# 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) - ]]> - - - - - - - - ^[A-Za-z][A-Za-z0-9]* - - - - - - - - - - - - - - - - - - - - - - -
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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) - ]]> - - - - - - - - ^[A-Za-z][A-Za-z0-9]* - - - - - - - - - - - - - - - - - - - - - - -
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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) - ]]> - - - - - - - - ^[A-Za-z][A-Za-z0-9]* - - - - - - - - - - - - - - - - - - - - - - -
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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) - ]]> - - - - - - - - ^[A-Za-z][A-Za-z0-9]* - - - - - - - - - - - - - - - - - - - - - - -
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