| Previous changeset 1:74b675f9d7c8 (2020-10-21) Next changeset 3:efaa93ed5a79 (2020-12-17) |
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Commit message:
"planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/fates-emerald commit c85f3e956d229848d22dd25c2da8482d2a8269e0" |
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removed:
ctsm-fates.xml.SLEEP ctsm-fates.xml.TRIC ctsm-fates.xml.binutils ctsm-fates.xml_detail |
| b |
| diff -r 74b675f9d7c8 -r b525b88bc941 ctsm-fates.xml.SLEEP --- a/ctsm-fates.xml.SLEEP Wed Oct 21 20:34:35 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,332 +0,0 @@\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 74b675f9d7c8 -r b525b88bc941 ctsm-fates.xml.TRIC --- a/ctsm-fates.xml.TRIC Wed Oct 21 20:34:35 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,338 +0,0 @@\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 74b675f9d7c8 -r b525b88bc941 ctsm-fates.xml.binutils --- a/ctsm-fates.xml.binutils Wed Oct 21 20:34:35 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,334 +0,0 @@\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 74b675f9d7c8 -r b525b88bc941 ctsm-fates.xml_detail --- a/ctsm-fates.xml_detail Wed Oct 21 20:34:35 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,331 +0,0 @@\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' |