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

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Revision 1877 - (hide annotations)
Tue Oct 14 02:58:39 2008 UTC (13 years ago) by ksteube
File size: 14170 byte(s)
convection.py checkpointing uses mkdir/rmdir, and under MPI there
was a race condition.

mkdir needs to be run on only one CPU and then a barrier to prevent
working processors from using the directory before it exists.

Added methods domain.MPIBarrier and domain.onMasterProcessor() to
implement this technique.

A more general solution might be possible in the future.

1 jgs 102
2 ksteube 1312 /*******************************************************
3 ksteube 1811 *
4     * Copyright (c) 2003-2008 by University of Queensland
5     * 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 jgs 474 #include "Data.h"
16     #include "FunctionSpace.h"
17     #include "FunctionSpaceFactory.h"
18     #include "DataFactory.h"
19     #include "AbstractContinuousDomain.h"
20     #include "AbstractDomain.h"
21     #include "Utils.h"
22 jgs 480 #include "AbstractSystemMatrix.h"
23 gross 1364 #include "AbstractTransportProblem.h"
24 gross 797 #include "DataVector.h"
25 ksteube 1800 #include "paso/Paso_MPI.h"
26 jgs 474
27 jfenwick 1872
28    
29 ksteube 1312 extern "C" {
30     #include "escript/blocktimer.h"
31     }
32    
33 robwdcock 682 #include "esysUtils/esysExceptionTranslator.h"
34 jgs 102
35     #include <boost/python.hpp>
36     #include <boost/python/module.hpp>
37     #include <boost/python/def.hpp>
38     #include <boost/python/object.hpp>
39     #include <boost/python/tuple.hpp>
40 gross 285 #include <boost/python/numeric.hpp>
41 jfenwick 1872 #include <boost/smart_ptr.hpp>
42 gross 285
43 jgs 102 using namespace boost::python;
44    
45 jgs 121 /*! \mainpage Esys Documentation
46     *
47     * \version 1.0.0
48     *
49     * - \ref escript
50     *
51     * - \ref esys_exception "Esys Exception"
52     *
53     * - \ref finley
54     *
55 cochrane 358 * - <a href=http://iservo.edu.au/esys/epydoc/index.html>Python module documentation (epydoc generated)</a>
56 jgs 122 *
57 jgs 121 */
58 jgs 102
59 jgs 121 /*! \page escript Escript
60     * Escript is the python module that contains the interfaces
61     * to the C++ side of escript.
62     *
63     * \version 1.0.0
64     *
65     * \section class_desc Class Description:
66     * Data
67     *
68     * \section class_limits Class Limitations:
69     * None
70     *
71     * \section class_conds Class Conditions of Use:
72     * None
73     *
74     * \section class_throws Throws:
75     * None
76     *
77     */
78 jgs 102
79     BOOST_PYTHON_MODULE(escriptcpp)
80     {
81 gross 391 def("setNumberOfThreads",escript::setNumberOfThreads);
82     def("getNumberOfThreads",escript::getNumberOfThreads);
83 gross 797 def("releaseUnusedMemory",escript::releaseUnusedMemory);
84 ksteube 1312 def("blocktimer_initialize",blocktimer_initialize);
85     def("blocktimer_reportSortByName",blocktimer_reportSortByName);
86     def("blocktimer_reportSortByTime",blocktimer_reportSortByTime);
87     def("blocktimer_increment",blocktimer_increment);
88     def("blocktimer_time",blocktimer_time);
89 ksteube 1247 def("getVersion",escript::getSvnVersion);
90 ksteube 1561 def("printParallelThreadCounts",escript::printParallelThreadCnt);
91 ksteube 1805 def("getMPISizeWorld",escript::getMPISizeWorld);
92     def("getMPIRankWorld",escript::getMPIRankWorld);
93 jgs 102
94 gross 797
95 jgs 102 //
96     // Interface for AbstractDomain
97     //
98 jfenwick 1872 class_<escript::AbstractDomain, escript::Domain_ptr>("Domain",no_init)
99 gross 1044 .def("setTagMap",&escript::AbstractDomain::setTagMap)
100     .def("getTag",&escript::AbstractDomain::getTag)
101     .def("isValidTagName",&escript::AbstractDomain::isValidTagName)
102     .def("showTagNames",&escript::AbstractDomain::showTagNames)
103 jgs 102 .def("getX",&escript::AbstractDomain::getX)
104 jfenwick 1803 .def("getDim",&escript::AbstractDomain::getDim)
105 jgs 102 .def("getNormal",&escript::AbstractDomain::getNormal)
106     .def("getSize",&escript::AbstractDomain::getSize)
107 jgs 153 .def("saveVTK",&escript::AbstractDomain::saveVTK)
108     .def("saveDX",&escript::AbstractDomain::saveDX)
109 ksteube 1312 .def("getMPISize",&escript::AbstractDomain::getMPISize)
110     .def("getMPIRank",&escript::AbstractDomain::getMPIRank)
111 ksteube 1877 .def("MPIBarrier",&escript::AbstractDomain::MPIBarrier)
112     .def("onMasterProcessor",&escript::AbstractDomain::onMasterProcessor)
113 ksteube 1312
114 jgs 102 .def(self == self)
115     .def(self != self);
116    
117     //
118     // Interface for AbstractContinuousDomain
119     //
120     class_<escript::AbstractContinuousDomain, bases<escript::AbstractDomain> >("ContinuousDomain",no_init)
121 gross 1859 .def("getSystemMatrixTypeId",&escript::AbstractContinuousDomain::getSystemMatrixTypeId)
122     .def("getTransportTypeId",&escript::AbstractContinuousDomain::getTransportTypeId);
123 jgs 102
124     //
125     // Interface for FunctionSpace
126     //
127 trankine 1426 class_<escript::FunctionSpace> fs_definer("FunctionSpace",init<>());
128     fs_definer.def("getDim",&escript::FunctionSpace::getDim);
129 jfenwick 1872 // fs_definer.def("getDomain",&escript::FunctionSpace::getDomain,
130     // return_internal_reference<>());
131     fs_definer.def("getDomain",&escript::FunctionSpace::getDomainPython);
132 trankine 1426 fs_definer.def("getX",&escript::FunctionSpace::getX);
133     fs_definer.def("getNormal",&escript::FunctionSpace::getNormal);
134     fs_definer.def("getSize",&escript::FunctionSpace::getSize);
135     fs_definer.def("setTags",&escript::FunctionSpace::setTags);
136     fs_definer.def("getTagFromDataPointNo",
137     &escript::FunctionSpace::getTagFromDataPointNo);
138 gross 1718 fs_definer.def("getReferenceIDFromDataPointNo", &escript::FunctionSpace::getReferenceIDFromDataPointNo);
139 gross 1716 fs_definer.def("getListOfTags",&escript::FunctionSpace::getListOfTags);
140 phornby 1628 fs_definer.def("__str__", &escript::FunctionSpace::toString);
141 trankine 1426 fs_definer.def(self == self);
142     fs_definer.def(self != self);
143 jgs 102 //
144     // Interface for Data
145     //
146 jfenwick 1872 class_<escript::Data>("Data","TEST DOCUMENTATION",init<>() )
147 jgs 102 // various constructors for Data objects
148     .def(init<const numeric::array&, optional<const escript::FunctionSpace&, bool> >(args("value","what","expand")))
149     .def(init<const object&, optional<const escript::FunctionSpace&, bool> >(args("value","what","expand")))
150     .def(init<const double, const tuple&, optional<const escript::FunctionSpace&, bool> >(args("value","shape","what","expand")))
151     .def(init<const escript::Data&, const escript::FunctionSpace&>(args("value","what")))
152     .def(init<const escript::Data&>())
153     // Note for Lutz, Need to specify the call policy in order to return a
154     // reference. In this case return_internal_reference.
155 ksteube 1312 .def("__str__",&escript::Data::toString)
156 jfenwick 1872 // .def("getDomain",&escript::Data::getDomain,return_internal_reference<>())
157     .def("getDomain",&escript::Data::getDomainPython)
158     .def("getFunctionSpace",&escript::Data::getFunctionSpace,return_value_policy<copy_const_reference>())
159 jgs 102 .def("isEmpty",&escript::Data::isEmpty)
160 gross 783 .def("isProtected",&escript::Data::isProtected)
161     .def("setProtection",&escript::Data::setProtection)
162 jgs 102 .def("getShape",&escript::Data::getShapeTuple)
163     .def("getRank",&escript::Data::getDataPointRank)
164 gross 950 .def("dump",&escript::Data::dump)
165 jgs 102 .def("copyWithMask",&escript::Data::copyWithMask)
166     .def("setTaggedValue",&escript::Data::setTaggedValue)
167 gross 1044 .def("setTaggedValue",&escript::Data::setTaggedValueByName)
168 gross 921 .def("getNumberOfDataPoints",&escript::Data::getNumDataPoints)
169 gross 1141 .def("isExpanded",&escript::Data::isExpanded)
170     .def("isTagged",&escript::Data::isTagged)
171 jgs 119 .def("expand",&escript::Data::expand)
172     .def("tag",&escript::Data::tag)
173 jgs 126 .def("copy",&escript::Data::copy)
174 jfenwick 1799 .def("copy",&escript::Data::copySelf,return_value_policy<manage_new_object>())
175 gross 1034 .def("setValueOfDataPoint",&escript::Data::setValueOfDataPointToPyObject)
176     .def("setValueOfDataPoint",&escript::Data::setValueOfDataPointToArray)
177 gross 921 .def("setValueOfDataPoint",&escript::Data::setValueOfDataPoint)
178     .def("getValueOfDataPoint",&escript::Data::getValueOfDataPoint)
179     .def("getValueOfGlobalDataPoint",&escript::Data::getValueOfGlobalDataPoint)
180 gross 1118 .def("setToZero",&escript::Data::setToZero)
181 gross 285 .def("interpolate",&escript::Data::interpolate)
182 gross 921 .def("minGlobalDataPoint",&escript::Data::minGlobalDataPoint)
183 gross 285 .def("saveDX",&escript::Data::saveDX)
184     .def("saveVTK",&escript::Data::saveVTK)
185 jgs 149 .def("getTagNumber",&escript::Data::getTagNumber)
186 gross 285 // Unary functions for Data
187     .def("_interpolate",&escript::Data::interpolate)
188     .def("_grad",&escript::Data::gradOn)
189     .def("_grad",&escript::Data::grad)
190     .def("_transpose",&escript::Data::transpose)
191     .def("_trace",&escript::Data::trace)
192     .def("_maxval",&escript::Data::maxval)
193     .def("_minval",&escript::Data::minval)
194 gross 698 .def("_wherePositive",&escript::Data::wherePositive)
195     .def("_whereNegative",&escript::Data::whereNegative)
196     .def("_whereNonNegative",&escript::Data::whereNonNegative)
197     .def("_whereNonPositive",&escript::Data::whereNonPositive)
198 jgs 571 .def("_whereZero",&escript::Data::whereZero,(arg("tol")=0.0))
199     .def("_whereNonZero",&escript::Data::whereNonZero,(arg("tol")=0.0))
200 ksteube 876 .def("_erf",&escript::Data::erf)
201 gross 285 .def("_sin",&escript::Data::sin)
202     .def("_cos",&escript::Data::cos)
203     .def("_tan",&escript::Data::tan)
204     .def("_asin",&escript::Data::asin)
205     .def("_acos",&escript::Data::acos)
206     .def("_atan",&escript::Data::atan)
207     .def("_sinh",&escript::Data::sinh)
208     .def("_cosh",&escript::Data::cosh)
209     .def("_tanh",&escript::Data::tanh)
210     .def("_asinh",&escript::Data::asinh)
211     .def("_acosh",&escript::Data::acosh)
212     .def("_atanh",&escript::Data::atanh)
213     .def("_exp",&escript::Data::exp)
214     .def("_sqrt",&escript::Data::sqrt)
215     .def("_log10",&escript::Data::log10)
216     .def("_log",&escript::Data::log)
217     .def("_sign",&escript::Data::sign)
218 ksteube 775 .def("_symmetric",&escript::Data::symmetric)
219     .def("_nonsymmetric",&escript::Data::nonsymmetric)
220 gross 800 .def("_trace",&escript::Data::trace)
221 gross 804 .def("_swap_axes",&escript::Data::swapaxes)
222 gross 576 .def("_eigenvalues",&escript::Data::eigenvalues)
223     .def("_eigenvalues_and_eigenvectors",&escript::Data::eigenvalues_and_eigenvectors,(arg("tol")=1.e-13))
224 gross 285 // functions returning a single real number:
225     .def("_Lsup",&escript::Data::Lsup)
226     .def("_sup",&escript::Data::sup)
227     .def("_inf",&escript::Data::inf)
228     .def("_integrate",&escript::Data::integrate)
229    
230     // following implements the python abs operator
231 jgs 108 .def("__abs__",&escript::Data::abs)
232 jgs 102 // following implements the python "-" negation operator
233     .def("__neg__",&escript::Data::neg)
234     // following implements the python "+" identity operator
235     .def("__pos__",&escript::Data::pos)
236     // following two functions implement the python [] operator
237     .def("__getitem__",&escript::Data::getItem)
238     .def("__setitem__",&escript::Data::setItemO)
239     .def("__setitem__",&escript::Data::setItemD)
240     // following two functions implement the python ** operator
241     .def("__pow__",&escript::Data::powO)
242     .def("__pow__",&escript::Data::powD)
243 gross 699 .def("__rpow__",&escript::Data::rpowO)
244 jgs 102 // NOTE:: The order of these declarations is important. Anything
245     // declared before the generic declaration isn't found so the generic
246     // version will be called.
247     .def(self + other<object>())
248     .def(other<object>() + self)
249     .def(self + self)
250 gross 285 .def(self += other<object>())
251     .def(self += self)
252    
253 jgs 102 .def(self - other<object>())
254     .def(other<object>() - self)
255     .def(self - self)
256 gross 285 .def(self -= other<object>())
257     .def(self -= self)
258    
259 jgs 102 .def(self * other<object>())
260     .def(other<object>() * self)
261     .def(self * self)
262 gross 285 .def(self *= other<object>())
263     .def(self *= self)
264    
265 jgs 102 .def(self / other<object>())
266     .def(other<object>() / self)
267     .def(self / self)
268 gross 285 .def(self /= other<object>())
269     .def(self /= self)
270 jgs 102 // Need scope resolution due to a bug either in the compiler or
271     // the boost code. This calls operator << for Data.
272     .def(self_ns::str(self));
273    
274     //
275     // Factory methods for function space
276     //
277     def("ContinuousFunction",escript::continuousFunction);
278 gross 1062 def("ReducedContinuousFunction",escript::reducedContinuousFunction);
279 jgs 102 def("Function",escript::function);
280 gross 1062 def("ReducedFunction",escript::reducedFunction);
281 jgs 102 def("FunctionOnBoundary",escript::functionOnBoundary);
282 gross 1062 def("ReducedFunctionOnBoundary",escript::reducedFunctionOnBoundary);
283 jgs 102 def("FunctionOnContactZero",escript::functionOnContactZero);
284 gross 1062 def("ReducedFunctionOnContactZero",escript::reducedFunctionOnContactZero);
285 jgs 102 def("FunctionOnContactOne",escript::functionOnContactOne);
286 gross 1062 def("ReducedFunctionOnContactOne",escript::reducedFunctionOnContactOne);
287 jgs 102 def("Solution",escript::solution);
288     def("ReducedSolution",escript::reducedSolution);
289     def("DiracDeltaFunction",escript::diracDeltaFunction);
290    
291     //
292     // Factory methods for Data
293     //
294 gross 950 def("load",escript::load);
295 gross 1023 def("loadIsConfigured",escript::loadConfigured);
296 jgs 102 def("Scalar",escript::Scalar,
297     (arg("value")=0.0,
298     arg("what")=escript::FunctionSpace(),
299     arg("expanded")=false));
300     def("Vector",escript::Vector,
301     (arg("value")=0.0,
302     arg("what")=escript::FunctionSpace(),
303     arg("expanded")=false));
304     def("Tensor",escript::Tensor,
305     (arg("value")=0.0,
306     arg("what")=escript::FunctionSpace(),
307     arg("expanded")=false));
308     def("Tensor3",escript::Tensor3,
309     (arg("value")=0.0,
310     arg("what")=escript::FunctionSpace(),
311     arg("expanded")=false));
312     def("Tensor4",escript::Tensor4,
313     (arg("value")=0.0,
314     arg("what")=escript::FunctionSpace(),
315     arg("expanded")=false));
316    
317     //
318 ksteube 813 // Binary operators
319     //
320     def("C_GeneralTensorProduct",escript::C_GeneralTensorProduct,
321     (arg("arg0")=escript::Data(),
322     arg("arg1")=escript::Data(),
323     arg("axis_offset")=0,
324     arg("transpose")=0));
325    
326     //
327 jgs 102 // Interface for AbstractSystemMatrix
328     //
329     class_<escript::AbstractSystemMatrix>("Operator",init<>())
330     .def("isEmpty",&escript::AbstractSystemMatrix::isEmpty)
331     .def("solve",&escript::AbstractSystemMatrix::solve)
332     .def("of",&escript::AbstractSystemMatrix::vectorMultiply)
333     .def("saveMM",&escript::AbstractSystemMatrix::saveMM)
334 jgs 123 .def("saveHB",&escript::AbstractSystemMatrix::saveHB)
335 jgs 149 .def("resetValues",&escript::AbstractSystemMatrix::resetValues)
336 jgs 102 .def(self*other<escript::Data>());
337 gross 1364 //
338     // Interface for AbstractTransportProblem
339     //
340     class_<escript::AbstractTransportProblem>("TransportProblem",init<>())
341     .def("isEmpty",&escript::AbstractTransportProblem::isEmpty)
342     .def("solve",&escript::AbstractTransportProblem::solve)
343 gross 1370 .def("setInitialValue",&escript::AbstractTransportProblem::setInitialValue)
344 gross 1417 .def("insertConstraint",&escript::AbstractTransportProblem::insertConstraint)
345     .def("reset",&escript::AbstractTransportProblem::resetTransport)
346 gross 1841 .def("resetValues",&escript::AbstractTransportProblem::resetTransport)
347 gross 1859 .def("getSafeTimeStepSize",&escript::AbstractTransportProblem::getSafeTimeStepSize)
348     .def("getUnlimitedTimeStepSize",&escript::AbstractTransportProblem::getUnlimitedTimeStepSize);
349 jgs 102
350     //
351     // Register esysExceptionTranslator
352     //
353     register_exception_translator<esysUtils::EsysException>(&esysUtils::esysExceptionTranslator);
354    
355     }

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