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bugfixes and updated files used in realtime for CCPP-Chem and CCPP-C384 experiments #29

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Sep 14, 2021
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bugfixes and updated files used in realtime for CCPP-Chem and CCPP-C384 experiments #29

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107 changes: 107 additions & 0 deletions FV3GFSwfm/rt_ccpp-chem/arch.xml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,107 @@
<?xml version="1.0"?>
<!DOCTYPE workflow
[
<!--
PROGRAM
Main workflow manager for Forecast only Global Forecast System

AUTHOR:
Rahul Mahajan
rahul.mahajan@noaa.gov

NOTES:
This workflow was automatically generated at 2021-04-11 13:25:05.897628
-->

<!-- Experiment parameters such as name, cycle, resolution -->
<!ENTITY PSLOT "rt_ccpp-chem">
<!ENTITY CDUMP "gfs">
<!ENTITY CASE "C384">

<!-- Experiment parameters such as starting, ending dates -->
<!ENTITY SDATE "202108030000">
<!ENTITY EDATE "202108140000">
<!ENTITY INTERVAL "24:00:00">

<!-- Run Envrionment -->
<!ENTITY RUN_ENVIR "emc">

<!-- Experiment related directories -->
<!ENTITY EXPDIR "/scratch1/BMC/gsd-fv3/rtruns/CCPP-Chem/FV3GFSwfm/rt_ccpp-chem">
<!ENTITY ROTDIR "/scratch1/BMC/gsd-fv3/rtruns/CCPP-Chem/FV3GFSrun/rt_ccpp-chem">
<!ENTITY ICSDIR "/scratch1/BMC/gsd-fv3/rtruns/CCPP-Chem/FV3ICS">

<!-- use RUNDIR1 as long as FV3-CHEM is still running in realtime -->
<!ENTITY RUNDIR1 "/scratch1/BMC/gsd-fv3/NCEPDEV/stmp3/rtfim/RUNDIRS/rt_fv3gfs_chem">
<!ENTITY RUNDIR "/scratch1/BMC/gsd-fv3/NCEPDEV/stmp3/rtfim/RUNDIRS/rt_ccpp-chem">

<!-- use lzhang GBBEPx directory as long as FV3-CHEM is still running in realtime -->
<!ENTITY EMIDIR "/scratch2/BMC/public/data/grids/sdsu/emissions">
<!ENTITY EMIDIR "/scratch1/BMC/gsd-fv3-dev/lzhang/GBBEPx">
<!ENTITY ARCEMI "/scratch2/BMC/gsd-fv3-dev/Judy.K.Henderson/sdsu_emissions">

<!-- Directories for driving the workflow -->
<!ENTITY HOMEgfs "/scratch1/BMC/gsd-fv3/rtruns/CCPP-Chem">
<!ENTITY JOBS_DIR "/scratch1/BMC/gsd-fv3/rtruns/CCPP-Chem/jobs/rocoto">

<!-- Machine related entities -->
<!ENTITY ACCOUNT "gsd-fv3">
<!ENTITY QUEUE "batch">
<!ENTITY PARTITION_ARCH "service">
<!ENTITY SCHEDULER "slurm">

<!-- Toggle HPSS archiving -->
<!ENTITY ARCHIVE_TO_HPSS "YES">

<!-- ROCOTO parameters that control workflow -->
<!ENTITY CYCLETHROTTLE "4">
<!ENTITY TASKTHROTTLE "25">
<!ENTITY MAXTRIES "2">

<!-- BEGIN: Resource requirements for the workflow -->

<!ENTITY QUEUE_ARCH_GFS "&QUEUE;">
<!ENTITY PARTITION_ARCH_GFS "&PARTITION_ARCH;">
<!ENTITY WALLTIME_ARCH_GFS "06:00:00">
<!ENTITY RESOURCES_ARCH_GFS "<nodes>1:ppn=1:tpp=1</nodes>">
<!ENTITY MEMORY_ARCH_GFS "2048M">
<!ENTITY NATIVE_ARCH_GFS "--export=NONE">

<!-- END: Resource requirements for the workflow -->

]>

<workflow realtime="F" scheduler="&SCHEDULER;" cyclethrottle="&CYCLETHROTTLE;" taskthrottle="&TASKTHROTTLE;">

<log verbosity="10"><cyclestr>&EXPDIR;/logs/@Y@m@d@H.log</cyclestr></log>

<!-- Define the cycles -->
<cycledef group="gfs">&SDATE; &EDATE; &INTERVAL;</cycledef>

<task name="gfsarch" cycledefs="gfs" maxtries="&MAXTRIES;" final="true">

<command>&JOBS_DIR;/arch_gsd.sh</command>

<jobname><cyclestr>&PSLOT;_gfsarch_@H</cyclestr></jobname>
<account>&ACCOUNT;</account>
<queue>&QUEUE_ARCH_GFS;</queue>
<partition>&PARTITION_ARCH_GFS;</partition>
&RESOURCES_ARCH_GFS;
<walltime>&WALLTIME_ARCH_GFS;</walltime>
<memory>&MEMORY_ARCH_GFS;</memory>
<native>&NATIVE_ARCH_GFS;</native>

<join><cyclestr>&ROTDIR;/logs/@Y@m@d@H/gfsarch.log</cyclestr></join>

<envar><name>RUN_ENVIR</name><value>&RUN_ENVIR;</value></envar>
<envar><name>HOMEgfs</name><value>&HOMEgfs;</value></envar>
<envar><name>EXPDIR</name><value>&EXPDIR;</value></envar>
<envar><name>CDATE</name><value><cyclestr>@Y@m@d@H</cyclestr></value></envar>
<envar><name>CDUMP</name><value>&CDUMP;</value></envar>
<envar><name>PDY</name><value><cyclestr>@Y@m@d</cyclestr></value></envar>
<envar><name>cyc</name><value><cyclestr>@H</cyclestr></value></envar>

</task>


</workflow>
107 changes: 107 additions & 0 deletions FV3GFSwfm/rt_ccpp-chem/archchem_other.xml
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@@ -0,0 +1,107 @@
<?xml version="1.0"?>
<!DOCTYPE workflow
[
<!--
PROGRAM
Main workflow manager for Forecast only Global Forecast System

AUTHOR:
Rahul Mahajan
rahul.mahajan@noaa.gov

NOTES:
This workflow was automatically generated at 2021-04-11 13:25:05.897628
-->

<!-- Experiment parameters such as name, cycle, resolution -->
<!ENTITY PSLOT "rt_ccpp-chem">
<!ENTITY CDUMP "gfs">
<!ENTITY CASE "C384">

<!-- Experiment parameters such as starting, ending dates -->
<!ENTITY SDATE "202103230000">
<!ENTITY EDATE "202107100000">
<!ENTITY INTERVAL "24:00:00">

<!-- Run Envrionment -->
<!ENTITY RUN_ENVIR "emc">

<!-- Experiment related directories -->
<!ENTITY EXPDIR "/scratch1/BMC/gsd-fv3/rtruns/CCPP-Chem/FV3GFSwfm/rt_ccpp-chem">
<!ENTITY ROTDIR "/scratch1/BMC/gsd-fv3/rtruns/CCPP-Chem/FV3GFSrun/rt_ccpp-chem">
<!ENTITY ICSDIR "/scratch1/BMC/gsd-fv3/rtruns/CCPP-Chem/FV3ICS">

<!-- use RUNDIR1 as long as FV3-CHEM is still running in realtime -->
<!ENTITY RUNDIR1 "/scratch1/BMC/gsd-fv3/NCEPDEV/stmp3/rtfim/RUNDIRS/rt_fv3gfs_chem">
<!ENTITY RUNDIR "/scratch1/BMC/gsd-fv3/NCEPDEV/stmp3/rtfim/RUNDIRS/rt_ccpp-chem">

<!-- use lzhang GBBEPx directory as long as FV3-CHEM is still running in realtime -->
<!ENTITY EMIDIR "/scratch2/BMC/public/data/grids/sdsu/emissions">
<!ENTITY EMIDIR "/scratch1/BMC/gsd-fv3-dev/lzhang/GBBEPx">
<!ENTITY ARCEMI "/scratch2/BMC/gsd-fv3-dev/Judy.K.Henderson/sdsu_emissions">

<!-- Directories for driving the workflow -->
<!ENTITY HOMEgfs "/scratch1/BMC/gsd-fv3/rtruns/CCPP-Chem">
<!ENTITY JOBS_DIR "/scratch1/BMC/gsd-fv3/rtruns/CCPP-Chem/jobs/rocoto">

<!-- Machine related entities -->
<!ENTITY ACCOUNT "gsd-fv3">
<!ENTITY QUEUE "batch">
<!ENTITY PARTITION_ARCH "service">
<!ENTITY SCHEDULER "slurm">

<!-- Toggle HPSS archiving -->
<!ENTITY ARCHIVE_TO_HPSS "YES">

<!-- ROCOTO parameters that control workflow -->
<!ENTITY CYCLETHROTTLE "4">
<!ENTITY TASKTHROTTLE "25">
<!ENTITY MAXTRIES "2">

<!-- BEGIN: Resource requirements for the workflow -->

<!ENTITY QUEUE_ARCH_GFS "&QUEUE;">
<!ENTITY PARTITION_ARCH_GFS "&PARTITION_ARCH;">
<!ENTITY WALLTIME_ARCH_GFS "06:00:00">
<!ENTITY RESOURCES_ARCH_GFS "<nodes>1:ppn=1:tpp=1</nodes>">
<!ENTITY MEMORY_ARCH_GFS "2048M">
<!ENTITY NATIVE_ARCH_GFS "--export=NONE">

<!-- END: Resource requirements for the workflow -->

]>

<workflow realtime="F" scheduler="&SCHEDULER;" cyclethrottle="&CYCLETHROTTLE;" taskthrottle="&TASKTHROTTLE;">

<log verbosity="10"><cyclestr>&EXPDIR;/logs/@Y@m@d@H.log</cyclestr></log>

<!-- Define the cycles -->
<cycledef group="gfs">&SDATE; &EDATE; &INTERVAL;</cycledef>

<task name="gfsarch" cycledefs="gfs" maxtries="&MAXTRIES;" final="true">

<command>&JOBS_DIR;/arch_gsd_other.sh</command>

<jobname><cyclestr>&PSLOT;_gfsarch_@H</cyclestr></jobname>
<account>&ACCOUNT;</account>
<queue>&QUEUE_ARCH_GFS;</queue>
<partition>&PARTITION_ARCH_GFS;</partition>
&RESOURCES_ARCH_GFS;
<walltime>&WALLTIME_ARCH_GFS;</walltime>
<memory>&MEMORY_ARCH_GFS;</memory>
<native>&NATIVE_ARCH_GFS;</native>

<join><cyclestr>&ROTDIR;/logs/@Y@m@d@H/gfsarch_other.log</cyclestr></join>

<envar><name>RUN_ENVIR</name><value>&RUN_ENVIR;</value></envar>
<envar><name>HOMEgfs</name><value>&HOMEgfs;</value></envar>
<envar><name>EXPDIR</name><value>&EXPDIR;</value></envar>
<envar><name>CDATE</name><value><cyclestr>@Y@m@d@H</cyclestr></value></envar>
<envar><name>CDUMP</name><value>&CDUMP;</value></envar>
<envar><name>PDY</name><value><cyclestr>@Y@m@d</cyclestr></value></envar>
<envar><name>cyc</name><value><cyclestr>@H</cyclestr></value></envar>

</task>


</workflow>
4 changes: 2 additions & 2 deletions FV3GFSwfm/rt_ccpp-chem/config.base.emc.dyn
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Original file line number Diff line number Diff line change
Expand Up @@ -85,7 +85,7 @@ export NCP="/bin/cp -p"
export NMV="/bin/mv"
export NLN="/bin/ln -sf"
export VERBOSE="YES"
export KEEPDATA="NO"
export KEEPDATA="YES"
export CHGRP_CMD="chgrp rstprod"
export NEMSIOGET="$HOMEgfs/exec/nemsio_get"
export NCDUMP="$NETCDF/bin/ncdump"
Expand Down Expand Up @@ -188,7 +188,7 @@ export restart_interval_gfs=0
export QUILTING=".true."
export OUTPUT_GRID="gaussian_grid"
export OUTPUT_FILE="nemsio" ## JKH
export WRITE_DOPOST=".true."
export WRITE_DOPOST=".false."

# suffix options depending on file format
if [ $OUTPUT_FILE = "netcdf" ]; then
Expand Down
17 changes: 9 additions & 8 deletions FV3GFSwfm/rt_ccpp-chem/noent_rtchem.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -22,18 +22,17 @@
<!ENTITY ICSDIR "/scratch1/BMC/gsd-fv3/rtruns/CCPP-Chem/FV3ICS">
<!-- use RUNDIR1 as long as FV3-CHEM is still running in realtime --><!ENTITY RUNDIR1 "/scratch1/BMC/gsd-fv3/NCEPDEV/stmp3/rtfim/RUNDIRS/rt_fv3gfs_chem">
<!ENTITY RUNDIR "/scratch1/BMC/gsd-fv3/NCEPDEV/stmp3/rtfim/RUNDIRS/rt_ccpp-chem">
<!-- use lzhang GBBEPx directory as long as FV3-CHEM is still running in realtime
<!ENTITY EMIDIR "/scratch2/BMC/public/data/grids/sdsu/emissions"> --><!ENTITY EMIDIR "/scratch1/BMC/gsd-fv3-dev/lzhang/GBBEPx">
<!-- use lzhang GBBEPx directory as long as FV3-CHEM is still running in realtime --><!ENTITY EMIDIR "/scratch1/BMC/gsd-fv3-dev/lzhang/GBBEPx">
<!ENTITY ARCEMI "/scratch2/BMC/gsd-fv3-dev/Judy.K.Henderson/sdsu_emissions">
<!-- Directories for driving the workflow --><!ENTITY HOMEgfs "/scratch1/BMC/gsd-fv3/rtruns/CCPP-Chem">
<!ENTITY JOBS_DIR "/scratch1/BMC/gsd-fv3/rtruns/CCPP-Chem/jobs/rocoto">
<!-- Machine related entities --><!ENTITY ACCOUNT "gsd-fv3">
<!ENTITY QUEUE "batch">
<!ENTITY QUEUE_ARCH "service">
<!ENTITY PARTITION_ARCH "service">
<!ENTITY SCHEDULER "slurm">
<!-- Toggle HPSS archiving --><!ENTITY ARCHIVE_TO_HPSS "YES">
<!-- ROCOTO parameters that control workflow --><!ENTITY CYCLETHROTTLE "2">
<!ENTITY TASKTHROTTLE "25">
<!-- ROCOTO parameters that control workflow --><!ENTITY CYCLETHROTTLE "5">
<!ENTITY TASKTHROTTLE "30">
<!ENTITY MAXTRIES "2">
<!-- BEGIN: Resource requirements for the workflow --><!ENTITY QUEUE_CALCINC "&QUEUE;">
<!ENTITY WALLTIME_CALCINC "00:30:00">
Expand All @@ -46,20 +45,21 @@
<!ENTITY MEMORY_PREP_CHEM_SRC "">
<!ENTITY NATIVE_PREP_CHEM_SRC "--export=NONE">
<!ENTITY QUEUE_FCST_GFS "&QUEUE;">
<!ENTITY WALLTIME_FCST_GFS "08:00:00">
<!ENTITY WALLTIME_FCST_GFS "06:00:00">
<!ENTITY RESOURCES_FCST_GFS "<nodes>8:ppn=40:tpp=1</nodes>">
<!ENTITY NATIVE_FCST_GFS "--export=NONE">
<!ENTITY QUEUE_POST_GFS "&QUEUE;">
<!ENTITY WALLTIME_POST_GFS "00:30:00">
<!ENTITY RESOURCES_POST_GFS "<nodes>4:ppn=12:tpp=1</nodes>">
<!ENTITY NATIVE_POST_GFS "--export=NONE">
<!ENTITY QUEUE_ARCH_GFS "&QUEUE;">
<!ENTITY PARTITION_ARCH_GFS "&PARTITION_ARCH;">
<!ENTITY WALLTIME_ARCH_GFS "06:00:00">
<!ENTITY RESOURCES_ARCH_GFS "<nodes>1:ppn=1:tpp=1</nodes>">
<!ENTITY MEMORY_ARCH_GFS "2048M">
<!ENTITY NATIVE_ARCH_GFS "--export=NONE">
<!-- END: Resource requirements for the workflow -->]>
<workflow realtime="T" scheduler="slurm" cyclethrottle="2" taskthrottle="25">
<workflow realtime="T" scheduler="slurm" cyclethrottle="5" taskthrottle="30">

<log verbosity="10"><cyclestr>/scratch1/BMC/gsd-fv3/rtruns/CCPP-Chem/FV3GFSwfm/rt_ccpp-chem/logs/@Y@m@d@H.log</cyclestr></log>

Expand Down Expand Up @@ -140,7 +140,7 @@
<account>gsd-fv3</account>
<queue>batch</queue>
<nodes>8:ppn=40:tpp=1</nodes>
<walltime>08:00:00</walltime>
<walltime>06:00:00</walltime>

<native>--export=NONE</native>

Expand Down Expand Up @@ -213,6 +213,7 @@
<jobname><cyclestr>rt_ccpp-chem_gfsarch_@H</cyclestr></jobname>
<account>gsd-fv3</account>
<queue>batch</queue>
<partition>service</partition>
<nodes>1:ppn=1:tpp=1</nodes>
<walltime>06:00:00</walltime>
<memory>2048M</memory>
Expand Down
14 changes: 8 additions & 6 deletions FV3GFSwfm/rt_ccpp-chem/rt_ccpp-chem.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -35,9 +35,9 @@
<!ENTITY RUNDIR1 "/scratch1/BMC/gsd-fv3/NCEPDEV/stmp3/rtfim/RUNDIRS/rt_fv3gfs_chem">
<!ENTITY RUNDIR "/scratch1/BMC/gsd-fv3/NCEPDEV/stmp3/rtfim/RUNDIRS/rt_ccpp-chem">

<!-- use lzhang GBBEPx directory as long as FV3-CHEM is still running in realtime
<!ENTITY EMIDIR "/scratch2/BMC/public/data/grids/sdsu/emissions"> -->
<!-- use lzhang GBBEPx directory as long as FV3-CHEM is still running in realtime -->
<!ENTITY EMIDIR "/scratch1/BMC/gsd-fv3-dev/lzhang/GBBEPx">
<!ENTITY EMIDIR "/scratch2/BMC/public/data/grids/sdsu/emissions">
<!ENTITY ARCEMI "/scratch2/BMC/gsd-fv3-dev/Judy.K.Henderson/sdsu_emissions">

<!-- Directories for driving the workflow -->
Expand All @@ -47,15 +47,15 @@
<!-- Machine related entities -->
<!ENTITY ACCOUNT "gsd-fv3">
<!ENTITY QUEUE "batch">
<!ENTITY QUEUE_ARCH "service">
<!ENTITY PARTITION_ARCH "service">
<!ENTITY SCHEDULER "slurm">

<!-- Toggle HPSS archiving -->
<!ENTITY ARCHIVE_TO_HPSS "YES">

<!-- ROCOTO parameters that control workflow -->
<!ENTITY CYCLETHROTTLE "2">
<!ENTITY TASKTHROTTLE "25">
<!ENTITY CYCLETHROTTLE "5">
<!ENTITY TASKTHROTTLE "30">
<!ENTITY MAXTRIES "2">

<!-- BEGIN: Resource requirements for the workflow -->
Expand All @@ -73,7 +73,7 @@
<!ENTITY NATIVE_PREP_CHEM_SRC "--export=NONE">

<!ENTITY QUEUE_FCST_GFS "&QUEUE;">
<!ENTITY WALLTIME_FCST_GFS "08:00:00">
<!ENTITY WALLTIME_FCST_GFS "06:00:00">
<!ENTITY RESOURCES_FCST_GFS "<nodes>8:ppn=40:tpp=1</nodes>">
<!ENTITY NATIVE_FCST_GFS "--export=NONE">

Expand All @@ -84,6 +84,7 @@
<!ENTITY NATIVE_POST_GFS "--export=NONE">

<!ENTITY QUEUE_ARCH_GFS "&QUEUE;">
<!ENTITY PARTITION_ARCH_GFS "&PARTITION_ARCH;">
<!ENTITY WALLTIME_ARCH_GFS "06:00:00">
<!ENTITY RESOURCES_ARCH_GFS "<nodes>1:ppn=1:tpp=1</nodes>">
<!ENTITY MEMORY_ARCH_GFS "2048M">
Expand Down Expand Up @@ -247,6 +248,7 @@
<jobname><cyclestr>&PSLOT;_gfsarch_@H</cyclestr></jobname>
<account>&ACCOUNT;</account>
<queue>&QUEUE_ARCH_GFS;</queue>
<partition>&PARTITION_ARCH_GFS;</partition>
&RESOURCES_ARCH_GFS;
<walltime>&WALLTIME_ARCH_GFS;</walltime>
<memory>&MEMORY_ARCH_GFS;</memory>
Expand Down
16 changes: 16 additions & 0 deletions FV3GFSwfm/rt_ccpp-chem/run_cmds
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Original file line number Diff line number Diff line change
Expand Up @@ -5,3 +5,19 @@ rocotostat -w /scratch1/BMC/gsd-fv3/rtruns/CCPP-Chem/FV3GFSwfm/rt_ccpp-chem/rt_

rocotorun -w /scratch1/BMC/gsd-fv3/rtruns/CCPP-Chem/FV3GFSwfm/rt_ccpp-chem/ccpp-chem.xml -d /home/rtfim/retro_dbfiles/ccpp-chem.db
rocotostat -w /scratch1/BMC/gsd-fv3/rtruns/CCPP-Chem/FV3GFSwfm/rt_ccpp-chem/ccpp-chem.xml -d /home/rtfim/retro_dbfiles/ccpp-chem.db | m

rocotorun -w /scratch1/BMC/gsd-fv3/rtruns/CCPP-Chem/FV3GFSwfm/rt_ccpp-chem/archchem_other.xml -d /home/rtfim/retro_dbfiles/archchem_other.db
rocotostat -w /scratch1/BMC/gsd-fv3/rtruns/CCPP-Chem/FV3GFSwfm/rt_ccpp-chem/archchem_other.xml -d /home/rtfim/retro_dbfiles/archchem_other.db

rocotorun -w urg_chem.xml -d urg_chem.db
rocotostat -w urg_chem.xml -d urg_chem.db

rocotorun -w urg_fcst.xml -d urg_fcst.db
rocotostat -w urg_fcst.xml -d urg_fcst.db

rocotorun -w urg_post.xml -d urg_post.db
rocotostat -w urg_post.xml -d urg_post.db

rocotorun -w arch.xml -d arch.db
rocotostat -w arch.xml -d arch.db

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