/[escript]/trunk/escript/src/Utils.cpp
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Annotation of /trunk/escript/src/Utils.cpp

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Revision 2644 - (hide annotations)
Wed Sep 2 04:14:03 2009 UTC (10 years, 7 months ago) by jfenwick
File size: 11914 byte(s)
Add unit tests for saveDataCSV which should be ready for use now.
Keyword args are now output in sorted order.

Removed some unneeded functions.
1 gross 391
2 ksteube 1312 /*******************************************************
3 ksteube 1811 *
4 jfenwick 2548 * Copyright (c) 2003-2009 by University of Queensland
5 ksteube 1811 * Earth Systems Science Computational Center (ESSCC)
6     * http://www.uq.edu.au/esscc
7     *
8     * Primary Business: Queensland, Australia
9     * Licensed under the Open Software License version 3.0
10     * http://www.opensource.org/licenses/osl-3.0.php
11     *
12     *******************************************************/
13 ksteube 1312
14 ksteube 1811
15 jfenwick 2641 #include <fstream>
16 ksteube 1806 #include <string.h>
17    
18 jfenwick 2635 // added for saveCSV
19     #include <boost/python.hpp>
20 jfenwick 2641 #include <boost/scoped_ptr.hpp>
21 jfenwick 2635 #include "Data.h"
22    
23 jgs 474 #include "Utils.h"
24 gross 797 #include "DataVector.h"
25 gross 391
26 jgs 478 #ifdef _OPENMP
27     #include <omp.h>
28     #endif
29    
30 ksteube 1561 #ifdef PASO_MPI
31     #include <mpi.h>
32     #endif
33    
34 phornby 1628 #ifdef _WIN32
35     #include <WinSock2.h>
36 phornby 1835 #else
37     #include <unistd.h>
38 phornby 1628 #endif
39    
40 gross 391 namespace escript {
41    
42 ksteube 1247 int getSvnVersion()
43     {
44     #ifdef SVN_VERSION
45     return SVN_VERSION;
46     #else
47     return 0;
48     #endif
49     }
50    
51 ksteube 1620 /* This is probably not very robust, but it works on Savanna today and is useful for performance analysis */
52     int get_core_id() {
53     int processor_num=-1;
54     #ifdef CORE_ID1
55     FILE *fp;
56     int i, count_spaces=0;
57     char fname[100];
58     char buf[1000];
59    
60     sprintf(fname, "/proc/%d/stat", getpid());
61     fp = fopen(fname, "r");
62     if (fp == NULL) return(-1);
63     fgets(buf, 1000, fp);
64     fclose(fp);
65    
66     for (i=strlen(buf)-1; i>=0; i--) {
67     if (buf[i] == ' ') count_spaces++;
68     if (count_spaces == 4) break;
69     }
70     processor_num = atoi(&buf[i+1]);
71     #endif
72     return(processor_num);
73     }
74    
75    
76 ksteube 1561 void printParallelThreadCnt()
77     {
78     int mpi_iam=0, mpi_num=1;
79 ksteube 1568 char hname[64];
80 ksteube 1561
81 ksteube 1705 #ifdef HAVE_GETHOSTNAME
82 ksteube 1568 gethostname(hname, 64);
83 ksteube 1806 hname[63] = '\0';
84 ksteube 1705 #else
85     strcpy(hname, "unknown host");
86     #endif
87 ksteube 1567
88 ksteube 1561 #ifdef PASO_MPI
89     MPI_Comm_rank(MPI_COMM_WORLD, &mpi_iam);
90     MPI_Comm_size(MPI_COMM_WORLD, &mpi_num);
91     #endif
92    
93     #pragma omp parallel
94     {
95     int omp_iam=0, omp_num=1;
96     #ifdef _OPENMP
97     omp_iam = omp_get_thread_num(); /* Call in a parallel region */
98     omp_num = omp_get_num_threads();
99     #endif
100 jfenwick 2607 #pragma omp critical (printthrdcount)
101 ksteube 1620 printf("printParallelThreadCounts: MPI=%03d/%03d OpenMP=%03d/%03d running on %s core %d\n",
102     mpi_iam, mpi_num, omp_iam, omp_num, hname, get_core_id());
103 ksteube 1561 }
104     }
105    
106 gross 391 void setNumberOfThreads(const int num_threads)
107     {
108    
109     #ifdef _OPENMP
110     omp_set_num_threads(num_threads);
111     #endif
112    
113     }
114    
115     int getNumberOfThreads()
116     {
117     #ifdef _OPENMP
118     return omp_get_max_threads();
119     #else
120     return 1;
121     #endif
122    
123     }
124    
125 gross 2313 ESCRIPT_DLL_API int getMPISizeWorld() {
126 ksteube 1805 int mpi_num = 1;
127     #ifdef PASO_MPI
128     MPI_Comm_size(MPI_COMM_WORLD, &mpi_num);
129     #endif
130     return mpi_num;
131     }
132    
133 gross 2313 ESCRIPT_DLL_API int getMPIRankWorld() {
134 ksteube 1805 int mpi_iam = 0;
135     #ifdef PASO_MPI
136     MPI_Comm_rank(MPI_COMM_WORLD, &mpi_iam);
137     #endif
138     return mpi_iam;
139     }
140    
141 gross 2308 ESCRIPT_DLL_API int getMPIWorldMax(const int val) {
142     #ifdef PASO_MPI
143     int val2 = val;
144     int out = val;
145     MPI_Allreduce( &val2, &out, 1, MPI_INT, MPI_MAX, MPI_COMM_WORLD );
146     #else
147     int out = val;
148     #endif
149     return out;
150     }
151    
152 jfenwick 2607 ESCRIPT_DLL_API int getMPIWorldSum(const int val) {
153     #ifdef PASO_MPI
154     int val2 = val;
155     int out = 0;
156     MPI_Allreduce( &val2, &out, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD );
157     #else
158     int out = val;
159     #endif
160     return out;
161     }
162 gross 2308
163 gross 2313 ESCRIPT_DLL_API double getMachinePrecision() {
164 gross 2100 return DBL_EPSILON;
165     }
166 gross 2313 ESCRIPT_DLL_API double getMaxFloat() {
167 gross 2100 return DBL_MAX;
168     }
169 gross 2313 ESCRIPT_DLL_API void MPIBarrierWorld() {
170     #ifdef PASO_MPI
171     MPI_Barrier(MPI_COMM_WORLD );
172     #endif
173     }
174 gross 2100
175 jfenwick 2642
176 jfenwick 2635 ESCRIPT_DLL_API
177     void
178     saveDataCSV(const std::string& filename, boost::python::dict arg, const std::string& sep, const std::string& csep,
179     bool append)
180     {
181     using std::cout;
182     using std::endl;
183     boost::python::list keys=arg.keys();
184     int numdata = boost::python::extract<int>(arg.attr("__len__")());
185 jfenwick 2637 bool hasmask=arg.has_key("mask");
186     Data mask;
187     if (hasmask)
188     {
189     mask=boost::python::extract<escript::Data>(arg["mask"]);
190     keys.remove("mask");
191     numdata--;
192     if (mask.getDataPointRank()!=0)
193     {
194     throw DataException("saveDataCSVcpp: masks must be scalar.");
195     }
196     }
197 jfenwick 2635 if (numdata<1)
198     {
199     throw DataException("saveDataCSVcpp: no data to save specified.");
200     }
201     std::vector<int> step(numdata);
202     std::vector<std::string> names(numdata);
203     std::vector<Data> data(numdata);
204     std::vector<const DataAbstract::ValueType::value_type*> samples(numdata);
205     std::vector<int> offset(numdata);
206     std::vector<int> fstypes(numdata); // FunctionSpace types for each data
207 gross 2100
208 jfenwick 2644 keys.sort(); // to get some predictable order to things
209    
210 jfenwick 2635 // We need to interpret the samples correctly even if they are different types
211     // for this reason, we should interate over samples
212     for (int i=0;i<numdata;++i)
213     {
214     names[i]=boost::python::extract<std::string>(keys[i]);
215     data[i]=boost::python::extract<escript::Data>(arg[keys[i]]);
216 jfenwick 2637 step[i]=(data[i].actsExpanded()?DataTypes::noValues(data[i].getDataPointShape()):0);
217 jfenwick 2635 fstypes[i]=data[i].getFunctionSpace().getTypeCode();
218     if (i>0)
219     {
220     if (data[i].getDomain()!=data[i-1].getDomain())
221     {
222     throw DataException("saveDataCSVcpp: all data must be on the same domain.");
223     }
224     }
225     }
226     int bestfnspace=0;
227     if (!data[0].getDomain()->commonFunctionSpace(fstypes, bestfnspace))
228     {
229     throw DataException("saveDataCSVcpp: FunctionSpaces of data are incompatible");
230     }
231     // now we interpolate all data to the same type
232     FunctionSpace best(data[0].getDomain(),bestfnspace);
233     for (int i=0;i<numdata;++i)
234     {
235     data[i]=data[i].interpolate(best);
236     }
237     int numsamples=data[0].getNumSamples(); // these must be the same for all data
238     int dpps=data[0].getNumDataPointsPerSample();
239    
240    
241 jfenwick 2641 std::ostringstream os;
242 jfenwick 2635
243 jfenwick 2641
244 jfenwick 2635 bool first=true;
245 jfenwick 2641
246     if (data[0].getDomain()->getMPIRank()==0)
247 jfenwick 2635 {
248 jfenwick 2641 for (int i=0;i<numdata;++i)
249     {
250 jfenwick 2635 const DataTypes::ShapeType& s=data[i].getDataPointShape();
251     switch (data[i].getDataPointRank())
252     {
253     case 0: if (!first)
254     {
255     os << sep;
256     }
257     else
258     {
259     first=false;
260     }
261     os << names[i]; break;
262     case 1: for (int j=0;j<s[0];++j)
263     {
264     if (!first)
265     {
266     os << sep;
267     }
268     else
269     {
270     first=false;
271     }
272     os << names[i] << csep << j;
273     }
274     break;
275     case 2: for (int j=0;j<s[0];++j)
276     {
277     for (int k=0;k<s[1];++k)
278     {
279     if (!first)
280     {
281     os << sep;
282     }
283     else
284     {
285     first=false;
286     }
287     os << names[i] << csep << k << csep << j;
288     }
289     }
290     break;
291     case 3: for (int j=0;j<s[0];++j)
292     {
293     for (int k=0;k<s[1];++k)
294     {
295     for (int l=0;l<s[2];++l)
296     {
297     if (!first)
298     {
299     os << sep;
300     }
301     else
302     {
303     first=false;
304     }
305     os << names[i] << csep << k << csep << j << csep << l;
306     }
307     }
308     }
309     break;
310     case 4: for (int j=0;j<s[0];++j)
311     {
312     for (int k=0;k<s[1];++k)
313     {
314     for (int l=0;l<s[2];++l)
315     {
316     for (int m=0;m<s[3];++m)
317     {
318     if (!first)
319     {
320     os << sep;
321     }
322     else
323     {
324     first=false;
325     }
326     os << names[i] << csep << k << csep << j << csep << l << csep << m;
327     }
328     }
329     }
330     }
331     break;
332     default:
333     throw DataException("saveDataCSV: Illegal rank");
334     }
335 jfenwick 2641 }
336     os << endl;
337 jfenwick 2635 }
338 jfenwick 2637 boost::scoped_ptr<BufferGroup> maskbuffer; // sample buffer for the mask [if we have one]
339     const double* masksample=0;
340     int maskoffset=0;
341 jfenwick 2635 //the use of shared_ptr here is just to ensure the buffer group is freed
342     //I would have used scoped_ptr but they don't work in vectors
343     std::vector<boost::shared_ptr<BufferGroup> > bg(numdata);
344     for (int d=0;d<numdata;++d)
345     {
346     bg[d].reset(data[d].allocSampleBuffer());
347     }
348    
349 jfenwick 2637 bool expandedmask=false; // does the mask act expanded. Are there mask value for each point in the sample
350     bool wantrow=true; // do we output this row?
351     if (hasmask)
352     {
353     maskbuffer.reset(mask.allocSampleBuffer());
354     if (mask.actsExpanded())
355     {
356     maskoffset=DataTypes::noValues(mask.getDataPointShape());
357     expandedmask=true;
358     }
359     }
360 jfenwick 2641 os.setf(std::ios_base::scientific, std::ios_base::floatfield);
361     os.precision(15);
362    
363     // errors prior to this point will occur on all processes anyway
364     // so there is no need to explicitly notify other ranks
365     int error=0;
366 jfenwick 2635 try{
367     for (int i=0;i<numsamples;++i)
368     {
369 jfenwick 2642 if (!best.ownSample(i))
370     {
371     continue;
372     }
373 jfenwick 2637 wantrow=true;
374 jfenwick 2635 for (int d=0;d<numdata;++d)
375     {
376     samples[d]=data[d].getSampleDataRO(i,bg[d].get());
377     }
378 jfenwick 2637 if (hasmask)
379     {
380     masksample=mask.getSampleDataRO(i, maskbuffer.get());
381     if (!expandedmask) // mask controls whole sample
382     {
383     if (masksample[0]<=0) // masks are scalar
384     {
385     wantrow=false;
386     }
387     }
388     }
389 jfenwick 2635 for (int j=0;j<dpps;++j)
390     {
391 jfenwick 2637 // now we need to check if this point is masked off
392     if (expandedmask)
393 jfenwick 2635 {
394 jfenwick 2637 wantrow=(masksample[j]>0); // masks are scalar to the relevant value is at [j]
395 jfenwick 2635 }
396 jfenwick 2637 if (wantrow)
397     {
398     bool needsep=false;
399     for (int d=0;d<numdata;++d)
400     {
401     DataTypes::pointToStream(os, samples[d], data[d].getDataPointShape(), offset[d], needsep, sep);
402     needsep=true;
403     offset[d]+=step[d];
404     }
405     os << endl;
406     }
407 jfenwick 2635 }
408     for (int d=0;d<numdata;++d)
409     {
410     offset[d]=0;
411     }
412     }
413     } catch (...)
414     {
415 jfenwick 2641 error=1;
416     #ifndef PASO_MPI
417 jfenwick 2635 throw;
418 jfenwick 2641 #endif
419 jfenwick 2635 }
420 jfenwick 2641 #ifdef PASO_MPI
421     MPI_Comm com=data[0].getDomain()->getMPIComm();
422     int rerror=0;
423     MPI_Allreduce( &error, &rerror, 1, MPI_INT, MPI_MAX, com );
424     error=rerror;
425     if (error)
426     {
427     throw DataException("saveDataCSVcpp: error building output");
428     }
429     #endif
430 jfenwick 2637
431 jfenwick 2641 // at this point os will contain the text to be written
432     #ifndef PASO_MPI
433 jfenwick 2637
434 jfenwick 2641 std::ofstream ofs;
435     if (append)
436     {
437     ofs.open(filename.c_str(), std::ios_base::app);
438     }
439     else
440     {
441     ofs.open(filename.c_str());
442     }
443     if (!ofs.is_open())
444     {
445     throw DataException("saveDataCSVcpp: unable to open file for writing");
446     }
447     ofs << os.str();
448     ofs.close();
449    
450     #else
451     // here we have MPI
452     const char* mpistr=0;
453     MPI_File mpi_fileHandle_p;
454     MPI_Status mpi_status;
455     MPI_Info mpi_info = MPI_INFO_NULL;
456     char* fname_c=new char[filename.size()+1];
457     strcpy(fname_c,filename.c_str());
458     boost::scoped_ptr<char> fname_p(fname_c);
459    
460     int amode = MPI_MODE_CREATE|MPI_MODE_WRONLY|MPI_MODE_UNIQUE_OPEN;
461     if (append)
462     {
463     amode |= MPI_MODE_APPEND;
464     }
465     else
466     {
467     if (data[0].getDomain()->getMPIRank()==0)
468     {
469     std::ifstream ifs(fname_p.get()); // if file exists, remove it
470     if (ifs.is_open())
471     {
472     ifs.close();
473 jfenwick 2642 if (remove(fname_p.get()))
474 jfenwick 2641 {
475     error=1;
476     }
477     }
478     }
479     data[0].getDomain()->MPIBarrier();
480     int rerror=0;
481     MPI_Allreduce( &error, &rerror, 1, MPI_INT, MPI_MAX, com );
482     if (rerror!=0)
483     {
484     std::ostringstream oss;
485     oss << "saveDataCSVcpp: File " << filename << " already exists and could not be removed in preparation for new output.";
486     throw DataException(oss.str());
487     }
488     }
489     int ierr;
490     ierr = MPI_File_open(com, fname_p.get(), amode, mpi_info, &mpi_fileHandle_p);
491     if (ierr != MPI_SUCCESS)
492     {
493     std::ostringstream oss;
494     oss << "saveDataCSVcpp: File " << filename << " could not be opened for writing in parallel";
495     // file is not open so we can throw
496     throw DataException(oss.str());
497     }
498     else
499     {
500     ierr=MPI_File_set_view(mpi_fileHandle_p,MPI_DISPLACEMENT_CURRENT,
501     MPI_CHAR, MPI_CHAR, "native", mpi_info);
502     // here we are assuming that std::string holds the same type of char as MPI_CHAR
503     }
504 jfenwick 2642
505 jfenwick 2641 std::string contents=os.str();
506     char* con=new char[contents.size()+1];
507     strcpy(con, contents.c_str());
508     boost::scoped_ptr<char> buff(con);
509     ierr=MPI_File_write_ordered(mpi_fileHandle_p, buff.get(), contents.size(), MPI_CHAR, &mpi_status);
510     if (ierr != MPI_SUCCESS)
511     {
512     error=1;
513     }
514    
515     if (MPI_File_close(&mpi_fileHandle_p)!= MPI_SUCCESS)
516     {
517     error=1;
518     }
519     data[0].getDomain()->MPIBarrier();
520     if (error) // any errors at this stage are from collective routines
521     { // so there is no need to reduce_all
522     throw DataException("saveDataCSVcpp: Error writing and closing file");
523     }
524    
525     #endif
526 jfenwick 2635 }
527    
528 jfenwick 2642
529 gross 391 } // end of namespace

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