Log of /branches/diaplayground/escriptcore/src/escriptcpp.cpp
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Revision
5136 -
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Modified
Tue Sep 9 07:13:55 2014 UTC
(4 years, 5 months ago)
by
caltinay
File length: 74894 byte(s)
Diff to
previous 5135
ripley now supports paso solvers again and returns an appropriate matrix type
id. Changed the getSystemMatrixTypeId() method to take a full SolverBuddy
instance and made some other simplifications.
Revision
5135 -
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Modified
Mon Sep 8 07:17:34 2014 UTC
(4 years, 5 months ago)
by
caltinay
File length: 74955 byte(s)
Diff to
previous 5130
Added and renamed Solver Options. Still need to update some tests.
Revision
5130 -
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Modified
Tue Sep 2 06:09:54 2014 UTC
(4 years, 5 months ago)
by
caltinay
File length: 74876 byte(s)
Diff to
previous 5122
Implemented transposed SpMV for DIA and CDS on CPU and GPU.
Added LSQR solver, not optimized yet but works in general.
Revision
5122 -
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Modified
Thu Aug 21 04:32:39 2014 UTC
(4 years, 5 months ago)
by
caltinay
File length: 74834 byte(s)
Diff to
previous 5084
Fast-forward to latest trunk to be able to use both Paso or cusp.
Revision
5084 -
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Modified
Sun Jun 29 23:29:51 2014 UTC
(4 years, 7 months ago)
by
caltinay
File length: 74769 byte(s)
Diff to
previous 5062
Fast forward to latest trunk which has had an impressive number of changes...
Revision
4949 -
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Modified
Mon May 19 05:54:58 2014 UTC
(4 years, 9 months ago)
by
caltinay
File length: 73549 byte(s)
Diff to
previous 4940
Fast forward to current trunk rev 4947.
All tests that don't require a direct solver pass without MPI.
Revision
4821 -
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Modified
Tue Apr 1 04:58:33 2014 UTC
(4 years, 10 months ago)
by
sshaw
Original Path:
trunk/escriptcore/src/escriptcpp.cpp
File length: 66944 byte(s)
Diff to
previous 4759
moved SolverOptions to c++, split into SolverOptions for the options and SolverBuddy as the state as a precursor to per-pde solving... does break some use cases (e.g. pde.getSolverOptions().DIRECT will now fail, new value access is with SolverOptions.DIRECT), examples and documentation updated to match
Revision
4603 -
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Modified
Wed Dec 18 02:24:32 2013 UTC
(5 years, 2 months ago)
by
jfenwick
Original Path:
trunk/escriptcore/src/escriptcpp.cpp
File length: 39860 byte(s)
Diff to
previous 4521
Added boost::noncopyable to remaining abstract base classes in the module file.
ie escriptcpp.cpp
Note I have not altered the c++ inheritance (this just just for the boost::python import)
Revision
4255 -
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Modified
Wed Feb 27 03:06:21 2013 UTC
(5 years, 11 months ago)
by
jfenwick
Original Path:
trunk/escript/src/escriptcpp.cpp
File length: 39582 byte(s)
Diff to
previous 4154
Hopefully, this will address the interpolation problems.
New canInterpolate() function exposed to python which calls probeInterpolation
AbstractDomain now has an additional virtual.
preferredIntrpolationOnDomain()
This will return 0 if interpolation is impossible, 1 if possible and preferred.
It will return -1 if interpolation is possible and preferred in the
oposite direction.
A value of -1 does not say that the proposed interpolation is possible or not.
Rather it indicates "please use the other way".
If you really _need_ to test it that way, use probeInterpolationOnDomain
Revision
3918 -
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Modified
Thu Jul 5 02:44:07 2012 UTC
(6 years, 7 months ago)
by
jfenwick
Original Path:
trunk/escript/src/escriptcpp.cpp
File length: 39006 byte(s)
Diff to
previous 3911
Added unit test which uses the TestDomain to check reduction.
TestDomains can no longer be created directly from python
(fixes problem I had earlier)
TestDomain can now create testdomains with aribtrarily sized
coordinate vectors.
Revision
2827 -
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Modified
Fri Dec 18 03:41:09 2009 UTC
(9 years, 2 months ago)
by
jfenwick
Original Path:
trunk/escript/src/escriptcpp.cpp
File length: 32543 byte(s)
Diff to
previous 2799
There is now a mechanism to pass a C function into escript and invoke it on each datapoint with:
applyBinaryCFunction
Warning in order to use this function your escript must be compiled with
scons ... iknowwhatimdoing=yes
---------------------
Because this code relies on casts that the C standard does not allow some code has been moved into Dodgy{.h .cpp}
Scons files have been modified to treat these files specially [Warnings are not errors for these files.]
Revision
2766 -
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Modified
Mon Nov 23 05:10:53 2009 UTC
(9 years, 2 months ago)
by
jfenwick
Original Path:
trunk/escript/src/escriptcpp.cpp
File length: 32211 byte(s)
Diff to
previous 2742
inf, sup and Lsup now correctly handle +-infinity.
They also will return NaN if any part of their input is NaN.
This will break unit tests since it exposes the hidden bug (#447 in mantis)
This code relies on the ability to test for NaNs.
To do this it makes use of macros and functions from C99.
If you do not have a C99 compiler, then you will probably get the old behaviour.
That is, you won't know when you have NaNs.
Also did minor tweak to saveDataCSV doco.
Revision
2742 -
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Modified
Thu Nov 12 06:03:37 2009 UTC
(9 years, 3 months ago)
by
jfenwick
Original Path:
trunk/escript/src/escriptcpp.cpp
File length: 32055 byte(s)
Diff to
previous 2673
Merging changes from the lapack branch.
The inverse() operation has been moved into c++. [No lazy support for this operation yet.]
Optional Lapack support has been added for matrices larger than 3x3.
service0 is set to use mkl_lapack.
Revision
2653 -
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Modified
Tue Sep 8 04:26:30 2009 UTC
(9 years, 5 months ago)
by
jfenwick
Original Path:
trunk/escript/src/escriptcpp.cpp
File length: 31627 byte(s)
Diff to
previous 2649
Fix bug in maxGlobalDataPoint and minGlobalDataPoint.
They now give the correct answers and the datapoint ids returned are globally
correct.
Removed some #defines from before COW
Removed hasNoSamples() - I don't trust myself to use that properly let alone anybody else.
Revision
2635 -
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Modified
Thu Aug 27 04:54:41 2009 UTC
(9 years, 5 months ago)
by
jfenwick
Original Path:
trunk/escript/src/escriptcpp.cpp
File length: 29940 byte(s)
Diff to
previous 2628
A bunch of changes related to saveDataCSV.
[Not completed or unit tested yet]
Added saveDataCSV to util.py
AbstractDomain (and MeshAdapter) have a commonFunctionSpace method to
take a group of FunctionSpaces and return something they can all be interpolated to.
Added pointToStream() in DataTypes to help print points.
added actsConstant() to data - required because DataConstant doesn't store samples the same way other Data do.
Revision
2607 -
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Modified
Tue Aug 18 01:02:56 2009 UTC
(9 years, 6 months ago)
by
jfenwick
Original Path:
trunk/escript/src/escriptcpp.cpp
File length: 16236 byte(s)
Diff to
previous 2602
Added getMPIWorldSum function to the esys.escript module.
This function takes an integer from each member of the MPIWorld.
This will hopefully address mantis issue 359
Added unit tests for most of the c++ free functions in the module.
Revision
2482 -
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Modified
Fri Jun 19 05:56:20 2009 UTC
(9 years, 8 months ago)
by
jfenwick
Original Path:
trunk/escript/src/escriptcpp.cpp
File length: 16004 byte(s)
Diff to
previous 2476
Added run_data_access.py to unit tests - tests things like toListOfTuples.
Corrected some doco comments.
Added TestDomain class to escript.
This should allow more testing without resorting to finley.
Revision
2308 -
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Modified
Mon Mar 16 01:20:56 2009 UTC
(9 years, 11 months ago)
by
gross
Original Path:
trunk/escript/src/escriptcpp.cpp
File length: 15717 byte(s)
Diff to
previous 2283
size_t may be 64 bits which is incompatible to MPI_INT. This problem is fixed by inserting a cast in Mesh_read.c.
Moreover a fix has been added making sure that gmsh and triangle are executed on one processor only.
Revision
2283 -
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Modified
Fri Feb 20 01:08:21 2009 UTC
(10 years ago)
by
jfenwick
Original Path:
trunk/escript/src/escriptcpp.cpp
File length: 15668 byte(s)
Diff to
previous 2271
doxygen doco now correctly reports global project revsion number.
link to epydoc is now via a relative URL (avoids the problem of nightly doxygen pointing at out of date release epydoc).
Revision
2100 -
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Modified
Wed Nov 26 08:13:00 2008 UTC
(10 years, 2 months ago)
by
gross
Original Path:
trunk/escript/src/escriptcpp.cpp
File length: 15470 byte(s)
Diff to
previous 2084
This commit cleans up the incompressible solver and adds a DarcyFlux solver in model module.
Some documentation for both classes has been added.
The convection code is only linear at the moment.
Revision
2084 -
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Modified
Fri Nov 21 05:20:42 2008 UTC
(10 years, 2 months ago)
by
jfenwick
Original Path:
trunk/escript/src/escriptcpp.cpp
File length: 15303 byte(s)
Diff to
previous 2078
Fixed a warning in cpp unit tests under dodebug
Pointed the url for python doco at shake200 rather than iservo.
Added support for trace and transpose to LazyData.
Fixed bug in trace to initialise running totals.
Revision
2078 -
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Modified
Thu Nov 20 16:10:10 2008 UTC
(10 years, 3 months ago)
by
phornby
Original Path:
trunk/escript/src/escriptcpp.cpp
File length: 15277 byte(s)
Diff to
previous 2076
Two changes.
1. Move blocktimer from escript to esysUtils.
2. Make it possible to link to paso as a DLL or .so.
Should have no effect on 'nix's
In respect of 1., blocktimer had begun to spring up everywhere, so
for the moment I thought it best to move it to the only other library that
pops up all over the place.
In respect of 2., paso needed to be a DLL in order to use the windows intelc /fast
option, which does aggressive multi-file optimisations. Even in its current form, it either
vectorises or parallelises hundreds more loops in the esys system than appear in the pragmas.
In achieving 2. I have not been too delicate in adding
PASO_DLL_API
declarations to the .h files in paso/src. Only toward the end of the process of
the conversion, when the number of linker errors dropped below 20, say, did I choosy about what
functions in a header I declared PASO_DLL_API. As a result, there are likely to be many routines
declared as external functions symbols that are in fact internal to the paso DLL.
Why is this an issue? It prevents the intelc compiler from getting aggressive on the paso module.
With pain there is sometimes gain. At least all the DLL rules in windows give good
(non-microsoft) compiler writers a chance to really shine.
So, if you should see a PASO_DLL_API on a function in a paso header file,
and think to yourself, "that function is only called in paso, why export it?", then feel free to
delete the PASO_DLL_API export declaration.
Here's hoping for no breakage.....
Revision
2076 -
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Modified
Thu Nov 20 12:34:17 2008 UTC
(10 years, 3 months ago)
by
phornby
Original Path:
trunk/escript/src/escriptcpp.cpp
File length: 15275 byte(s)
Diff to
previous 2064
I may get into trouble for this.
boost-python 1.34 does have a docstring_options class,
but does not have a 3 argument constructor for
it. So the test has been modified to
#if ((BOOST_VERSION/100)%1000 > 34) || (BOOST_VERSION/100000 >1)
If you wish to make things more delicate, one can define a 2 argument construction
of docopt just for 1.34 (with an #elif). Probably not worth the effort frankly.
Hope that this has not broken anything for anyone else. The SVN logs suggest this is a
little fragile.....
Also, please be aware that much of our chemistry interface code, that we wish to use with
escript, makes extensive use of boost python.
Having two different boost versions mucking with the python interpreter sounds
like a really bad idea, I'm sure you'll agree.
The problem is that it is not a simple task for us to build new versions of boost-python
on all our platforms. Consequently, it would be nice to be informed when you guys
intend to upgrade a support library of this nature so that we can plan and allocate
resources to keep up.
Cheers.
Revision
2005 -
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Modified
Mon Nov 10 01:21:39 2008 UTC
(10 years, 3 months ago)
by
jfenwick
Original Path:
trunk/escript/src/escriptcpp.cpp
File length: 14626 byte(s)
Diff to
previous 1897
Bringing all changes across from schroedinger.
(Note this does not mean development is done, just that it will happen
on the trunk for now).
If anyone notices any problems please contact me.
Revision
1897 -
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Modified
Mon Oct 20 00:32:30 2008 UTC
(10 years, 4 months ago)
by
jfenwick
Original Path:
trunk/escript/src/escriptcpp.cpp
File length: 14407 byte(s)
Diff to
previous 1877
Modified Data::toString() so it doesn't throw on DataEmpty.
Added setEscriptParamInt and getEscriptParamInt as free functions.
At the moment all they do is allow you to set the param TOO_MANY_LINES.
This is used to determine when printing a Data object will show you the
points and when it will print a summary.
I've set the default value back to 80 lines.
If you need to see more lines use (in python):
setEscriptParamInt("TOO_MANY_LINES",80000)
Revision
1877 -
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Modified
Tue Oct 14 02:58:39 2008 UTC
(10 years, 4 months ago)
by
ksteube
Original Path:
trunk/escript/src/escriptcpp.cpp
File length: 14170 byte(s)
Diff to
previous 1872
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.
Revision
1805 -
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Modified
Wed Sep 24 23:39:00 2008 UTC
(10 years, 4 months ago)
by
ksteube
Original Path:
trunk/escript/src/escriptcpp.cpp
File length: 13601 byte(s)
Diff to
previous 1803
Added python-level methods getMPISizeWorld() and getMPIRankWorld() for MPI process info.
Test suite run_inputOutput.py runs on any number of cores now, hybrid may still be a problem.
Revision
1803 -
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Modified
Wed Sep 24 06:20:29 2008 UTC
(10 years, 4 months ago)
by
jfenwick
Original Path:
trunk/escript/src/escriptcpp.cpp
File length: 13499 byte(s)
Diff to
previous 1801
All about making DataEmpty instances throw.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Exposed getDim from AbstractDomain to python to fix bug.
Added isEmpty member to DataAbstract to allow it to throw is queries are
made about a DataEmpty instance.
Added exceptions to DataAbstract, DataEmpty and Data to prevent calls
being made against DataEmpty objects.
The following still work as expected on DataEmpty instances
copy, getDomain, getFunctionSpace, isEmpty, isExpanded, isProtected,
isTagged, setprotection.
You can also call interpolate, however it should throw if you try to
change FunctionSpaces.
Revision
1800 -
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Modified
Thu Sep 18 05:28:20 2008 UTC
(10 years, 5 months ago)
by
ksteube
Original Path:
trunk/escript/src/escriptcpp.cpp
File length: 13507 byte(s)
Diff to
previous 1799
Serialized parallel I/O when writing mesh or data to NetCDF file on multiple MPI processors.
Added domain method getMPIComm() to complement getMPISize() and getMPIRank().
Revision
1799 -
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Modified
Wed Sep 17 06:33:18 2008 UTC
(10 years, 5 months ago)
by
jfenwick
Original Path:
trunk/escript/src/escriptcpp.cpp
File length: 13419 byte(s)
Diff to
previous 1796
Added Data::copySelf() [Note: this is exposed as copy() in python].
This method returns a pointer to a deep copy of the target.
There are c++ tests but no python tests for this yet.
All DataAbstracts now have a deepCopy() which simplifies the
implementation of the compy methods.
Revision
1628 -
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Modified
Fri Jul 11 13:12:46 2008 UTC
(10 years, 7 months ago)
by
phornby
Original Path:
trunk/escript/src/escriptcpp.cpp
File length: 13259 byte(s)
Diff to
previous 1561
Merge in /branches/windows_from_1456_trunk_1620_merged_in branch.
You will find a preserved pre-merge trunk in tags under tags/trunk_at_1625.
That will be useful for diffing & checking on my stupidity.
Here is a list of the conflicts and their resolution at this
point in time.
=================================================================================
(LLWS == looks like white space).
finley/src/Assemble_addToSystemMatrix.c - resolve to branch - unused var. may be wrong.....
finley/src/CPPAdapter/SystemMatrixAdapter.cpp - resolve to branch - LLWS
finley/src/CPPAdapter/MeshAdapter.cpp - resolve to branch - LLWS
paso/src/PCG.c - resolve to branch - unused var fixes.
paso/src/SolverFCT.c - resolve to branch - LLWS
paso/src/FGMRES.c - resolve to branch - LLWS
paso/src/Common.h - resolve to trunk version. It's omp.h's include... not sure it's needed,
but for the sake of saftey.....
paso/src/Functions.c - resolve to branch version, indentation/tab removal and return error
on bad unimplemented Paso_FunctionCall.
paso/src/SolverFCT_solve.c - resolve to branch version, unused vars
paso/src/SparseMatrix_MatrixVector.c - resolve to branch version, unused vars.
escript/src/Utils.cpp - resloved to branch, needs WinSock2.h
escript/src/DataExpanded.cpp - resolved to branch version - LLWS
escript/src/DataFactory.cpp - resolve to branch version
=================================================================================
This currently passes tests on linux (debian), but is not checked on windows or Altix yet.
This checkin is to make a trunk I can check out for windows to do tests on it.
Known outstanding problem is in the operator=() method of exceptions
causing warning messages on the intel compilers.
May the God of doughnuts have mercy on my soul.
Revision
1312 -
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Modified
Mon Sep 24 06:18:44 2007 UTC
(11 years, 4 months ago)
by
ksteube
Original Path:
trunk/escript/src/escriptcpp.cpp
File length: 12514 byte(s)
Diff to
previous 1247
The MPI branch is hereby closed. All future work should be in trunk.
Previously in revision 1295 I merged the latest changes to trunk into trunk-mpi-branch.
In this revision I copied all files from trunk-mpi-branch over the corresponding
trunk files. I did not use 'svn merge', it was a copy.
Revision
1141 -
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Modified
Tue May 15 04:24:51 2007 UTC
(11 years, 9 months ago)
by
gross
Original Path:
trunk/escript/src/escriptcpp.cpp
File length: 12126 byte(s)
Diff to
previous 1137
Some changes to make things run on windows. There is still a problem with netcdf an long file names on windows but there is the suspicion that this is a bigger problem related to boost (compiler options). In fact runs with large numbers of iteration/time steps tend to create seg faults.
Revision
1034 -
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Modified
Wed Mar 14 23:49:20 2007 UTC
(11 years, 11 months ago)
by
gross
Original Path:
trunk/escript/src/escriptcpp.cpp
File length: 11286 byte(s)
Diff to
previous 1023
In VC++ boost has problems with numarray arguments from python. This
fixes that problem by taking python::object arguments from the python
level and converting it into python::numeric::array on the C++ level.
This hasn't been tested with VC++ yet.
Moreover the two Data methods dealing with big numarrays as argument and
return value have been removed.
Revision
964 -
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Modified
Tue Feb 13 05:10:26 2007 UTC
(12 years ago)
by
gross
Original Path:
trunk/escript/src/escriptcpp.cpp
File length: 11283 byte(s)
Diff to
previous 950
The set/getRefVal functions of Data objects have been removed (mainly to avoid later problems with MPI).
Moreover, a faster access to the reference id of samples has been introduced. I don't think that anybody will
profit form this at this stage but it will allow a faster dump of data objects.
Revision
950 -
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Modified
Tue Feb 6 07:01:11 2007 UTC
(12 years ago)
by
gross
Original Path:
trunk/escript/src/escriptcpp.cpp
File length: 11443 byte(s)
Diff to
previous 922
escript data objects can now be saved to netCDF files, see http://www.unidata.ucar.edu/software/netcdf/.
Currently only constant data are implemented with expanded and tagged data to follow.
There are two new functions to dump a data object
s=Data(...)
s.dump(<filename>)
and to recover it
s=load(<filename>, domain)
Notice that the function space of s is recovered but domain is still need.
dump and load will replace archive and extract.
The installation needs now the netCDF installed.
Revision
921 -
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Modified
Fri Jan 5 00:54:37 2007 UTC
(12 years, 1 month ago)
by
gross
Original Path:
trunk/escript/src/escriptcpp.cpp
File length: 11245 byte(s)
Diff to
previous 914
I have done some clarification on functions that allow to access individual data point values in a Data object.
The term "data point number" is always local on a MPI process and referes to the value (data_point_in_sample, sample)
as a single identifyer (data_point_in_sample + sample * number_data_points_per_sample). a "global data point number"
referes to a tuple of a processour id and local data point number.
The function convertToNumArrayFromSampleNo has been removed now and convertToNumArrayFromDPNo renamed to getValueOfDataPoint.
There are two new functions:
getNumberOfDataPoints
setValueOfDataPoint
This allows you to do things like:
in=Data(..)
out=Data(..)
for i in xrange(in.getNumberOfDataPoints())
in_loc=in.getValueOfDataPoint(i)
out_loc=< some operations on in_loc>
out.setValueOfDataPoint(i,out_loc)
Also mindp is renamed to minGlobalDataPoint and there is a new function getValueOfGlobalDataPoint. While in MPI the functions getNumberOfDataPoints and getValueOfDataPoint are working locally on each process (so the code above is executed in parallel).
the latter allows getting a single value across all processors.
Revision
813 -
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Modified
Mon Aug 21 02:08:47 2006 UTC
(12 years, 6 months ago)
by
ksteube
Original Path:
trunk/escript/src/escriptcpp.cpp
File length: 11067 byte(s)
Diff to
previous 804
Tensor products for Data objects are now computed by a C++ method
C_GeneralTensorProduct, which calls C function matrix_matrix_product
to do the actual calculation.
Can perform product with either input transposed in place, meaning
without first computing the transpose in a separate step.
Revision
783 -
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Modified
Tue Jul 18 01:32:50 2006 UTC
(12 years, 7 months ago)
by
gross
Original Path:
trunk/escript/src/escriptcpp.cpp
File length: 10720 byte(s)
Diff to
previous 775
coordinates, element size and normals returned by corresponding
FunctionSpace mesthods are now protected against updates. So
+=, -=, *=, /=, setTaggedValue, fillFromNumArray will through an
excpetion.
The FunctionSpace class does nut buffer the oordinates, element size and
normals yet.
Revision
775 -
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Modified
Mon Jul 10 04:00:08 2006 UTC
(12 years, 7 months ago)
by
ksteube
Original Path:
trunk/escript/src/escriptcpp.cpp
File length: 10612 byte(s)
Diff to
previous 767
Modified the following python methods in escript/py_src/util.py to
call faster C++ methods:
escript_trace
escript_transpose
escript_symmetric
escript_nonsymmetric
Revision
682 -
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Modified
Mon Mar 27 02:43:09 2006 UTC
(12 years, 10 months ago)
by
robwdcock
Original Path:
trunk/escript/src/escriptcpp.cpp
File length: 10452 byte(s)
Diff to
previous 615
+ NEW BUILD SYSTEM
This commit contains the new build system with cross-platform support.
Most things work are before though you can have more control.
ENVIRONMENT settings have changed:
+ You no longer require LD_LIBRARY_PATH or PYTHONPATH to point to the
esysroot for building and testing performed via scons
+ ACcESS altix users: It is recommended you change your modules to load
the latest intel compiler and other libraries required by boost to match
the setup in svn (you can override). The correct modules are as follows
module load intel_cc.9.0.026
export
MODULEPATH=${MODULEPATH}:/data/raid2/toolspp4/modulefiles/gcc-3.3.6
module load boost/1.33.0/python-2.4.1
module load python/2.4.1
module load numarray/1.3.3
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