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Polish standard output messages#69

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SeanBryan51 merged 4 commits intomasterfrom
67-polished-messaging-to-standard-output
May 17, 2023
Merged

Polish standard output messages#69
SeanBryan51 merged 4 commits intomasterfrom
67-polished-messaging-to-standard-output

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@SeanBryan51 SeanBryan51 commented May 2, 2023

Currently, benchcab outputs stdout from other commands such as svn and ./build3.sh, but does not output anything when running ./cable or when generating particular directory structures.

This commit improves the messages output to stdout by benchcab for all sub-commands. We also add a boolean flag to specify verbose output for each sub-command.

Write the standard output from CABLE to the tasks/<task_name>/out.txt directory instead of writing to /dev/null so that it is accessible to the user.

Remove wd9 dependence in source code.

Fixes #67 and #64

@SeanBryan51 SeanBryan51 linked an issue May 2, 2023 that may be closed by this pull request
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Standard output from benchcab run:

$ 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/<task_name>_log.txt
The CABLE standard output for each task is written to runs/site/tasks/<task_name>/out.txt
The NetCDF output for each task is written to runs/site/outputs/<task_name>_out.nc

Captured stdout from job:

Running FLUXNET tasks...
Successfully ran FLUXNET tasks

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Standard out from benchcab run -v (verbose):

$ benchcab run -v
Creating src directory: /scratch/tm70/sb8430/bench_example/src
Checking out repositories...
svn checkout https://trac.nci.org.au/svn/cable/trunk /scratch/tm70/sb8430/bench_example/src/trunk
A    src/trunk/offline
A    src/trunk/offline/cable_pft_params.F90
A    src/trunk/offline/.Hytiallia.sumbal
A    src/trunk/offline/pft_params.nml
A    src/trunk/offline/cable_input.F90
A    src/trunk/offline/TumbaFluxnet.1.3_met.nc
A    src/trunk/offline/cable_checks.F90
A    src/trunk/offline/cable_mpidrv.F90
A    src/trunk/offline/cable_parameters.F90
A    src/trunk/offline/.GSWP2.log_cable
A    src/trunk/offline/cable_site.F90
A    src/trunk/offline/gridinfo_CSIRO_1x1.nc
A    src/trunk/offline/cable_metutils.F90
A    src/trunk/offline/cbl_model_driver_offline.F90
A    src/trunk/offline/casa_cable.F90
A    src/trunk/offline/cable_abort.F90
A    src/trunk/offline/cable.nml
A    src/trunk/offline/build3.sh
A    src/trunk/offline/cable_soil_params.F90
A    src/trunk/offline/file.txt
A    src/trunk/offline/cable_define_types.F90
A    src/trunk/offline/cable_cru_TRENDY.F90
A    src/trunk/offline/cable_mpiworker.F90
A    src/trunk/offline/landuse_inout.F90
A    src/trunk/offline/.Tumba.sumbal
A    src/trunk/offline/CASAONLY_LUC.F90
A    src/trunk/offline/cable_plume_mip.F90
A    src/trunk/offline/cable_write.F90
A    src/trunk/offline/cable_initialise.F90
A    src/trunk/offline/pftlookup.csv
A    src/trunk/offline/cable_namelist_input.F90
A    src/trunk/offline/cable_mpicommon.F90
A    src/trunk/offline/parallel_cable
A    src/trunk/offline/cable_output.F90
A    src/trunk/offline/.Ampero.sumbal
A    src/trunk/offline/cable_mpimaster.F90
A    src/trunk/offline/casa_offline_inout.F90
A    src/trunk/offline/cable_iovars.F90
A    src/trunk/offline/cable_phenology.F90
A    src/trunk/offline/run.ksh
A    src/trunk/offline/cable_weathergenerator.F90
A    src/trunk/offline/CSIRO_BSD_MIT_License_v2.0_CABLE.txt
A    src/trunk/offline/cable_read.F90
A    src/trunk/offline/casa_ncdf.F90
A    src/trunk/offline/spincasacnp.F90
A    src/trunk/offline/cable_soilparm.nml
A    src/trunk/offline/serial_cable
A    src/trunk/offline/cable_LUC_EXPT.F90
A    src/trunk/offline/Makefile
A    src/trunk/offline/cable_driver.F90
A    src/trunk/params
A    src/trunk/params/cable_other_constants_mod.F90
A    src/trunk/params/cable_phys_constants_mod.F90
A    src/trunk/params/cable_params_mod.F90
A    src/trunk/params/cable_photo_constants_mod.F90
A    src/trunk/params/cable_maths_constants_mod.F90
A    src/trunk/params/grid_constants_cbl.F90
A    src/trunk/science
A    src/trunk/science/casa-cnp
A    src/trunk/science/casa-cnp/casa_feedback.F90
A    src/trunk/science/casa-cnp/casa_phenology.F90
A    src/trunk/science/casa-cnp/casa_dimension.F90
A    src/trunk/science/casa-cnp/casa_variable.F90
A    src/trunk/science/casa-cnp/casa_sumcflux.F90
A    src/trunk/science/casa-cnp/casa_readbiome.F90
A    src/trunk/science/casa-cnp/casa_inout.F90
A    src/trunk/science/casa-cnp/bgcdriver.F90
A    src/trunk/science/casa-cnp/casa_cnp.F90
A    src/trunk/science/casa-cnp/casa_param.F90
A    src/trunk/science/casa-cnp/casa_rplant.F90
A    src/trunk/science/casa-cnp/biogeochem_casa.F90
A    src/trunk/science/albedo
A    src/trunk/science/albedo/cbl_albedo.F90
A    src/trunk/science/albedo/cbl_snow_albedo.F90
A    src/trunk/science/albedo/cbl_soilColour_albedo.F90
A    src/trunk/science/sli
A    src/trunk/science/sli/cable_sli_utils.F90
A    src/trunk/science/sli/cable_sli_main.F90
A    src/trunk/science/sli/cable_sli_roots.F90
A    src/trunk/science/sli/cable_sli_solve.F90
A    src/trunk/science/sli/cable_sli_numbers.F90
A    src/trunk/science/canopy
A    src/trunk/science/canopy/cbl_SurfaceWetness.F90
A    src/trunk/science/canopy/cbl_friction_vel.F90
A    src/trunk/science/canopy/cbl_fwsoil.F90
A    src/trunk/science/canopy/cbl_photosynthesis.F90
A    src/trunk/science/canopy/cbl_pot_evap_snow.F90
A    src/trunk/science/canopy/cbl_zetar.F90
A    src/trunk/science/canopy/cbl_LAI_canopy_height.F90
A    src/trunk/science/canopy/cbl_dryLeaf.F90
A    src/trunk/science/canopy/cbl_wetleaf.F90
A    src/trunk/science/canopy/cbl_latent_heat.F90
A    src/trunk/science/canopy/cbl_qsat.F90
A    src/trunk/science/canopy/cbl_within_canopy.F90
A    src/trunk/science/canopy/cable_canopy.F90
A    src/trunk/science/radiation
A    src/trunk/science/radiation/cbl_radiation.F90
A    src/trunk/science/radiation/cbl_spitter.F90
A    src/trunk/science/radiation/cbl_init_radiation.F90
A    src/trunk/science/radiation/cbl_rhoch.F90
A    src/trunk/science/radiation/cbl_sinbet.F90
A    src/trunk/science/landuse
A    src/trunk/science/landuse/landuse3.F90
A    src/trunk/science/landuse/landuse_constant.F90
A    src/trunk/science/misc
A    src/trunk/science/misc/cable_carbon.F90
A    src/trunk/science/misc/cable_air.F90
A    src/trunk/science/misc/cable_climate.F90
A    src/trunk/science/roughness
A    src/trunk/science/roughness/cable_roughness.F90
A    src/trunk/science/roughness/roughnessHGT_effLAI_cbl.F90
A    src/trunk/science/soilsnow
A    src/trunk/science/soilsnow/cbl_soilsnow_data.F90
A    src/trunk/science/soilsnow/cbl_soilfreeze.F90
A    src/trunk/science/soilsnow/cbl_surfbv.F90
A    src/trunk/science/soilsnow/cbl_snowMelt.F90
A    src/trunk/science/soilsnow/cbl_snowl_adjust.F90
A    src/trunk/science/soilsnow/cbl_trimb.F90
A    src/trunk/science/soilsnow/cbl_GW.F90
A    src/trunk/science/soilsnow/cbl_stempv.F90
A    src/trunk/science/soilsnow/cbl_smoisturev.F90
A    src/trunk/science/soilsnow/cbl_soilsnow_main.F90
A    src/trunk/science/soilsnow/cbl_Oldconductivity.F90
A    src/trunk/science/soilsnow/cbl_conductivity.F90
A    src/trunk/science/soilsnow/cbl_snowCheck.F90
A    src/trunk/science/soilsnow/cbl_snowDensity.F90
A    src/trunk/science/soilsnow/cbl_hyd_redistrib.F90
A    src/trunk/science/soilsnow/cbl_snow_aging.F90
A    src/trunk/science/soilsnow/cbl_thermal.F90
A    src/trunk/science/soilsnow/cbl_snowAccum.F90
A    src/trunk/science/soilsnow/cbl_soilsnow_init_special.F90
A    src/trunk/science/soilsnow/cbl_remove_trans.F90
A    src/trunk/science/pop
A    src/trunk/science/pop/pop_def.F90
A    src/trunk/science/pop/POP.F90
A    src/trunk/science/pop/POPLUC.F90
A    src/trunk/science/pop/pop_types.F90
A    src/trunk/science/pop/pop_mpi.F90
A    src/trunk/science/pop/pop_io.F90
A    src/trunk/science/pop/pop_constants.F90
A    src/trunk/science/gw_hydro
A    src/trunk/science/gw_hydro/cable_psm.F90
A    src/trunk/science/gw_hydro/cable_gw_hydro.F90
A    src/trunk/coupled
A    src/trunk/coupled/JAC
A    src/trunk/coupled/JAC/map_veg_parameters_cbl.F90
A    src/trunk/coupled/JAC/control
A    src/trunk/coupled/JAC/control/util
A    src/trunk/coupled/JAC/control/util/pack_mod_cbl.F90
A    src/trunk/coupled/JAC/control/util/activeTile_mask_cbl.F90
A    src/trunk/coupled/JAC/control/interface
A    src/trunk/coupled/JAC/control/interface/radiation
A    src/trunk/coupled/JAC/control/interface/radiation/rad_driver_cbl.F90
A    src/trunk/coupled/JAC/control/interface/radiation/rad_unpack_cbl.F90
A    src/trunk/coupled/JAC/control/cable_land
A    src/trunk/coupled/JAC/control/cable_land/radiation
A    src/trunk/coupled/JAC/control/cable_land/radiation/cable_land_albedo_mod_cbl.F90
A    src/trunk/coupled/JAC/control/cable_land/radiation/alloc_rad_albedo_vars_cbl.F90
A    src/trunk/coupled/JAC/control/cable
A    src/trunk/coupled/JAC/control/cable/shared
A    src/trunk/coupled/JAC/control/cable/shared/progs_cbl_vars_mod.F90
A    src/trunk/coupled/JAC/control/cable/shared/params_io_cbl.F90
A    src/trunk/coupled/JAC/control/cable/shared/work_vars_mod_cbl.F90
A    src/trunk/coupled/JAC/control/cable/shared/cable_surface_types_mod.F90
A    src/trunk/coupled/JAC/control/cable/standalone
A    src/trunk/coupled/JAC/control/cable/standalone/cable_fields_mod.F90
A    src/trunk/coupled/JAC/control/shared
A    src/trunk/coupled/JAC/control/shared/cable_surface_types_mod.F90
A    src/trunk/coupled/JAC/control/shared/progs_cbl_vars_mod.F90
A    src/trunk/coupled/JAC/control/shared/LAI_canopy_height_cbl.F90
A    src/trunk/coupled/JAC/control/shared/params_io_cbl.F90
A    src/trunk/coupled/JAC/control/shared/cable_fields_mod.F90
A    src/trunk/coupled/JAC/control/shared/work_vars_mod_cbl.F90
A    src/trunk/coupled/JAC/control/standalone
A    src/trunk/coupled/JAC/initialisation
A    src/trunk/coupled/JAC/initialisation/init_cable_working_vars.F90
A    src/trunk/coupled/JAC/initialisation/init_vegin_cbl.inc
A    src/trunk/coupled/JAC/initialisation/init_soilin_cbl.inc
A    src/trunk/coupled/JAC/initialisation/prognostics
A    src/trunk/coupled/JAC/initialisation/prognostics/init_cable_progs.F90
A    src/trunk/coupled/JAC/initialisation/prognostics/read_cable_progs.F90
A    src/trunk/coupled/ACCESS-CM2
A    src/trunk/coupled/ACCESS-CM2/cable_soil_params.F90
A    src/trunk/coupled/ACCESS-CM2/cable_pft_params.F90
A    src/trunk/coupled/ACCESS-CM2/control
A    src/trunk/coupled/ACCESS-CM2/control/implicit
A    src/trunk/coupled/ACCESS-CM2/control/implicit/cable_implicit_unpack.F90
A    src/trunk/coupled/ACCESS-CM2/control/implicit/cable_implicit_main.F90
A    src/trunk/coupled/ACCESS-CM2/control/implicit/cable_implicit_driver.F90
A    src/trunk/coupled/ACCESS-CM2/control/radiation
A    src/trunk/coupled/ACCESS-CM2/control/radiation/cable_rad_main.F90
A    src/trunk/coupled/ACCESS-CM2/control/radiation/cable_rad_driver.F90
A    src/trunk/coupled/ACCESS-CM2/control/hydrology
A    src/trunk/coupled/ACCESS-CM2/control/hydrology/cable_hyd_driver.F90
A    src/trunk/coupled/ACCESS-CM2/control/hydrology/cable_hyd_main.F90
A    src/trunk/coupled/ACCESS-CM2/control/hydrology/cable_wblake_fix.F90
A    src/trunk/coupled/ACCESS-CM2/control/utils
A    src/trunk/coupled/ACCESS-CM2/control/utils/cable_gather_UM_data_decs.F90
A    src/trunk/coupled/ACCESS-CM2/control/explicit
A    src/trunk/coupled/ACCESS-CM2/control/explicit/cable_explicit_driver.F90
A    src/trunk/coupled/ACCESS-CM2/control/explicit/cable_explicit_unpack.F90
A    src/trunk/coupled/ACCESS-CM2/control/explicit/cable_explicit_main.F90
A    src/trunk/coupled/ACCESS-CM2/control/casa
A    src/trunk/coupled/ACCESS-CM2/control/casa/casa_um_inout.F90
A    src/trunk/coupled/ACCESS-CM2/control/casa/casa_main.F90
A    src/trunk/coupled/ACCESS-CM2/control/casa/casa_types.F90
A    src/trunk/coupled/ACCESS-CM2/utils
A    src/trunk/coupled/ACCESS-CM2/utils/cable_jules_links_mod.F90
A    src/trunk/coupled/ACCESS-CM2/utils/cable_unpack_checks.F90
A    src/trunk/coupled/ACCESS-CM2/utils/cable_logs.F90
A    src/trunk/coupled/ACCESS-CM2/utils/cable_um_tech.F90
A    src/trunk/coupled/ACCESS-CM2/utils/cable_decs.F90
A    src/trunk/coupled/ACCESS-CM2/utils/cable_write_logs.F90
A    src/trunk/coupled/ACCESS-CM2/cable_define_types.F90
A    src/trunk/coupled/ACCESS-CM2/init
A    src/trunk/coupled/ACCESS-CM2/init/cable_um_init_subrs.F90
A    src/trunk/coupled/ACCESS-CM2/init/cable_um_init.F90
A    src/trunk/coupled/ACCESS-CM2/cable_cbm.F90
A    src/trunk/coupled/ACCESS-CM2/cable_iovars_CMIP6.F90
A    src/trunk/coupled/shared
A    src/trunk/coupled/shared/cable_canopy_type_mod.F90
A    src/trunk/coupled/shared/cable_soilsnow_type_mod.F90
A    src/trunk/coupled/ESM1.5
A    src/trunk/coupled/ESM1.5/casa_um_inout.F90
A    src/trunk/coupled/ESM1.5/CABLEfilesFromESM1.5
A    src/trunk/coupled/ESM1.5/CABLEfilesFromESM1.5/cable_data.F90
A    src/trunk/coupled/ESM1.5/CABLEfilesFromESM1.5/cable_explicit_driver.F90
A    src/trunk/coupled/ESM1.5/CABLEfilesFromESM1.5/cable_define_types.F90
A    src/trunk/coupled/ESM1.5/CABLEfilesFromESM1.5/cable_hyd_driver.F90
A    src/trunk/coupled/ESM1.5/CABLEfilesFromESM1.5/cable_cbm.F90
A    src/trunk/coupled/ESM1.5/CABLEfilesFromESM1.5/cable_rad_driver.F90
A    src/trunk/coupled/ESM1.5/CABLEfilesFromESM1.5/allocate_veg_params_cbl.F90
A    src/trunk/coupled/ESM1.5/CABLEfilesFromESM1.5/cable_um_init_subrs.F90
A    src/trunk/coupled/ESM1.5/CABLEfilesFromESM1.5/cable_iovars.F90
A    src/trunk/coupled/ESM1.5/CABLEfilesFromESM1.5/cable_um_init.F90
A    src/trunk/coupled/ESM1.5/CABLEfilesFromESM1.5/cable_um_tech.F90
A    src/trunk/coupled/ESM1.5/CABLEfilesFromESM1.5/cable_implicit_driver.F90
A    src/trunk/coupled/ESM1.5/CABLEfilesFromESM1.5/allocate_soil_params_cbl.F90
A    src/trunk/coupled/ESM1.5/casa_types.F90
A    src/trunk/coupled/ESM1.5/cable_soil_params.F90
A    src/trunk/coupled/ESM1.5/cable_pft_params.F90
A    src/trunk/coupled/ESM1.5/casa_landuse.F90
A    src/trunk/util
A    src/trunk/util/cable_runtime_opts_mod.F90
A    src/trunk/util/cable_common.F90
A    src/trunk/util/masks_cbl.F90
A    src/trunk/util/cable_climate_type_mod.F90
 U   src/trunk
Checked out revision 9550.
Successfully checked out trunk at revision 9550
svn checkout https://trac.nci.org.au/svn/cable/branches/Users/sb8430/test-branch /scratch/tm70/sb8430/bench_example/src/test-branch
A    src/test-branch/offline
A    src/test-branch/offline/gridinfo_CSIRO_1x1.nc
A    src/test-branch/offline/cable_weathergenerator.F90
A    src/test-branch/offline/cable_abort.F90
A    src/test-branch/offline/CSIRO_BSD_MIT_License_v2.0_CABLE.txt
A    src/test-branch/offline/build3.sh
A    src/test-branch/offline/cable.nml
A    src/test-branch/offline/cable_soil_params.F90
A    src/test-branch/offline/cable_read.F90
A    src/test-branch/offline/cable_soilparm.nml
A    src/test-branch/offline/cable_mpiworker.F90
A    src/test-branch/offline/serial_cable
A    src/test-branch/offline/cable_LUC_EXPT.F90
A    src/test-branch/offline/landuse_inout.F90
A    src/test-branch/offline/.Tumba.sumbal
A    src/test-branch/offline/cable_plume_mip.F90
A    src/test-branch/offline/Makefile
A    src/test-branch/offline/cable_write.F90
A    src/test-branch/offline/pftlookup.csv
A    src/test-branch/offline/cable_driver.F90
A    src/test-branch/offline/cable_pft_params.F90
A    src/test-branch/offline/cable_mpicommon.F90
A    src/test-branch/offline/pft_params.nml
A    src/test-branch/offline/cable_checks.F90
A    src/test-branch/offline/cable_mpimaster.F90
A    src/test-branch/offline/cable_mpidrv.F90
A    src/test-branch/offline/cable_parameters.F90
A    src/test-branch/offline/.GSWP2.log_cable
A    src/test-branch/offline/cable_site.F90
A    src/test-branch/offline/cable_phenology.F90
A    src/test-branch/offline/run.ksh
A    src/test-branch/offline/cable_metutils.F90
A    src/test-branch/offline/casa_cable.F90
A    src/test-branch/offline/cbl_model_driver_offline.F90
A    src/test-branch/offline/file.txt
A    src/test-branch/offline/casa_ncdf.F90
A    src/test-branch/offline/spincasacnp.F90
A    src/test-branch/offline/cable_cru_TRENDY.F90
A    src/test-branch/offline/cable_define_types.F90
A    src/test-branch/offline/CASAONLY_LUC.F90
A    src/test-branch/offline/cable_initialise.F90
A    src/test-branch/offline/cable_namelist_input.F90
A    src/test-branch/offline/.Hytiallia.sumbal
A    src/test-branch/offline/cable_input.F90
A    src/test-branch/offline/TumbaFluxnet.1.3_met.nc
A    src/test-branch/offline/parallel_cable
A    src/test-branch/offline/cable_output.F90
A    src/test-branch/offline/.Ampero.sumbal
A    src/test-branch/offline/casa_offline_inout.F90
A    src/test-branch/offline/cable_iovars.F90
A    src/test-branch/params
A    src/test-branch/params/grid_constants_cbl.F90
A    src/test-branch/params/cable_other_constants_mod.F90
A    src/test-branch/params/cable_phys_constants_mod.F90
A    src/test-branch/params/cable_params_mod.F90
A    src/test-branch/params/cable_photo_constants_mod.F90
A    src/test-branch/params/cable_maths_constants_mod.F90
A    src/test-branch/science
A    src/test-branch/science/gw_hydro
A    src/test-branch/science/gw_hydro/cable_psm.F90
A    src/test-branch/science/gw_hydro/cable_gw_hydro.F90
A    src/test-branch/science/casa-cnp
A    src/test-branch/science/casa-cnp/casa_feedback.F90
A    src/test-branch/science/casa-cnp/casa_phenology.F90
A    src/test-branch/science/casa-cnp/casa_dimension.F90
A    src/test-branch/science/casa-cnp/casa_variable.F90
A    src/test-branch/science/casa-cnp/casa_sumcflux.F90
A    src/test-branch/science/casa-cnp/casa_readbiome.F90
A    src/test-branch/science/casa-cnp/casa_inout.F90
A    src/test-branch/science/casa-cnp/bgcdriver.F90
A    src/test-branch/science/casa-cnp/casa_cnp.F90
A    src/test-branch/science/casa-cnp/casa_param.F90
A    src/test-branch/science/casa-cnp/casa_rplant.F90
A    src/test-branch/science/casa-cnp/biogeochem_casa.F90
A    src/test-branch/science/albedo
A    src/test-branch/science/albedo/cbl_snow_albedo.F90
A    src/test-branch/science/albedo/cbl_soilColour_albedo.F90
A    src/test-branch/science/albedo/cbl_albedo.F90
A    src/test-branch/science/sli
A    src/test-branch/science/sli/cable_sli_solve.F90
A    src/test-branch/science/sli/cable_sli_numbers.F90
A    src/test-branch/science/sli/cable_sli_utils.F90
A    src/test-branch/science/sli/cable_sli_main.F90
A    src/test-branch/science/sli/cable_sli_roots.F90
A    src/test-branch/science/canopy
A    src/test-branch/science/canopy/cbl_friction_vel.F90
A    src/test-branch/science/canopy/cbl_fwsoil.F90
A    src/test-branch/science/canopy/cbl_photosynthesis.F90
A    src/test-branch/science/canopy/cbl_pot_evap_snow.F90
A    src/test-branch/science/canopy/cbl_zetar.F90
A    src/test-branch/science/canopy/cbl_LAI_canopy_height.F90
A    src/test-branch/science/canopy/cbl_dryLeaf.F90
A    src/test-branch/science/canopy/cbl_wetleaf.F90
A    src/test-branch/science/canopy/cbl_latent_heat.F90
A    src/test-branch/science/canopy/cbl_qsat.F90
A    src/test-branch/science/canopy/cbl_within_canopy.F90
A    src/test-branch/science/canopy/cable_canopy.F90
A    src/test-branch/science/canopy/cbl_SurfaceWetness.F90
A    src/test-branch/science/radiation
A    src/test-branch/science/radiation/cbl_rhoch.F90
A    src/test-branch/science/radiation/cbl_sinbet.F90
A    src/test-branch/science/radiation/cbl_radiation.F90
A    src/test-branch/science/radiation/cbl_spitter.F90
A    src/test-branch/science/radiation/cbl_init_radiation.F90
A    src/test-branch/science/landuse
A    src/test-branch/science/landuse/landuse3.F90
A    src/test-branch/science/landuse/landuse_constant.F90
A    src/test-branch/science/misc
A    src/test-branch/science/misc/cable_air.F90
A    src/test-branch/science/misc/cable_climate.F90
A    src/test-branch/science/misc/cable_carbon.F90
A    src/test-branch/science/roughness
A    src/test-branch/science/roughness/cable_roughness.F90
A    src/test-branch/science/roughness/roughnessHGT_effLAI_cbl.F90
A    src/test-branch/science/soilsnow
A    src/test-branch/science/soilsnow/cbl_remove_trans.F90
A    src/test-branch/science/soilsnow/cbl_soilsnow_data.F90
A    src/test-branch/science/soilsnow/cbl_soilfreeze.F90
A    src/test-branch/science/soilsnow/cbl_surfbv.F90
A    src/test-branch/science/soilsnow/cbl_snowMelt.F90
A    src/test-branch/science/soilsnow/cbl_snowl_adjust.F90
A    src/test-branch/science/soilsnow/cbl_GW.F90
A    src/test-branch/science/soilsnow/cbl_trimb.F90
A    src/test-branch/science/soilsnow/cbl_stempv.F90
A    src/test-branch/science/soilsnow/cbl_smoisturev.F90
A    src/test-branch/science/soilsnow/cbl_soilsnow_main.F90
A    src/test-branch/science/soilsnow/cbl_Oldconductivity.F90
A    src/test-branch/science/soilsnow/cbl_snowCheck.F90
A    src/test-branch/science/soilsnow/cbl_conductivity.F90
A    src/test-branch/science/soilsnow/cbl_snowDensity.F90
A    src/test-branch/science/soilsnow/cbl_snow_aging.F90
A    src/test-branch/science/soilsnow/cbl_hyd_redistrib.F90
A    src/test-branch/science/soilsnow/cbl_thermal.F90
A    src/test-branch/science/soilsnow/cbl_snowAccum.F90
A    src/test-branch/science/soilsnow/cbl_soilsnow_init_special.F90
A    src/test-branch/science/pop
A    src/test-branch/science/pop/pop_def.F90
A    src/test-branch/science/pop/POP.F90
A    src/test-branch/science/pop/POPLUC.F90
A    src/test-branch/science/pop/pop_types.F90
A    src/test-branch/science/pop/pop_mpi.F90
A    src/test-branch/science/pop/pop_io.F90
A    src/test-branch/science/pop/pop_constants.F90
A    src/test-branch/coupled
A    src/test-branch/coupled/shared
A    src/test-branch/coupled/shared/cable_canopy_type_mod.F90
A    src/test-branch/coupled/shared/cable_soilsnow_type_mod.F90
A    src/test-branch/coupled/ESM1.5
A    src/test-branch/coupled/ESM1.5/cable_pft_params.F90
A    src/test-branch/coupled/ESM1.5/casa_landuse.F90
A    src/test-branch/coupled/ESM1.5/casa_um_inout.F90
A    src/test-branch/coupled/ESM1.5/CABLEfilesFromESM1.5
A    src/test-branch/coupled/ESM1.5/CABLEfilesFromESM1.5/cable_explicit_driver.F90
A    src/test-branch/coupled/ESM1.5/CABLEfilesFromESM1.5/cable_define_types.F90
A    src/test-branch/coupled/ESM1.5/CABLEfilesFromESM1.5/cable_hyd_driver.F90
A    src/test-branch/coupled/ESM1.5/CABLEfilesFromESM1.5/cable_cbm.F90
A    src/test-branch/coupled/ESM1.5/CABLEfilesFromESM1.5/cable_rad_driver.F90
A    src/test-branch/coupled/ESM1.5/CABLEfilesFromESM1.5/allocate_veg_params_cbl.F90
A    src/test-branch/coupled/ESM1.5/CABLEfilesFromESM1.5/cable_um_init_subrs.F90
A    src/test-branch/coupled/ESM1.5/CABLEfilesFromESM1.5/cable_iovars.F90
A    src/test-branch/coupled/ESM1.5/CABLEfilesFromESM1.5/cable_um_init.F90
A    src/test-branch/coupled/ESM1.5/CABLEfilesFromESM1.5/cable_um_tech.F90
A    src/test-branch/coupled/ESM1.5/CABLEfilesFromESM1.5/cable_implicit_driver.F90
A    src/test-branch/coupled/ESM1.5/CABLEfilesFromESM1.5/allocate_soil_params_cbl.F90
A    src/test-branch/coupled/ESM1.5/CABLEfilesFromESM1.5/cable_data.F90
A    src/test-branch/coupled/ESM1.5/casa_types.F90
A    src/test-branch/coupled/ESM1.5/cable_soil_params.F90
A    src/test-branch/coupled/JAC
A    src/test-branch/coupled/JAC/map_veg_parameters_cbl.F90
A    src/test-branch/coupled/JAC/control
A    src/test-branch/coupled/JAC/control/cable
A    src/test-branch/coupled/JAC/control/cable/standalone
A    src/test-branch/coupled/JAC/control/cable/standalone/cable_fields_mod.F90
A    src/test-branch/coupled/JAC/control/cable/shared
A    src/test-branch/coupled/JAC/control/cable/shared/cable_surface_types_mod.F90
A    src/test-branch/coupled/JAC/control/cable/shared/progs_cbl_vars_mod.F90
A    src/test-branch/coupled/JAC/control/cable/shared/params_io_cbl.F90
A    src/test-branch/coupled/JAC/control/cable/shared/work_vars_mod_cbl.F90
A    src/test-branch/coupled/JAC/control/shared
A    src/test-branch/coupled/JAC/control/shared/cable_surface_types_mod.F90
A    src/test-branch/coupled/JAC/control/shared/progs_cbl_vars_mod.F90
A    src/test-branch/coupled/JAC/control/shared/LAI_canopy_height_cbl.F90
A    src/test-branch/coupled/JAC/control/shared/params_io_cbl.F90
A    src/test-branch/coupled/JAC/control/shared/cable_fields_mod.F90
A    src/test-branch/coupled/JAC/control/shared/work_vars_mod_cbl.F90
A    src/test-branch/coupled/JAC/control/standalone
A    src/test-branch/coupled/JAC/control/util
A    src/test-branch/coupled/JAC/control/util/activeTile_mask_cbl.F90
A    src/test-branch/coupled/JAC/control/util/pack_mod_cbl.F90
A    src/test-branch/coupled/JAC/control/interface
A    src/test-branch/coupled/JAC/control/interface/radiation
A    src/test-branch/coupled/JAC/control/interface/radiation/rad_driver_cbl.F90
A    src/test-branch/coupled/JAC/control/interface/radiation/rad_unpack_cbl.F90
A    src/test-branch/coupled/JAC/control/cable_land
A    src/test-branch/coupled/JAC/control/cable_land/radiation
A    src/test-branch/coupled/JAC/control/cable_land/radiation/cable_land_albedo_mod_cbl.F90
A    src/test-branch/coupled/JAC/control/cable_land/radiation/alloc_rad_albedo_vars_cbl.F90
A    src/test-branch/coupled/JAC/initialisation
A    src/test-branch/coupled/JAC/initialisation/init_cable_working_vars.F90
A    src/test-branch/coupled/JAC/initialisation/init_vegin_cbl.inc
A    src/test-branch/coupled/JAC/initialisation/init_soilin_cbl.inc
A    src/test-branch/coupled/JAC/initialisation/prognostics
A    src/test-branch/coupled/JAC/initialisation/prognostics/read_cable_progs.F90
A    src/test-branch/coupled/JAC/initialisation/prognostics/init_cable_progs.F90
A    src/test-branch/coupled/JAC/params
A    src/test-branch/coupled/JAC/params/cable_photo_constants_mod.F90
A    src/test-branch/coupled/JAC/params/cable_maths_constants_mod.F90
A    src/test-branch/coupled/JAC/params/cable_other_constants_mod.F90
A    src/test-branch/coupled/JAC/params/cable_phys_constants_mod.F90
A    src/test-branch/coupled/ACCESS-CM2
A    src/test-branch/coupled/ACCESS-CM2/cable_pft_params.F90
A    src/test-branch/coupled/ACCESS-CM2/control
A    src/test-branch/coupled/ACCESS-CM2/control/hydrology
A    src/test-branch/coupled/ACCESS-CM2/control/hydrology/cable_hyd_main.F90
A    src/test-branch/coupled/ACCESS-CM2/control/hydrology/cable_wblake_fix.F90
A    src/test-branch/coupled/ACCESS-CM2/control/hydrology/cable_hyd_driver.F90
A    src/test-branch/coupled/ACCESS-CM2/control/utils
A    src/test-branch/coupled/ACCESS-CM2/control/utils/cable_gather_UM_data_decs.F90
A    src/test-branch/coupled/ACCESS-CM2/control/explicit
A    src/test-branch/coupled/ACCESS-CM2/control/explicit/cable_explicit_driver.F90
A    src/test-branch/coupled/ACCESS-CM2/control/explicit/cable_explicit_unpack.F90
A    src/test-branch/coupled/ACCESS-CM2/control/explicit/cable_explicit_main.F90
A    src/test-branch/coupled/ACCESS-CM2/control/casa
A    src/test-branch/coupled/ACCESS-CM2/control/casa/casa_um_inout.F90
A    src/test-branch/coupled/ACCESS-CM2/control/casa/casa_main.F90
A    src/test-branch/coupled/ACCESS-CM2/control/casa/casa_types.F90
A    src/test-branch/coupled/ACCESS-CM2/control/implicit
A    src/test-branch/coupled/ACCESS-CM2/control/implicit/cable_implicit_driver.F90
A    src/test-branch/coupled/ACCESS-CM2/control/implicit/cable_implicit_unpack.F90
A    src/test-branch/coupled/ACCESS-CM2/control/implicit/cable_implicit_main.F90
A    src/test-branch/coupled/ACCESS-CM2/control/radiation
A    src/test-branch/coupled/ACCESS-CM2/control/radiation/cable_rad_main.F90
A    src/test-branch/coupled/ACCESS-CM2/control/radiation/cable_rad_driver.F90
A    src/test-branch/coupled/ACCESS-CM2/utils
A    src/test-branch/coupled/ACCESS-CM2/utils/cable_decs.F90
A    src/test-branch/coupled/ACCESS-CM2/utils/cable_write_logs.F90
A    src/test-branch/coupled/ACCESS-CM2/utils/cable_jules_links_mod.F90
A    src/test-branch/coupled/ACCESS-CM2/utils/cable_unpack_checks.F90
A    src/test-branch/coupled/ACCESS-CM2/utils/cable_logs.F90
A    src/test-branch/coupled/ACCESS-CM2/utils/cable_um_tech.F90
A    src/test-branch/coupled/ACCESS-CM2/cable_define_types.F90
A    src/test-branch/coupled/ACCESS-CM2/init
A    src/test-branch/coupled/ACCESS-CM2/init/cable_um_init_subrs.F90
A    src/test-branch/coupled/ACCESS-CM2/init/cable_um_init.F90
A    src/test-branch/coupled/ACCESS-CM2/cable_cbm.F90
A    src/test-branch/coupled/ACCESS-CM2/cable_iovars_CMIP6.F90
A    src/test-branch/coupled/ACCESS-CM2/cable_soil_params.F90
A    src/test-branch/util
A    src/test-branch/util/cable_climate_type_mod.F90
A    src/test-branch/util/cable_runtime_opts_mod.F90
A    src/test-branch/util/cable_common.F90
A    src/test-branch/util/masks_cbl.F90
 U   src/test-branch
Checked out revision 9550.
Successfully checked out test-branch at revision 9550
svn checkout https://trac.nci.org.au/svn/cable/branches/Share/CABLE-AUX /scratch/tm70/sb8430/bench_example/src/CABLE-AUX
A    src/CABLE-AUX/core
A    src/CABLE-AUX/core/biogeochem
A    src/CABLE-AUX/core/biogeochem/poolcnpInTumbarumba.csv
A    src/CABLE-AUX/core/biogeochem/modis_phenology_csiro.txt
A    src/CABLE-AUX/core/biogeochem/pftlookup_csiro_v16_17tiles.csv
A    src/CABLE-AUX/core/biogeochem/pftlookup_csiro_v16_17tiles_Ticket2.csv
A    src/CABLE-AUX/core/biogeophys
A    src/CABLE-AUX/core/biogeophys/def_veg_params.txt
A    src/CABLE-AUX/core/biogeophys/veg_params_vbeta1.txt
A    src/CABLE-AUX/core/biogeophys/def_soil_params.txt
A    src/CABLE-AUX/core/biogeophys/def_veg_params_Ticket2.txt
A    src/CABLE-AUX/core/biogeophys/def_veg_params_zr_clitt_albedo_fix.txt
A    src/CABLE-AUX/core/biogeophys/def_veg_params_medlyn_mean.txt
A    src/CABLE-AUX/core/biogeophys/veg_params_vbeta1_Ticket2.txt
A    src/CABLE-AUX/core/biogeophys/def_veg_params_zr_clitt.txt
A    src/CABLE-AUX/UMUI
A    src/CABLE-AUX/UMUI/cable_handedits.ed
A    src/CABLE-AUX/UMUI/nci_libcable.ovr
A    src/CABLE-AUX/UM
A    src/CABLE-AUX/UM/qxreconf
A    src/CABLE-AUX/UM/cable_start.ksh
A    src/CABLE-AUX/UM/cable.nml
A    src/CABLE-AUX/UM/libcable.a
A    src/CABLE-AUX/UM/ACCESS-1.3+CABLE-2.0.exe
A    src/CABLE-AUX/UM/cable_end.ksh
A    src/CABLE-AUX/offline
A    src/CABLE-AUX/offline/TumbaFluxnet.1.3_met.nc
A    src/CABLE-AUX/offline/cable.nml.TicketV
A    src/CABLE-AUX/offline/cable.nml.CMIP6-bios3
A    src/CABLE-AUX/offline/sites.txt
A    src/CABLE-AUX/offline/cru_936pts_landmask_0.5x0.5.nc
A    src/CABLE-AUX/offline/gridinfo_CSIRO_1x1.nc
A    src/CABLE-AUX/offline/ConvertMetForLSM.R
A    src/CABLE-AUX/offline/cable.nml.CMIP6-MOSRS
A    src/CABLE-AUX/offline/cable.nml
A    src/CABLE-AUX/offline/plumber_landmask_.5x.5.nc
A    src/CABLE-AUX/offline/soilcolor_global_1x1.nc
A    src/CABLE-AUX/offline/gridinfo_CSIRO_CRU05x05_4tiles.nc
A    src/CABLE-AUX/offline/cable.nml.bu
Checked out 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...
./my_build.ksh

Building cable (serial)

ERROR: Multiple (2) conda environments have been loaded, cannot unload with module
ERROR: Try 'conda deactivate' first

Unloading conda/analysis3-22.10
  ERROR: Module evaluation aborted

Build setup complete.
Compiling now ...


Building from source common across serial and MPI applications


Building drivers for either serial or MPI application

ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c grid_constants_cbl.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_maths_constants_mod.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_phys_constants_mod.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_other_constants_mod.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_photo_constants_mod.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_runtime_opts_mod.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_define_types.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_pft_params.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_soil_params.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c masks_cbl.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_iovars.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_common.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c casa_ncdf.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_soilColour_albedo.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_snow_albedo.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_rhoch.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_albedo.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_spitter.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_sinbet.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_init_radiation.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_radiation.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_abort.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c pop_def.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c pop_constants.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c pop_types.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c POP.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c casa_dimension.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c casa_param.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c casa_variable.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_LUC_EXPT.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c casa_phenology.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_parameters.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_read.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_initialise.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_checks.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c POPLUC.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c landuse_constant.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c casa_cnp.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c casa_offline_inout.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c casa_inout.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_metutils.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c casa_readbiome.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_input.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_write.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_output.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_soilsnow_data.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_soilfreeze.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_snowMelt.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_snowl_adjust.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_snowDensity.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_snowCheck.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_snowAccum.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_remove_trans.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_hyd_redistrib.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_conductivity.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_Oldconductivity.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_trimb.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_GW.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_thermal.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_smoisturev.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_surfbv.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_stempv.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_soilsnow_main.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_soilsnow_init_special.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_snow_aging.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_air.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c roughnessHGT_effLAI_cbl.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_roughness.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_carbon.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_friction_vel.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_qsat.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_pot_evap_snow.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_zetar.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_latent_heat.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_wetleaf.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_within_canopy.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_SurfaceWetness.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_photosynthesis.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_fwsoil.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_dryLeaf.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_sli_numbers.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_sli_utils.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_sli_roots.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_sli_solve.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_sli_main.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_gw_hydro.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_psm.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_climate_type_mod.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_canopy.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c pop_io.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_weathergenerator.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_plume_mip.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_climate.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_phenology.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_cru_TRENDY.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_namelist_input.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_site.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c casa_rplant.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c biogeochem_casa.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c casa_cable.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c spincasacnp.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c CASAONLY_LUC.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_model_driver_offline.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c landuse3.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c landuse_inout.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c bgcdriver.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c casa_feedback.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c casa_sumcflux.F90

BUILD OK

Successfully compiled CABLE for realisation trunk
Compiling CABLE serially for realisation test-branch...
./my_build.ksh

Building cable (serial)

ERROR: Multiple (2) conda environments have been loaded, cannot unload with module
ERROR: Try 'conda deactivate' first

Unloading conda/analysis3-22.10
  ERROR: Module evaluation aborted

Build setup complete.
Compiling now ...


Building from source common across serial and MPI applications


Building drivers for either serial or MPI application

ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c grid_constants_cbl.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_maths_constants_mod.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_phys_constants_mod.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_other_constants_mod.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_photo_constants_mod.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_runtime_opts_mod.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_define_types.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_pft_params.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_soil_params.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c masks_cbl.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_iovars.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_common.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c casa_ncdf.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_soilColour_albedo.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_snow_albedo.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_rhoch.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_albedo.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_spitter.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_sinbet.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_init_radiation.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_radiation.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_abort.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c pop_def.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c pop_constants.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c pop_types.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c POP.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c casa_dimension.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c casa_param.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c casa_variable.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_LUC_EXPT.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c casa_phenology.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_parameters.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_read.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_initialise.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_checks.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c POPLUC.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c landuse_constant.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c casa_cnp.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c casa_offline_inout.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c casa_inout.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_metutils.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c casa_readbiome.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_input.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_write.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_output.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_soilsnow_data.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_soilfreeze.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_snowMelt.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_snowl_adjust.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_snowDensity.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_snowCheck.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_snowAccum.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_remove_trans.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_hyd_redistrib.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_conductivity.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_Oldconductivity.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_trimb.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_GW.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_thermal.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_smoisturev.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_surfbv.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_stempv.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_soilsnow_main.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_soilsnow_init_special.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_snow_aging.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_air.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c roughnessHGT_effLAI_cbl.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_roughness.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_carbon.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_friction_vel.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_qsat.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_pot_evap_snow.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_zetar.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_latent_heat.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_wetleaf.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_within_canopy.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_SurfaceWetness.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_photosynthesis.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_fwsoil.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_dryLeaf.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_sli_numbers.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_sli_utils.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_sli_roots.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_sli_solve.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_sli_main.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_gw_hydro.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_psm.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_climate_type_mod.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_canopy.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c pop_io.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_weathergenerator.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_plume_mip.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_climate.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_phenology.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_cru_TRENDY.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_namelist_input.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cable_site.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c casa_rplant.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c biogeochem_casa.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c casa_cable.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c spincasacnp.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c CASAONLY_LUC.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c cbl_model_driver_offline.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c landuse3.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c landuse_inout.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c bgcdriver.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c casa_feedback.F90
ifort -O2 -fp-model precise  -I/apps/netcdf/4.7.4/include/Intel -c casa_sumcflux.F90

BUILD OK

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...
Creating runs/site/tasks/AU-Tum_2002-2017_OzFlux_Met_R0_S0: /scratch/tm70/sb8430/bench_example/runs/site/tasks/AU-Tum_2002-2017_OzFlux_Met_R0_S0
Creating runs/site/tasks/AU-Tum_2002-2017_OzFlux_Met_R1_S0: /scratch/tm70/sb8430/bench_example/runs/site/tasks/AU-Tum_2002-2017_OzFlux_Met_R1_S0
Setting up tasks...
Setting up task: AU-Tum_2002-2017_OzFlux_Met_R0_S0
  Cleaning task
  Copying namelist files from /scratch/tm70/sb8430/bench_example/namelists to /scratch/tm70/sb8430/bench_example/runs/site/tasks/AU-Tum_2002-2017_OzFlux_Met_R0_S0
  Copying CABLE executable from /scratch/tm70/sb8430/bench_example/src/trunk/offline/cable to /scratch/tm70/sb8430/bench_example/runs/site/tasks/AU-Tum_2002-2017_OzFlux_Met_R0_S0/cable
  Adjusting namelist file: applying patch to CABLE namelist file /scratch/tm70/sb8430/bench_example/runs/site/tasks/AU-Tum_2002-2017_OzFlux_Met_R0_S0/cable.nml
Setting up task: AU-Tum_2002-2017_OzFlux_Met_R1_S0
  Cleaning task
  Copying namelist files from /scratch/tm70/sb8430/bench_example/namelists to /scratch/tm70/sb8430/bench_example/runs/site/tasks/AU-Tum_2002-2017_OzFlux_Met_R1_S0
  Copying CABLE executable from /scratch/tm70/sb8430/bench_example/src/test-branch/offline/cable to /scratch/tm70/sb8430/bench_example/runs/site/tasks/AU-Tum_2002-2017_OzFlux_Met_R1_S0/cable
  Adjusting namelist file: applying patch to CABLE namelist file /scratch/tm70/sb8430/bench_example/runs/site/tasks/AU-Tum_2002-2017_OzFlux_Met_R1_S0/cable.nml
Successfully setup FLUXNET tasks
Creating PBS job script to run FLUXNET tasks on compute nodes: benchmark_cable_qsub.sh
PBS job submitted: 82479540.gadi-pbs
The CABLE log file for each task is written to runs/site/logs/<task_name>_log.txt
The CABLE standard output for each task is written to runs/site/tasks/<task_name>/out.txt
The NetCDF output for each task is written to runs/site/outputs/<task_name>_out.nc

Captured stdout from job:

Running FLUXNET tasks...
Running task AU-Tum_2002-2017_OzFlux_Met_R0_S0... CABLE standard output saved in /scratch/tm70/sb8430/bench_example/runs/site/tasks/AU-Tum_2002-2017_OzFlux_Met_R0_S0/out.txt
cd /scratch/tm70/sb8430/bench_example/runs/site/tasks/AU-Tum_2002-2017_OzFlux_Met_R0_S0
./cable cable.nml > out.txt
Adding attributes to output file: /scratch/tm70/sb8430/bench_example/runs/site/outputs/AU-Tum_2002-2017_OzFlux_Met_R0_S0_out.nc
cd /scratch/tm70/sb8430/bench_example
Running task AU-Tum_2002-2017_OzFlux_Met_R1_S0... CABLE standard output saved in /scratch/tm70/sb8430/bench_example/runs/site/tasks/AU-Tum_2002-2017_OzFlux_Met_R1_S0/out.txt
cd /scratch/tm70/sb8430/bench_example/runs/site/tasks/AU-Tum_2002-2017_OzFlux_Met_R1_S0
./cable cable.nml > out.txt
Adding attributes to output file: /scratch/tm70/sb8430/bench_example/runs/site/outputs/AU-Tum_2002-2017_OzFlux_Met_R1_S0_out.nc
cd /scratch/tm70/sb8430/bench_example
Successfully ran FLUXNET tasks

Currently, `benchcab` outputs stdout from other commands such as `svn`
and `./build3.sh`, but does not output anything when running `./cable`
or when generating particular directory structures.

This commit improves the messages output to stdout by `benchcab` for all
sub-commands. We also add a boolean flag to specify verbose output for
each sub-command.

Write the standard output from CABLE to the `tasks/<task_name>/out.txt`
directory instead of writing to `/dev/null` so that it is accessible to
the user.

Fixes #67
@SeanBryan51 SeanBryan51 force-pushed the 67-polished-messaging-to-standard-output branch from 919e4de to f8c12f0 Compare May 3, 2023 01:07
@SeanBryan51 SeanBryan51 marked this pull request as ready for review May 3, 2023 01:09
@SeanBryan51 SeanBryan51 requested a review from ccarouge May 3, 2023 01:09
@ccarouge
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ccarouge commented May 5, 2023

I've noticed this output in the build part:

Compiling CABLE serially for realisation trunk...
./my_build.ksh

Building cable (serial)

ERROR: Multiple (2) conda environments have been loaded, cannot unload with module
ERROR: Try 'conda deactivate' first

Unloading conda/analysis3-22.10
  ERROR: Module evaluation aborted

Build setup complete.
Compiling now ...

Do you know where it comes from? I don't see it happening for me. Just checking it is due to your setup and not a problem for users.

@SeanBryan51
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I think the error message is due to a custom conda environment being activated and so we cannot module unload conda until we run conda deactivate (I currently use a custom conda environment for testing benchcab). When the error occurs, the conda module remains loaded. I don't think I have had any issues with this so far.

Comment thread benchcab/benchtree.py Outdated

src_dir = Path(root_dir, internal.SRC_DIR)
if not src_dir.exists():
print(f"Creating src directory: {src_dir}")
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Suggested change
print(f"Creating src directory: {src_dir}")
print(f"Creating {src_dir.relative_to(root_dir)} directory: {src_dir}")

Should we replace all the relative path in the print statements like above? This means if we change the directory tree, we wouldn't have to change the printed messages.

Comment thread benchcab/job_script.py Outdated
#PBS -P {project}
#PBS -j oe
#PBS -M {email_address}
#PBS -l storage=gdata/ks32+gdata/wd9+gdata/hh5+gdata/{project}+{curdir_root}/{curdir_proj}
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Suggested change
#PBS -l storage=gdata/ks32+gdata/wd9+gdata/hh5+gdata/{project}+{curdir_root}/{curdir_proj}
#PBS -l storage=gdata/ks32+gdata/hh5+gdata/{project}+{curdir_root}/{curdir_proj}

Remove wd9 now if we change the formatting here

- use `relative_to()` method to print relative paths
- remove `wd9` dependency

In `Task.patch_namelist_file()` print verbose message before doing file
manipulations in case an exception is raised.

Changes requested by @ccarouge

Fixes #64
@SeanBryan51 SeanBryan51 force-pushed the 67-polished-messaging-to-standard-output branch from dc668c7 to 7952f47 Compare May 14, 2023 23:44
@SeanBryan51 SeanBryan51 linked an issue May 14, 2023 that may be closed by this pull request
@SeanBryan51 SeanBryan51 requested a review from ccarouge May 14, 2023 23:47
Add verbose standard output when compiling with a custom build script.
@SeanBryan51 SeanBryan51 force-pushed the 67-polished-messaging-to-standard-output branch from f75ecb4 to c1d5ef1 Compare May 15, 2023 03:30
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ccarouge commented May 16, 2023

  • add indentation to verbose output within running a task
  • blank line between steps of the workflow in all cases (verbose True/False)

- Add indentation to verbose output within running a task to improve
stdout readability
- Add blank line between steps of the workflow in all cases (verbose
True/False) to improve stdout readability
@SeanBryan51 SeanBryan51 requested a review from ccarouge May 16, 2023 07:14
@SeanBryan51 SeanBryan51 merged commit 7d4c94a into master May 17, 2023
@SeanBryan51 SeanBryan51 deleted the 67-polished-messaging-to-standard-output branch May 17, 2023 06:09
@SeanBryan51 SeanBryan51 mentioned this pull request Jul 14, 2023
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Polished messaging to standard output Remove wd9 from required projects

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