Add self hosted runner to get GPU testing on CSD3

.github/workflows/check_tests.sh

@@ -0,0 +1,7 @@
+#!/bin/bash
+/home/js2430/rds/hpc-work/OceanBioME-runner/_work/_temp/julia-1.9.3/bin/julia -O0 --color=yes --project test/gpu_runtests.jl > "output.test"; ec=$?
+if [ $ec -eq 0 ]; then
+    echo "1" > "results.test"; 
+else 
+    echo "0" > "results.test"; 
+fi

.github/workflows/gpu-test.sbatch

@@ -0,0 +1,105 @@
+#!/bin/bash
+#!
+#! Example SLURM job script for Wilkes3 (AMD EPYC 7763, ConnectX-6, A100)
+#! Last updated: Fri 30 Jul 11:07:58 BST 2021
+#!
+
+#!#############################################################
+#!#### Modify the options in this section as appropriate ######
+#!#############################################################
+
+#! sbatch directives begin here ###############################
+#! Name of the job:
+#SBATCH -J OceanBioME-testing
+#! Which project should be charged (NB Wilkes2 projects end in '-GPU'):
+#SBATCH -A taylor-sl3-gpu
+#! How many whole nodes should be allocated?
+#SBATCH --nodes=1
+#! How many (MPI) tasks will there be in total?
+#! Note probably this should not exceed the total number of GPUs in use.
+#SBATCH --ntasks=1
+#! Specify the number of GPUs per node (between 1 and 4; must be 4 if nodes>1).
+#! Note that the job submission script will enforce no more than 32 cpus per GPU.
+#SBATCH --gres=gpu:1
+#! How much wallclock time will be required?
+#SBATCH --time=02:00:00
+#! What types of email messages do you wish to receive?
+#SBATCH --mail-type=NONE
+#! Uncomment this to prevent the job from being requeued (e.g. if
+#! interrupted by node failure or system downtime):
+##SBATCH --no-requeue
+
+#! Do not change:
+#SBATCH -p ampere
+
+#! sbatch directives end here (put any additional directives above this line)
+
+#! Notes:
+#! Charging is determined by GPU number*walltime. 
+
+#! Number of nodes and tasks per node allocated by SLURM (do not change):
+numnodes=$SLURM_JOB_NUM_NODES
+numtasks=$SLURM_NTASKS
+mpi_tasks_per_node=$(echo "$SLURM_TASKS_PER_NODE" | sed -e  's/^\([0-9][0-9]*\).*$/\1/')
+#! ############################################################
+#! Modify the settings below to specify the application's environment, location 
+#! and launch method:
+
+#! Optionally modify the environment seen by the application
+#! (note that SLURM reproduces the environment at submission irrespective of ~/.bashrc):
+. /etc/profile.d/modules.sh                # Leave this line (enables the module command)
+module purge                               # Removes all modules still loaded
+module load rhel8/default-amp              # REQUIRED - loads the basic environment
+
+#! Insert additional module load commands after this line if needed:
+
+#! Full path to application executable: 
+#! TODO - workout how to make version get passed to this script
+application="./check_tests.sh"
+
+#! Run options for the application:
+options=""
+
+#! Work directory (i.e. where the job will run):
+workdir="$SLURM_SUBMIT_DIR"  # The value of SLURM_SUBMIT_DIR sets workdir to the directory
+                             # in which sbatch is run.
+
+#! Are you using OpenMP (NB this is unrelated to OpenMPI)? If so increase this
+#! safe value to no more than 128:
+export OMP_NUM_THREADS=1
+
+#! Number of MPI tasks to be started by the application per node and in total (do not change):
+np=$[${numnodes}*${mpi_tasks_per_node}]
+
+#! Choose this for a pure shared-memory OpenMP parallel program on a single node:
+#! (OMP_NUM_THREADS threads will be created):
+CMD="$application $options"
+
+
+###############################################################
+### You should not have to change anything below this line ####
+###############################################################
+
+cd $workdir
+echo -e "Changed directory to `pwd`.\n"
+
+JOBID=$SLURM_JOB_ID
+
+echo -e "JobID: $JOBID\n======"
+echo "Time: `date`"
+echo "Running on master node: `hostname`"
+echo "Current directory: `pwd`"
+
+if [ "$SLURM_JOB_NODELIST" ]; then
+        #! Create a machine file:
+        export NODEFILE=`generate_pbs_nodefile`
+        cat $NODEFILE | uniq > machine.file.$JOBID
+        echo -e "\nNodes allocated:\n================"
+        echo `cat machine.file.$JOBID | sed -e 's/\..*$//g'`
+fi
+
+echo -e "\nnumtasks=$numtasks, numnodes=$numnodes, mpi_tasks_per_node=$mpi_tasks_per_node (OMP_NUM_THREADS=$OMP_NUM_THREADS)"
+
+echo -e "\nExecuting command:\n==================\n$CMD\n"
+
+eval $CMD 

.github/workflows/gpu-tests.yml

@@ -0,0 +1,36 @@
+name: CSD3 tests
+
+on:
+  #push:
+  #  branches:
+  #    - main
+  pull_request:
+    branches: 
+      - main
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ github.ref != 'refs/heads/main' }}
+
+env:
+  DATADEPS_ALWAYS_ACCEPT: true
+  JULIA_VERSION: "1.9.3"
+  JULIA_MINOR_VERSION: "1.9"
+  RDS_HOME: "/home/js2430/rds/hpc-work/OceanBioME-runner/_work"
+
+jobs:
+  test:
+    name: Deploy CSD3 tests
+    runs-on: self-hosted
+    steps:
+      - name: Download Julia
+        run: "wget -N -P $RDS_HOME/_temp https://julialang-s3.julialang.org/bin/linux/x64/$JULIA_MINOR_VERSION/julia-$JULIA_VERSION-linux-x86_64.tar.gz;
+              tar xf $RDS_HOME/_temp/julia-$JULIA_VERSION-linux-x86_64.tar.gz -C $RDS_HOME/_temp"
+      - name: Clean repo
+        run: "git checkout main; git pull --force; git checkout $GITHUB_HEAD_REF; git pull --force"
+      - name: Run tests
+        run: "sbatch .github/workflows/gpu-test.sbatch;
+              /home/js2430/rds/hpc-work/OceanBioME-runner/_work/_temp/julia-1.9.3/bin/julia -O0 --color=yes --project test/check_results.jl"
+      - name: Clean up
+        if: always()
+        run: "rm -rf $RDS_HOME/_temp/julia-$JULIA_VERSION; rm results.test; rm output.test" # presumably this happens anyway

.github/workflows/tests.yml

@@ -1,4 +1,5 @@
 name: Tests
+
 on:
   push:
     branches:

test/check_results.jl

@@ -0,0 +1,18 @@
+file_exists = isfile("results.test")
+
+while !(file_exists)
+    sleep(10)
+    global file_exists = isfile("results.test")
+end
+
+result = open("results.test") do file
+    parse(Int, read(file, String))
+end
+
+output = open("output.test") do file
+    read(file, String)
+end
+
+println(output)
+
+result == 0 ? error("Tests failed") : nothing

test/gpu_runtests.jl

@@ -0,0 +1,13 @@
+using Pkg
+
+Pkg.instantiate()
+
+Pkg.add("Test", "CUDA", "DataDeps", "Documenter", "Statistics", "JLD2")
+
+Pkg.precompile()
+
+using Oceananigans
+
+arch = GPU()
+
+include("runtests.jl")

test/runtests.jl

@@ -1,4 +1,8 @@
-using OceanBioME, Documenter, Test
+using OceanBioME, Documenter, Test, Oceananigans
+
+if !(@isdefined arch)
+    arch = CPU()
+end
 
 include("test_utils.jl")
 include("test_light.jl")
@@ -8,6 +12,8 @@ include("test_gasexchange.jl")
 include("test_slatissima.jl")
 include("test_sediments.jl")
 
-@testset "Doctests" begin
-    doctest(OceanBioME)
-end
+if isa(arch, CPU)
+    @testset "Doctests" begin
+        doctest(OceanBioME)
+    end
+end

test/test_LOBSTER.jl

@@ -114,14 +114,13 @@ end
 
 n_timesteps = 100
 
-for arch in (CPU(), )
-    grid = RectilinearGrid(arch; size=(1, 1, 1), extent=(1, 1, 2))
-    for open_bottom = (false, true), sinking = (false, true), variable_redfield = (false, true), oxygen = (false, true), carbonates = (false, true)
-        if !(sinking && open_bottom) # no sinking is the same with and without open bottom
-            @info "Testing on $(typeof(arch)) with carbonates $(carbonates ? :✅ : :❌), oxygen $(oxygen ? :✅ : :❌), variable redfield $(variable_redfield ? :✅ : :❌), sinking $(sinking ? :✅ : :❌), open bottom $(open_bottom ? :✅ : :❌))"
-            @testset "$arch, $carbonates, $oxygen, $variable_redfield, $sinking, $open_bottom" begin
-                test_LOBSTER(grid, carbonates, oxygen, variable_redfield, sinking, open_bottom, n_timesteps)
-            end
+grid = RectilinearGrid(arch; size=(1, 1, 1), extent=(1, 1, 2))
+
+for open_bottom = (false, true), sinking = (false, true), variable_redfield = (false, true), oxygen = (false, true), carbonates = (false, true)
+    if !(sinking && open_bottom) # no sinking is the same with and without open bottom
+        @info "Testing on $(typeof(arch)) with carbonates $(carbonates ? :✅ : :❌), oxygen $(oxygen ? :✅ : :❌), variable redfield $(variable_redfield ? :✅ : :❌), sinking $(sinking ? :✅ : :❌), open bottom $(open_bottom ? :✅ : :❌))"
+        @testset "$arch, $carbonates, $oxygen, $variable_redfield, $sinking, $open_bottom" begin
+            test_LOBSTER(grid, carbonates, oxygen, variable_redfield, sinking, open_bottom, n_timesteps)
         end
     end
 end

test/test_NPZD.jl

@@ -47,14 +47,13 @@ function test_NPZD(grid, sinking, open_bottom)
     return nothing
 end
 
-for arch in (CPU(), )
-    grid = RectilinearGrid(arch; size=(3, 3, 6), extent=(1, 1, 2))
-    for sinking = (false, true), open_bottom = (false, true)
-        if !(sinking && open_bottom) # no sinking is the same with and without open bottom
-            @info "Testing on $(typeof(arch)) with sinking $(sinking ? :✅ : :❌), open bottom $(open_bottom ? :✅ : :❌))"
-            @testset "$arch, $sinking, $open_bottom" begin
-                test_NPZD(grid, sinking, open_bottom)
-            end
+grid = RectilinearGrid(arch; size=(3, 3, 6), extent=(1, 1, 2))
+
+for sinking = (false, true), open_bottom = (false, true)
+    if !(sinking && open_bottom) # no sinking is the same with and without open bottom
+        @info "Testing on $(typeof(arch)) with sinking $(sinking ? :✅ : :❌), open bottom $(open_bottom ? :✅ : :❌))"
+        @testset "$arch, $sinking, $open_bottom" begin
+            test_NPZD(grid, sinking, open_bottom)
         end
     end
 end

test/test_light.jl

@@ -42,11 +42,9 @@ function test_two_band(grid, bgc, model_type)
     return all(results_PAR .≈ reverse(expected_PAR))
 end
 
-archs = (CPU(), )
 
 @testset "Light attenuaiton model" begin 
     for model in (NonhydrostaticModel, HydrostaticFreeSurfaceModel),
-        arch in archs,
         grid in (RectilinearGrid(arch; size = (2, 2, 2), extent = (2, 2, 2)), 
                  LatitudeLongitudeGrid(arch; size = (5, 5, 2), longitude = (-180, 180), latitude = (-85, 85), z = (-2, 0))),
         bgc in (LOBSTER, NutrientPhytoplanktonZooplanktonDetritus) # this is now redundant since each model doesn't deal with the light separatly

test/test_sediments.jl

@@ -112,31 +112,30 @@ display_name(::ImmersedBoundaryGrid) = "Immersed boundary grid"
 
 bottom_height(x, y) = -1000 + 500 * exp(- (x^2 + y^2) / 250) # a perfect hill
 
+grids = [RectilinearGrid(architecture; size=(3, 3, 50), extent=(10, 10, 500)),
+         LatitudeLongitudeGrid(architecture; size = (3, 3, 16), latitude = (0, 10), longitude = (0, 10), z = (-500, 0)),
+         ImmersedBoundaryGrid(
+            LatitudeLongitudeGrid(architecture; size = (3, 3, 16), latitude = (0, 10), longitude = (0, 10), z = (-500, 0)), 
+            ridFittedBottom(bottom_height))]
+
 @testset "Sediment integration" begin
-    for architecture in (CPU(), )
-        grids = [RectilinearGrid(architecture; size=(3, 3, 50), extent=(10, 10, 500)),
-                 LatitudeLongitudeGrid(architecture; size = (3, 3, 16), latitude = (0, 10), longitude = (0, 10), z = (-500, 0)),
-                 ImmersedBoundaryGrid(
-                    LatitudeLongitudeGrid(architecture; size = (3, 3, 16), latitude = (0, 10), longitude = (0, 10), z = (-500, 0)), 
-                    GridFittedBottom(bottom_height))]
-        for grid in grids
-            for timestepper in (:QuasiAdamsBashforth2, :RungeKutta3),
-                sediment_model in (InstantRemineralisation(; grid), SimpleMultiG(; grid)),
-                model in (NonhydrostaticModel, HydrostaticFreeSurfaceModel)
-                for biogeochemistry in (NutrientPhytoplanktonZooplanktonDetritus(; grid, sediment_model),
-                                        LOBSTER(; grid,
-                                                  carbonates = ifelse(isa(sediment_model, SimpleMultiG), true, false), 
-                                                  oxygen = ifelse(isa(sediment_model, SimpleMultiG), true, false), 
-                                                  variable_redfield = ifelse(isa(sediment_model, SimpleMultiG), true, false), 
-                                                  sediment_model))
-                    # get rid of incompatible combinations
-                    run = ifelse((model == NonhydrostaticModel && (isa(grid, ImmersedBoundaryGrid) || isa(grid, LatitudeLongitudeGrid))) ||
-                                 (model == HydrostaticFreeSurfaceModel && timestepper == :RungeKutta3) ||
-                                 (isa(sediment_model, SimpleMultiG) && isa(biogeochemistry.underlying_biogeochemistry, NutrientPhytoplanktonZooplanktonDetritus)), false, true)
-                    if run
-                        @info "Testing sediment on $(typeof(architecture)) with $timestepper and $(display_name(sediment_model)) on $(display_name(biogeochemistry.underlying_biogeochemistry))"
-                        @testset "$architecture, $timestepper, $(display_name(sediment_model)), $(display_name(biogeochemistry.underlying_biogeochemistry))" test_flat_sediment(grid, biogeochemistry, model; timestepper)
-                    end
+    for grid in grids
+        for timestepper in (:QuasiAdamsBashforth2, :RungeKutta3),
+            sediment_model in (InstantRemineralisation(; grid), SimpleMultiG(; grid)),
+            model in (NonhydrostaticModel, HydrostaticFreeSurfaceModel)
+            for biogeochemistry in (NutrientPhytoplanktonZooplanktonDetritus(; grid, sediment_model),
+                                    LOBSTER(; grid,
+                                              carbonates = ifelse(isa(sediment_model, SimpleMultiG), true, false), 
+                                              oxygen = ifelse(isa(sediment_model, SimpleMultiG), true, false), 
+                                              variable_redfield = ifelse(isa(sediment_model, SimpleMultiG), true, false), 
+                                              sediment_model))
+                # get rid of incompatible combinations
+                run = ifelse((model == NonhydrostaticModel && (isa(grid, ImmersedBoundaryGrid) || isa(grid, LatitudeLongitudeGrid))) ||
+                             (model == HydrostaticFreeSurfaceModel && timestepper == :RungeKutta3) ||
+                             (isa(sediment_model, SimpleMultiG) && isa(biogeochemistry.underlying_biogeochemistry, NutrientPhytoplanktonZooplanktonDetritus)), false, true)
+                if run
+                    @info "Testing sediment on $(typeof(architecture)) with $timestepper and $(display_name(sediment_model)) on $(display_name(biogeochemistry.underlying_biogeochemistry))"
+                    @testset "$architecture, $timestepper, $(display_name(sediment_model)), $(display_name(biogeochemistry.underlying_biogeochemistry))" test_flat_sediment(grid, biogeochemistry, model; timestepper)
                 end
             end
         end

test/test_slatissima.jl

@@ -10,7 +10,6 @@ function intercept_tendencies!(model, intercepted_tendencies)
 end
 
 @testset "SLatissima particle setup and conservations" begin
-    arch = CPU()
     grid = RectilinearGrid(arch; size=(1, 1, 1), extent=(1, 1, 1))
 
     # Initial properties

test/test_utils.jl

@@ -46,9 +46,7 @@ function test_negative_zeroing(arch)
 end
 
 @testset "Test Utils" begin
-    for arch in (CPU(), )
-        @test test_column_diffusion_timescale(arch)
-        @test test_negative_scaling(arch)
-        @test test_negative_zeroing(arch)
-    end
+    @test test_column_diffusion_timescale(arch)
+    @test test_negative_scaling(arch)
+    @test test_negative_zeroing(arch)
 end