Merge pull request #764 from ProjectTorreyPines/dev

Major update to the multi_objective and database generator studies

Makefile

@@ -16,7 +16,7 @@ else
 endif
 
 GENERAL_REGISTRY_PACKAGES := CoordinateConventions FuseExchangeProtocol MillerExtendedHarmonic IMASdd IMASutils
-FUSE_PACKAGES_MAKEFILE := ADAS BalanceOfPlantSurrogate BoundaryPlasmaModels CHEASE CoordinateConventions EPEDNN FiniteElementHermite FusionMaterials FuseExchangeProtocol IMAS IMASdd IMASutils MXHEquilibrium MeshTools MillerExtendedHarmonic NEO NNeutronics QED RABBIT SimulationParameters TEQUILA TGLFNN TJLF VacuumFields
+FUSE_PACKAGES_MAKEFILE := ADAS BalanceOfPlantSurrogate BoundaryPlasmaModels CHEASE CoordinateConventions EPEDNN FiniteElementHermite FRESCO FusionMaterials FuseExchangeProtocol IMAS IMASdd IMASutils MXHEquilibrium MeshTools MillerExtendedHarmonic NEO NNeutronics QED RABBIT SimulationParameters TEQUILA TGLFNN TJLF TroyonBetaNN VacuumFields
 FUSE_PACKAGES_MAKEFILE_EXTENSION := ThermalSystemModels
 ifndef NO_FUSE_EXTENSION
 	FUSE_PACKAGES_MAKEFILE := $(FUSE_PACKAGES_MAKEFILE) $(FUSE_PACKAGES_MAKEFILE_EXTENSION)
@@ -69,25 +69,25 @@ help: header help_info
 ADAS:
 	$(call clone_pull_repo,$@)
 
-FUSE:
-	$(call clone_pull_repo,$@)
+BalanceOfPlantSurrogate:
+	$(call clone_pull_repo$@)
 
-IMAS:
+BoundaryPlasmaModels:
 	$(call clone_pull_repo,$@)
 
-IMASdd:
+CHEASE:
 	$(call clone_pull_repo,$@)
 
 CoordinateConventions:
 	$(call clone_pull_repo,$@)
 
-MillerExtendedHarmonic:
+EPEDNN:
 	$(call clone_pull_repo,$@)
 
-IMASutils:
+FiniteElementHermite:
 	$(call clone_pull_repo,$@)
 
-FuseUtils:
+FRESCO:
 	$(call clone_pull_repo,$@)
 
 FusionMaterials:
@@ -96,7 +96,13 @@ FusionMaterials:
 FuseExchangeProtocol:
 	$(call clone_pull_repo,$@)
 
-VacuumFields:
+IMAS:
+	$(call clone_pull_repo,$@)
+
+IMASdd:
+	$(call clone_pull_repo,$@)
+
+IMASutils:
 	$(call clone_pull_repo,$@)
 
 MXHEquilibrium:
@@ -105,46 +111,45 @@ MXHEquilibrium:
 MeshTools:
 	$(call clone_pull_repo,$@)
 
-TGLFNN:
+MillerExtendedHarmonic:
 	$(call clone_pull_repo,$@)
 
-TJLF:
+NEO:
 	$(call clone_pull_repo,$@)
 
-EPEDNN:
+NNeutronics:
 	$(call clone_pull_repo,$@)
 
 QED:
 	$(call clone_pull_repo,$@)
 
-FiniteElementHermite:
+RABBIT:
 	$(call clone_pull_repo,$@)
 
-CHEASE:
+SimulationParameters:
 	$(call clone_pull_repo,$@)
 
 TEQUILA:
 	$(call clone_pull_repo,$@)
 
-BalanceOfPlantSurrogate:
-	$(call clone_pull_repo$@)
-
-NNeutronics:
+TGLFNN:
 	$(call clone_pull_repo,$@)
 
-SimulationParameters:
+TJLF:
 	$(call clone_pull_repo,$@)
 
-BoundaryPlasmaModels:
+TroyonBetaNN:
 	$(call clone_pull_repo,$@)
 
-NEO:
+VacuumFields:
 	$(call clone_pull_repo,$@)
 
-XSteam:
+# ========
+
+FUSE:
 	$(call clone_pull_repo,$@)
 
-RABBIT:
+XSteam:
 	$(call clone_pull_repo,$@)
 
 ThermalSystemModels:

docs/src/install.md

@@ -43,9 +43,11 @@ For installation start your Julia interpreter by typing `julia` at the terminal,
 1. Exit julia and clone [`FUSE examples`](https://github.com/ProjectTorreyPines/FuseExamples) in the current working directory. To see/run those `.ipynb` files, you'll need to use Jupyter-Lab or VScode.
 
    ```bash
-   fusebot install_examples
+   git clone https://github.com/ProjectTorreyPines/FuseExamples
    ```
 
+   This is a git repository that you are in control of. Do a `git fetch && git reset --hard origin/master` to gather the latest updates (**NOTE: this will wipe out any changes you have made to those examples!**)
+
 ## Install Jupyter-Lab with Julia support
 
 1. You will need to [install `jupyter-lab`](https://jupyterlab.readthedocs.io/en/stable/getting_started/installation.html) if that's not already available on your system 

generate_dd/data_structures_extra/mhd_linear.json

@@ -0,0 +1,8 @@
+{
+ "mhd_linear.time_slice[:].toroidal_mode[:].metric": {
+  "data_type": "FLT_0D",
+  "documentation": "MHD stability metric, to be defined by user",
+  "type": "dynamic",
+  "units": "-"
+ }
+}

src/actors.jl

@@ -172,15 +172,15 @@ end
 #= ============= =#
 #  actor_logging  #
 #= ============= =#
-function actor_logging(dd::IMAS.dd)
+function actor_logging(dd::IMAS.DD)
     aux = getfield(dd, :_aux)
     if :fuse_actor_logging ∉ keys(aux)
         aux[:fuse_actor_logging] = true
     end
     return aux[:fuse_actor_logging]
 end
 
-function actor_logging(dd::IMAS.dd, value::Bool)
+function actor_logging(dd::IMAS.DD, value::Bool)
     aux = getfield(dd, :_aux)
     old_value = actor_logging(dd)
     aux[:fuse_actor_logging] = value
@@ -219,14 +219,14 @@ end
 
 function enter_workflow(actor::AbstractActor)
     aux = _aux_workflow(actor.dd)
-    h = goto_worflow_depth(aux[:fuse_workflow], aux[:fuse_workflow_depth])
-    aux[:fuse_workflow_count] += 1
-    aux[:fuse_workflow_depth] += 1
-    return h[(name(actor), aux[:fuse_workflow_count])] = Workflow(name(actor))
+    h = goto_worflow_depth(aux[:fuse_workflow], aux[:fuse_workflow_depth][1])
+    aux[:fuse_workflow_count][1] += 1
+    aux[:fuse_workflow_depth][1] += 1
+    return h[(name(actor), aux[:fuse_workflow_count][1])] = Workflow(name(actor))
 end
 
 function exit_workflow(actor::AbstractActor)
-    return _aux_workflow(actor.dd)[:fuse_workflow_depth] -= 1
+    return _aux_workflow(actor.dd)[:fuse_workflow_depth][1] -= 1
 end
 
 function goto_worflow_depth(workflow::Workflow, depth::Int)
@@ -237,20 +237,35 @@ function goto_worflow_depth(workflow::Workflow, depth::Int)
     return h
 end
 
-function workflow_depth(dd::IMAS.dd)
-    return _aux_workflow(dd)[:fuse_workflow_depth]
+function workflow_depth(dd::IMAS.DD)
+    return _aux_workflow(dd)[:fuse_workflow_depth][1]
 end
 
-function workflow(dd::IMAS.dd)
+function workflow(dd::IMAS.DD)
     return _aux_workflow(dd)[:fuse_workflow]
 end
 
-function _aux_workflow(dd::IMAS.dd)
+function _aux_workflow(dd::IMAS.DD)
     aux = getfield(dd, :_aux)
     if :fuse_workflow ∉ keys(aux)
         aux[:fuse_workflow] = Workflow("Main")
-        aux[:fuse_workflow_depth] = 0
-        aux[:fuse_workflow_count] = 0
+        aux[:fuse_workflow_depth] = [0]
+        aux[:fuse_workflow_count] = [0]
     end
     return aux
 end
+
+"""
+    copy_workflow!(dd_out::IMAS.DD, dd_in::IMAS.DD)
+
+Copy (:fuse_workflow, :fuse_workflow_depth, :fuse_workflow_count, :fuse_actor_logging) from `dd_in` to `dd_out`
+
+This is useful when continuing the execution of a FUSE workflow on different dd's
+"""
+function copy_workflow!(dd_out::IMAS.DD, dd_in::IMAS.DD)
+    for item in (:fuse_workflow, :fuse_workflow_depth, :fuse_workflow_count, :fuse_actor_logging)
+        if item in keys(getfield(dd_in, :_aux))
+            getfield(dd_out, :_aux)[item] = getfield(dd_in, :_aux)[item]
+        end
+    end
+end

src/actors/costing/costing_actor.jl

@@ -46,6 +46,7 @@ function ActorCosting(dd::IMAS.dd, par::FUSEparameters__ActorCosting, act::Param
     empty!(dd.costing)
 
     ddR = IMAS.get_timeslice(Measurement{Float64}, dd)
+    copy_workflow!(ddR, dd) # to let FUSE continue tracking the execution workflow on ddR
 
     ddR.costing.construction_start_year = act.ActorCosting.construction_start_year
     ddR.costing.future.inflation_rate = act.ActorCosting.future_inflation_rate

src/actors/stability/vertical_actor.jl

@@ -105,17 +105,17 @@ function _finalize(actor::ActorVerticalStability)
 
     # Stability margin
     mode = mhd.toroidal_mode[1]
-    mode.perturbation_type.description = "Vertical stability margin, > 0.15 for stability (N.B., not in Hz)"
+    mode.perturbation_type.description = "Vertical stability margin, > 0.15 for stability"
     mode.perturbation_type.name = "m_s"
     mode.n_tor = 0
-    mode.growthrate = actor.stability_margin # not in Hz
+    mode.stability_metric = actor.stability_margin
 
     # Normalized growth rate
     mode = mhd.toroidal_mode[2]
-    mode.perturbation_type.description = "Normalized vertical growth rate, < 10 for stability (N.B., not in Hz)"
+    mode.perturbation_type.description = "Normalized vertical growth rate, < 10 for stability"
     mode.perturbation_type.name = "γτ"
     mode.n_tor = 0
-    mode.growthrate = actor.normalized_growth_rate # not in Hz
+    mode.stability_metric = actor.normalized_growth_rate
 
     # plot
     if par.do_plot

src/optimization.jl

@@ -150,12 +150,13 @@ function optimization_engine(
     constraint_functions::AbstractVector{<:IMAS.ConstraintFunction},
     save_folder::AbstractString,
     save_dd::Bool,
-    p::ProgressMeter.Progress)
+    p::ProgressMeter.Progress,
+    generation_offset::Int)
 
     # parallel evaluation of a generation
     ProgressMeter.next!(p)
     tmp = Distributed.pmap(
-        x -> _optimization_engine(ini, act, actor_or_workflow, x, objective_functions, constraint_functions, save_folder, p.counter, save_dd),
+        x -> _optimization_engine(ini, act, actor_or_workflow, x, objective_functions, constraint_functions, save_folder, p.counter + generation_offset, save_dd),
         [X[k, :] for k in 1:size(X)[1]]
     )
     F = zeros(size(X)[1], length(tmp[1][1]))

src/parameters/parameters_studies.jl

@@ -12,11 +12,11 @@ function study_common_parameters(; kw...)
     name = first(keys(kw))
     default = first(values(kw))
     if name == :server
-        return Switch{String}(["localhost", "omega", "saga"], "-", "Where to run"; default)
+        return Switch{String}(["localhost", "omega", "saga", "feynman"], "-", "Where to run"; default)
     elseif name == :n_workers
         return Entry{Int}("-", "Number of workers to run with"; default)
     elseif name == :file_save_mode
-        return Switch{Symbol}([:safe_write, :overwrite], "-", "Saving file policy, `safe_write` only writes when the folder is empty"; default)
+        return Switch{Symbol}([:safe_write, :overwrite, :append], "-", "Saving file policy, `safe_write` only writes when the folder is empty"; default)
     elseif name == :release_workers_after_run
         return Entry{Bool}("-", "Releases the workers after running the study"; default)
     elseif name == :save_dd
@@ -57,9 +57,9 @@ function setup(study::AbstractStudy)
     return _setup(study)
 end
 
-function analyze(study::AbstractStudy)
+function analyze(study::AbstractStudy; kw...)
     # here you can add timing info and more
-    return _analyze(study)
+    return _analyze(study; kw...)
 end
 
 function run(study::T, args...; kw...) where {T<:AbstractStudy}
@@ -89,7 +89,10 @@ function check_and_create_file_save_mode(sty)
             @assert !isfile(sty.save_folder) "$(sty.save_folder) can't be a file"
             mkdir(sty.save_folder)
         end
-    elseif sty.file_save_mode == :overwrite && !isdir(sty.save_folder)
+    elseif sty.file_save_mode == :overwrite
+        rm(sty.save_folder; force=true, recursive=true)
         mkdir(sty.save_folder)
+    elseif sty.file_save_mode == :append
+        # this is fine
     end
 end

src/utils_begin.jl

@@ -244,6 +244,33 @@ function parallel_environment(cluster::String="localhost", nworkers::Integer=0,
             error("Not running on saga cluster")
         end
 
+    elseif cluster == "feynman"
+        if occursin("feynman", gethostname())
+            gigamem_per_node = 800
+            cpus_per_node = 30
+            if nworkers > 0
+                nodes = 1
+                nprocs_max = cpus_per_node * nodes
+                nworkers = min(nworkers, nprocs_max)
+            end
+            np = nworkers + 1
+            gigamem_per_cpu = Int(ceil(memory_usage_fraction * gigamem_per_node / cpus_per_node * cpus_per_task))
+            ENV["JULIA_WORKER_TIMEOUT"] = "360"
+            if Distributed.nprocs() < np
+                Distributed.addprocs(
+                    ClusterManagers.SlurmManager(np - Distributed.nprocs());
+                    partition="LocalQ",
+                    topology=:master_worker,
+                    time="99:99:99",
+                    cpus_per_task,
+                    exeflags=["--threads=$(cpus_per_task)", "--heap-size-hint=$(gigamem_per_cpu)G"],
+                    kw...
+                )
+            end
+        else
+            error("Not running on feynman cluster")
+        end
+
     elseif cluster == "localhost"
         mem_size = Int(ceil(localhost_memory() * memory_usage_fraction))
 
@@ -298,4 +325,5 @@ struct MissingExtensionError <: Exception
     package_name::String
 end
 
-Base.showerror(io::IO, e::MissingExtensionError) = print(io, "The FUSE actor $(e.actor_name) cannot be run because the Julia package $(e.package_name).jl is not loaded. Please load it to enable this feature.")
+Base.showerror(io::IO, e::MissingExtensionError) =
+    print(io, "The FUSE actor $(e.actor_name) cannot be run because the Julia package $(e.package_name).jl is not loaded. Please load it to enable this feature.")