-
Notifications
You must be signed in to change notification settings - Fork 41
/
md_openmp.html
377 lines (326 loc) · 9.91 KB
/
md_openmp.html
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
<html>
<head>
<title>
MD_OPENMP - Molecular Dynamics using OpenMP
</title>
</head>
<body bgcolor="#EEEEEE" link="#CC0000" alink="#FF3300" vlink="#000055">
<h1 align = "center">
MD_OPENMP <br> Molecular Dynamics using OpenMP
</h1>
<hr>
<p>
<b>MD_OPENMP</b>
is a C++ program which
carries out a molecular dynamics simulation,
using OpenMP for parallel execution.
</p>
<p>
On an Apple PowerPC G5 with two processors, the following results were
observed for a run with 400 steps and 1000 particles:
<table border="1" align="center">
<tr>
<th>Threads</th><th>Time</th>
</tr>
<tr>
<td>1</td><td>183.517 secconds</td>
</tr>
<tr>
<td>2</td><td>94.037 seconds</td>
</tr>
<tr>
<td>4</td><td>93.164 seconds</td>
</tr>
</table>
</p>
<h3 align = "center">
Usage:
</h3>
<p>
In the BASH shell, the program could be run with 2 threads using the commands:
<pre>
export OMP_NUM_THREADS=2
./md_openmp
</pre>
</p>
<h3 align = "center">
Licensing:
</h3>
<p>
The computer code and data files described and made available on this web page
are distributed under
<a href = "../../txt/gnu_lgpl.txt">the GNU LGPL license.</a>
</p>
<h3 align = "center">
Languages:
</h3>
<p>
<b>MD_OPENMP</b> is available in
<a href = "../../c_src/md_openmp/md_openmp.html">a C version</a> and
<a href = "../../cpp_src/md_openmp/md_openmp.html">a C++ version</a> and
<a href = "../../f77_src/md_openmp/md_openmp.html">a FORTRAN77 version</a> and
<a href = "../../f_src/md_openmp/md_openmp.html">a FORTRAN90 version</a>.
</p>
<h3 align = "center">
Related Data and Programs:
</h3>
<p>
<a href = "../../cpp_src/dijkstra_openmp/dijkstra_openmp.html">
DIJKSTRA_OPENMP</a>,
a C++ program which
uses OpenMP to parallelize a simple example of Dijkstra's
minimum distance algorithm for graphs.
</p>
<p>
<a href = "../../cpp_src/fft_openmp/fft_openmp.html">
FFT_OPENMP</a>,
a C++ program which
demonstrates the computation of a Fast Fourier Transform
in parallel, using OpenMP.
</p>
<p>
<a href = "../../cpp_src/heated_plate_openmp/heated_plate_openmp.html">
HEATED_PLATE_OPENMP</a>,
a C++ program which
solves the steady (time independent) heat equation in a 2D
rectangular region, using OpenMP to run in parallel.
</p>
<p>
<a href = "../../cpp_src/hello_openmp/hello_openmp.html">
HELLO_OPENMP</a>,
a C++ program which
prints out "Hello, world!" using the OpenMP parallel programming environment.
</p>
<p>
<a href = "../../cpp_src/md/md.html">
MD</a>,
a C++ program which
carries out a molecular dynamics simulation, and is intended as
a starting point for implementing an OpenMP parallel version.
</p>
<p>
<a href = "../../m_src/md_parfor/md_parfor.html">
MD_PARFOR</a>,
a MATLAB program which
is intended to be run in parallel using MATLAB's "PARFOR" feature.
</p>
<p>
<a href = "../../f_src/md1/md1.html">
MD1</a>,
a FORTRAN90 program which
carries out a molecular dynamics simulation.
</p>
<p>
<a href = "../../f_src/md2/md2.html">
MD2</a>,
a FORTRAN90 program which
carries out a molecular dynamics simulation.
</p>
<p>
<a href = "../../f_src/md3/md3.html">
MD3</a>,
a FORTRAN90 program which
carries out a molecular dynamics simulation.
</p>
<p>
<a href = "../../f_src/md3glue/md3glue.html">
MD3GLUE</a>,
a FORTRAN90 program which
carries out a molecular dynamics simulation.
</p>
<p>
<a href = "../../f77_src/mdbnch/mdbnch.html">
MDBNCH</a>,
a FORTRAN77 program which
is a benchmark molecular simulation calculation.
</p>
<p>
<a href = "../../cpp_src/multitask_openmp/multitask_openmp.html">
MULTITASK_OPENMP</a>,
a C++ program which
demonstrates how to "multitask", that is, to execute several unrelated
and distinct tasks simultaneously, using OpenMP for parallel execution.
</p>
<p>
<a href = "../../cpp_src/mxv_openmp/mxv_openmp.html">
MXM_OPENMP</a>,
a C++ program which
computes a dense matrix product C=A*B,
using OpenMP for parallel execution.
<p>
<p>
<a href = "../../cpp_src/mxv_openmp/mxv_openmp.html">
MXV_OPENMP</a>,
a C++ program which
compares the performance of plain vanilla Fortran and the FORTRAN90
intrinsic routine MATMUL, for the matrix multiplication problem
y=A*x, with and without parallelization by OpenMP.
<p>
<p>
<a href = "../../cpp_src/openmp/openmp.html">
OPENMP</a>,
C++ programs which
illustrate the use of OpenMP.
<p>
<p>
<a href = "../../cpp_src/poisson_openmp/poisson_openmp.html">
POISSON_OPENMP</a>,
a C++ program which
computes an approximate solution to the Poisson equation in a rectangle,
using the Jacobi iteration to solve the linear system, and OpenMP to
carry out the Jacobi iteration in parallel.
</p>
<p>
<a href = "../../cpp_src/prime_openmp/prime_openmp.html">
PRIME_OPENMP</a>,
a C++ program which
counts the number of primes between 1 and N, using OpenMP for parallel execution.
</p>
<p>
<a href = "../../cpp_src/quad_openmp/quad_openmp.html">
QUAD_OPENMP</a>,
a C++ program which
approximates an integral using a quadrature rule, and carries out the
computation in parallel using OpenMP.
</p>
<p>
<a href = "../../cpp_src/random_openmp/random_openmp.html">
RANDOM_OPENMP</a>,
a C++ program which
illustrates how a parallel program using OpenMP can generate multiple
distinct streams of random numbers.
</p>
<p>
<a href = "../../cpp_src/satisfy_openmp/satisfy_openmp.html">
SATISFY_OPENMP</a>,
a C++ program which
demonstrates, for a particular circuit, an exhaustive search
for solutions of the circuit satisfy problem,
using OpenMP for parallel execution.
<p>
<p>
<a href = "../../cpp_src/schedule_openmp/schedule_openmp.html">
SCHEDULE_OPENMP</a>,
a C++ program which
demonstrates the default, static, and dynamic methods of "scheduling"
loop iterations in OpenMP to avoid work imbalance.
<p>
<p>
<a href = "../../cpp_src/sgefa_openmp/sgefa_openmp.html">
SGEFA_OPENMP</a>,
a C++ program which
reimplements the SGEFA/SGESL linear algebra routines from
LINPACK for use with OpenMP.
</p>
<p>
<a href = "../../cpp_src/ziggurat_openmp/ziggurat_openmp.html">
ZIGGURAT_OPENMP</a>,
a C++ program which
demonstrates how the ZIGGURAT library can be used to generate random numbers
in an OpenMP parallel program.
</p>
<h3 align = "center">
Reference:
</h3>
<p>
<ol>
<li>
Peter Arbenz, Wesley Petersen,<br>
Introduction to Parallel Computing - A practical guide with examples in C,<br>
Oxford University Press,<br>
ISBN: 0-19-851576-6,<br>
LC: QA76.58.P47.
</li>
<li>
Rohit Chandra, Leonardo Dagum, Dave Kohr, Dror Maydan,
Jeff McDonald, Ramesh Menon,<br>
Parallel Programming in OpenMP,<br>
Morgan Kaufmann, 2001,<br>
ISBN: 1-55860-671-8,<br>
LC: QA76.642.P32.
</li>
<li>
Barbara Chapman, Gabriele Jost, Ruud vanderPas, David Kuck,<br>
Using OpenMP: Portable Shared Memory Parallel Processing,<br>
MIT Press, 2007,<br>
ISBN13: 978-0262533027,<br>
LC: QA76.642.C49.
</li>
</ol>
</p>
<h3 align = "center">
Source Code:
</h3>
<p>
<ul>
<li>
<a href = "md_openmp.cpp">md_openmp.cpp</a>,
the source code;
</li>
</ul>
</p>
<h3 align = "center">
Examples and Tests:
</h3>
<p>
<b>MD_LOCAL</b> runs the program locally.
<ul>
<li>
<a href = "md_local.sh">md_local.sh</a>,
commands to compile the program and run with 1, 2, 4, and 8 threads.
</li>
<li>
<a href = "md_local_output.txt">md_local_output.txt</a>,
the output file.
</li>
</ul>
</p>
<p>
<b>MD_ITHACA</b> runs the program through ITHACA's batch system.
<ul>
<li>
<a href = "md_ithaca.sh">md_ithaca.sh</a>,
commands to compile the program and run with 1, 2, 4, and 8 threads.
</li>
<li>
<a href = "md_ithaca_output.txt">md_ithaca_output.txt</a>,
the output file.
</li>
</ul>
</p>
<h3 align = "center">
List of Routines:
</h3>
<p>
<ul>
<li>
<b>MAIN</b> is the main program for MD_OPENMP.
</li>
<li>
<b>COMPUTE</b> computes the forces and energies.
</li>
<li>
<b>DIST</b> computes the displacement and distance between two particles.
</li>
<li>
<b>INITIALIZE</b> initializes the positions, velocities, and accelerations.
</li>
<li>
<b>TIMESTAMP</b> prints the current YMDHMS date as a time stamp.
</li>
<li>
<b>UPDATE</b> updates positions, velocities and accelerations.
</li>
</ul>
</p>
<p>
You can go up one level to <a href = "../cpp_src.html">
the C++ source codes</a>.
</p>
<hr>
<i>
Last revised on 02 September 2009.
</i>
<!-- John Burkardt -->
</body>
</html>