job_settings
- Burkhardt Rockel (Unlicensed)
This file includes the main settings for the simulation and is called at the beginning of each script in the job chain.
Environment Variable | Description |
SPDIR | Absolut parent path of the SPICE directory. SPDIR only occurs in job_settings. This is not necessary to set if you define the different paths by yourself. |
EXPID | job identification |
Main directory settings | |
PFDIR | Parent directory where the scripts for the experiment are stored. PFDIR should be on a disk partition that is saved frequently as a copy. |
WORKDIR | NONE of the created files under this directory will be deleted at the end of the simulation. The disk partition should have enough remaining disk space. |
SCRATCHDIR | ALL created files under this directory will be deleted at the end of the job chain. This disk partition is only for temporary file storage. |
SRCDIR | directory of supplementary programs |
DATADIR | directory holding supplementary data (grid descriptions etc.) |
ARCHIVE_OUTDIR | Directory where the results should be archived. "Results" are the output of the ICON output streams define in the namelist block output_nml. |
RESDIR | Directory where the restart files will be stored |
INIDIR | Directory where some initial data of the simulation will be stored |
Information on the time period of the simulation | |
YDATE_START_ISO | Start date of simulation in ISO8601 format: YYYY-MM-DDTHH:MM:SSZ |
YDATE_STOP_ISO | End date of simulation in ISO8601 format: YYYY-MM-DDTHH:MM:SSZ |
INC_DATE | Time increment for the ICON-CLM job. Standard is one month 01:00:00 . You may want to use a higher frequency, e.g. if a monthly increment exceeds the batch job limits of your computing system. |
ITYPE_CALENDAR | Calendar settings. 0 = proleptic gregorian, 1 = 360 day year, 2 = 365 day year |
Email, notification and account settings | |
EMAIL_ADDRESS | Replace this with your email address or leave the environment variable empty to prevent getting emails from your batch system |
NOTIFICATION_ADDRESS | SPICE scripts send notifications to this address, in case it is set. In case of |
NOTIFICATION_SCRIPT | The script holding the notification instruction including the whole absolute path to the script. It is called like so ${NOTIFICATION_SCRIPT} ${NOTIFICATION_ADDRESS} subject message-fileThe following scripts are available under You can also define your own notification script holding your favorite notification system. |
PROJECT_ACCOUNT | On the computer systems at DKRZ you need to set you project account ID. If your computings system does not have this feature you can leave it open |
Directory and binary path settings for utilities | |
CFU | cfu (climate fortran utilities) program including the absolute path. These are part of SPICE |
UTILS_BINDIR | Absolute path to the directory of utility binaries (ccaf2icaf and correct_cf). These are part of SPICE |
CDO | cdo program including the absolute path. |
NCO_BINDIR | Absolute path to the directory of NCO utility binaries (e.g. ncks, ncrcat, ncatted ...) |
NC_BINDIR | Absolute path to the directory of netCDF standard binaries (e.g. ncdump, nccopy) |
PIGZ | pigz program including the absolute path in case your computing system supports parallel gzip. |
PYTHON | python interpreter including the absolute path |
Special script settings | |
ITYPE_CONV2ICON | Choose whether to run conv2icon (=1) or use already existing conv2icon output (=0) |
ITYPE_ICON_ARCH_PAR | Submit icon.job.sh in arch.job.sh directly after checking the ICON output (=1, i.e. icon simulation and archiving job are running in parallel after the file checking) or at the end of arch.job.sh (=0, i.e. are running sequentially). |
ITYPE_COMPRESS_POST | Compression type of output in post-processing |
ITYPE_COMPRESS_ARCH | Compression type of output in archiving |
ITYPE_TS | How timeseries are combined |
ITYPE_SAMOVAR | choose SAMOVAR check for original ICON output |
SAMOVAR_EXE | Name of SAMOVAR executable including full path |
SAMOVAR_SH | Name of the SAMOVAR shell script including the path. Default: |
SAMOVAR_LIST | File in csv format including the maximal value ranges of the output quantities of original ICON output. Default: |
ITYPE_SAMOVAR_TS | chosse SAMOVAR check for time series |
SAMOVAR_LIST_TS | File in csv format including the maximal value ranges of the output quantities in the time series file. Quantity names defined as in |
Initial and boundary data input | |
GCM_DATADIR | Directory of the initial and boundary data |
GCM_PREFIX | prefix of the data (e.g., caf or cas) |
HINCBOUND | boundary data temporal increment in hours |
ICON_INPUT_OPTIONAL | e.g. 'QC,Qi' for ERAInterim or 'QC,QI,QR,QS' for ERA5 |
SMI_DEFAULT | In case the coarse grid data do not contain the soil moisture index (SMI), a default value can be set here. The environment variable has to be exported in order to be read in the pre-processing by ccaf2icaf. The setting has no effect on ICON, ERAInterim, ERA5 reanalysis input since they include values for SMI. |
GCM_REMAP | The default remapping of coarse grid data in the conv2icon.job.sh script. CDO is used for remapping, therefore the name must be given accordingly. Only remapping options that conserves the dependencies of the fields in the vertical structure should be used here (e.g. remapnn, remaplaf) |
Grid description, climatological and other supplemental data | |
INI_BASEDIR | Directory where the grid description, climatological and other supplemental data are stored |
LAM_GRID | Grid description of the limited area dynamic grid (can be generated with the ICON Grid Generator + ExtPar Web Frontend) |
PARENT_GRID | Grid description of the parent grid (can be generated with the ICON Grid Generator + ExtPar Web Frontend) |
ECRADDIR | Directory containing supplemental files for the ECRAD radiation scheme. Can point to the directory in the ICON distribution |
GHG_FILENAME | File name of greenhouse gas concentrations. Needed by the radiation scheme. Possible data files are available under |
EXTPAR | External parameters on ICON grid (can be generated with the ICON Grid Generator + ExtPar Web Frontend) |
OUTPUT_MAPPING_FILE | Mapping of ICON parameter names to those given in the mapping file. These names have to be consistent with those in correct_cf.f90, functions.sh and post.job.sh |
TARGET_GRID | External data file holding information on the domain in rotated coordinates. This information is needed in the post-processing for interpolation from ICON grid to rotated lat/lon grid |
ICON specific settings | |
BINARY_ICON | Full path and name of ICON executable |
DTIME | Time step in seconds (if not defined it will be calculated in icon.job.sh) |
ZML_SOIL | Values of soil levels |
HOUT_INC | HOUT_INC is an array. Each index holds the output frequency of one output stream given in the ICON namelist |
PRECIP_INTERVAL | Interval for accumulating precipitation in ISO8601 format (must be consistent with HOUT_INC) |
RUNOFF_INTERVAL | Interval for accumulating runoff in ISO8601 format (must be consistent with HOUT_INC) |
SUNSHINE_INTERVAL | Interval for accumulating sunshine duration after the definition from WMO "threshold for bright sunshine is 120 W m-2 in a plane perpendicular to the direct solar beam" |
MAXT_INTERVAL | Interval for min/max of 2m-temperature in ISO8601 ( must be consistent with HOUT_INC) |
GUST_INTERVAL | Interval for maximum of wind gust |
OPERATION | OPERATION is an array. Each index holds the operation of one output stream given in the ICON namelist. The operation parameter affect all variables defined in an output stream. The variables must be instantaneous variables. Depending on the name of the operation ("mean", "max", or "min") the variables are averaged over the output interval or the maximum or minimum over the output interval is calculated, respectively. No value, expressed as "", means no operation is performed. |
NESTING_STREAM | Output stream to save quantities as input for further downscaling. Put the number of the output stream here. This chosen output stream is saved as is. A value of 0 means no output stream is saved as input for further downscaling. This output stream cannot be used in post.job.sh for building time series. |
PLEVS | List of pressure levels. Must be the same as or a subset of the p_levels in icon namelist !! BUT: in hPa instead of Pa !! |
ZLEVS | List of altitude levels (height over NN). Must be the same as or a subset of the h_levels in icon namelist. |
HLEV_STREAM | Output stream that contains 4D prognostic quantities plus the height on full level z_mc. Put the number of the output stream here. In case |
HLEVS | Array holding the height levels over ground in meter |
Global attribute settings in the ICON netCDF output | |
GA_INSTITUTION | Name of the institution where the simulation has been performed |
GA_TITLE | Title of the simulation |
GA_PROJECT_ID | Project ID |
GA_REALIZATION | Realization number of the simulation |
GA_CONVENTIONS | The conventions the ICON output uses (e.g. "CF-1.4") |
GA_CONVENTIONSURL | Website address of the conventions description |
GA_CONTACT | Contact address in case of questions on the simulation |
GA_ICON_CLM_VERSION | Stable ICON-CLM version used for the simulation |
Parallelization settings ⚠️ Not all variables are available on each computing system ⚠️ | |
PARTITION_PREP | Select specific node type/partition for prep.job.sh. This can be different from computing system to computing system. At DKRZ is can be compute or shared. |
TASKS_PREP | Number of parallel tasks in prep.job.sh |
CPUS_PER_TASK_PREP | Number of tasks per cpu for prep.job.sh |
TIME_PREP | requested time in batch queue for prep.job.sh |
PARTITION_CONV2ICON | Select specific node type/partition for conv2icon.job.sh. This can be different from computing system to computing system. At DKRZ is can be compute or shared. |
TASKS_CONV2ICON | Number of parallel tasks in conv2icon.job.sh |
OMP_THREADS_CONV2ICON | Number of OPENMP threads (used in CDO commands) in conv2icon.job.sh |
NODES_CONV2ICON | Number of nodes requested for conv2icon.job.sh ⚠️ conv2icon.job.sh can be run only on 1 node presently ⚠️ |
TIME_CONV2ICON | requested time in batch queue for conv2icon.job.sh |
PARTITION_ARCH | Select specific node type/partition for arch.job.sh. This can be different from computing system to computing system. At DKRZ is can be compute or shared. |
TASKS_ARCH | Number of parallel tasks in arch.job.sh |
CPUS_PER_TASK_ARCH | Number of tasks per cpu for arch.job.sh |
TIME_ARCH | requested time in batch queue for arch.job.sh |
PARTITION_POST | Select specific node type/partition for post.job.sh. This can be different from computing system to computing system. At DKRZ is can be compute or shared. |
TASKS_POST | Number of parallel tasks in post.job.sh |
OMP_THREADS_POST | Number of OPENMP threads (used in CDO commands) in post.job.sh |
TIME_POST | requested time in batch queue for post.job.sh |
TIME_POST_YEARLY | requested time in batch queue for post.job.sh when yearly time series are computed |
PARTITION_ICON | Select specific node type/partition for icon.job.sh. This can be different from computing system to computing system. At DKRZ is can be compute or shared. |
NP_ICON | Number of processors for ICON |
NODES_ICON | Number of nodes for ICON |
NUM_THREAD_ICON | Number of OpenMP threads: choose one of the following values 1 (without hyperthreading), 2, 3 (without hyperthreading), 4, 6, 8 (compute only), 9 (compute2 only) |
HT_ICON | hyperthreading: 0 - off, 1 - on |
TIME_ICON | requested time in batch queue for ICON simulation |
NUM_IO_PROCS | num_io_procs: 1,2 specified in namelist parallel_nml (icon.job.sh) |
NUM_RESTART_PROCS | num_restart_procs: number of processors for restart (on DWD NEC) |
NUM_PREFETCH_PROC | num_prefetch_proc: number of processors for LBC prefetching (on DWD NEC) |