Proceedings of the IASTED International Conference
Advances in Computer Science and Engineering (ACSE 2009)
March 16 - 18, 2009 Phuket, Thailand
A DYNAMIC PDE SOLVER FOR BREASTS’ CANCEROUS CELL
VISUALIZATION ON DISTRIBUTED PARALLEL COMPUTING SYSTEMS
Norma Alias1, Md. Rajibul Islam1, Nur Syazana Rosly2
1
Institute of Ibnu Sina, Faculty of Science, Universiti Teknologi Malaysia, Johor
2
Department of Mathematics, Faculty of Science, University Technology Malaysia, Johor
E-mail: norma@ibnusina.utm.my, md.rajibul.islam05@mmu.edu.my, sya_zana953@yahoo.com
ABSTRACT
Since distributed parallel computing system offers users
with more spread computing and storage resources, it
provides us a prospect to propose new efficient and
dynamic solvers for the numerical solutions of partial
differential equations (PDEs) in order to visualize breasts’
cancerous cell. Partial differential equations (PDEs) can
be classified as parabolic equation, elliptic equation and
hyperbolic equation. Partial differential equations are used
commonly as mathematical models for solving all of the
science and engineering fields. This research will focus on
the study of elliptic equations, particularly Helmholtz’s
wave equation and hyperbolic equations. The numerical
finite-difference method is chosen as a platform for
discretizating the elliptic equations and to solve the
hyperbolic equations. The elliptic equation can be used as
mathematical models for biological aspects of
electromagnetic wave. Breast cancer is the commonest
female malignancy in Malaysia as well as all over the
world. The incidence of breast cancer in Malaysia is
estimated to be around 27 per 100,000 populations, with
close to 3,000 new cases annually. Parallel Virtual
Machine (PVM) is emphasized as communication open
source software on distributed parallel computing system,
which results in a performance gain. The parallel
performance measurements of the parallel computing is
analysed in this study.
KEY WORDS
2D Helmholtz’s Wave Equation, Distributed Parallel
Computing, Numerical Finite-Difference Method,
Hyperbolic PDE, and Breast Cancer.
1. Introduction
Breast cancer is the most general disease among women,
except for non-melanoma skin cancers. Due to early
detection and increased awareness, resulting deaths have
been decreasing recently. The second leading reason of
cancer death in women is breast cancer. The possibility
that breast cancer will be responsible for a woman’s death
is about 1 in 33. Early detection is the key to successful
treatment. Alternative methods for tumor recognition have
been researched to couple with Thermal Simulation (F.J.
Gonźalez, 2007), Microwave Imaging system through
646-073
Space Time beamformer (Essex J. Bond et al., 2003) and
2D Finite-Difference Time Domain (FDTD) (Xu Li and
Susan C. Hagness, 2001). Panagiotis Kosmas et al. (2004)
have developed a novel implementation of the uniaxial
perfectly matched layer (UPML) absorbing boundary
condition (ABC). The interpretation of mammography is
difficult in that it involves the identification of tissue
abnormalities such as microcalcifications, architectural
distortions, asymmetrical densities, masses and densities
that have developed since the previous mammogram (M.
Patlak et. al., 2000).
This paper is organised as follows. First, the mathematical
models for breast tumor and implement the model with
the real-life problems is reviewed. This study is to
construct a mathematical model in order to detect and
predict breast tumor position and growth. This means that,
to relate the Helmholtz’s wave equation and hyperbolic
equations with the early detection of breasts’ cancerous
cell under electromagnetic field. The computational part
of the wave equations and hyperbolic equations is solved
by finite-difference technique. Then some numerical
methods called Red Black Gauss-Seidel method are
developed in the direction of formulate the PDEs. This
discretization is evaluated and analysed to detect breast
tumor. The realistic mathematical modelling is
represented the importance of biological phenomena. In
this study we use the parallel computing system with the
PVM communication platform and C programming to
solve the complex mathematical problems. The
distributed parallel computer system is performed using
38 CPUs with Pentium IV Processor, 512MB RAM each,
connected with local area network on LINUX operating
system. The implementation of the algorithm and large
sparse matrices on a distributed parallel computer system
are convenient in solving the high scale calculations.
Finally the performance of the parallel computing is
analysed to evaluate the efficiency and advantages of the
approach, early detection of breast tumor and the results
are visualized.
1.1 Numerical Approximation Methods for Breast
Tumor Detection
The mathematical modelling could be advantage solutions
in terms of insights and predictions. Beside comparison
138
with the real-life results, the model can be transforms to Subject to the boundary conditions
more precisely imitate the biological process. There are u (0, t ) = u ( L, t ) = 0, t > 0
some techniques are implementing now a days to detect and the initial conditions
breast tumor and some limitations have been
acknowledges by the medical community.
u ( x,0) = f ( x),0 ≤ x ≤ L,
∂u
( x,0) = g ( x),0 ≤ x ≤ L
1.1.1 1D Problem Formulating
∂t
Here hyperbolic equation leading the ultrasound pressure
where α is a constant.
fields. The problem gained from the hyperbolic equation
To set up the finite-difference method, assume u = f (x) is
which is a wave equation integrated with a frequency-
a function of the independent variables x and t. Subdivide
dependent attenuation is as equation (1).
the x-plane into sets of equal rectangles if sides δx = h
1 ∂ 2 p ( x, t ) ∂p ( x, t ) and δt = k.
+γ = ∇.(c∇p ( x, t )) (1)
Writing this set of equations in matrix form gives,
c 2
∂t 2
∂t
where,
p – pressure
x – space variable
t – time variable
c – sound speed of the traversed tissue
γ – damping or attenuation parameter

1.1.2 2D Problem Formulating Two Dimensional Elliptic Equation

The two dimensional elliptic equation ∂ r + ∂ r = 0 can
2 2
The wave equation of PDEs are presenting the time
harmonic electrical field. The problem is derived into two ∂x ∂y 2
2

dimensional problem as the following equation. be further implemented to solve the large scale
(∇ 2 + k 2 (r ))e(r ) = 0 (2) mathematical problem. Generally, finite-difference
k- the wave number of the electromagnetic approximation to two dimensional elliptic equation is
e(r)- total electric field given by
r- current in the electrical field ri −1, j − 2ri , j + ri +1, j ri , j −1 − 2ri , j + ri , j +1
x- x direction of the space variable + =0 (5)
( Δx ) ( Δy )
2 2
y- y direction of the space variable
Then we will have the finite-difference approximation
Equation (2) can then transform into Equation (3) by equation from (5) as follows,
using Finite Difference Method in three points θ ri , j −1 + ri −1, j − (2 + 2θ )ri , j + ri +1, j + θ ri , j +1 = 0 (6)
discretization.
⎛ ri −1, j − 2ri , j + ri +1, j ri , j −1 − 2ri , j + ri , j +1 ⎞ For 0 ≤ θ ≤ 1
⎜ + + k 2 ( ri , j ) ⎟ e ( ri , j ) = 0
(3)
⎜ ( Δx )
2
( Δy )
2
⎟
⎝ ⎠

1.2 The Mathematical Modelling For Breast Cancer 2. Iteration point methods for solving the
cells Finite Difference Equations
The method to solve Helmholtz’s equation and hyperbolic Iterative methods are used to solved the linear algebraic
PDE are introduced in this section that are utilizing to the when the number of unknown is large but each equation
early detection of breast tumor by Gauss-Seidel iteration involves only a few of them. It is mean by when the
and Red Black Gauss-Seidel iterative methods. The matrix of coefficients consists mainly of zeros and the
electromagnetic of Helmholtz’s equation and hyperbolic iterative methods take advantage of the zeros, where as a
PDE are discretized to transform the model in a matrix great deal of the work of direct elimination methods is
form. concerned. So that, the finite-difference equations
associated with partial differential equations are suitable
1.2.1 Hyperbolic Partial Differential Equations to be solved using iterative methods. In this section,
Hyperbolic differential equations, includes the “wave Gauss-Seidel iterative methods are presented.
equation” which is fundamental to the study of vibrating
systems. It is instructive to outline the derivation of the 2.1 Gauss Seidel Iterative Method
simple wave equation in one dimension problem.
The wave equation is given by the differential equation One of our interests in this study is hyperbolic equation,
∂ 2u by consider the wave equation give,
2 ∂ u
2
( x , t ) − α ( x, t ) = 0,0 < x < L, t > 0 (4)
∂t 2 ∂x 2

139
 ii. Grid calculation at Ω :
B
∂ 2u 2 ∂ u
2
( x , t ) − α ( x, t ) = 0 (7)
∂t 2 ∂x 2 w ( n +1)
i =λ w2 ( n +1)
i +1 + 2(1 − λ2 ) wi( n ) + λ2 wi(−n1+1) − bi
Using finite-difference method, the equation become i=2,4,6,…,m-1 (15)
wi , j +1 − 2 wi , j + wi , j −1 wi +1, j + 2 wi , j − wi −1, j Red Black Gauss Seidel algorithm is used to implement
−α 2 =0 (8)
k 2
h2 the parallel algorithm in solving the finite difference
This is called gauss-seidel iterative for equation (8) equation. The iterative method contains 2-sub domain,
wi( n+1) = λ2 wi(+n1) + 2(1 − λ2 ) wi( n ) + λ2 wi(−n1+1) − bi (9) Ω R and Ω B . There is a communication between
For elliptic equation, from equation (10) solving the left Ω R and Ω B (B. Wilkinson and M. Allen, 2004). The
side for ri , j +1 gives, calculation of this method is shown as follow:
i. Grid calculation at Ω :
R
1
ri , j +1 = [(2 + 2θ )ri , j − ri +1, j − ri −1, j − θ ri , j −1 ] (10) 1
θ ri ( n +1) = [(2 + 2θ )ri( n ) − ri (+n1) − ri (−n1+1) ] − bi ,
The unknowns ri +1, j , ri , j , ri −1, j are converted simply as
θ
i =1, 3, 5,…, n (16)
ri +1, , ri , ri −1 , respectively. This enables to express the ii. Grid calculation at Ω :
B

relationship between these unknowns as 1

1 ri ( n +1) = [(2 + 2θ )ri( n ) − ri (+n1) − ri (−n1+1) ] − bi ,
ri = [(2 + 2θ ) ri − ri +1 − ri −1 − θ bi ] θ
θ (11) i =2, 4, 6,…, n + 1 (17)
1 Gauss-Seidel update approaches are more preferable than
ri = [(2 + 2θ ) ri − ri +1 − ri −1 ] − bi (12)
θ Jacobi strategies for sequential because they permit
precise solutions to be obtained through less iteration.
where, bi = ri , j −1
The simple Gauss-Seidel update strategy is more
Denote the first approximation to ri by ri , the second
(1) appropriate in sequential program while Red Black
Gauss-Seidel parallel algorithm is more appropriate for
approximation by ri(2) , and the n approximation by ri( n ) . the solution of large mathematical problem compares to
the Gauss-Seidel with sequential algorithm.
Assume that n of then have been calculated, ri( n ) is known The Red Black Gauss Seidel iterative via parallel
for all i. By Equation (11), rewrite iterative formula as computing is converging very speedy compares to the
the following, sequential algorithm by Gauss-Seidel iterative. Red Black
1 Gauss-Seidel is a data decomposition approach that
ri ( n +1) = [(2 + 2θ )ri( n ) − ri (+n1) − ri (−n1) ] − bi (13) divides arrays among local processors to minimize the
θ communication. The data structure has to be decomposed
A further improvement in the rate at which where given set of ranges assigned to particular
( n +1)
r converges to the next exact solution can be processors must be physically sent to those processors in
achieved by using the most recent iterates as soon as they order for the processing to be done. The result must be
(n) ( n +1) sent back to whichever processors which are responsible
are available. It can replace r by r immediately
they have been computed. Assume we have calculated for coordinating the final result.
r ( n ) at each mesh point along a given space row. 2.3 The Discretization
Working systematically from left to right,
r1( n +1) , r2( n +1) ,... .Now, assume ri (−n1+1) have been calculated We introduce a time grid tn = nΔt for n = 0, 1, 2, … and
and then about to compute ri ( n +1)
. Δt is the time step size.
We set pn(x) = p(x, tn) as the nth iterate of the pressure at
the global point x. The time derivatives in (1) are
2.2 Red Black Gauss-Seidel Iteration Method discretized by centered difference formula, which
gives the semi-discrete scheme as the following,
To implement the parallel algorithm in solving the finite
difference equation, Red Black Gauss Seidel algorithm is P n +1 − 2 P n + P n −1 P n +1 − P n −1
+ γc 2 = c 2 Δ2 P n (18)
used (Malik Silva, 2003). The iterative method contains 2 Δt 2
2Δt
sub-domain, Ω R and Ω B. There are a communication
between, ΩR and ΩB. The calculation of this method is The discretization of the mathematical model based on the
show by the equation (14) and (15), finite-difference approximation to equation (4) can be
written as,
i. Grid calculation at Ω :
R
⎡ ⎛ h2 ⎞ 2⎤ ⎛ h2 ⎞ ⎛ h2 ⎞
w ( n +1)
i =λ w 2 (n)
i +1 + 2(1 − λ2 ) wi( n ) + λ2 wi(−n1+1) − bi ri +1, j + ri −1, j − ⎢ 2 + 2 ⎜ 2 ⎟ − h 2 k ⎥ ri , j + ⎜ 2 ⎟ ri , j +1 + ⎜ 2 ⎟ ri , j −1 = 0
⎣ ⎝k ⎠ ⎦ ⎝k ⎠ ⎝k ⎠
i=1,3,5,…..,m (14)
(19)

140
⎡ ⎛ h2 ⎞ 2 2 ⎤ ⎛ h2 ⎞
⎢ 2 + 2 ⎜ 2 ⎟ − h k ⎥ ri , j = ri +1, j + ri −1, j + ⎜ 2 ⎟ ri , j +1 + ⎜ 2 ⎟ ri , j −1
⎣ ⎝k ⎠ ⎦ ⎝k ⎠
3. Numerical Analysis of the Problem
The numerical analysis of time execution, speedup,
efficiency, effectiveness and temporal performance is
used to measure the parallel algorithm performance for
proving the significances of parallel is better that the
sequential algorithms. The parallel strategies make the
iterative methods converges faster to the solution. This is
because of the parallel implementation of an algorithm
involves the division of total workload into a number of
smaller tasks, which can be assigned to different
processors and executed concurrently and simultaneously.
Parallel strategies typically attempt to distribute
computational work by breaking a large domain of PDE
into a number of smaller subdomain. When solving a
PDE on a parallel computer system the communication
requirement of the numerical solver is minimized and the
amount of subdomain to be performed on each processor
is approximately equal. The analysis of the executive time
by parallel program helps to understand the barriers to
high performance and predict how much of the
improvement can be realized by increasing the number of
processors. This approach increases the modularity of
parallel schemes, provides flexibility, integrated, accurate
and fast enough for real time implementations.
3.1 Visualization of the Two Dimensional Breast
Cancer
In this study, we are applying the explicit method to solve
the mathematical model by using a suitable sequence
iteration method of Gauss-Seidel sequential algorithms
with some minimize requirements such as PVM, C
programming and Linux environment on distributed
parallel computing system. The results from the
sequential algorithm in solving the two-dimensional
elliptic equation using C programming are shown in Table
1.
When visualizing the existence of breast cancer cells, it
shows that the cells were being affected by cancer when
the current of electric field (the r-terms) Gunnarsson T.
(2007) has performed the approaches of microwave
imaging using tomography methods where a cross-
sectional slice of dielectric properties is generated.
⎛ h2 ⎞
⎝k ⎠
(20)
Figure 1: The Detection of Breast Cancer in Two Dimensional with
dx/dy=1
When visualizing the existence of breast cancer cells, it
shows that the cells were being affected by cancer when
the current of electric field (the r-terms) Gunnarsson T.
(2007) has performed the approaches of microwave
imaging using tomography methods where a cross-
sectional slice of dielectric properties is generated. The
major reason for this is that the potentially high dielectric
contrast between cancerous tissues and normal breast
tissues. When expose to microwaves, breast tumor
exhibits electrical properties that are significantly
different from a healthy breast tissues. Besides that, the
high water content of malignant breast tissues cause
significantly microwave scattering than normal fatty
breast tissues that have low water content.
For the straight line segments of the edges of a shape, a
solution is integrable or predictable in closed-form as long
as it is expressible as a finite linear combination of plane
waves that satisfy the boundary conditions (zero at the
boundary, i.e., membrane clamped). In figure 1, it shows
that the graph has form the lower half of and elliptic shape
where the electric force approaching 0.6 volts as the wave
space increases.
Figure 2: The Visualization of the Detection of the Breast Cancer
Cells using Sequential Algorithm with C programming
In running the sequential program, take the k values as
0.1, the Δx = 0.1 and Δy = 0.1 . Small tumors are
successfully detected even when a significant mismatch
exists between the average normal breast-tissue dielectric
141
properties assumed in the beamformer design and the The core work of master task is to split the model domain
actual average dielectric properties of the breast being into sub domains and allocate them to worker tasks. After
scanned. This may be conclude as there exist an error with each time step, the worker tasks communicate and execute
the Helmholtz’s equation in predicting early detection of time marching. The parallel algorithm’s performance will
breast cancer. be evaluated respecting the efficiency, effectiveness,
speedup and temporal performance with number of
Table 1: The Pressure of Breast Cancer for 30 days
processor and time execution.
The following definitions are used to measure the parallel
Days strategies in term of (Zomaya,1996):
Grid Speedup : L(p)=t1 / tp (21)
efficiency : C(p)=L(p)/ p (22)
5 10 15 20 25 30
effectiveness: K(p)=L(p)/ ptp (23)
1 152.000 202.000 334.000 739.000 1652.000 4160.000 where t1 is the execution time on a serial machine and tp
2 229.153 280.307 431.460 812.613 1733.765 4234.918 is the computing time on a parallel machine with p
308.613 363.226 517.839 922.452 1827.064 4331.676
3 processors. The temporal performance F(p) is used to
4 391.551 453.136 614.756 1026.410 1938.099 4449.822
479.172 552.223 726.143 1149.942 2073.950 4598.166
investigate the performance of difference algorithms. The
5
6 572.735 654.206 856.412 1299.357 2243.041 4787.465 definition is F(p)=1/ tp.
7 673.570 791.111 1010.635 1482.153 2455.679 5031.230
8 783.097 936.659 1194.741 1707.400 2724.700 5346.680 Execution time is the amount of time needed for a
9 902.846 1104.700 1415.750 1986.200 3066.220 5756.030 complete run of a computer program routine. The time
10 1034.48 1299.650 1682.050 2332.210 3500.670 6287.990 required for a computer to decode and perform a compiled
instruction. The time execution for one CPU to compute
Table 1 shows that the pressure of the breast cancer the programming using time.h from the parallel
computed using parallel programming with PVM and C programming is as shown in Table 2.
of mathematical model in this research (A. Bounaïm at el,
2004). The pressure in Table 1 will be used to visualize Table 2: Time execution, speedup, efficiency, effectiveness, temporal
the growth of the breast cancer within 30 days more performances against different number of processors
obviously. According to Table 1, the pressure of breast Number Time Speedup Efficiency Effectiveness Temporal
cancer increasing from 150 to 6000 within 1 month. This of execution Performance
processor (Second)
shows that the diffusive of the cancer cells is very fast. 1 97.61890 1 1 0.01024 0.01024
4 42.31848 2.30677 0.57669 0.01363 0.02363
8 32.56302 2.99785 0.37473 0.01151 0.03071
12 25.62441 3.80961 0.31747 0.01239 0.03903
16 10.49781 9.29898 0.58119 0.05537 0.09257
20 06.96519 14.01525 0.70076 0.10061 0.14357

The execution time is decreasing with the increasing of

the number of processors. The time execution with one
processor is 97.61890 second. However, the time
execution with 20 processors is more quickly at 6.96519
second. It is because the distributed memory hierarchy
reduces the time consuming access to a cluster of
workstations. According to Amdahl’s Law, the speedup
increases with the number of processors increase up to the
certain level.
Figure 3: The Growth Rate of Breast Cancer

Figure 3 shows the pressure inside the breast for every 5
days within 1 month. The graph has shown that in the first
5 days, the pressure is low. However, after 20 days, the
pressure increases drastically. The pressure becomes
higher after 30 days. As a conclusion, the pressure is
increasing with the tumor size. Therefore, the growth of
breast cancer can be visualized from its pressure.
4. Results and Discussion
4.1 The Performance Analysis
There is a master task in the PVM execution of the
modelling codes and there are number of worker tasks.
The efficiency decreases with the increasing of number of
processors. As known, efficiency is the ratio of speedup
with number of processors. So, efficiency is a
performance closely related to speedup. But in this case,
it can be summarized as the system has reach it’s
maximum efficiency at 12 number of processor. The
effectiveness is escalating with the increasing of the
number of processors. In addition, the adding of the
number of processors is to make the graph increasing.
Table 2 shows that the temporal performance graph is
proportional to the number of processors increase. It is
because the execute time is decreasing versus the number
of processors.

142
Finally, the analysis from the aspect of execution time,
speedup, efficiency, effectiveness and temporal
performance show that the performance of the parallel
algorithm is improved by the increasing of the number of
processors. Besides, we can also conclude that
communication and execute times is always affecting the
performance of parallel computing. Parallel computing is
becoming more popular since that it is a low cost
supercomputer and save a lot of time in solving a large
problem. The Red Black Gauss Seidel which is effective
is found to be well suited for parallel implementation on
the PVM where data decomposition is run synchronously
and concurrently at every time level.
5. Conclusion
Every woman in the world is at risk for breast cancer. So,
we must take the action to predict it. Early detection of
breast cancer significantly reduces the risk of death.
Finding a breast cancer as early as possible improves the
likelihood that treatment will be successful.
The Key purpose of this study is being able to visualize
the breast cancer cells in one-dimensional and two-
dimensional space. We have identified the one-
dimensional hyperbolic PDE and two-dimensional elliptic
equation described the breast tumor cells in r and space,
x, and y the physical state of the system. Both of the
hyperbolic equations and elliptic equations are derived
using the numerical finite difference method. By
developing the sequential C programming, the iterative
methods namely Gauss-Seidel method is applied to solve
the equations. The GSRB is established appropriate for
parallel implementation on the Parallel Virtual Machine
(S.Y Ping, 2006). The parallel computing with PVM
system can be concluded as a well suite performance tools
in solving the grand challenge of mathematical problem.
It can save a lot of execute time compare to the sequence
processing.
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