From a2d174cc96e1d1f10c1390c74ec750a0e79ae104 Mon Sep 17 00:00:00 2001 From: "C. Carouge" Date: Mon, 15 May 2023 11:55:49 +1000 Subject: [PATCH] Add example of expected output --- docs/user_guide/expected_output.md | 37 ++++++++++++++++++++++++++++++ docs/user_guide/index.md | 10 +++++--- mkdocs.yml | 1 + 3 files changed, 45 insertions(+), 3 deletions(-) create mode 100644 docs/user_guide/expected_output.md diff --git a/docs/user_guide/expected_output.md b/docs/user_guide/expected_output.md new file mode 100644 index 00000000..069fb8b1 --- /dev/null +++ b/docs/user_guide/expected_output.md @@ -0,0 +1,37 @@ +# Expected output from benchcab + +Below you will find examples of the expected output printed by `benchcab` to the screen when running the full workflow, with `benchcab run`. + +Other sub-commands should print out part of this output. + +``` +$ benchcab run +Creating src directory: /scratch/tm70/sb8430/bench_example/src +Checking out repositories... +Successfully checked out trunk at revision 9550 +Successfully checked out test-branch at revision 9550 +Successfully checked out CABLE-AUX at revision 9550 +Writing revision number info to rev_number-1.log +Compiling CABLE serially for realisation trunk... +Successfully compiled CABLE for realisation trunk +Compiling CABLE serially for realisation test-branch... +Successfully compiled CABLE for realisation test-branch +Setting up run directory tree for FLUXNET tests... +Creating runs/site/logs directory: /scratch/tm70/sb8430/bench_example/runs/site/logs +Creating runs/site/outputs directory: /scratch/tm70/sb8430/bench_example/runs/site/outputs +Creating runs/site/tasks directory: /scratch/tm70/sb8430/bench_example/runs/site/tasks +Creating task directories... +Setting up tasks... +Successfully setup FLUXNET tasks +Creating PBS job script to run FLUXNET tasks on compute nodes: benchmark_cable_qsub.sh +PBS job submitted: 82479088.gadi-pbs +The CABLE log file for each task is written to runs/site/logs/_log.txt +The CABLE standard output for each task is written to runs/site/tasks//out.txt +The NetCDF output for each task is written to runs/site/outputs/_out.nc +``` + +The PBS schedule job should print out the following to the job log file: +``` +Running FLUXNET tasks... +Successfully ran FLUXNET tasks +``` diff --git a/docs/user_guide/index.md b/docs/user_guide/index.md index a8e0d68e..86074325 100644 --- a/docs/user_guide/index.md +++ b/docs/user_guide/index.md @@ -78,7 +78,7 @@ cd bench_example `benchcab` will stop if it is not run within a work directory with the proper structure. -Currently, `benchcab` can only run CABLE for flux sites. To run the flux site tests, run +Currently, `benchcab` can only run CABLE for flux sites. **To run the whole workflow**, run ```bash benchcab run @@ -90,13 +90,17 @@ The tool will follow the steps: 2. Compile the source code from all branches 3. Setup and launch a PBS job to run the simulations in parallel. When `benchcab` launches the PBS job, it will print out the job ID to the terminal. You can check the status of the job with `qstat`. `benchcab` will not warn you when the simulations are over. -For help on the available options for `benchcab`: +!!! tip "Expected output" + + You can see [an example of the expected output](expected_output.md) printed out to the screen by `benchcab run` to check if the tool has worked as expected. + +For help on the **available options** for `benchcab`: ```bash benchcab -h ``` -!!! Tip +!!! Tip "Running parts of the workflow" It is possible to run each step of the workflow separately using sub-commands for `benchcab`. Refer to the help message to learn more. ## Directory structure and files diff --git a/mkdocs.yml b/mkdocs.yml index c776e3ad..23e8abad 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -69,3 +69,4 @@ nav: - user_guide/index.md - user_guide/config_options.md - user_guide/default_science_configurations.md + - user_guide/expected_output.md