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15 Apr 2020  NERSC Directory Change Notice  

Due to project's name change at NERSC from 'ACME' to 'E3SM' and NERSC’s file system update, the directory  '/project/projectdirs/acme/' is now '/cfs/cdirs/e3sm'

Table of Contents

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atm_grid_file=ne4.g
ocn_grid_file=/projectglobal/cfs/projectdirscdirs/acmee3sm/inputdata/cpl/gridmaps/oQU240/ocean.QU.240km.scrip.151209.nc
cd ${output_root} && ncremap -P mwf -s $ocn_grid_file -g $atm_grid_file --nm_src=oQU240 --nm_dst=ne4np4 --dt_sng=20181114

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#!/bin/bash

# Setup environment
source /global/projectcfs/projectdirscdirs/acmee3sm/software/anaconda_envs/load_latest_e3sm_unified.sh
e3sm_root=${HOME}/codes/e3sm/branches/master

# Build gen_domain tool
export USER_FFLAGS='-traceback -g -O0'
gen_domain=${e3sm_root}/cime/tools/mapping/gen_domain_files/gen_domain
cd `dirname ${gen_domain}`/src
../../../configure --macros-format Makefile --mpilib mpi-serial
(. ./.env_mach_specific.sh ; gmake)

# Set paths to mapping files
mapping_root="/global/homes/b/bhillma/cscratch/e3sm/grids/ne4"
ocn_grid_name=oQU240
atm_grid_name=ne4np4
lnd_grid_name=${atm_grid_name}

# run domain generation tool (from output directory)
domain_root=${mapping_root} 
mkdir -p ${domain_root} && cd ${domain_root}
for target_grid_name in ${lnd_grid_name} ${atm_grid_name}; do
    
    # Find conservative mapping files, use the latest file generated    
    map_ocn_to_target=`ls ${mapping_root}/map_${ocn_grid_name}_to_${target_grid_name}_monotr.*.nc | tail -n1`

    # Run domain tool code
    ${gen_domain} -m ${map_ocn_to_target} -o ${ocn_grid_name} -l ${target_grid_name}

done

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• land grid descriptor file in SCRIP format 

• ESMF_RegridWeightGen

• geographic distribution for each land surface type along with grid descriptor files for each of those surface types

• mkmapdata.sh (found in components/clm/tools/shared/mkmapdata/)

• mksurfdata.pl (found in components/clm/tools/clm4_5/mksurfdata_map/)

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1. Create mapping files for each land surface type if needed. An (older and deprecated) example of doing this can be found here. Updated instructions follow:
   
   

   1. Obtain or generate a target grid file in SCRIP format. For these example, we will use a ne1024pg2 grid file, which we will need to create (note that most np4 grid files can be found within the inputdata repository, for example, the ne1024np4 grid file is at https://web.lcrc.anl.gov/public/e3sm/mapping/grids/ne1024np4_scrip_c20191023.nc). To generate the pg2 SCRIP file: 

      Code Block
      ${tempest_root}/bin/GenerateCSMesh --alt --res 1024 --file ne1024.g ${tempest_root}/bin/GenerateVolumetricMesh --in ne1024.g --out ne1024pg2.g --np 2 --uniform ${tempest_root}/bin/ConvertExodusToSCRIP --in ne1024pg2.g --out ne1024pg2_scrip.nc

   2. Get list of input grid files for each land surface input data file. This is done by running the components/clm/tools/shared/mkmapdata/mkmapdata.sh script in debug mode to output a list of needed files (along with the commands that will be used to generate each map file; also make sure GRIDFILE is set to the SCRIP file from the above step): 

      Code Block
      language bash
      cd ${e3sm_root}/components/clm/tools/shared/mkmapdata ./mkmapdata.sh --gridfile ${GRIDFILE} --inputdata-path ${INPUTDATA_ROOT} --res ne1024pg2 --gridtype global --output-filetype 64bit_offset --debug -v --list

   3. Download needed input grid files. The above command will output a list of needed files to clm.input_data_list. We need to download all of these before calling the script without the debug flag to actually perform the mapping. This is possible using check_input_data in CIME, but needs to be done from a dummy case directory. So, one can create a dummy case, cd to that case, and then call ./check_input_data --data-list-dir <path where mkmapdata was run from> --download. However, this failed to connect to the CESM SVN server for me. So instead, I used the following one-off script: 

      Code Block

      #!/bin/bash e3sm_inputdata_repository="https://web.lcrc.anl.gov/public/e3sm" cesm_inputdata_repository="https://svn-ccsm-inputdata.cgd.ucar.edu/trunk" inputdata_list=clm.input_data_list cat $inputdata_list | while read line; do localpath=`echo ${line} | sed 's:.* = \(.*\):\1:'` url1=${e3sm_inputdata_repository}/`echo ${line} | sed 's:.*\(inputdata/lnd/.*\):\1:'` url2=${cesm_inputdata_repository}/`echo ${line} | sed 's:.*\(inputdata/lnd/.*\):\1:'` if [ ! -f ${localpath} ]; then echo "${url1} -> ${localpath}" mkdir -p `dirname ${localpath}` cd `dirname ${localpath}` # Try to download using first URL, if that fails then use the second wget ${url1} || wget ${url2} else echo "${localpath} exists, skipping." fi done

   4. Create mapping files. Should just be able to run the above mkmapdata.sh command without the –debug --list flags. We need to append the --outputfile-type 64bit_offset flag for our large files (no reason not to do this by default anyways):

      Code Block
      ./mkmapdata.sh --gridfile ${GRIDFILE} --inputdata-path ${INPUTDATA_ROOT} --res ne1024pg2 --gridtype global --output-filetype 64bit_offset -v

2. Compile surface dataset source code (NOTE: ${e3sm_root}/components/clm/tools/clm4_5/mksurfdata_map/src/Makefile.common needs to be edited to build on most machines; this is fixed in https://github.com/E3SM-Project/E3SM/pull/2757):

   Code Block

   # Setup environment (should work on any E3SM-supported machine) ${e3sm_dir}/cime/tools/configure --macros-format=Makefile && source .env_mach_specific.sh # Set environent variables expected by mksurfdata_map Makefile; # Note that NETCDF_DIR is probably specific to NERSC and may need # to be adjusted for other systems export LIB_NETCDF=$NETCDF_DIR/lib export INC_NETCDF=$NETCDF_DIR/include export USER_FC=ifort export USER_CC=icc # Build mksurfdata_map cd $e3sm_dir/components/clm/tools/clm4_5/mksurfdata_map/src/ && gmake

   
   

3. Run the mksurfdata.pl script in "debug" mode to generate the namelist (use year 2010 on ne120np4 grids as an example). 

   Code Block

   # For supported resolutions #(use year 2010 on ne120np4 grids as an example) cd $e3sm_dir/components/clm/tools/clm4_5/mksurfdata_map ./mksurfdata.pl -res ne120np4 -y 2010 -d -dinlc /global/projectcfs/projectdirscdirs/acmee3sm/inputdata -usr_mapdir /global/projectcfs/projectdirscdirs/acmee3sm/inputdata/lnd/clm2/mappingdata/maps/ne120np4 # For unsupported, user-specified resolutions # (use year 2010 on ne50np4 grid as an example) # (Assuming the mapping files created in step 1 has a time stamp of '190409' in the filenames and the location of mapping files are '/whatever/directory/you/put/mapping/files') ./mksurfdata.pl -res usrspec -usr_gname ne50np4 -usr_gdate 190409 -y 2010 -d -dinlc /global/projectcfs/projectdirscdirs/acmee3sm/inputdata -usr_mapdir /whatever/directory/you/put/mapping/files

   (However, ./mksurfdata.pl -h shows -y is by default 2010. When running without "-y" option, standard output says sim_year 2000. I suspect the mksurfdata.pl help information is wrong. To be confirmed.)
   
   

4. Modify namelist file
   (Should the correct namelist settings be automatically picked up if the default land build name list settings are modified accordingly?)

   Time-evolving Land use land cover change (LULCC) data should not be used for fixed-time compsets, but the LULCC information for that particular year should be used (right?)
   Manually change to mksrf_fvegtyp = '/global/projectcfs/projectdirscdirs/acmee3sm/inputdata/lnd/clm2/rawdata/AA_mksrf_landuse_rc_1850-2015_06062017_LUH2/AA_mksrf_landuse_rc_2010_06062017.nc' for the F2010 ne120 compset.
   
   

5. Create the land surface data by interactive or batch job

   Code Block

   rm -f surfdata_ne120np4_simyr2010.bash cat <<EOF >> surfdata_ne120np4_simyr2010.bash #!/bin/bash #SBATCH --job-name=mksurfdata2010 #SBATCH --account=acme #SBATCH --nodes=1 #SBATCH --output=mksurfdata.o%j #SBATCH --exclusive #SBATCH --time=00:30:00 #SBATCH --qos=debug # Load modules module load nco module load ncl module load cray-netcdf module load cray-hdf5 # mksurfdata_map is dynamically linked export LIB_NETCDF=$NETCDF_DIR/lib export INC_NETCDF=$NETCDF_DIR/include export USER_FC=ifort export USER_CC=icc export USER_LDFLAGS="-L$NETCDF_DIR/lib -lnetcdf -lnetcdff -lnetcdf_intel" export USER_LDFLAGS=$USER_LDFLAGS" -L$HDF5_DIR/lib -lhdf5 -lhdf5_fortran -lhdf5_cpp -lhdf5_fortran_intel -lhdf5_hl_intel -lhdf5hl_fortran_intel" cd /global/homes/t/tang30/ACME_code/MkLandSurf/components/clm/tools/clm4_5/mksurfdata_map CDATE=c`date +%y%m%d` # current date ./mksurfdata_map < namelist EOF sbatch surfdata_ne120np4_simyr2010.bash

   The land surface data in NetCDF format will be created at current directory. (How to verify the file is correct?)

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