( nthreads = 1)\n+(seq_comm_joincomm) init ID ( 8 CPLALLLNDID ) join IDs = 2 7 ( npes = 1) ( nthreads = 1)\n+(seq_comm_setcomm) init ID ( 13 ICE ) pelist = 0 0 1 ( npes = 1) ( nthreads = 1)( suffix =)\n+(seq_comm_joincomm) init ID ( 14 CPLICE ) join IDs = 2 13 ( npes = 1) ( nthreads = 1)\n+(seq_comm_jcommarr) init ID ( 11 ALLICEID ) join multiple comp IDs ( npes = 1) ( nthreads = 1)\n+(seq_comm_joincomm) init ID ( 12 CPLALLICEID ) join IDs = 2 11 ( npes = 1) ( nthreads = 1)\n+(seq_comm_setcomm) init ID ( 17 OCN ) pelist = 0 0 1 ( npes = 1) ( nthreads = 1)( suffix =)\n+(seq_comm_joincomm) init ID ( 18 CPLOCN ) join IDs = 2 17 ( npes = 1) ( nthreads = 1)\n+(seq_comm_jcommarr) init ID ( 15 ALLOCNID ) join multiple comp IDs ( npes = 1) ( nthreads = 1)\n+(seq_comm_joincomm) init ID ( 16 CPLALLOCNID ) join IDs = 2 15 ( npes = 1) ( nthreads = 1)\n+(seq_comm_setcomm) init ID ( 21 ROF ) pelist = 0 0 1 ( npes = 1) ( nthreads = 1)( suffix =)\n+(seq_comm_joincomm) init ID ( 22 CPLROF ) join IDs = 2 21 ( npes = 1) ( nthreads = 1)\n+(seq_comm_jcommarr) init ID ( 19 ALLROFID ) join multiple comp IDs ( npes = 1) ( nthreads = 1)\n+(seq_comm_joincomm) init ID ( 20 CPLALLROFID ) join IDs = 2 19 ( npes = 1) ( nthreads = 1)\n+(seq_comm_setcomm) init ID ( 25 GLC ) pelist = 0 0 1 ( npes = 1) ( nthreads = 1)( suffix =)\n+(seq_comm_joincomm) init ID ( 26 CPLGLC ) join IDs = 2 25 ( npes = 1) ( nthreads = 1)\n+(seq_comm_jcommarr) init ID ( 23 ALLGLCID ) join multiple comp IDs ( npes = 1) ( nthreads = 1)\n+(seq_comm_joincomm) init ID ( 24 CPLALLGLCID ) join IDs = 2 23 ( npes = 1) ( nthreads = 1)\n+(seq_comm_setcomm) init ID ( 29 WAV ) pelist = 0 0 1 ( npes = 1) ( nthreads = 1)( suffix =)\n+(seq_comm_joincomm) init ID ( 30 CPLWAV ) join IDs = 2 29 ( npes = 1) ( nthreads = 1)\n+(seq_comm_jcommarr) init ID ( 27 ALLWAVID ) join multiple comp IDs ( npes = 1) ( nthreads = 1)\n+(seq_comm_joincomm) init ID ( 28 CPLALLWAVID ) join IDs = 2 27 ( npes = 1) ( nthreads = 1)\n+('..b'\n+ clmfates_interfaceMod.F90:: reading fates_mort_bmort\n+ clmfates_interfaceMod.F90:: reading fates_mort_r_size_senescence\n+ clmfates_interfaceMod.F90:: reading fates_mort_ip_size_senescence\n+ clmfates_interfaceMod.F90:: reading fates_mort_r_age_senescence\n+ clmfates_interfaceMod.F90:: reading fates_mort_ip_age_senescence\n+ clmfates_interfaceMod.F90:: reading fates_mort_scalar_coldstress\n+ clmfates_interfaceMod.F90:: reading fates_mort_scalar_cstarvation\n+ clmfates_interfaceMod.F90:: reading fates_mort_scalar_hydrfailure\n+ clmfates_interfaceMod.F90:: reading fates_mort_hf_sm_threshold\n+ clmfates_interfaceMod.F90:: reading fates_mort_hf_flc_threshold\n+ clmfates_interfaceMod.F90:: reading fates_leaf_vcmaxha\n+ clmfates_interfaceMod.F90:: reading fates_leaf_jmaxha\n+ clmfates_interfaceMod.F90:: reading fates_leaf_tpuha\n+ clmfates_interfaceMod.F90:: reading fates_leaf_vcmaxhd\n+ clmfates_interfaceMod.F90:: reading fates_leaf_jmaxhd\n+ clmfates_interfaceMod.F90:: reading fates_leaf_tpuhd\n+ clmfates_interfaceMod.F90:: reading fates_leaf_vcmaxse\n+ clmfates_interfaceMod.F90:: reading fates_leaf_jmaxse\n+ clmfates_interfaceMod.F90:: reading fates_leaf_tpuse\n+ clmfates_interfaceMod.F90:: reading fates_seed_germination_rate\n+ clmfates_interfaceMod.F90:: reading fates_seed_decay_rate\n+ clmfates_interfaceMod.F90:: reading fates_trim_limit\n+ clmfates_interfaceMod.F90:: reading fates_trim_inc\n+ clmfates_interfaceMod.F90:: reading fates_leaf_diameter\n+ clmfates_interfaceMod.F90:: reading fates_z0mr\n+ clmfates_interfaceMod.F90:: reading fates_displar\n+ clmfates_interfaceMod.F90:: reading fates_phenflush_fraction\n+ clmfates_interfaceMod.F90:: reading fates_phen_cold_size_threshold\n+ clmfates_interfaceMod.F90:: reading fates_phen_stem_drop_fraction\n+ clmfates_interfaceMod.F90:: reading fates_eca_decompmicc\n+ clmfates_interfaceMod.F90:: reading fates_eca_km_nh4\n+ clmfates_interfaceMod.F90:: reading fates_eca_vmax_nh4\n+ clmfates_interfaceMod.F90:: reading fates_eca_km_no3\n+ clmfates_interfaceMod.F90:: reading fates_eca_vmax_no3\n+ clmfates_interfaceMod.F90:: reading fates_eca_km_p\n+ clmfates_interfaceMod.F90:: reading fates_eca_vmax_p\n+ clmfates_interfaceMod.F90:: reading fates_eca_km_ptase\n+ clmfates_interfaceMod.F90:: reading fates_eca_vmax_ptase\n+ clmfates_interfaceMod.F90:: reading fates_eca_alpha_ptase\n+ clmfates_interfaceMod.F90:: reading fates_eca_lambda_ptase\n+ clmfates_interfaceMod.F90:: reading fates_prescribed_nuptake\n+ clmfates_interfaceMod.F90:: reading fates_prescribed_puptake\n+ clmfates_interfaceMod.F90:: reading fates_rholvis\n+ clmfates_interfaceMod.F90:: reading fates_rholnir\n+ clmfates_interfaceMod.F90:: reading fates_rhosvis\n+ clmfates_interfaceMod.F90:: reading fates_rhosnir\n+ clmfates_interfaceMod.F90:: reading fates_taulvis\n+ clmfates_interfaceMod.F90:: reading fates_taulnir\n+ clmfates_interfaceMod.F90:: reading fates_tausvis\n+ clmfates_interfaceMod.F90:: reading fates_tausnir\n+ clmfates_interfaceMod.F90:: reading fates_hydr_avuln_node\n+ clmfates_interfaceMod.F90:: reading fates_hydr_p50_node\n+ clmfates_interfaceMod.F90:: reading fates_hydr_thetas_node\n+ clmfates_interfaceMod.F90:: reading fates_hydr_epsil_node\n+ clmfates_interfaceMod.F90:: reading fates_hydr_pitlp_node\n+ clmfates_interfaceMod.F90:: reading fates_hydr_resid_node\n+ clmfates_interfaceMod.F90:: reading fates_hydr_fcap_node\n+ clmfates_interfaceMod.F90:: reading fates_hydr_pinot_node\n+ clmfates_interfaceMod.F90:: reading fates_hydr_kmax_node\n+ clmfates_interfaceMod.F90:: reading fates_leaf_vcmax25top\n+ NetCDF: Variable not found\n+ NetCDF: Invalid dimension ID or name\n+ NetCDF: Invalid dimension ID or name\n+ NetCDF: Invalid dimension ID or name\n+ NetCDF: Invalid dimension ID or name\n+ NetCDF: Invalid dimension ID or name\n+ NetCDF: Invalid dimension ID or name\n+ NetCDF: Invalid dimension ID or name\n+ NetCDF: Invalid dimension ID or name\n+ NetCDF: Invalid dimension ID or name\n+ NetCDF: Invalid dimension ID or name\n+ NetCDF: Variable not found\n+ NetCDF: Variable not found\n' |
| b |
| diff -r 000000000000 -r 8c7414c07367 test-data/cpl.log |
| b |
| Binary file test-data/cpl.log has changed |
| b |
| diff -r 000000000000 -r 8c7414c07367 test-data/inputdata_test.tar |
| b |
| Binary file test-data/inputdata_test.tar has changed |
| b |
| diff -r 000000000000 -r 8c7414c07367 test-data/lnd.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/lnd.log Wed Oct 21 20:30:35 2020 +0000 |
| b |
| b'@@ -0,0 +1,2106 @@\n+(lnd_init_mct) :CLM land model initialization\n+ unknown\n+\n+ Attempting to initialize the land model .....\n+\n+ Attempting to initialize run control settings .....\n+ Read in clm_inparm namelist from: lnd_in\n+ \n+ rooting_profile settings:\n+ rooting_profile_method_water = 1\n+ (rooting_profile_varindex_water = 1 )\n+ rooting_profile_method_carbon = 1\n+ (rooting_profile_varindex_carbon = 2 )\n+ \n+ soilwater_movement settings:\n+ soilwater_movement_method = 1\n+ upper_boundary_condition = 1\n+ lower_boundary_condition = 2\n+ use_bedrock = F\n+ dtmin = 60.000000000000000 \n+ verySmall = 1.0000000000000000E-008\n+ xTolerUpper = 0.10000000000000001 \n+ xTolerLower = 1.0000000000000000E-002\n+ expensive = 42\n+ inexpensive = 1\n+ flux_calculation = 1\n+ \n+ soil_resis settings:\n+ soil_resis_method = 1\n+ Read in canopyfluxes_inparm namelist\n+ (OPNFIL): Successfully opened file lnd_in on unit= 96\n+ \n+ canopyfluxes_inparm settings:\n+&CANOPYFLUXES_INPARM\n+ USE_UNDERCANOPY_STABILITY=F,\n+ ITMAX_CANOPY_FLUXES= 40,\n+ /\n+ \n+ Read in clm_CanopyHydrology_inparm namelist\n+ (OPNFIL): Successfully opened file lnd_in on unit= 96\n+ \n+ canopyhydrology settings:\n+ interception_fraction = 1.0000000000000000 \n+ maximum_leaf_wetted_fraction = 5.0000000000000003E-002\n+ use_clm5_fpi = T\n+ Read in surfacealbedo_inparm namelist\n+ (OPNFIL): Successfully opened file lnd_in on unit= 96\n+\n+ surfacealbedo_inparm settings\n+&SURFACEALBEDO_INPARM\n+ SNOWVEG_AFFECTS_RADIATION=T,\n+ /\n+\n+ Read in clm_SnowHydrology_inparm namelist\n+ (OPNFIL): Successfully opened file lnd_in on unit= 96\n+ \n+ SnowHydrology settings:\n+&CLM_SNOWHYDROLOGY_INPARM\n+ WIND_DEPENDENT_SNOW_DENSITY=T,\n+ SNOW_OVERBURDEN_COMPACTION_METHOD="Vionnet2012 ",\n+ LOTMP_SNOWDENSITY_METHOD="Slater2017 ",\n+ UPPLIM_DESTRUCT_METAMORPH= 175.00000000000000 ,\n+ OVERBURDEN_COMPRESS_TFACTOR= 8.0000000000000002E-002,\n+ MIN_WIND_SNOWCOMPACT= 5.0000000000000000 ,\n+ RESET_SNOW=F,\n+ RESET_SNOW_GLC=F,\n+ RESET_SNOW_GLC_ELA= 1000000000.0000000 ,\n+ SNOW_DZMIN_1= 1.0000000000000000E-002,\n+ SNOW_DZMAX_L_1= 2.9999999999999999E-002,\n+ SNOW_DZMAX_U_1= 2.0000000000000000E-002,\n+ SNOW_DZMIN_2= 1.4999999999999999E-002,\n+ SNOW_DZMAX_L_2= 7.0000000000000007E-002,\n+ SNOW_DZMAX_U_2= 5.0000000000000003E-002,\n+ /\n+ \n+ Read in clmu_inparm namelist\n+ (OPNFIL): Successfully opened file lnd_in on unit= 96\n+ urban air conditioning/heating and wasteheat = ON_WASTEHEAT \n+ urban traffic flux = F\n+ Read in clm_humanindex_inparm namelist\n+ (OPNFIL): Successfully opened file lnd_in on unit= 96\n+ Read in luna namelist\n+ (OPNFIL): Successfully opened file lnd_in on unit= 96\n+ \n+ luna settings:\n+&LUNA\n+ JMAXB1= 0.10000000000000001 ,\n+ /\n+ \n+ Read in soilhydrology_inparm namelist\n+ (OPNFIL): Successfully opened file lnd_in on unit= 96\n+ \n+ soilhydrology_inparm settings:\n+&SOILHYDROLOGY_INPARM\n+ BASEFLOW_SCALAR= 1.0000000000000000E-003,\n+ /\n+ \n+ Read in CENTURY_soilBGCDecompCascade namelist\n+ (OPNFIL): Successfully opened file lnd_in on unit= 96\n+ \n+ CENTURY_soilBGCDecompCascade settings:\n+&CENTURY_SOILBGCDECOMPCASCADE\n+ INITIAL_CSTOCKS= 3*200.00000000000000 ,\n+ INITIAL_CSTOCKS_DEPTH= 1.5000000000000000 ,\n+ /\n+ \n+ Successfully initialized run control settings\n+\n+ Attempting to read maxsoil_patches and numcft from the surface data .....\n+ (GETFIL): attempting to find local file surfdata_ALP1_simyr2000.nc\n+ (GETFIL): using /opt/uio/tmp/tmpqayq__51/job_working_directory/000/2/working'..b'OI_10CM 1 A \n+ 396 TSOI_ICE 25 A \n+ 397 TV 1 A \n+ 398 TWS 1 A \n+ 399 T_SCALAR 20 A \n+ 400 U10 1 A \n+ 401 U10_DUST 1 A \n+ 402 URBAN_AC 1 A \n+ 403 URBAN_HEAT 1 A \n+ 404 VOLR 1 A \n+ 405 VOLRMCH 1 A \n+ 406 WA 1 A \n+ 407 WASTEHEAT 1 A \n+ 408 WBT 1 A \n+ 409 WBT_R 1 A \n+ 410 WBT_U 1 A \n+ 411 WIND 1 A \n+ 412 W_SCALAR 20 A \n+ 413 ZBOT 1 A \n+ 414 ZWT 1 A \n+ 415 ZWT_PERCH 1 A \n+ There will be a total of 1 history tapes\n+\n+ History tape 1 write frequency is MONTHLY\n+ All fields on history tape 1 are grid averaged\n+ Number of time samples on history tape 1 is 120\n+ Output precision on history tape 1 = 2\n+\n+ hist_htapes_build hist tape = 1 written with dov2xy= T\n+ hist_htapes_build Successfully initialized clm2 history files\n+------------------------------------------------------------\n+ Successfully initialized the land model\n+ begin initial run at: \n+ nstep= 0 year= 2000 month= 1 day= 1 seconds= 0\n+\n+************************************************************\n+\n+ dtime_sync= 1800 dtime_clm= 1800 mod = 0\n+ clm: completed timestep 0\n+ clm: calling FATES model 1\n+FATES Dynamics: 2000-01-01\n+ clm: leaving fates model 1 1\n+ clm: completed timestep 1\n+ hist_htapes_wrapup : history tape 1 : no open file to close\n+ writing restart file ./test.clm2.r.2000-01-01-01800.nc for model date = 2000-01-01-01800 \n+\n+ restFile_open: writing restart dataset at ./test.clm2.r.2000-01-01-01800.nc at nstep = 1\n+\n+ Opened file ./test.clm2.r.2000-01-01-01800.nc to write 458752\n+ htape_create : Opening netcdf rhtape ./test.clm2.rh0.2000-01-01-01800.nc\n+ Opened file ./test.clm2.rh0.2000-01-01-01800.nc to write 589824\n+ htape_create : Successfully defined netcdf restart history file 1\n+ Successfully wrote local restart file ./test.clm2.r.2000-01-01-01800.nc\n+------------------------------------------------------------\n+\n+ (OPNFIL): Successfully opened file ./rpointer.lnd on unit= 95\n+ Successfully wrote local restart pointer file\n+ Successfully wrote out restart data at nstep = 1\n+------------------------------------------------------------\n' |
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| diff -r 000000000000 -r 8c7414c07367 test-data/restart.tar |
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| Binary file test-data/restart.tar has changed |
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| diff -r 000000000000 -r 8c7414c07367 test-data/restart_info.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/restart_info.txt Wed Oct 21 20:30:35 2020 +0000 |
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| @@ -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 |
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| diff -r 000000000000 -r 8c7414c07367 test-data/rof.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rof.log Wed Oct 21 20:30:35 2020 +0000 |
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| @@ -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 |