# HG changeset patch
# User climate
# Date 1603313359 0
# Node ID b525b88bc9410dd13cd2173fcce73b49ad255b67
# Parent 74b675f9d7c868f6c1abeaade55b1acf8ba02a80
"planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/fates-emerald commit c85f3e956d229848d22dd25c2da8482d2a8269e0"
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
@@ -1,332 +0,0 @@
-
- Functionally Assembled Terrestrial Ecosystem Simulator
-
- fates-emerald
- tar
- binutils
- python
- perl-xml-libxml
-
- $case_info 2>&1 &&
- #if (str($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)
- ]]>
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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
@@ -1,338 +0,0 @@
-
- Functionally Assembled Terrestrial Ecosystem Simulator
-
- fates-emerald
- tar
- python
- perl-xml-libxml
-
- $case_info 2>&1 &&
- #if (str($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)
- ]]>
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- topic_3318
- topic_3050
- topic_0610
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- operation_3946
- operation_2426
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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
@@ -1,334 +0,0 @@
-
- Functionally Assembled Terrestrial Ecosystem Simulator
-
- fates-emerald
- tar
- binutils
- python
- perl-xml-libxml
-
- $case_info 2>&1 &&
- #if (str($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)
- ]]>
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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
@@ -1,331 +0,0 @@
-
- Functionally Assembled Terrestrial Ecosystem Simulator
-
- fates-emerald
- tar
- binutils
- python
- perl-xml-libxml
-
- $case_info 2>&1 &&
- #if (str($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)
- ]]>
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