jube_TSMP2

This JUBE file installs TSMP2 and runs the test case from TSMP2_workflow-engine. The JUBE file also compare the results with a reference.

For developing use

You must explicitly change the parameter userInfo and bin_storage in Lines 45-46:

  - name: userInfo
    parameter:
      - {name: branch_name, _: master}
      - {name: bin_storage, _: "/p/project1/cslts/shared_data/CI_TSMP2/bin"}

For this example, the jube file is using the master-branch and the binaries of build will be saved in the cslts_project folder. The complete path to the saved binaries is:

${bin_storage}/${branch_name}/${system_name}_${model_id}_${env_str}

How to use it

If the working directory to the benchmark is:

working_dir = path_to_benchmark_folder/benchmark/jube

1. Upload JUBE:

ml JUBE

2. Run JUBE:

In the working_dir that contains the “jube_filename.yml” file, submit the following command, replacing the tags (see section Tags below):

jube -v run --tag system_tag execution_mode_tag download_data_tag tsmp_combination_tag(s) environment_tag --outpath ./outpath -r -e jube_filename.yml

NOTE: Tags must be provided after --tag (in any order).

-v is verbose, displays the log-output during the run

-e jube run will exit if there is an error

-r run result after finishing run command (this will also start analysis)

--outpath defines where the benchmark is going to be stored

For more details on how to run JUBE, have a look at the JUBE documentation.

3. Continue an existing benchmark (after running the simulation is finished):

jube continue ./outpath -r -e

After step (3), JUBE will produce a results table. For instance:

system,version,queue,account,variant,components,jobid,nodes,ntasks,taskspernode,threadspertask,runtime_sec,runtime,success,comparison_eclm
jurecadc,2024.01,dc-cpu,slts,single,eCLM,14230309,1,128,128,128,85,00:01:25,true,SUCCESSFUL

Tags

system_name: machine where the benchmark runs.

execution_mode: allows to choose among full (build + run), build (only build), and run (only run). If no execution mode is defined, it will only build. To be able to use the run mode, the combination build must have been built previously. The builts are saved here ${bin_storage}=/path_to_binaries/bin/. The built is saved as <machine_components_environment>, for instance JURECADC_ICON-eCLM_jsc.2025.intel.psmpi.

download_data: allows to choose between data (downloads data) and nodata (no data is downloaded). The data downloaded is the data needed to run the EUR-11 case. Data is available here. If no download data mode is defined, the data will not be downloaded. To use the nodata mode, data must have been downloaded previously, otherwise it the simulation run will fail.

TSMP_components: allows to choose the components for the build. Components: icon, eclm, parflow. If no component-combination is specified, it will build by default eclm.

environment: allows to choose among several defined environments. When no environment is spcified, it will use jsc.2025.intel.psmpi.

Tag Name	Tag Options	Default Tag	Type of Tag
system_name	jureca, juwels, jupiter, jusuf	no default option, needs to be defined	exclusive (only one can be selected)
execution_mode	full, build, run	build	exclusive (only one can be selected)
download_data	data, nodata	nodata	exclusive (only one can be selected)
TSMP_components	icon, eclm, parflow	eclm	multiple choices allowed
environment	jsc.2025.intel.psmpi jsc.2025.gnu.openmpi jsc.2025.gnu.psmpi jsc.2024.intel.psmpi jsc.2023.intel.psmpi default.2025.env ubuntu.gnu.openmpi uni-bonn.gnu.openmpi	jsc.2025.intel.psmpi	exclusive (only one can be selected)

Examples of jube commands

1. To build and run TSMP2 with icon + eclm on jureca using the environment jsc.2025.gnu.openmpi, the jube command would be:

jube -v run -r -e --tag jureca full icon eclm jsc.2025.gnu.openmpi --outpath ./outpath jube_filename.yml

Since no download_data is defined, it will NOT download the data (since it uses the default option).

2. To only build a fully-coupled TSMP2 (icon + eclm + parflow) on juwels using the environment jsc.2025.intel.psmpi and no download data, the jube command would be:

jube -v run -r -e --tag juwels build icon eclm parflow nodata jsc.2025.intel.psmpi --outpath ./outpath jube_filename.yml

3. If only the system name is provided (e.g., juwels):

jube -v run -r -e --tag juwels --outpath ./outpath jube_filename.yml

It will use the default options on juwels: build, eclm, jsc.2025.intel.psmpi, and won't download data.

Comparison of results

Reference case was produced on jureca using the jsc.2025.intel.psmpi. Reference results are here:

/p/project1/cslts/shared_data/rcmod_TSMP2_WFE_reference_CORDEX_JURECADC/simres/${model_id_sim}_20170701/

Scripts used to compare the outputs from eclm, parflow, and icon use a threshold of 1E-8 and are stored here:

working_dir/../../usecompare/

usecompare]$ tree
.
├── compare_nc_eclm.sh
├── compare_nc_icon.sh
└── compare_nc_parflow.sh

Threshold can easily be modified on their respective scripts, as well as, the output variables to read.

• eclm compares the following variables of the output eCLM_eur-11u.clm2.h0.2017-07-01-00000.nc:

VARS=("TWS" "H2OSOI" "TSOI" "TG" "EFLX_LH_TOT" "FSH" "FSA" "FSR" "FIRA" "Rnet" "EFLX_SOIL_GRND")

• parflow compares the following variables of the output eur-11u.out.00001.nc:

VARS=("pressure" "saturation" "evaptrans")

• icon compares the following variables of the output ICON_out_EU-R13B5_inst_DOM01_ML_20170702T000000Z_1h.nc:

VARS=("w" "theta_v" "qv" "shfl_s" "lhfl_s")

There are three possible outputs of the comparison:

• SUCCESSFUL: variables' differences are below the threshold.
• FAILED: differences are greater than the threshold.
• MISSING-NC-FILES: reference and/or test output files are missing.

Directories

• Results of the benchmark will be stored at outpath:

working_dir/outpath

• Builds will take place here:

working_dir/outpath/0000##/000001_build/work/TSMP2/bin/

Where ## stands for the benchmark ID-number. For instance, 000000 or 000005.

• Copy of binaries. When a build is carried out, as mentioned above, a copy of the binaries will be stored (to be used later) here:

/p/project1/cslts/shared_data/CI_TSMP2/bin/

• Runs will take place here:

working_dir/outpath/0000##/000003_execute/work/TSMP2_workflow-engine/run

• Comparison results (as a csv file) will be here:

working_dir/outpath/0000##/000005_compare/work/

• Results table will be saved here:

working_dir/outpath/0000##/result

• Data will be downloaded here:

working_dir/download_data