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‎LICENSE

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BSD 2-Clause License
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Copyright (c) 2021, PIK - Infrastructure and Complex Networks
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All rights reserved.
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Redistribution and use in source and binary forms, with or without
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modification, are permitted provided that the following conditions are met:
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1. Redistributions of source code must retain the above copyright notice, this
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list of conditions and the following disclaimer.
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2. Redistributions in binary form must reproduce the above copyright notice,
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this list of conditions and the following disclaimer in the documentation
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and/or other materials provided with the distribution.
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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
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FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
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DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
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CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
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OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

‎README.md

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This repository contains scripts for benchmarking dynamical systems on networks. Usage Instructions are found below. Details on our methodology are reported in our paper on [NetworkDynamics.jl -- Composing and simulating complex networks in Julia](https://arxiv.org/abs/2012.12696). Below you see a plot of competing runtimes simulating a Kuramoto network of 1000 oscillators with Dormand-Prince's 5th order method.
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![](utils/plotting/WPD1000.pdf)
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# Instructions
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## High level Requirements
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- sqlite
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- make
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- python3
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- Julia 1.5
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## Setup python environment
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We suggest a virtual env for python
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```
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python3 -m venv .env
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```
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activate and install the requirements
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```
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source .env/bin/activate
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pip install -r src/python/requirements.pip
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```
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## Setup Julia enviroment
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The julia env should be activated automatically by the scripts.
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## Compile fortran program
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If you would like to run the fortran benchmarks, you must have a Fortran
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2003 compiler. In the example we use GFortran. If you do not wish to run
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the fortran benchmark, bypass this section.
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The fortran program uses FPM, the fortran package manager. Install from
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https://github.com/fortran-lang/fpm
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Using this tool, you can build the fortran program with fpm
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```
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cd src/fortran
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fpm build --flag -ldl --flag -lpthread
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```
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now, set KURABENCH_FEXE to the newly built binary
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```
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cd ../../
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export
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KURABENCH_FEXE=`pwd`/src/fortran/build/<compiler>_<uuid>/app/FKuraBenchmark
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```
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where compiler and uuid are the details of your compilation process
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resulting from the fpm build command.
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## Prepare Database
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In these benchmarks, we use an SQLite database to store the setup of
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each system (node parameters, edge parameters, system parameters,
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connectivity) and also the experiment log and trajectory outputs.
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You may place your database at a location of your choosing. Each program
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uses the environmental variable KURABENCH_DB to identify the location of
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the database. In this case, we will place the database in the `data`
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directory.
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```
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export KURABENCH_DB=`pwd`/data/kurabench.db
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make database
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```
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## Generate systems
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Be sure that your python virtual env is activated
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```
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make systems
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```
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## Generate reference trajectories
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The "ground-truth" trajectories are generated using the (implicit) radau
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solver at low tolerance settings. Julia is used to run this generation
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step. Some timing information will be printed to stdout during the
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program execution. Compute the trajectories with:
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```
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make reference
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```
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## Generate benchmarks
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Now, generate any benchmarks of interest by running
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```
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make <X>
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```
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where `<X>` is one of
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networkdynamics
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diffeq
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jitcode
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scipy
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fortran
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The resulting experiment summary is stored in the database in the
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experiments table. The trajectory of each state is stored in the
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`states` table, indexed by the experiment id found in the `experiments`
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table.
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The `experiments` table includes the timing and `err_v_ref`, the average
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deviation (across all states) of the experiment trajectory and the
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reference (radau-computed) trajectory for that system and initial
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condition.

‎data/KuraBench.sql

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CREATE TABLE edges (system integer NOT NULL, id integer NOT NULL, source integer, dest integer, PRIMARY KEY (system, id));
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CREATE TABLE IF NOT EXISTS "systems" (
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"id" INTEGER,
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"name" TEXT,
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"nodes" INTEGER,
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"edges" INTEGER,
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"q" NUMERIC,
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"c" NUMERIC,
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"coupling_constant" NUMERIC,
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PRIMARY KEY("id")
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);
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CREATE TABLE IF NOT EXISTS "nodes" (
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"system" integer NOT NULL,
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"id" integer NOT NULL,
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"omega" DOUBLE,
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"initialCondition" DOUBLE,
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FOREIGN KEY("system") REFERENCES "systems"("id"),
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PRIMARY KEY("system","id")
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);
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CREATE TABLE IF NOT EXISTS "states" (
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"experimentid" INTEGER NOT NULL,
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"time" NUMERIC,
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"idx" INTEGER,
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"node" INTEGER,
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"state" DOUBLE,
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PRIMARY KEY("experimentid","idx","time"),
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FOREIGN KEY("experimentid") REFERENCES "experiments"("experimentid")
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);
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CREATE TABLE IF NOT EXISTS "experiments" (
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"experimentid" INTEGER NOT NULL PRIMARY KEY AUTOINCREMENT,
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"runtime" TEXT,
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"datetime" TEXT,
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"githash" TEXT,
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"gitchanges" TEXT,
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"commandline" TEXT,
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"host" TEXT,
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"system" INTEGER,
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"solver" TEXT,
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"atol" NUMERIC,
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"rtol" NUMERIC,
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"tstart" INTEGER,
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"tend" INTEGER,
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"nfcn" INTEGER,
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"njac" INTEGER,
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"nstep" INTEGER,
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"naccept" INTEGER,
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"nreject" INTEGER,
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"ndec" INTEGER,
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"nsol" INTEGER,
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"tstartup" NUMERIC,
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"tload" NUMERIC,
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"tjit" NUMERIC,
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"tintegration" NUMERIC,
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"ttotal" NUMERIC,
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"peak_mem" NUMERIC,
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"err_v_ref" NUMERIC,
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"refeid" INTEGER,
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"notes" TEXT,
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FOREIGN KEY("system") REFERENCES "systems"("id")
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);

‎data/KuraBenchXeon.db

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‎makefile

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database:
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@echo "Building database.."
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@sqlite3 ${KURABENCH_DB} < ./data/KuraBench.sql
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systems:
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@echo "Generating systems.."
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@KURABENCH_DB=${KURABENCH_DB} python3 ./utils/generate_systems.py
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reference:
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@echo "Computing reference trajectories"
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@KURABENCH_DB=${KURABENCH_DB} ./utils/gen_ref.sh
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jitcode:
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@echo "Computing jitcode trajectories"
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@KURABENCH_DB=${KURABENCH_DB} ./utils/run_jitcode.sh
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scipy:
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@echo "Computing scipy trajectories"
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@KURABENCH_DB=${KURABENCH_DB} ./utils/run_scipy.sh
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networkdynamics:
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@echo "Computing networkdynamics trajectories"
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@KURABENCH_DB=${KURABENCH_DB} ./utils/run_nd.sh
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diffeq:
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@echo "Computing pure diffeq.jl trajectories"
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@KURABENCH_DB=${KURABENCH_DB} ./utils/run_diffeq.sh
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fortran:
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@echo "Computing fortran trajectories"
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@KURABENCH_DB=${KURABENCH_DB} ./utils/run_f.sh
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clean:
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@rm ${KURABENCH_DB} || echo "Nothing to cleanup.."

‎src/fortran/LICENSE.txt

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Fortran Kuramoto System Benchmark (c) 2021, Lucas Lincoln
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"BSD 3-Clause"
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Redistribution and use in source and binary forms, with or without
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modification, are permitted provided that the following conditions are met:
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1. Redistributions of source code must retain the above copyright notice, this
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list of conditions and the following disclaimer.
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2. Redistributions in binary form must reproduce the above copyright notice,
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this list of conditions and the following disclaimer in the documentation
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and/or other materials provided with the distribution.
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3. Neither the name of the copyright holder nor the names of its contributors
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may be used to endorse or promote products derived from this software without
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specific prior written permission.
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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
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ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
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WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
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FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
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DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
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CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
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OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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Original dopri5.f by Ernst Hairer (now embedded in dopri5.f90) is included
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under the following license:
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Copyright (c) 2004, UNIGE
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Redistribution and use in source and binary forms, with or without
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modification, are permitted provided that the following conditions are
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met:
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- Redistributions of source code must retain the above copyright
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notice, this list of conditions and the following disclaimer.
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- Redistributions in binary form must reproduce the above copyright
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notice, this list of conditions and the following disclaimer in the
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documentation and/or other materials provided with the distribution.
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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS “AS
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IS” AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
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TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
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PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR
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CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
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EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
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PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
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LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
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NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
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SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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‎src/fortran/README.md

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# kurabenchmark
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Benchmark for the kuramoto system, in pure fortran 2003
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Compile using FPM (https://github.com/fortran-lang/fpm)

‎src/fortran/app/DopriWrap.f90

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module dopriWrap
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!======= Inclusions ===========
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use KuraNetwork
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use LoadNetwork
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use iso_fortran_env, only: real64
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!======= Declarations =========
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implicit none
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!type(KuramotoNetwork(:,:)),allocatable :: net
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type(KuramotoNetwork) :: net
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real(real64),parameter :: dt = 2.0_real64
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contains
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subroutine dopri_loadNet(database, systemid)
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implicit none
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character(len=*), intent(in) :: database
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integer, intent(in) :: systemid
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integer :: state_length
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!real(kind=real64),dimension(:), allocatable :: y,dy
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call get_system_info(database,systemid)
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!call load_network(net)
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net = load_network()
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return
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end subroutine dopri_loadNet
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! ----------------------------------------------------------------
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! RhsFn provides the right hand side function for the
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! ODE: dy/dt = f(t,y)
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! Here wrapped for use with the dopri5 solver
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! ----------------------------------------------------------------
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subroutine dopri_RhsFn(N,t,y,dy,rpar,ipar)
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implicit none
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integer, intent(in) :: N
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real(real64) ,intent(in) :: t
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real(real64) ,dimension(N),intent(in) :: y
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real(real64) ,dimension(N),intent(out) :: dy
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real(real64), dimension(:), intent(in),optional :: rpar ! real params
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integer, dimension(:), intent(in),optional :: ipar ! integer params
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! fill RHS vector fvec
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call f(net,t,y,dy)
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! return success
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end subroutine dopri_RhsFn
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end module dopriWrap

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