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Rifat

Multi-core architecture refers to processors with multiple cores that can execute functions simultaneously, enhancing performance and efficiency compared to single-core processors. Advantages include improved response times for CPU-intensive tasks and reduced power consumption. The document also discusses the use of OpenMP for parallel programming, particularly in matrix multiplication, and its relevance to computational biology problems.

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Geetharani Prabahar
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11 views26 pages

Rifat

Multi-core architecture refers to processors with multiple cores that can execute functions simultaneously, enhancing performance and efficiency compared to single-core processors. Advantages include improved response times for CPU-intensive tasks and reduced power consumption. The document also discusses the use of OpenMP for parallel programming, particularly in matrix multiplication, and its relevance to computational biology problems.

Uploaded by

Geetharani Prabahar
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Download as PDF, TXT or read online on Scribd
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What is Multi Core Architecture?

When a processor has more than one core to


execute all the necessary functions of a computer,
it’s processor is known to be a multi core
architecture.
In other words, a chip with more than one
CPU’s(Central Processing Unit).
What is the difference between a
single core processor and a multi core
processor?


Advantages of multi core CPU

the largest boost in performance will likely be noticed


in improved response-time while running CPU-
intensive processes, like anti-virus scans,
ripping/burning media.
assuming that the die can fit into the package,
physically, the multi-core CPU designs require much
less printed Circuit Board(PCB) space than multi-chip
SMP designs. Also, a dual core processor uses slightly
less power than two coupled single core processors,
principally because of the decreased power required to
drive signals external to the chip.
Bio-grid Cluster
How it works!!!
 DEMO TIME !!!
OpenMP example

• When writing a program in C or C++, you


must import the library #include<omp.h> to
include the openMP library on your program
to allow parallelization during compile time.
• some sample OpenMP runtime Functions:
• omp_set_num_threads (Sets number of
threads)
• omp_set_max_active_levels (Sets number
of active parallel regions)
OpenMP Example Continued..
 #include <omp.h>
 #include <stdio.h>
 #include <stdlib.h>

 #define NRA 62 /* number of rows in matrix A */


 #define NCA 15 /* number of columns in matrix A */
 #define NCB 7 /* number of columns in matrix B */
OpenMP Example Continued..

 int main (int argc, char *argv[])


 {
 int tid, nthreads, i, j, k, chunk;
 double a[NRA][NCA], /* matrix A to be
multiplied */
 b[NCA][NCB], /* matrix B to be multiplied
*/
 c[NRA][NCB]; /* result matrix C */

 chunk = 10; /* set loop iteration chunk size


*/
OpenMP Example Continued..
 /*** Spawn a parallel region explicitly scoping all variables ***/
 #pragma omp parallel shared(a,b,c,nthreads,chunk) private(tid,i,j,k)
 {
 tid = omp_get_thread_num();
 if (tid == 0)
 {
 nthreads = omp_get_num_threads();
 printf("Starting matrix multiple example with %d threads\n",nthreads);
 printf("Initializing matrices...\n");
 printf("Hello");
 }
OpenMP Example Continued..
 /*** Initialize matrices ***/
 #pragma omp for schedule (static, chunk)
 for (i=0; i<NRA; i++)
 for (j=0; j<NCA; j++)
 a[i][j]= i+j;
 #pragma omp for schedule (static, chunk)
 for (i=0; i<NCA; i++)
 for (j=0; j<NCB; j++)
 b[i][j]= i*j;
 #pragma omp for schedule (static, chunk)
 for (i=0; i<NRA; i++)
 for (j=0; j<NCB; j++)
 c[i][j]= 0;
OpenMP Example Continued..
 /*** Do matrix multiply sharing iterations on outer loop ***/
 /*** Display who does which iterations for demonstration purposes ***/
 printf("Thread %d starting matrix multiply...\n",tid);
 #pragma omp for schedule (static, chunk)
 for (i=0; i<NRA; i++)
 {
 printf("Thread=%d did row=%d\n",tid,i);
 for(j=0; j<NCB; j++)
 for (k=0; k<NCA; k++)
 c[i][j] += a[i][k] * b[k][j];
 }
 } /*** End of parallel region ***/
OpenMP Example Continued..
 /*** Print results ***/
 printf("******************************************************\n");
 printf("Result Matrix:\n");
 for (i=0; i<NRA; i++)
 {
 for (j=0; j<NCB; j++)
 printf("%6.2f ", c[i][j]);
 printf("\n");
 }
 printf("******************************************************\n");
 printf ("Done.\n");

 }
The relevance…

Using the algorithm derived from solving the


Matrix multiplication problem using OpenMP, we
can extend this algorithm to solve computational
biology problems. Such as
 “ developing Algorithms for Identifying Boolean
Networks and
 Related Biological Networks Based on Matrix
 Multiplication and Fingerprint Function”…1
The relevance continued…
By doing so we can analyze gene expression data
Understanding matrix multiplication problem and
it can be applied to solve cient algorithms for
identifying Boolean networks of bounded
indegree and related biological networks,
where identification of a Boolean network can
be formalized as a problem of identifying many
Boolean functions simultaneously.”1
How to extend my project…
 Add MPI library and functions to send task to different
processors
 Extend this algorithm to solve computational biology
problems as stated on previous two slides.
Acknowledgements
 Special thanks to NSF for providing us with this
wonderful opportunity to do research under BioGrid
 Also, Special Acknowledgements to Dr. Chun-His
Huang for all his effort, patience and help towards
helping me understand and implement the contents of
this research!
 It was a fun summer indeed 
Source Citation

1. JOURNAL OF COMPUTATIONAL BIOLOGY


 Volume 7, Numbers 3/4, 2000
 Mary Ann Liebert, Inc.
 Pp. 331–343
 Algorithms for Identifying Boolean Networks and
 Related Biological Networks Based on Matrix
 Multiplication and Fingerprint Function
 TATSUYA AKUTSU,1SATORU MIYANO,a nd SATORU
KUHARA1
 2. wikipedia.org
Source Citation
 http://openmp.org/wp/
 http://www.compunity.org/training/tutorials/2%20Ba
sic_Concepts_Parallelization.pdf
 https://iwomp.zih.tu-
dresden.de/downloads/2.Overview_OpenMP.pdf

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