New benchmark for cluster

foam/cavityParallel/0/U

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+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  plus                                  |
+|   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       volVectorField;
+    object      U;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions      [0 1 -1 0 0 0 0];
+
+internalField   uniform (0 0 0);
+
+boundaryField
+{
+    movingWall
+    {
+        type            fixedValue;
+        value           uniform (1 0 0);
+    }
+
+    fixedWalls
+    {
+        type            noSlip;
+    }
+
+    frontAndBack
+    {
+        type            empty;
+    }
+}
+
+// ************************************************************************* //

foam/cavityParallel/0/p

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+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  plus                                  |
+|   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       volScalarField;
+    object      p;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions      [0 2 -2 0 0 0 0];
+
+internalField   uniform 0;
+
+boundaryField
+{
+    movingWall
+    {
+        type            zeroGradient;
+    }
+
+    fixedWalls
+    {
+        type            zeroGradient;
+    }
+
+    frontAndBack
+    {
+        type            empty;
+    }
+}
+
+// ************************************************************************* //

foam/cavityParallel/Allclean

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+rm -rf processor*

foam/cavityParallel/ExecutionTime-512.csv

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+,amount_processor,time_max,speedup,efficiency
+0,1,880.53,0.0,0.0
+1,2,507.05,1.7365743023370475,0.8682871511685237
+2,4,414.59,2.1238573048071587,0.5309643262017897
+3,8,215.96,4.077282830153732,0.5096603537692165
+4,12,162.28,5.4259921123983235,0.45216600936652696
+5,16,153.04,5.753593831677993,0.35959961447987454

foam/cavityParallel/README.md

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+Benchmarking for cluster environment with openFOAM and SLURM as job Scheduler
+
+The environment should be run as follows:
+
+1 - OpenMPI/3.0.0 or another MPI compiler (such as MPICH and Intel) configured;
+
+2 - OpenFOAM tool;
+
+3 - Cluster environment configured;
+
+4 - scipy or matplotlib, numpy and pandas dependencies (python >= 2.7);
+
+steps to test:
+```
+$ source /foam-directory/etc/bashrc 
+
+$ ./Allclean
+```
+
+Edit system/decomposeParDict where numberOfSubdomains = $number_of_processors_available
+
+and
+
+```
+simpleCoeffs
+{
+        n               ( 4 4 1 );
+            delta           0.0001;
+}
+```
+for this example has been used n ( 4 4 ...) this parameters should be change as of total of your processors. In this case, the total is 4 x 4 = 16
+
+```
+$ blockMesh (to create mesh for processing)
+
+$ decomposePar -force (to split the mesh as of total processors able)
+```
+
+Configure "jobslurm.sh" according to what your hardware and resources.
+
+```
+$ sbatch jobslurm.sh (to running simulation)
+```
+

foam/cavityParallel/constant/polyMesh/blockMeshDict

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+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  plus                                  |
+|   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    object      blockMeshDict;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+scale   0.1;
+
+vertices
+(
+    (0 0 0)
+    (1 0 0)
+    (1 1 0)
+    (0 1 0)
+    (0 0 0.1)
+    (1 0 0.1)
+    (1 1 0.1)
+    (0 1 0.1)
+);
+
+blocks
+(
+    hex (0 1 2 3 4 5 6 7) (1024 1024 1) simpleGrading (1 1 1)
+);
+
+edges
+(
+);
+
+boundary
+(
+    movingWall
+    {
+        type wall;
+        faces
+        (
+            (3 7 6 2)
+        );
+    }
+    fixedWalls
+    {
+        type wall;
+        faces
+        (
+            (0 4 7 3)
+            (2 6 5 1)
+            (1 5 4 0)
+        );
+    }
+    frontAndBack
+    {
+        type empty;
+        faces
+        (
+            (0 3 2 1)
+            (4 5 6 7)
+        );
+    }
+);
+
+mergePatchPairs
+(
+);
+
+// ************************************************************************* //

foam/cavityParallel/constant/transportProperties

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+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  2.3.0                                 |
+|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    location    "constant";
+    object      transportProperties;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+nu              nu [ 0 2 -1 0 0 0 0 ] 0.001;
+
+
+// ************************************************************************* //

foam/cavityParallel/jobslurm.sh

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+#!/bin/bash
+
+# Copy/paste this job script into a text file and submit with the command:
+#    sbatch thefilename
+
+#SBATCH --time=20:00:00   # walltime limit (HH:MM:SS)
+#SBATCH --nodes=4   # number of nodes
+#SBATCH --ntasks-per-node=4   # 4 processor core(s) per node
+#SBATCH --job-name="nativa-jobs"
+#SBATCH --output="slurm-%j.out.log" # job standard output file (%j replaced by job id)
+#SBATCH --error="slurm-%j.err.out.log" # job standard error file (%j replaced by job id)
+
+# LOAD MODULES, INSERT CODE, AND RUN YOUR PROGRAMS HERE
+module load gnu7
+
+mpiexec --hostfile machines -np 16 --allow-run-as-root /home/admceltab/OpenFOAM-v1712/bin/foamExec icoFoam -parallel

foam/cavityParallel/machines

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+n1
+n2
+n3
+n4

foam/cavityParallel/metrics.sh

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+#!/bin/bash
+echo "Filtering log files of openFOAM simulation..."
+
+if [ $# -lt 1 ]; then
+   echo "Faltou utilizar pelo menos um argumento!"
+   exit 1
+fi
+
+ls $1 | grep out > /tmp/files
+cd $1
+while read line; do
+    progs=($line)
+    cut -d: -f 10,10 ${progs[0]} | grep ExecutionTime | sed 's/[a-z A-Z]\+//g' | cut -d= -f 1,2 | sed 's/[a-z A-Z =,]\+//g' > log-${progs[0]}
+    sed -i '1 i\time' log-${progs[0]}
+done < /tmp/files
+rm /tmp/files
+
+echo "Finishing filter"

foam/cavityParallel/plot.py

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+'''
+This file is a test for shared mpi4py libraries in a cluster environment.
+The application can be run...
+'''
+__author__ = 'Fernando Demarchi Natividade Luiz'
+__email__ = '[email protected]'
+
+import matplotlib.pyplot as plt
+import csv
+import pandas as pd
+import numpy as np
+
+class BenchMarkMetrics:
+	def __init__(self):
+		self.df1 = pd.read_csv('results-512/log-out-1x1.txt')
+		self.df2 = pd.read_csv('results-512/log-out-2x1.txt')
+		self.df3 = pd.read_csv('results-512/log-out-2x2.txt')
+		self.df4 = pd.read_csv('results-512/log-out-4x2.txt')
+		self.df5 = pd.read_csv('results-512/log-out-6x2.txt')
+		self.df6 = pd.read_csv('results-512/log-out-4x4.txt')
+
+	def plot_graph_execution_time(self):
+		# plt.plot(self.df1['time'])
+		plt.plot(self.df1['time'], label='1 processor')
+		plt.plot(self.df2['time'], label='2 processors')
+		plt.plot(self.df3['time'], label='4 processors')
+		plt.plot(self.df4['time'], label='8 processors')
+		plt.plot(self.df5['time'], label='12 processors')
+		plt.plot(self.df6['time'], label='16 processors')
+		plt.title('CELTAB Cluster Metrics')
+		plt.legend(loc='upper left')
+		plt.xlabel('epochs')
+		plt.ylabel('execution time (sec)')
+   		plt.grid(True)
+        	plt.savefig('assets/benchmark-512.png')
+
+	def print_execution_time(self):
+		with open('ExecutionTime-512.csv', 'w') as csvfile:
+    			writer = csv.DictWriter(csvfile, fieldnames= ['amount_processor', 'time_max', 'speedup', 'efficiency'])
+    			writer.writeheader()
+    			writer.writerow({'amount_processor': 1, 'time_max': self.df1['time'].max()})
+    			writer.writerow({'amount_processor': 2, 'time_max': self.df2['time'].max()})
+    			writer.writerow({'amount_processor': 4, 'time_max': self.df3['time'].max()})
+    			writer.writerow({'amount_processor': 8, 'time_max': self.df4['time'].max()})
+    			writer.writerow({'amount_processor': 12, 'time_max': self.df5['time'].max()})
+    			writer.writerow({'amount_processor': 16, 'time_max': self.df6['time'].max()})
+			self.clear_buffer_plt()
+			print(self.df1.describe())
+
+	def speedup_calculation(self):
+		# s(p) = t(1) / t(p)
+		data = pd.read_csv('ExecutionTime-512.csv')
+		for i in range(1, data['amount_processor'].count()):
+			data['speedup'][i] = (data['time_max'][0] / data['time_max'][i])
+			data['efficiency'][i] = (data['speedup'][i] / data['amount_processor'][i])
+		data = self.clean_nan_values(data)
+		data.to_csv('ExecutionTime-512.csv')
+
+	def plot_graph_speedup(self):
+		data = pd.read_csv('ExecutionTime-512.csv')
+		plt.plot(data['amount_processor'], data['speedup'], label="IcoFoam Cavity Simulation", marker='o', linestyle='--', color='g')
+		plt.title('CELTAB Cluster Metrics')
+		plt.legend(loc='upper left')
+		plt.xlabel('cores')
+		plt.ylabel('speedup')
+		plt.grid(True)
+		plt.savefig('assets/speedup-512.png')
+		self.clear_buffer_plt()
+
+	def plot_graph_efficiency(self):
+		data = pd.read_csv('ExecutionTime-512.csv')
+		plt.plot(data['amount_processor'], data['efficiency'], label="IcoFoam Cavity Simulation", marker='o', linestyle='--', color='r')
+		plt.title('CELTAB Cluster Metrics')
+		plt.legend(loc='upper right')
+		plt.xlabel('cores')
+		plt.ylabel('efficiency')
+		plt.grid(True)
+		plt.savefig('assets/efficiency-512.png')
+		self.clear_buffer_plt()
+
+	def clean_nan_values(self, dataset):
+		dataset = dataset.fillna(0)
+		return dataset
+
+	def clear_buffer_plt(self):
+		plt.cla()
+		plt.clf()
+
+
+if __name__ == '__main__':
+	plot = BenchMarkMetrics()
+	plot.plot_graph_execution_time()
+	plot.print_execution_time()
+	plot.speedup_calculation()
+	plot.plot_graph_speedup()
+	plot.plot_graph_efficiency()

foam/cavityParallel/system/.#decomposeParDict

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+[email protected]:1526471467