| 1 | Making initial condition files for icosa_lmdz.exe from |
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| 2 | an LMDZ start_archive.nc file |
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| 3 | |
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| 4 | What you need to do/know before: |
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| 5 | --------------------------- |
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| 6 | Run a dynamico simulation (with startphy_file=false for example) with the desired resolution to get |
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| 7 | start.nc and startfi.nc. These files will be used as reference (rename as *_ref.nc) in the script. |
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| 8 | |
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| 9 | Job_mpi is the file you need to run start_archive2icosa on Occigen |
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| 10 | |
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| 11 | Warning: the input start_archive.nc file must include SSO parameters in this version, which is only available with a modified start2archive: start2archive_SSO |
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| 12 | |
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| 13 | This script is currently under development and still needs to be finalized. |
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| 14 | So you must be careful to adapt the script to your own needs and replace hardcoded variables. |
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| 15 | Any suggestion for improvement is welcome. |
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| 16 | |
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| 17 | In a nutshell: |
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| 18 | -------------- |
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| 19 | 1) input file start_archive.nc needs some minor adaptations: |
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| 20 | - variable "nivsigs" needs be renamed "sigs" (XIOS requires CF-compliant files) |
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| 21 | ncrename -vnivsigs,sigs start_archive.nc |
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| 22 | - input file start_archive.nc need be converted to NetCDF4 format |
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| 23 | nccopy -k 'netCDF-4' start_archive.nc start_archive_nc4.nc |
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| 24 | 2) script "compile" can be used to compile main tool start_archive2icosa.f90 |
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| 25 | as well as rearrange_startphy.f90 |
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| 26 | 3) to run, start_archive2icosa needs input files: |
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| 27 | - "start_archive_nc4.nc" : from step 1 |
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| 28 | - "start_icosa_ref.nc" : a start.nc file from an icosa_lmdz.exe run (contains |
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| 29 | all the necessary information about the icosaedral grid at that resolution) |
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| 30 | - "startphy_icosa_ref.nc" : a startfi.nc file from an icosa_lmdz.exe run (contains |
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| 31 | all the necessary information about colums from physics) |
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| 32 | - "surface_nc4.nc" : Mars topography file (also needs to be in NetCDF4 format) |
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| 33 | - "iodef.xml" : information about field names and grids for XIOS |
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| 34 | NB: interpolation of HR topography requires lots of memory; see e.g. job_mpi |
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| 35 | job script where 2 nodes (56 cores) are requested but only 28 processes |
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| 36 | are run. |
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| 37 | 4) start_archive2icosa outputs files "start_icosa_prefinalize.nc" and "startfi_prefinalize.nc" |
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| 38 | require a couple of extra modifications. Script "icosa_finalize.bash" does |
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| 39 | the required changes and generates files "start_icosa.nc" and "startfi.nc" that |
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| 40 | can be used as inputs by icosa_lmdz.exe |
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| 41 | 5) When using these start one must add in run_icosa.def the extra flag |
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| 42 | etat0_start_file_colocated = true |
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| 43 | |
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| 44 | Additional comments: |
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| 45 | -------------------- |
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| 46 | - script "compile" assumes XIOS is to be found in "/scratch/cnt0027/lmd1167/adelavois/models/code/XIOS" |
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| 47 | to be adapted to your own settings |
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| 48 | - "nccopy" is a standard netcdf tool available via e.g.: |
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| 49 | module load intel/17.0 intelmpi/2017.0.098 hdf5/1.8.17 netcdf/4.4.0_fortran-4.4.2 |
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| 50 | - "nco" tools (ncrename, ncks, ...) are available via e.g.: |
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| 51 | module load intel/17.0 openmpi/intel/2.0.1 hdf5/1.8.17 netcdf/4.4.0_fortran-4.4.2 nco/4.4.6 |
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| 52 | - in start_archive2icosa.f90, rearrange_startphy.f90, iodef.xml and |
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| 53 | icosa_finalize.bash input/output file names are hard-coded. |
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| 54 | Modify/adapt with caution! |
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