Merge branch 'init' into 'master'

Initialize the Julia framework

See merge request !1

Project.toml

+
+name = "Exio"
+uuid = "0525473d-17b7-4fd3-beb1-bf17216ddbac"
+version = "0.0.1"
+
+[deps]
+Glob = "c27321d9-0574-5035-807b-f59d2c89b15c"
+
+[compat]
+julia = "1"
+JuliaFormatter = "0.6.2"
+
+[extras]
+Test = "eaa6fafa-8011-46e2-b288-c2f1e2a8ee56"
+JuliaFormatter = "98e50ef6-434e-11e9-1051-2b60c6c9e899"
+
+[targets]
+test = ["Test"]
+
+
+
+

README.md

 # jexio
 
+Julia Extractor for Input Output. 
+Set of scripts to generate I/O patterns understanding for particular applications. 
+Supported:
+
+- [AMReX-Astro Castro](https://amrex-astro.github.io/Castro/)
+
+
+For simple usage see tests:
+
+1. Install requirements (run once):
+	`$ julia scripts/requirements.jl`
+
+2. Run tests:
+	`$ julia --project=. test/runtests.jl`
+
+
+Formatting the code:
+
+	`$ julia scripts/formatter.jl`

scripts/formatter.jl

+
+# Usage run from root project 
+# julia ./scripts/formatter.jl
+# Requires the JuliaFormatter package see scripts/requirements.jl  
+
+using JuliaFormatter
+
+format(".")

scripts/requirements.jl

+
+# Use to install dependencies for this project
+# Run:
+# > julia scripts/requirements.jl
+
+using Pkg
+
+Pkg.add("JuliaFormatter")
+Pkg.add("Glob")
+
+exit()

src/Exio.jl

+module Exio
+
+export ExioH, exio_init, input_parser
+
+include("extractor/Extractor.jl")
+
+mutable struct ExioH
+    extractor::AbstractExtractor
+
+    ExioH() = new()
+end
+
+
+function exio_init(app::String, outputPrefix::String)::ExioH
+
+    exioH = ExioH()
+    if app == "AmrexCastro"
+        println("Hello AmrexCastro")
+        exioH.extractor = AmrexCastro()
+        init!(exioH.extractor, outputPrefix)
+    end
+
+    return exioH
+end
+
+
+end

src/extractor/Amrex.jl

+
+abstract type AbstractAmrex <: AbstractExtractor end
+
+mutable struct Amrex <: AbstractAmrex
+    app::String
+    outputPrefix::String
+    degreesOfFreedom::Any
+
+    Amrex() = new()
+end
+
+"""
+   
+   initialize members of the extractor::Amrex type
+   Using bang convention as init modifies the extractor::Amrex
+   https://docs.julialang.org/en/v1/manual/style-guide/index.html#bang-convention-1
+"""
+function init!(extractor::Amrex, outputPrefix::String)
+    extractor.app = "Amrex"
+    extractor.outputPrefix = outputPrefix
+    extractor.degreesOfFreedom =
+        ["max_step", "amr.check_int", "amr.plot_int", "amr.n_cell", "amr.max_level"]
+end
+
+"""
+    Parses an input file with entries key = value, returns all entries in a Dict
+    # Arguments
+    - `extractor::AbstractAmrex` : input type extending AbstractAmrex
+    - `inputFile::String` : input file to be parsed, absolute path is preferred
+"""
+function input_parser(extractor::AbstractAmrex, inputFile::String)::Dict{String,String}
+
+    parameters = Dict{String,String}()
+    # get file contents in a single iterable type, \n newline is removed 
+    fileContents = readlines(inputFile)
+
+    # go through each line
+    for line in fileContents
+        if isempty(line)
+            continue
+        end
+
+        # remove comments marked with #
+        result = findfirst("#", line)
+
+        if isnothing(result) == false
+            line = SubString(line, 1, result[1] - 1)
+            if isempty(line)
+                continue
+            end
+        end
+
+        parameter = split(line, "=")
+        parameters[strip(parameter[1])] = strip(parameter[2])
+
+    end
+
+    return parameters
+end
+
+"""
+    Get actual independent variables for I/O characterization: 
+    number of cells or ncells, output frequency or nplots, ncheckpoints, etc.    
+    from input parameters 
+    # Arguments
+    - `extractor::AbstractAmrex` : input type extending AbstractAmrex
+    - `parameters::Dict{String,String}` : input file to be parsed, absolute path is preferred
+"""
+function get_independent_variables(extractor::AbstractAmrex, parameters)::Dict
+
+    independentVariables = Dict()
+
+    # Number of output events, 
+    # get is the safe way. 3rd argument is a default fallback if key not found
+    maxStepStr = get(parameters, "max_step", "")
+
+    if maxStepStr != ""
+        
+      # safe string conversion to a type
+        maxStep = parse(Int64, maxStepStr)
+
+        plotIntStr = get(parameters, "amr.plot_int", "")
+        if plotIntStr != ""
+            plotFrequency = parse(Int64, plotIntStr)
+            independentVariables["amr.nplot_files"] = floor(Int32, maxStep / plotFrequency)
+        else
+            throw(NoSuchFieldException("jexio Amrex: Can't find amr.plot_int"))
+        end
+
+        checkIntStr = get(parameters, "amr.check_int", "")
+        if checkIntStr != ""
+            checkpointFrequency = parse(Int64, checkIntStr)
+            independentVariables["amr.ncheck_files"] = floor(Int32, maxStep / checkpointFrequency)
+        else
+            throw(NoSuchFieldException("jexio Amrex: Can't find amr.check_int"))
+        end
+
+    end
+
+    # Using the dot "." operator to apply it on an element-by-element basis (like a dot product)
+    # input is a dictionary with key="amr.ncell" and value = {"nx" "ny" "nz"},  
+    # output is nx*ny*nz
+    # Example:  
+    # input Dict[ "amr.n_cell" => ["16" "16"] ], if key not found return 0
+    # >ncells
+    #   256
+    ncells = prod(parse.(Int64, split(get(parameters, "amr.n_cell", ["0"]))))
+    independentVariables["amr.ncells"] = ncells
+
+    maxLevel = get(parameters, "amr.max_level", "")
+    independentVariables["amr.max_level"] = maxLevel == "" ? 1 : parse(Int32, maxLevel)
+      
+    regrid = get(parameters, "amr.regrid_int", "")
+    independentVariables["amr.regrid_int"] = regrid == "" ? 1 : parse(Int32, regrid)
+    
+    return independentVariables
+
+end

src/extractor/AmrexCastro.jl

+
+import Glob
+
+mutable struct AmrexCastro <: AbstractAmrex
+    app::String
+    degreesOfFreedom::Any
+    outputPrefix::String
+
+    AmrexCastro() = new()
+end
+
+"""
+   init!
+   initialize members of the extractor::AmrexCastro type
+   Using bang convention as init modifies the extractor::Amrex
+   https://docs.julialang.org/en/v1/manual/style-guide/index.html#bang-convention-1
+"""
+function init!(extractor::AmrexCastro, outputPrefix::String)
+    extractor.app = "AmrexCastro"
+    extractor.degreesOfFreedom = [
+        "max_step",
+        "amr.check_int",
+        "amr.plot_int",
+        "amr.n_cell",
+        "amr.max_level",
+        "castro.cfl",
+        "castro.max_grid_size",
+    ]
+    extractor.outputPrefix = outputPrefix
+end
+
+
+
+function get_dependent_variable_datasize(extractor::AmrexCastro)
+   
+   findDelimiter = findlast("/",extractor.outputPrefix)
+   println(extractor.outputPrefix)
+   println(findDelimiter)
+   
+   searchDirectory = extractor.outputPrefix[ 1: findDelimiter[1]-1 ]
+   prefix =  extractor.outputPrefix[ findDelimiter[1]+1:end]
+   println("Search directory: ", searchDirectory, " prefix: ", prefix)
+   outputDirs = Glob.glob( string(prefix,"*"), searchDirectory )
+   println(outputDirs)
+  
+end
+
+
+
+
+

src/extractor/Extractor.jl

+
+abstract type AbstractExtractor end
+
+include("Amrex.jl")
+include("AmrexCastro.jl")

test/data/amrexCastro/LICENSE

+Copyright (c) 2017, The Regents of the University of California,
+through Lawrence Berkeley National Laboratory and the Alliance for
+Sustainable Energy, LLC., through National Renewable Energy Laboratory
+(subject to receipt of any required approvals from the U.S. Dept. of
+Energy).  All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+(1) Redistributions of source code must retain the above copyright
+notice, this list of conditions and the following disclaimer.
+
+(2) Redistributions in binary form must reproduce the above copyright
+notice, this list of conditions and the following disclaimer in the
+documentation and/or other materials provided with the distribution.
+
+(3) Neither the name of the University of California, Lawrence
+Berkeley National Laboratory, Alliance for Sustainable Energy, LLC.,
+National Renewable Energy Laboratory, U.S. Dept. of Energy nor the
+names of its contributors may be used to endorse or promote products
+derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE 
+ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE 
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL 
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR 
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER 
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, 
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
\ No newline at end of file

test/data/amrexCastro/test_data_AmrexCastro_inputs.2d.cyl_in_cartcoords

+# ------------------  INPUTS TO MAIN PROGRAM  -------------------
+max_step = 20
+stop_time = 0.1
+
+# PROBLEM SIZE & GEOMETRY
+geometry.is_periodic =  0 0
+geometry.coord_sys   =  0       # 0 => cart
+geometry.prob_lo     =  0    0
+geometry.prob_hi     =  1    1
+amr.n_cell           = 16   16
+
+# >>>>>>>>>>>>>  BC FLAGS <<<<<<<<<<<<<<<<
+# 0 = Interior           3 = Symmetry
+# 1 = Inflow             4 = SlipWall
+# 2 = Outflow            5 = NoSlipWall
+# >>>>>>>>>>>>>  BC FLAGS <<<<<<<<<<<<<<<<
+castro.lo_bc       =  2   2
+castro.hi_bc       =  2   2
+
+# WHICH PHYSICS
+castro.do_hydro = 1
+castro.do_react = 0
+
+# TIME STEP CONTROL
+castro.cfl            = 0.5     # cfl number for hyperbolic system Courant-Friedrichs-Lewy condition
+castro.init_shrink    = 0.01    # scale back initial timestep
+castro.change_max     = 1.1     # maximum increase in dt over successive steps
+
+# DIAGNOSTICS & VERBOSITY
+castro.sum_interval   = 1       # timesteps between computing mass
+castro.v              = 1       # verbosity in Castro.cpp
+amr.v                 = 1       # verbosity in Amr.cpp 
+#amr.grid_log         = grdlog  # name of grid logging file
+
+# REFINEMENT / REGRIDDING
+amr.max_level       = 2       # maximum level number allowed
+amr.ref_ratio       = 2 2 2 2 # refinement ratio
+amr.regrid_int      = 2       # how often to regrid
+amr.blocking_factor = 8       # block factor in grid generation
+amr.max_grid_size   = 128
+
+# CHECKPOINT FILES
+amr.check_file      = sedov_2d_cyl_in_cart_chk   # root name of checkpoint file
+amr.check_int       = 20       # number of timesteps between checkpoints
+
+# PLOTFILES
+amr.plot_file       = sedov_2d_cyl_in_cart_plt
+amr.plot_int        = 20
+amr.derive_plot_vars=ALL
+
+# PROBIN FILENAME
+amr.probin_file = probin.2d.cyl_in_cartcoords

test/runtests.jl

+
+using Test, Base.Filesystem
+
+import Exio
+
+@testset "test_amrexCastro" begin
+    include("test_AmrexCastro.jl")
+end;
+
+@testset "test_Exio.input_parser_docstring" begin
+    @test println(@doc Exio.input_parser) === nothing
+end;

test/test_AmrexCastro.jl

+
+"""
+workaround function to update counter if scalar
+Julia doesn't pass values by reference "address"
+"""
+function test_value(
+    counter,
+    parameters::Dict{String,String},
+    key::String,
+    test_value::String,
+)
+    value = parameters[key]
+    @test value == test_value
+    counter += 1
+    return counter
+end
+
+function test_AmrexCastro()
+    exio = Exio.exio_init("AmrexCastro", "/home/wgodoy/workspace/Castro/Exec/hydro_tests/Sedov/case")
+
+    @test typeof(exio) == Exio.ExioH
+
+    println("Current directory: ", Filesystem.pwd())
+    inputFile = string(
+        Filesystem.pwd(),
+        "/test/data/amrexCastro/test_data_AmrexCastro_inputs.2d.cyl_in_cartcoords",
+    )
+    println("Input file: ", inputFile)
+
+    parameters = Exio.input_parser(exio.extractor, inputFile)
+
+    # keys counter
+    counter = 0
+    counter = test_value(counter, parameters, "max_step", "20")
+    counter = test_value(counter, parameters, "stop_time", "0.1")
+    counter = test_value(counter, parameters, "geometry.is_periodic", "0 0")
+    counter = test_value(counter, parameters, "geometry.coord_sys", "0")
+    counter = test_value(counter, parameters, "geometry.prob_lo", "0    0")
+    counter = test_value(counter, parameters, "geometry.prob_hi", "1    1")
+    counter = test_value(counter, parameters, "amr.n_cell", "16   16")
+    counter = test_value(counter, parameters, "castro.lo_bc", "2   2")
+    counter = test_value(counter, parameters, "castro.hi_bc", "2   2")
+    counter = test_value(counter, parameters, "castro.do_hydro", "1")
+    counter = test_value(counter, parameters, "castro.do_react", "0")
+    counter = test_value(counter, parameters, "castro.cfl", "0.5")
+    counter = test_value(counter, parameters, "castro.init_shrink", "0.01")
+    counter = test_value(counter, parameters, "castro.change_max", "1.1")
+    counter = test_value(counter, parameters, "castro.sum_interval", "1")
+    counter = test_value(counter, parameters, "castro.v", "1")
+    counter = test_value(counter, parameters, "amr.v", "1")
+    counter = test_value(counter, parameters, "amr.max_level", "2")
+    counter = test_value(counter, parameters, "amr.ref_ratio", "2 2 2 2")
+    counter = test_value(counter, parameters, "amr.regrid_int", "2")
+    counter = test_value(counter, parameters, "amr.blocking_factor", "8")
+    counter = test_value(counter, parameters, "amr.max_grid_size", "128")
+    counter = test_value(counter, parameters, "amr.check_file", "sedov_2d_cyl_in_cart_chk")
+    counter = test_value(counter, parameters, "amr.check_int", "20")
+    counter = test_value(counter, parameters, "amr.plot_file", "sedov_2d_cyl_in_cart_plt")
+    counter = test_value(counter, parameters, "amr.derive_plot_vars", "ALL")
+    counter =
+        test_value(counter, parameters, "amr.probin_file", "probin.2d.cyl_in_cartcoords")
+
+    @test counter == 27
+
+    independent_variables = Exio.get_independent_variables(exio.extractor, parameters)
+    println(independent_variables)
+    
+    Exio.get_dependent_variable_datasize(exio.extractor)
+
+end
+
+
+test_AmrexCastro()