Adds notes about generating surface dataset and initial condition for ELM #6582
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| # Creating an ELM initial condition file | ||
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| An ELM initial condition (IC) file can be created by remapping an existing IC file from | ||
| one resolution to another using the `interpinic`, located at | ||
| `components/elm/tools/interpinic`. An ELM IC file is in the same format as an ELM restart file. | ||
| The composet of the remapped IC file will be the same as that of the input IC file. | ||
| So, for a new ELM SP-mode IC file, use an ELM input file corresponding to the SP-mode. | ||
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| The steps involved in creating a new IC files are as follows: | ||
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| 1. Identifying an input ELM IC or restart file that will be remapped. | ||
| 2. Obtaining an ELM restart file at the new resolution. | ||
| 3. Compiling `interpinic` on the machine of interest. | ||
| 4. Running `interpinic` to perform the interpolation. | ||
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| The notes below provide an example of creating 1850 ELM IC file for the NARRM grid using E3SM v3 LR piControl from year = 0101. These notes are provided for Chrysalis. | ||
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| ## 1. Identification of the input ELM IC file | ||
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| The identified input land condition file for this case is the following: | ||
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| ```bash | ||
| /lcrc/group/e3sm2/ac.golaz/E3SMv3/v3.LR.piControl/archive/rest/0101-01-01-00000/v3.LR.piControl.elm.r.0101-01-01-00000.nc | ||
| ``` | ||
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| ## 2. Obtaining an ELM restart file | ||
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| Using an existing NARRM land IC and making a copy of it | ||
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| ```bash | ||
| cd components/elm/tools/interpinic | ||
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| cp /lcrc/group/e3sm/data/inputdata/lnd/clm2/initdata_map/elmi.v3-NARRM.northamericax4v1pg2_r025_IcoswISC30E3r5.1870-01-01-00000.c20240704.nc \ | ||
| elmi.v3-NARRM.northamericax4v1pg2_r025_IcoswISC30E3r5.1850-01-01-00000.c`date "+%Y%m%d"`.nc | ||
| ``` | ||
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| ## 3. Compiling `interpinic` | ||
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| ```bash | ||
| # Load relevant modules | ||
| cd <e3sm-dir> | ||
| eval $(./cime/CIME/Tools/get_case_env) | ||
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| # change directory | ||
| cd components/elm/tools/interpinic/src | ||
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| export USER_LDFLAGS="-L$NETCDF_C_DIR/lib -lnetcdf -L$NETCDF_F_DIR/lib -lnetcdff -L$HDF5_DIR/lib -lhdf5" | ||
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| USER_FC=ifort LIB_NETCDF="`nc-config --flibs`" INC_NETCDF="`nf-config --includedir`" make VERBOSE=1 | ||
| ``` | ||
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| ## 4. Run `interpinic` | ||
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| The `interpinic` can then be run via the following batch job (e.g., `remap.r025_RRSwISC6to18E3r4.1850.batch`) to generate the initial condition. | ||
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| ```bash | ||
| >cat remap.r025_RRSwISC6to18E3r4.1850.batch | ||
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| #!/bin/sh | ||
| #SBATCH --job-name=remap | ||
| #SBATCH --nodes=1 | ||
| #SBATCH --exclusive | ||
| #SBATCH --time 24:00:00 | ||
| #SBATCH -p slurm | ||
| #SBATCH --account esmd | ||
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| # Load relevant modules. | ||
| cd <e3sm-dir> | ||
| eval $(./cime/CIME/Tools/get_case_env/get_case_env) | ||
|
There was a problem hiding this comment. extra 'get_case_env' in path. |
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| # Change dir to `interpinic` | ||
| cd components/elm/tools/interpinic/src | ||
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There was a problem hiding this comment. When I tried this, the executable was one directory up (not in /src). |
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| srun -n 1 ./interpinic \ | ||
| -i /lcrc/group/e3sm2/ac.golaz/E3SMv3/v3.LR.piControl/archive/rest/0101-01-01-00000/v3.LR.piControl.elm.r.0101-01-01-00000.nc \ | ||
| -o elmi.v3-NARRM.northamericax4v1pg2_r025_IcoswISC30E3r5.1850-01-01-00000.c20240903.nc | ||
| ``` | ||
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,56 @@ | ||
| # Creating an ELM surface dataset | ||
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| The notes describe the steps in creating an ELM surface dataset at 0.5x0.5 resolution for 1950 on Perlmutter. | ||
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| ## 1. Load the appropriate modules | ||
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| ```bash | ||
| cd <e3ms-dir> | ||
| eval $(./cime/CIME/Tools/get_case_env) | ||
| ``` | ||
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| ## 2. Compile `mksurfdata_map` | ||
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| ```bash | ||
| cd components/elm/tools/mksurfdata_map/src/ | ||
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| make clean | ||
| export USER_LDFLAGS="-L$NETCDF_DIR/lib -lnetcdf -lnetcdff -lnetcdf_intel" | ||
| export USER_LDFLAGS=$USER_LDFLAGS" -L$HDF5_DIR/lib -lhdf5 -lhdf5_fortran -lhdf5_hl_intel -lhdf5hl_fortran_intel" | ||
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| USER_FC=ifort LIB_NETCDF="`nc-config --flibs`" INC_NETCDF="`nf-config --includedir`" make VERBOSE=1 | ||
| ``` | ||
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| ## Build the namelist | ||
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| This step assumes that the resolution for which the new surface dataset is being created is a supported resolution. | ||
| If the surface dataset is being created for an unsupported resolution, 16 mapping files will have to be created to map the raw datasets | ||
| onto this unsupported resolution. The `namelist` file with default number of glaciers (equal to zero) can be generated as: | ||
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| ```bash | ||
| cd ../ | ||
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| RES=0.5x0.5 | ||
| YR=1950 | ||
| DIN_LOC_ROOT=/global/cfs/cdirs/e3sm/inputdata | ||
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| ./mksurfdata.pl -res $RES -years $YR -d -dinlc $DIN_LOC_ROOT | ||
| ``` | ||
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| An example of generating the namelist for 0.25 deg (`r025`) resolution for 1980 with 10 glacier layers is as follows: | ||
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| ```bash | ||
| RES=r025 | ||
| YR=1980 | ||
| DIN_LOC_ROOT=/global/cfs/cdirs/e3sm/inputdata | ||
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| ./mksurfdata.pl -res $RES -years $YR -d -dinlc $DIN_LOC_ROOT -glc_nec 10 | ||
| ``` | ||
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| ## Run `mksurfdata_map` via an interactive job | ||
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| ```bash | ||
| salloc --nodes 1 --qos interactive --time 01:00:00 --constraint cpu --account e3sm | ||
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| srun -n 1 ./mksurfdata_map < namelist | ||
| ``` |
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missing "export" ?