format, docs fixes

CliMA · Jul 17, 2024 · 92d9618 · 92d9618
1 parent 3fc571c
commit 92d9618
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diff --git a/docs/src/api.md b/docs/src/api.md
@@ -14,21 +14,23 @@ ClimaCalibrate.observation_map
 ClimaCalibrate.get_backend
 ClimaCalibrate.calibrate
 ClimaCalibrate.model_run
+ClimaCalibrate.module_load_string
 ```
 
 ## Job Scheduler
 ```@docs
 ClimaCalibrate.wait_for_jobs
-log_member_error
-kill_job
-job_status
+ClimaCalibrate.log_member_error
+ClimaCalibrate.kill_job
+ClimaCalibrate.job_status
 ClimaCalibrate.kwargs
 ClimaCalibrate.slurm_model_run
-generate_sbatch_script
-submit_slurm_job
+ClimaCalibrate.generate_sbatch_script
+ClimaCalibrate.generate_sbatch_directives
+ClimaCalibrate.submit_slurm_job
 ClimaCalibrate.pbs_model_run
 ClimaCalibrate.generate_pbs_script
-submit_pbs_job
+ClimaCalibrate.submit_pbs_job
 ```
 
 ## EnsembleKalmanProcesses Interface

diff --git a/src/backends.jl b/src/backends.jl
@@ -35,7 +35,7 @@ function get_backend()
 end
 
 """
-    module_load_string(T) where {T<:Type{SlurmBackend}}
+    module_load_string(backend)
 
 Return a string that loads the correct modules for a given backend when executed via bash.
 """

diff --git a/src/pbs.jl b/src/pbs.jl
@@ -24,7 +24,7 @@ function generate_pbs_script(
     hpc_kwargs = Dict(),
 )
     member_log = path_to_model_log(output_dir, iter, member)
-    
+
     queue = get(hpc_kwargs, :queue, "main")
     walltime = format_pbs_time(get(hpc_kwargs, :time, 45))
     num_nodes = get(hpc_kwargs, :ntasks, 1)
@@ -47,22 +47,23 @@ function generate_pbs_script(
     total_ranks = num_nodes * ranks_per_node
 
 
-    qsub_contents = file -> """
-    #!/bin/bash
-    #PBS -N run_$(iter)_$member
-    #PBS -j oe
-    #PBS -A UCIT0011
-    #PBS -q $queue
-    #PBS -o $member_log
-    #PBS -l walltime=$walltime
-    #PBS -l select=$num_nodes:ncpus=$cpus_per_node:ngpus=$gpus_per_node:ompthreads=1
+    qsub_contents =
+        file -> """
+#!/bin/bash
+#PBS -N run_$(iter)_$member
+#PBS -j oe
+#PBS -A UCIT0011
+#PBS -q $queue
+#PBS -o $member_log
+#PBS -l walltime=$walltime
+#PBS -l select=$num_nodes:ncpus=$cpus_per_node:ngpus=$gpus_per_node:ompthreads=1
 
-    $module_load_str
+$module_load_str
 
-    export CLIMACOMMS_DEVICE="$climacomms_device"
-    export CLIMACOMMS_CONTEXT="MPI"
-    \$MPITRAMPOLINE_MPIEXEC -n $total_ranks -ppn $ranks_per_node $set_gpu_rank julia --project=$experiment_dir $file
-    """
+export CLIMACOMMS_DEVICE="$climacomms_device"
+export CLIMACOMMS_CONTEXT="MPI"
+\$MPITRAMPOLINE_MPIEXEC -n $total_ranks -ppn $ranks_per_node $set_gpu_rank julia --project=$experiment_dir $file
+"""
 
     julia_script = """\
     import ClimaCalibrate as CAL
@@ -86,7 +87,7 @@ function pbs_model_run(
     model_interface,
     module_load_str;
     hpc_kwargs,
-    debug = false
+    debug = false,
 )
     # Type and existence checks
     @assert isdir(output_dir) "Output directory does not exist: $output_dir"

diff --git a/src/slurm.jl b/src/slurm.jl
@@ -193,7 +193,7 @@ function generate_sbatch_script(
     $slurm_directives
     $module_load_str
 
-    export CLIMACOMMS_DEVICE=$climacomms_device
+    export CLIMACOMMS_DEVICE="$climacomms_device"
     export CLIMACOMMS_CONTEXT="MPI"
 
     srun --output=$member_log --open-mode=append julia --project=$experiment_dir -e '

diff --git a/test/hpc_backend_e2e.jl b/test/hpc_backend_e2e.jl
@@ -5,7 +5,13 @@ using Pkg;
 Pkg.instantiate(; verbose = true);
 
 import ClimaCalibrate:
-    get_backend, HPCBackend, JuliaBackend, calibrate, get_prior, kwargs, DerechoBackend
+    get_backend,
+    HPCBackend,
+    JuliaBackend,
+    calibrate,
+    get_prior,
+    kwargs,
+    DerechoBackend
 using Test
 import EnsembleKalmanProcesses: get_ϕ_mean_final, get_g_mean_final
 

diff --git a/test/pbs_unit_tests.jl b/test/pbs_unit_tests.jl
@@ -11,8 +11,12 @@ const GPUS_PER_TASK = 2
 const EXPERIMENT_DIR = "exp/dir"
 const MODEL_INTERFACE = "model_interface.jl"
 const MODULE_LOAD_STR = CAL.module_load_string(CAL.DerechoBackend)
-const hpc_kwargs =
-    CAL.kwargs(time = TIME_LIMIT, ntasks = NTASKS, cpus_per_task = CPUS_PER_TASK, gpus_per_task = GPUS_PER_TASK)
+const hpc_kwargs = CAL.kwargs(
+    time = TIME_LIMIT,
+    ntasks = NTASKS,
+    cpus_per_task = CPUS_PER_TASK,
+    gpus_per_task = GPUS_PER_TASK,
+)
 
 # Time formatting tests
 @test CAL.format_pbs_time(TIME_LIMIT) == "01:30:00"
-Original file line number
+Diff line change
@@ Expand Up / @@ -35,7 +35,7 @@ function get_backend() @@
     end
     """
-        module_load_string(T) where {T<:Type{SlurmBackend}}
+        module_load_string(backend)
     Return a string that loads the correct modules for a given backend when executed via bash.
     """
@@ Expand Down @@