init

add error up climacommons

test error

test

wait

split cmds

split cmds

split to diff steps

gp fix

no {

rm init

one ln cmd

clean

options

now sol passes

test to fail on BK

revs

try

try

pip fix

try

no bl ln

try

try

sep script

sep script

sep script

sep script

try

try

try

revert fail test

.buildkite/pipeline.yml

@@ -1,6 +1,6 @@
 agents:
   queue: new-central
-  slurm_time: 24:00:00
+  slurm_time: 4:00:00
   modules: climacommon/2024_03_18
 
 env:
@@ -344,8 +344,6 @@ steps:
           slurm_ntasks: 2
           slurm_mem: 16GB
 
-      - label: "batch script"
-        command: "sbatch test/mpi_tests/local_checks.sh"
 
       # short high-res performance test
       - label: "Unthreaded AMIP FINE" # also reported by longruns with a flame graph
@@ -431,9 +429,13 @@ steps:
           slurm_mem: 20GB
           slurm_gpus: 1
 
-
-
-      - wait
+  - group: "Bash scripts"
+    steps:
+      - label: "Submit and Monitor sbatch Job on Caltech HPC"
+        # check that (1) the script can be succesfully submitted, (2) it runs successfully
+        command: "test/mpi_tests/test_sbatch_script.sh"
+        agents:
+          slurm_ntasks: 1
 
   - wait
 

.gitignore

@@ -50,7 +50,7 @@ experiments/AMIP/output/*
 *.so
 
 # internal tests
-testdel.jl
+slurm-*.out
 
 # ignore vscode artifacts
 *.vscode

config/model_configs/coarse_single_ft64_hourly_checkpoints_restart.yml

@@ -0,0 +1,19 @@
+anim: false
+apply_limiter: false
+dt: "400secs"
+dt_cpl: 400
+dt_save_restart: "10days"
+dt_save_to_sol: "1days"
+energy_check: false
+h_elem: 6
+hourly_checkpoint: true
+hourly_checkpoint_dt: 1
+job_id: "coarse_single_ft64_hourly_checkpoints_restart"
+mode_name: "amip"
+moist: "equil"
+mono_surface: false
+precip_model: "0M"
+rad: "gray"
+run_name: "coarse_single_ft64_hourly_checkpoints_restart"
+t_end: "800secs"
+vert_diff: "true"

experiments/AMIP/cli_options.jl

@@ -38,6 +38,10 @@ function argparse_settings()
         help = "Boolean flag indicating whether to checkpoint at intervals of 1 hour or multiple hours"
         arg_type = Bool
         default = false
+        "--hourly_checkpoint_dt"
+        help = "Time interval for hourly checkpointing in hours (20 days by default)"
+        arg_type = Int
+        default = 480
         "--coupler_output_dir"
         help = "Directory to save output files. Note that TempestRemap fails if interactive and paths are too long."
         arg_type = String

experiments/AMIP/coupler_driver.jl

@@ -131,6 +131,7 @@ saveat = Float64(time_to_seconds(config_dict["dt_save_to_sol"]))
 date0 = date = DateTime(config_dict["start_date"], dateformat"yyyymmdd")
 mono_surface = config_dict["mono_surface"]
 hourly_checkpoint = config_dict["hourly_checkpoint"]
+hourly_checkpoint_dt = config_dict["hourly_checkpoint_dt"]
 restart_dir = config_dict["restart_dir"]
 restart_t = Int(config_dict["restart_t"])
 evolving_ocean = config_dict["evolving_ocean"]
@@ -526,8 +527,13 @@ The currently implemented callbacks are:
   being approximated from wind speed). It is updated at the same frequency as the atmospheric radiation.
   NB: Eventually, we will call all of radiation from the coupler, in addition to the albedo calculation.
 =#
-checkpoint_cb =
-    HourlyCallback(dt = FT(480), func = checkpoint_sims, ref_date = [dates.date[1]], active = hourly_checkpoint) # 20 days
+
+checkpoint_cb = HourlyCallback(
+    dt = hourly_checkpoint_dt,
+    func = checkpoint_sims,
+    ref_date = [dates.date[1]],
+    active = hourly_checkpoint,
+) # 20 days
 update_firstdayofmonth!_cb =
     MonthlyCallback(dt = FT(1), func = update_firstdayofmonth!, ref_date = [dates.date1[1]], active = true)
 dt_water_albedo = parse(FT, filter(x -> !occursin(x, "hours"), dt_rad))

test/mpi_tests/local_checks.sh

@@ -1,29 +1,25 @@
 #!/bin/bash
-#SBATCH --time=24:00:00
-#SBATCH --nodes=1
-#SBATCH --job-name=mpi_restart_test
-#SBATCH --reservation=clima
-#SBATCH --mem=32GB
 #SBATCH --ntasks=2
+#SBATCH --job-name=mpi_amip
+#SBATCH --time=24:00:00
+#SBATCH --mem-per-cpu=16G
+#SBATCH --partition=expansion
 
-# TODO: this needs to be updated (+ implement better tests that are caught on Buildkite) #667
-
+export MODULE_PATH=/groups/esm/modules:$MODULE_PATH
 module purge
-module load julia/1.10.1
-export JULIA_MPI_BINARY=system
-export JULIA_NUM_THREADS=${SLURM_CPUS_PER_TASK:=1}
-export CLIMACORE_DISTRIBUTED="MPI"
-export JULIA_HDF5_PATH=""
+module load climacommon/2024_03_18
 
-export RUN_NAME=amip_restart_mpi_test
+export CC_PATH=$(pwd)/ # adjust this to the path of your ClimaCoupler.jl directory
+export RUN_NAME=coarse_single_ft64_hourly_checkpoints_restart
+export CONFIG_FILE=${CC_PATH}config/model_configs/${RUN_NAME}.yml
 export RESTART_DIR=experiments/AMIP/output/amip/${RUN_NAME}_artifacts/
-export RESTART_T=200
 
-julia -e 'using Pkg; Pkg.add("MPIPreferences"); using MPIPreferences; use_system_binary()'
-julia --project -e 'using Pkg; Pkg.instantiate()'
-julia --project -e 'using Pkg; Pkg.build("MPI")'
-julia --project -e 'using Pkg; Pkg.build("HDF5")'
-julia --project -e 'using Pkg; Pkg.API.precompile()'
+export OPENBLAS_NUM_THREADS=1
+export JULIA_NVTX_CALLBACKS=gc
+export OMPI_MCA_opal_warn_on_missing_libcuda=0
+export JULIA_MAX_NUM_PRECOMPILE_FILES=100
+export JULIA_CPU_TARGET='broadwell;skylake;icelake;cascadelake;epyc'
+export SLURM_KILL_BAD_EXIT=1
 
 julia --project=experiments/AMIP/ -e 'using Pkg; Pkg.instantiate(;verbose=true)'
 julia --project=experiments/AMIP/ -e 'using Pkg; Pkg.precompile()'
@@ -34,10 +30,28 @@ julia --project=artifacts -e 'using Pkg; Pkg.precompile()'
 julia --project=artifacts -e 'using Pkg; Pkg.status()'
 julia --project=artifacts artifacts/download_artifacts.jl
 
-# run spin up
-# - specify `--hourly_checkpoint true` to save monthly checkpoints of all model prognostic states
-mpiexec julia --color=yes --project=experiments/AMIP/ experiments/AMIP/coupler_driver.jl --run_name $RUN_NAME --coupled true   --start_date 19790101 --hourly_checkpoint true  --anim true --surface_setup PrescribedSurface --dt_cpl 200 --energy_check false --mode_name amip --mono_surface false --vert_diff true --moist equil --rad clearsky --precip_model 0M --z_elem 35 --dz_bottom 50 --h_elem 12 --rayleigh_sponge true --alpha_rayleigh_uh 0 --dt 200secs --t_end 0.1days --job_id $RUN_NAME --dt_save_to_sol 1000days --dt_save_state_to_disk 10days --apply_limiter false --FLOAT_TYPE Float64
+srun -K julia --project=experiments/AMIP/ experiments/AMIP/coupler_driver.jl --config_file $CONFIG_FILE
+
+# restart from simulation time of 400 seconds
+export RESTART_T=400
+
+# setup the new config file with ammened checkpointing frequency
+export RESTART_CONFIG_FILE=${CONFIG_FILE::-4}_tmp.yml
+cp $CONFIG_FILE $RESTART_CONFIG_FILE
+sed -i 's/t_end: \"800secs\"/t_end: \"3600secs\"/g' $RESTART_CONFIG_FILE
+
+# rerun the model
+srun -K julia --project=experiments/AMIP/ experiments/AMIP/coupler_driver.jl --config_file $RESTART_CONFIG_FILE --restart_dir $RESTART_DIR --restart_t $RESTART_T
+
+# throw an error if no restart checkpoint files are found
+if [ $(ls -1 $RESTART_DIR/checkpoint | wc -l) -lt 5 ]; then
+  echo "RESTART_DIR does not contain enough files"
+  exit 1
+else
+  echo "RESTART_DIR contains $(ls -1 $RESTART_DIR/checkpoint | wc -l) files"
+fi
 
-# init using a restart
-# - specify the directory of the `checkpoint/` folder (i.e.,  `--restart_dir`) and time (in secs; `--restart_t`) of the restart file
-mpiexec julia --color=yes --project=experiments/AMIP/ experiments/AMIP/coupler_driver.jl --run_name $RUN_NAME --coupled true --restart_dir $RESTART_DIR --restart_t $RESTART_T --start_date 19790102 --anim true --surface_setup PrescribedSurface --dt_cpl 200 --energy_check false --mode_name amip --mono_surface false --vert_diff true --moist equil --rad clearsky --precip_model 0M --z_elem 35 --dz_bottom 50 --h_elem 12 --rayleigh_sponge true --alpha_rayleigh_uh 0 --dt 200secs --t_end 0.1days --job_id $RUN_NAME --dt_save_to_sol 1000days --dt_save_state_to_disk 10days --apply_limiter false --FLOAT_TYPE Float64
+# Trouble shooting?
+# - ensure you're using the latest module file of climacommon
+# - ensure you're using the latest version of ClimaCoupler.jl
+# - did you cd to your version of ClimaCoupler.jl?

test/mpi_tests/test_sbatch_script.sh

@@ -0,0 +1,25 @@
+#!/bin/bash
+
+# Submit the sbatch script and capture its job ID
+JOB_ID=$(sbatch  test/mpi_tests/local_checks.sh | awk '{print $4}')
+echo "Submitted job with ID: $JOB_ID, output log: slurm-$JOB_ID.out"
+START_TIME=$(date +%s)
+# Loop until the job finishes
+while true; do
+    # Check the status of the job
+    STATUS=$(squeue -j $JOB_ID | grep $JOB_ID | awk '{print $5}')
+    ELAPSED_TIME=$(( $(date +%s) - $START_TIME ))
+    # If the job status is 'PD' (pending) or 'R' (running), wait and continue checking
+    if [ "$STATUS" == "PD" ] || [ "$STATUS" == "R" ]; then
+        sleep 60
+        echo "Job is still running... Elapsed time: $ELAPSED_TIME seconds."
+    # If the job status is 'CF' (completed successfully), print success message and exit
+    elif [ "$STATUS" == "CF" ]; then
+        echo "Job completed successfully."
+        exit 0
+    # If the job status is anything else, print error message and exit
+    else
+        echo "Error: Job failed or terminated. See slurm-$JOB_ID.out for more information."
+        exit 1
+    fi
+done