Install
Software Requirements
Fortran 90/95 and C compiler
MPI or OpenMP libraries
netCDF4 library linked with HDF5 and zip libraries and extended by the Fortran netCDF package (The netCDF4 package comes with the programs ncdump and nccopy)
UNIX utilities: make, ksh, uname, sed, awk, wget, etc.
For post-processing: Climate Data Operators (CDO) and netCDF Operators (NCO)
- An ICON binary
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CCLM_SP uses netCDF I/O of COSMO-CLM |
The starter package is written for the HRLE–3 Mistral at DKRZ. Additional changes need to be applied on other machines. On the Mistral the Simple Linux Utility for Resource Management SLURM ist installed.
On mistral please use OPENMPI by setting
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module load intel/17.0.2 module load openmpi/2.0.2p1_hpcx-intel14 export OMPI_MCA_pml=cm export OMPI_MCA_mtl=mxm export MCM_RDMA_PORTS=mlx5_0:1 |
To install the starter package, follow these steps:
1. Copy the starter package from RedC.
2. Unpack the starter package:
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./config.sh -a addon1,addon2,… |
1 Get the source code
Goto https://redc.clm-community.eu/projects/icon-clm-starter-package/wiki and download the latest revision, i.e. tag (e.g. 1.0 in the following), as tarball, copy spice-v1.0.tar.gz to your computing system and proceed like so:
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$ cd ${SPDIR}/data
$ ./get_spice_rcm.sh |
A directory rcm is created holding the necessary data to run the ICON-CLM test experiment.
3 Configure SPICE and run the test examples
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Call the script
or at DWD like so
This will create two directories including the basic scripts. You find them under Run the test examplesThere are two tests, one for testing ICON with GCM or reanalysis data as initial and boundary conditions ( Before you start the experiment look for the following environment variables in the
Now you should be ready to start the first experiment:
This experiment is a two month simulation, 50 km / Europe / driven bei ERAInterim After successful completion start the second one:
This experiment is a two month simulation, 3km / region around Hamburg / driven by ICON output of |
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3.1 Create the supplemental programs a. Create the fortran library |
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$ cd ${SPDIR}/src/fortran-csv-lib
$ cp LOCAL/Fopts.dkrz Fopts |
Adopt the Fopts file to your system and type:
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$ make |
After successful compilation you find the libcsv in ${SPDIR}/src/fortran-csv-lib/lib.
b. Create the cfu executable
The climate fortran utilities contain several functions needed in the runtime environment.
Choose a Fopts file in the directory LOCAL and copy it to the base directory of libcsv (here we choose Fopts.dkrz as an example):
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$ cd ${SPDIR}/src/cfu
$ cp LOCAL/Fopts.dkrz Fopts |
Adopt the Fopts file to your system and type:
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$ make |
After successful compilation you find the cfu executable in ${SPDIR}/src/cfu/bin
c. Create additional conversion programs
The programs are used to convert COSMO-CLM caf-files to ICON-CLM compatible caf-file (ccaf2icaf) and to correct the netCDF output of ICON-CLM (correct_cf).
Choose a Fopts file in the directory LOCAL and copy it to the base directory of libcsv (here we choose Fopts.dkrz as an example):
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$ cd ${SPDIR}/src/utils
$ cp LOCAL/Fopts.dkrz Fopts |
Adopt the Fopts file to your system and type:
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$ make |
After successful compilation you find the executables ccaf2icaf and correct_cf in ${SPDIR}/src/utils/bin
3.2 Configure SPICE on your computing system
If you intent not to run ICON-CLM at DKRZ or DWD you have to perform some adoptions. First, find out which batch system comes nearest to your system. DKRZ uses SLURM (i.e. SBATCH commands) and DWD uses the Portable Batch Commands (i.e. PBS commands). Lets suppose as an example in the following that you use SLURM on your computing system and therefore you use "dkrz" as a template.
a. Change into the configure_scripts directory:
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$ cd ${SPDIR}/configure_scripts |
b. Adopt the dkrz part in the system_settings.tmpl file to the settings on your system.
c. Run the config.sh script:
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$ cd ${SPDIR}/configure_scripts
$ ./config.sh -s dkrz |
This will create two directories including the basic scripts. You find them under ${SPDIR}/chain/gcm2icon/sp001 and ${SPDIR}/chain/icon2icon/sp002
Now comes the hardest part: you have to dive into the scripts in the directories and adopt the scripts to your system (e.g. modify batch commands, program calls etc.). Start with adopting the experiment ${SPDIR}/chain/gcm2icon/sp001 .
Run the test examples
There are two tests, one for testing ICON with GCM or reanalysis data as initial and boundary conditions (${SPDIR}/chain/gcm2icon/sp001) and one for testing ICON with coarse grid ICON data as initial and boundary conditions (${SPDIR}/chain/icon2icon/sp002). Actually sp001 creates the necessary input data for sp002.
SP001 is a two month simulation, 50 km / Europe / driven bei ERAInterim
SP002 This experiment is a two month simulation, 3km / region around Hamburg / driven by ICON output of sp001 .
Before you start the experiment look for the following environment variables in the job_settings of and adopt them to your needs.
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PROJECT_ACCOUNT= # your project account EMAIL_ADDRESS= # your email address if you want to get information when your job crashes or finishes BINARY_ICON= # ICON executable including full path ECRADDIR= # path to the ECRAD data directory, if you plan to use the ECRAD radiation scheme |
Adopt the input directory of the ERAInterim data
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GCM_DATADIR=/pool/data/CCLM/reanalyses/ERAInterim |
and probably the de-tar part in prep.job.sh.
Now you should be ready to start the first experiment:
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$ cd ${SPDIR}/chain/gcm2icon/sp001
$ ./subchain start |
In SPICE the scripts are called in the order prep.job.sh, conv2icon.job.sh, icon.job.sh, arch.job.sh, post.job.sh. If your job crashes in one of the scripts you do not have to run all the successful scripts again, but can start this script again after you made the corrections by submitting the appropriate command from the following list:
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./subchain prep ./subchain conv2icon ./subchain icon noprep ./subchain arch ./subchain post |
After successful completion of the SP001 experiment adopt the scripts in SP002 and start this experiment:
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$ cd ${SPDIR}/chain/icon2icon/sp002
$ ./subchain start |
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