Update README and test script

README.md

@@ -1,24 +1,41 @@
 # NorCPM_esp
-
-# NorCPM Structure
-
 ### Scientific description:
   [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1169902.svg)](https://doi.org/10.5281/zenodo.1169902)
 
 ### Overview
-  NorCPM do ensemble data assimilation with NorESM1 and 2. NorCPM_ESP apply the process as an ESP component in NorESM2. Which modify model data in memory to reduce overhead time from restarting model.
+  NorCPM_esp runs as a ESP (External System Processing) component, which is introduced since CESM2. Also in NorESM2
 
-  For now NorCPM_ESP is only DA for BLOM component.
-
-  It is still under development.
+  This component runs after all other componets at every time step, and takes no effect by default.
 
-### Usage
-  The content in cime_config/config_compsets.xml is needed to insert to NorESM/cime_config/config_compsets.xml
+  In NorCPM_esp, this is used to run data assimilation. Including read observation data, calculation EnKF and feedback to model.
+
+  For the EnKF (Ensemble Kalman Filter), which is necessary to have multiple ensemble members. 
+
+  The multiple instances function is also introduced in CESM2. Which runs multiple copies of model.
 
-  Check the test script in 'testscript/'.
+
+### Required settings
+  1. Compset need be set to NHISTNCPM or NHISTNCPMfrc2
+  2. NINST must larger than 1. 10 is suggested for scientific meaning.
+  3. NTASKS can be default but need to be multiple to NINST. 
+     However, it is suggested to use one node per instance (Betzy)
+     The NTASKS_ESP need to cover all CPUs.
+
+  Detail setting can be found in doc/create_norcpm_esp.sh
+
+### Usage
+  Please start from [NorESM repo](https://github.com/NorESMhub/NorESM). 
+  In file Externals.cfg, [norcpm] section, set the required from False to True.
+  Then use manage_externals/checkout_externals to download components.
+  The test script can be found in NorESM/components/norcpm/doc/create_norcpm_esp.sh.
+  Most of the settings are in env_run.xml, start with NORCPM_.
 
 ### Portability
   It only tested on Betzy.
 
   The SST DA needs monthly file named as YYYY_MM_DD.nc and placed at specific structure of directory.
 
+### Issues
+  1. Only OISST(daily), EN4 profiles(monthly, temperature and salnity) supported.
+  2. Data assimilation(DA) only when middle day of model (43200) instead of day begin (00000) due to the restart time.
+  3. EN4 DA takes more than 20 secs. Which is due to parallel method.

doc/create_norcpm_esp.sh

@@ -0,0 +1,87 @@
+#!/bin/bash -e
+
+case=norcpm_esp_test01
+    NINST=10
+    compset=NHISTNCPM
+    STOP_N=1
+    STOP_OPTION=nmonth
+    NTASKS_CPL=$((128*$NINST))   
+    NTASKS_ATM=$((128*$NINST))   
+    NTASKS_LND=$((128*$NINST))   
+    NTASKS_ICE=$((128*$NINST))   
+    NTASKS_OCN=$((123*$NINST)) #### blom_dimensions: Available processor counts: 32 42 63 77 91 123 156 186 256 354
+    NTASKS_ROF=$((128*$NINST))   
+    NTASKS_GLC=$((128*$NINST))   
+    NTASKS_WAV=$((128*$NINST))   
+    NTASKS_ESP=$((128*$NINST))
+    ROOTPE_CPL=0
+    ROOTPE_ATM=0
+    ROOTPE_LND=0
+    ROOTPE_ICE=0
+    ROOTPE_OCN=0
+    ROOTPE_ROF=0
+    ROOTPE_GLC=0
+    ROOTPE_WAV=0
+    ROOTPE_ESP=0
+
+    MULTI_DRIVER=FALSE
+    ## DO NOT set anything about PAUSE
+
+pecount=S
+compset=${compset:-NHIST} ## NorESM
+res=${res:-f19_tn14}  ## NorESM
+noresmdir="./NorESM"
+caseroot=.
+
+## cleaning old build
+echo "To clean old build:"
+echo "    rm -rf ~/work/{archive,noresm,.}/${case}"
+if [ "$1" == "delete" ] ;then
+    echo 'cleaning old bld'
+    rm -rf ~/work/{archive,noresm,.}/${case}
+    rm -rf ${caseroot}/${case}/
+    if [ "$2" == "only" ] ;then
+        exit
+    fi
+fi
+
+${noresmdir}/cime/scripts/./create_newcase --case ${case} --mach betzy --res ${res} --compset ${compset} --project nn9039k 
+
+
+cd ${caseroot}/${case}
+
+## set NTASKS and ROOTPE
+    ./xmlchange NTASKS_ATM=$NTASKS_ATM,ROOTPE_ATM=$ROOTPE_ATM
+    ./xmlchange NTASKS_LND=$NTASKS_LND,ROOTPE_LND=$ROOTPE_LND
+    ./xmlchange NTASKS_ICE=$NTASKS_ICE,ROOTPE_ICE=$ROOTPE_ICE
+    ./xmlchange NTASKS_OCN=$NTASKS_OCN,ROOTPE_OCN=$ROOTPE_OCN
+    ./xmlchange NTASKS_CPL=$NTASKS_CPL,ROOTPE_CPL=$ROOTPE_CPL
+    ./xmlchange NTASKS_GLC=$NTASKS_GLC,ROOTPE_GLC=$ROOTPE_GLC
+    ./xmlchange NTASKS_ROF=$NTASKS_ROF,ROOTPE_ROF=$ROOTPE_ROF
+    ./xmlchange NTASKS_WAV=$NTASKS_WAV,ROOTPE_WAV=$ROOTPE_WAV
+    ./xmlchange NTASKS_ESP=$NTASKS_ESP,ROOTPE_ESP=$ROOTPE_ESP
+
+## multi-instance
+    ./xmlchange NINST_ATM=$NINST
+    ./xmlchange NINST_LND=$NINST
+    ./xmlchange NINST_ICE=$NINST
+    ./xmlchange NINST_ROF=$NINST
+    ./xmlchange NINST_GLC=$NINST
+    ./xmlchange NINST_OCN=$NINST
+    ./xmlchange NINST_WAV=$NINST
+    ./xmlchange NINST_ESP=$NINST
+
+./xmlchange STOP_N=STOP_N
+./xmlchange STOP_OPTION=STOP_OPTION
+./xmlchange  --subgroup case.run  JOB_WALLCLOCK_TIME=72:00:00
+./xmlchange RUN_STARTDATE=1982-01-01
+
+## soft link makes life easier
+ln -s $(./xmlquery RUNDIR --value)      ./run
+ln -s $(./xmlquery EXEROOT --value)     ./bld
+ln -s $(./xmlquery DOUT_S_ROOT --value) ./archive
+
+./case.setup
+#./preview_namelists
+./case.build
+./case.submit