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38 package ffx.algorithms.optimize.manybody;
39
40 import static java.lang.String.format;
41
42 import edu.rit.mp.DoubleBuf;
43 import edu.rit.pj.Comm;
44 import edu.rit.pj.IntegerSchedule;
45 import edu.rit.pj.MultipleParallelException;
46 import edu.rit.pj.WorkerIntegerForLoop;
47 import edu.rit.pj.WorkerRegion;
48 import ffx.algorithms.optimize.RotamerOptimization;
49 import ffx.potential.Utilities;
50 import ffx.potential.bonded.Residue;
51 import ffx.potential.bonded.Rotamer;
52 import java.io.BufferedWriter;
53 import java.io.IOException;
54 import java.util.Collection;
55 import java.util.Map;
56 import java.util.Set;
57 import java.util.logging.Level;
58 import java.util.logging.Logger;
59
60
61 public class SelfEnergyRegion extends WorkerRegion {
62
63 private static final Logger logger = Logger.getLogger(SelfEnergyRegion.class.getName());
64 private final Residue[] residues;
65 private final RotamerOptimization rO;
66 private final EnergyExpansion eE;
67 private final EliminatedRotamers eR;
68
69 private final Map<Integer, Integer[]> selfEnergyMap;
70
71 private final BufferedWriter energyWriter;
72
73 private final Comm world;
74
75 private final int numProc;
76
77 private final boolean pruneClashes;
78
79 private final boolean master;
80
81 private final int rank;
82
83 private final boolean verbose;
84
85 private final boolean writeEnergyRestart;
86
87
88
89
90 private final boolean printFiles;
91
92 private Set<Integer> keySet;
93
94 public SelfEnergyRegion(RotamerOptimization rO, EnergyExpansion eE, EliminatedRotamers eR,
95 Residue[] residues, BufferedWriter energyWriter, Comm world,
96 int numProc, boolean pruneClashes, boolean master, int rank, boolean verbose,
97 boolean writeEnergyRestart, boolean printFiles) {
98 this.rO = rO;
99 this.eE = eE;
100 this.eR = eR;
101 this.residues = residues;
102 this.energyWriter = energyWriter;
103 this.world = world;
104 this.numProc = numProc;
105 this.pruneClashes = pruneClashes;
106 this.master = master;
107 this.rank = rank;
108 this.verbose = verbose;
109 this.writeEnergyRestart = writeEnergyRestart;
110 this.printFiles = printFiles;
111
112 this.selfEnergyMap = eE.getSelfEnergyMap();
113 logger.info(format("\n Number of self energies: %d", selfEnergyMap.size()));
114 }
115
116 @Override
117 public void finish() {
118
119 eR.prePruneSelves(residues);
120
121
122 if (pruneClashes) {
123 eR.pruneSingleClashes(residues);
124 }
125
126
127 if (master && verbose) {
128 for (int i = 0; i < residues.length; i++) {
129 Residue residue = residues[i];
130 Rotamer[] rotamers = residue.getRotamers();
131 for (int ri = 0; ri < rotamers.length; ri++) {
132 logger.info(format(" Self energy %8s %-2d: %s", residues[i].toString(rotamers[ri]), ri,
133 rO.formatEnergy(eE.getSelf(i, ri))));
134 }
135 }
136 }
137 }
138
139 @Override
140 public void run() throws Exception {
141 if (!keySet.isEmpty()) {
142 try {
143 execute(0, keySet.size() - 1, new SelfEnergyLoop());
144 } catch (MultipleParallelException mpx) {
145 Collection<Throwable> subErrors = mpx.getExceptionMap().values();
146 logger.info(format(" MultipleParallelException caught: %s\n Stack trace:\n%s", mpx,
147 Utilities.stackTraceToString(mpx)));
148 for (Throwable subError : subErrors) {
149 logger.info(format(" Exception %s\n Stack trace:\n%s", subError,
150 Utilities.stackTraceToString(subError)));
151 }
152 throw mpx;
153 } catch (Throwable t) {
154 Throwable cause = t.getCause();
155 logger.info(
156 format(" Throwable caught: %s\n Stack trace:\n%s", t, Utilities.stackTraceToString(t)));
157 if (cause != null) {
158 logger.info(
159 format(" Cause: %s\n Stack trace:\n%s", cause, Utilities.stackTraceToString(cause)));
160 }
161 throw t;
162 }
163 }
164 }
165
166 @Override
167 public void start() {
168
169 int numSelf = selfEnergyMap.size();
170 int remainder = numSelf % numProc;
171
172 Integer[] padding = {-1, -1};
173
174 int padKey = numSelf;
175 while (remainder != 0) {
176 selfEnergyMap.put(padKey++, padding);
177 remainder = selfEnergyMap.size() % numProc;
178 }
179
180 numSelf = selfEnergyMap.size();
181 if (numSelf % numProc != 0) {
182 logger.severe(" Logic error padding self energies.");
183 }
184
185
186 keySet = selfEnergyMap.keySet();
187
188
189 double backboneEnergy = 0.0;
190 try {
191 backboneEnergy = rO.computeBackboneEnergy(residues);
192 } catch (ArithmeticException ex) {
193 logger.severe(format(" Error in calculation of backbone energy %s", ex.getMessage()));
194 }
195 rO.logIfRank0(format(" Backbone energy: %s\n", rO.formatEnergy(backboneEnergy)));
196 eE.setBackboneEnergy(backboneEnergy);
197 }
198
199 private class SelfEnergyLoop extends WorkerIntegerForLoop {
200
201 final DoubleBuf[] resultBuffer;
202 final DoubleBuf myBuffer;
203
204 SelfEnergyLoop() {
205 resultBuffer = new DoubleBuf[numProc];
206 for (int i = 0; i < numProc; i++) {
207 resultBuffer[i] = DoubleBuf.buffer(new double[3]);
208 }
209 myBuffer = resultBuffer[rank];
210 }
211
212 @Override
213 public void run(int lb, int ub) {
214 for (int key = lb; key <= ub; key++) {
215 Integer[] job = selfEnergyMap.get(key);
216 int i = job[0];
217 int ri = job[1];
218
219 myBuffer.put(0, i);
220 myBuffer.put(1, ri);
221 myBuffer.put(2, 0.0);
222
223 if (i >= 0 && ri >= 0) {
224 if (!eR.check(i, ri)) {
225 long time = -System.nanoTime();
226 Rotamer[] rotamers = residues[i].getRotamers();
227 double selfEnergy;
228 try {
229 selfEnergy = eE.computeSelfEnergy(residues, i, ri);
230 time += System.nanoTime();
231 logger.info(
232 format(" Self %8s %-2d: %s in %6.4f (sec).", residues[i].toString(rotamers[ri]),
233 ri, rO.formatEnergy(selfEnergy), time * 1.0e-9));
234 } catch (ArithmeticException ex) {
235 selfEnergy = Double.NaN;
236 time += System.nanoTime();
237 logger.info(format(" Self %8s %-2d:\t pruned in %6.4f (sec).",
238 residues[i].toString(rotamers[ri]), ri, time * 1.0e-9));
239 }
240 myBuffer.put(2, selfEnergy);
241 }
242 } else {
243
244
245
246 myBuffer.put(2, 0.0);
247 }
248
249
250 if (numProc > 1) {
251 try {
252 world.allGather(myBuffer, resultBuffer);
253 } catch (Exception e) {
254 logger.log(Level.SEVERE, " Exception communicating self energies.", e);
255 }
256 }
257
258
259 for (DoubleBuf doubleBuf : resultBuffer) {
260 int resI = (int) doubleBuf.get(0);
261 int rotI = (int) doubleBuf.get(1);
262 double energy = doubleBuf.get(2);
263
264 if (resI >= 0 && rotI >= 0) {
265 if (Double.isNaN(energy)) {
266 logger.info(" Rotamer eliminated: " + resI + ", " + rotI);
267 eR.eliminateRotamer(residues, resI, rotI, false);
268 }
269 eE.setSelf(resI, rotI, energy);
270 if (rank == 0 && writeEnergyRestart && printFiles) {
271 try {
272 energyWriter.append(format("Self %d %d: %16.8f", resI, rotI, energy));
273 energyWriter.newLine();
274 energyWriter.flush();
275 } catch (IOException ex) {
276 logger.log(Level.SEVERE, " Exception writing energy restart file.", ex);
277 }
278 }
279 }
280 }
281 }
282 }
283
284 @Override
285 public IntegerSchedule schedule() {
286
287 return IntegerSchedule.fixed();
288 }
289 }
290 }