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/*****************************************************************************
*
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* Copyright (c) 2000 - 2008, Lawrence Livermore National Security, LLC
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* Produced at the Lawrence Livermore National Laboratory
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* LLNL-CODE-400142
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* All rights reserved.
*
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* This file is  part of VisIt. For  details, see https://visit.llnl.gov/.  The
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* full copyright notice is contained in the file COPYRIGHT located at the root
* of the VisIt distribution or at http://www.llnl.gov/visit/copyright.html.
*
* Redistribution  and  use  in  source  and  binary  forms,  with  or  without
* modification, are permitted provided that the following conditions are met:
*
*  - Redistributions of  source code must  retain the above  copyright notice,
*    this list of conditions and the disclaimer below.
*  - Redistributions in binary form must reproduce the above copyright notice,
*    this  list of  conditions  and  the  disclaimer (as noted below)  in  the
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*    documentation and/or other materials provided with the distribution.
*  - Neither the name of  the LLNS/LLNL nor the names of  its contributors may
*    be used to endorse or promote products derived from this software without
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*    specific prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT  HOLDERS AND CONTRIBUTORS "AS IS"
* AND ANY EXPRESS OR  IMPLIED WARRANTIES, INCLUDING,  BUT NOT  LIMITED TO, THE
* IMPLIED WARRANTIES OF MERCHANTABILITY AND  FITNESS FOR A PARTICULAR  PURPOSE
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* ARE  DISCLAIMED. IN  NO EVENT  SHALL LAWRENCE  LIVERMORE NATIONAL  SECURITY,
* LLC, THE  U.S.  DEPARTMENT OF  ENERGY  OR  CONTRIBUTORS BE  LIABLE  FOR  ANY
* DIRECT,  INDIRECT,   INCIDENTAL,   SPECIAL,   EXEMPLARY,  OR   CONSEQUENTIAL
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* DAMAGES (INCLUDING, BUT NOT  LIMITED TO, PROCUREMENT OF  SUBSTITUTE GOODS OR
* SERVICES; LOSS OF  USE, DATA, OR PROFITS; OR  BUSINESS INTERRUPTION) HOWEVER
* CAUSED  AND  ON  ANY  THEORY  OF  LIABILITY,  WHETHER  IN  CONTRACT,  STRICT
* LIABILITY, OR TORT  (INCLUDING NEGLIGENCE OR OTHERWISE)  ARISING IN ANY  WAY
* OUT OF THE  USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
* DAMAGE.
*
*****************************************************************************/

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// ************************************************************************* //
//                              NetworkManager.C                             //
// ************************************************************************* //

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#include <snprintf.h>
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#include <AttributeSubject.h>
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#include <NetworkManager.h>
#include <DataNetwork.h>
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#include <ClonedDataNetwork.h>
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#include <DebugStream.h>
#include <avtDatabaseFactory.h>
#include <LoadBalancer.h>
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#include <ConstructDDFAttributes.h>
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#include <DBOptionsAttributes.h>
#include <ExportDBAttributes.h>
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#include <MaterialAttributes.h>
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#include <MeshManagementAttributes.h>
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#include <avtExpressionEvaluatorFilter.h>
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#include <avtNamedSelectionFilter.h>
#include <avtNamedSelectionManager.h>
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#include <ImproperUseException.h>
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#include <InvalidVariableException.h>
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#include <DatabaseException.h>
#include <NoInputException.h>
#include <avtPluginFilter.h>
#include <OperatorPluginManager.h>
#include <OperatorPluginInfo.h>
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#include <AnnotationObjectList.h>
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#include <AnnotationAttributes.h>
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#include <PickAttributes.h>
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#include <VisualCueInfo.h>
#include <VisualCueList.h>
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#include <avtApplyDDFExpression.h>
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#include <avtCallback.h>
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#include <avtColorTables.h>
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#include <avtDebugDumpOptions.h>
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#include <avtExtents.h>
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#include <avtNullData.h>
#include <avtDataObjectQuery.h>
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#include <avtMultipleInputQuery.h>
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#include <avtAreaBetweenCurvesQuery.h>
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#include <avtFileWriter.h>
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#include <avtDatabaseWriter.h>
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#include <avtL2NormBetweenCurvesQuery.h>
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#include <avtLocateQuery.h>
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#include <avtLocateCellQuery.h>
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#include <avtLocateNodeQuery.h>
#include <avtActualCoordsQuery.h>
#include <avtActualNodeCoordsQuery.h>
#include <avtActualZoneCoordsQuery.h>
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#include <avtPickQuery.h>
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#include <avtNodePickQuery.h>
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#include <avtParallel.h>
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#include <avtPickByNodeQuery.h>
#include <avtPickByZoneQuery.h>
#include <avtZonePickQuery.h>
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#include <avtCurvePickQuery.h>
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#include <avtSoftwareShader.h>
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#include <avtDDF.h>
#include <avtDDFConstructor.h>
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#include <avtSourceFromAVTImage.h>
#include <avtSourceFromImage.h>
#include <avtSourceFromNullData.h>
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#include <avtTiledImageCompositor.h>
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#include <avtWholeImageCompositerWithZ.h>
#include <avtWholeImageCompositerNoZ.h>
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#include <avtPlot.h>
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#include <avtQueryOverTimeFilter.h>
#include <avtQueryFactory.h>
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#include <CompactSILRestrictionAttributes.h>
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#include <VisWindow.h>
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#include <VisWinRendering.h> // for SetStereoEnabled
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#include <ParsingExprList.h>
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#include <avtExprNode.h>
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#include <DatabasePluginManager.h>
#include <DatabasePluginInfo.h>
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#include <PlotPluginManager.h>
#include <PlotPluginInfo.h>
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#include <StackTimer.h>
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#ifdef PARALLEL
#include <mpi.h>
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#include <parallel.h>
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#endif
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#include <visit-config.h>
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#include <TimingsManager.h>
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#include <SaveWindowAttributes.h>
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#include <set>
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#include <map>
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#include <algorithm>
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#include <climits>

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#include <vtkImageData.h>

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using std::set;

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//
// Static functions.
//
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static void   DumpImage(avtDataObject_p, const char *fmt, bool allprocs=true);
static void   DumpImage(avtImage_p, const char *fmt, bool allprocs=true);
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static ref_ptr<avtDatabase> GetDatabase(void *, const std::string &,
                                        int, const char *);
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static avtDDF *GetDDFCallbackBridge(void *arg, const char *name);
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static bool OnlyRootNodeHasData(avtImage_p &);
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static void BroadcastImage(avtImage_p &, bool, int);
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#ifdef PARALLEL
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static bool IsBlankImage(avtImage_p img);
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static std::vector<int> BuildBlankImageVector(avtImage_p img);
#endif
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//
// Static data members of the NetworkManager class.
//
InitializeProgressCallback NetworkManager::initializeProgressCallback = NULL;
void                      *NetworkManager::initializeProgressCallbackArgs=NULL;
ProgressCallback           NetworkManager::progressCallback = NULL;
void                      *NetworkManager::progressCallbackArgs = NULL;



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// ****************************************************************************
//  Method: NetworkManager default constructor
//
//  Programmer: Jeremy Meredith
//  Creation:   September 29, 2000
//
//  Modifications:
//
//    Kathleen Bonnell, Tue Nov 20 12:35:54 PST 2001
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//    Initialize requireOriginalCells.
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//
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//    Hank Childs, Mon Jan  5 16:04:57 PST 2004
//    Initialize uniqueNetworkId.
//
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//    Hank Childs, Thu Mar  4 09:11:46 PST 2004
//    Change instantiation of vis window, since it is now assumed to be nowin.
//
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//    Mark C. Miller, Thu Apr 29 16:15:25 PDT 2004
//    Added missing initialization of dumpRenders
//
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//    Mark C. Miller, Tue May 25 20:44:10 PDT 2004
//    Removed unnecessary scope. Set annotationAttributes data member
//
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//    Kathleen Bonnell, Wed Jun  2 09:48:29 PDT 2004
//    Initialize requireOriginalNodes.
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//
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//    Mark C. Miller, Tue Jan  4 10:23:19 PST 2005
//    Made the viswin part of a map of EngineVisWinInfo objects
//    Removed some unnecessary initialization
//
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//    Mark C. Miller, Wed Jan  5 10:14:21 PST 2005
//    Added call to NewVisWindow
//
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//    Hank Childs, Mon Feb 28 16:56:20 PST 2005
//    Initialize inQueryMode.
//
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//    Hank Childs, Fri Aug 26 15:44:48 PDT 2005
//    Register a callback to get databases.
//
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//    Hank Childs, Sat Feb 18 11:31:23 PST 2006
//    Added a call back for the apply ddf expression.
//
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//    Cyrus Harrison, Tue Feb 19 08:42:51 PST 2008
//    Removed dumpRenders (now controled by avtDebugDumpOptions)
//
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//    Brad Whitlock, Tue Jun 24 15:40:29 PDT 2008
//    Added plugin managers.
//
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// ****************************************************************************
NetworkManager::NetworkManager(void) : virtualDatabases()
{
    workingNet = NULL;
    loadBalancer = NULL;
    requireOriginalCells = false;
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    requireOriginalNodes = false;
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    inQueryMode = false;
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    uniqueNetworkId = 0;
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    // stuff to support scalable rendering. We always have window 0
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    NewVisWindow(0);
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    avtCallback::RegisterGetDatabaseCallback(GetDatabase, this);
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    avtApplyDDFExpression::RegisterGetDDFCallback(GetDDFCallbackBridge, this);
    avtExpressionEvaluatorFilter::RegisterGetDDFCallback(
                                                  GetDDFCallbackBridge, this);
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    databasePlugins = new DatabasePluginManager;
    operatorPlugins = new OperatorPluginManager;
    plotPlugins = new PlotPluginManager;
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}

// ****************************************************************************
//  Method: NetworkManager destructor
//
//  Programmer: Jeremy Meredith
//  Creation:   September 29, 2000
//
//  Modifications:
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//    Sean Ahern, Fri May 24 11:12:25 PDT 2002
//    Got rid of deletion of the database cache, since all DBs in there
//    will be deleted by deleting the network cache.
//
//    Hank Childs, Mon Jan  5 16:30:04 PST 2004
//    Don't assume the caches are valid.
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//
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//    Mark C. Miller, Tue Jan  4 10:23:19 PST 2005
//    Added code to delete VisWindow objects
//
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//    Hank Childs, Mon Feb 13 23:14:23 PST 2006
//    Delete the DDFs.
//
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//    Brad Whitlock, Tue Jun 24 15:41:08 PDT 2008
//    Added plugin managers.
//
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// ****************************************************************************
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NetworkManager::~NetworkManager(void)
{
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    for (size_t i = 0; i < networkCache.size(); i++)
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        if (networkCache[i] != NULL)
            delete networkCache[i];
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    std::map<int, EngineVisWinInfo>::iterator it;
    for (it = viswinMap.begin(); it != viswinMap.end(); it++)
        delete it->second.viswin;
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    for (size_t d = 0 ; d < ddf.size() ; d++)
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        delete ddf[d];
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    delete databasePlugins;
    delete operatorPlugins;
    delete plotPlugins;
}

// ****************************************************************************
// Method: NetworkManager::GetDatabasePluginManager
//
// Purpose: 
//   Return the database plugin manager.
//
// Returns:    the database plugin manager.
//
// Programmer: Brad Whitlock
// Creation:   Tue Jun 24 15:25:41 PDT 2008
//
// Modifications:
//   
// ****************************************************************************

DatabasePluginManager *
NetworkManager::GetDatabasePluginManager() const
{
    return databasePlugins;
}

// ****************************************************************************
// Method: NetworkManager::GetOperatorPluginManager
//
// Purpose: 
//   Return the operator plugin manager.
//
// Returns:    the operator plugin manager.
//
// Programmer: Brad Whitlock
// Creation:   Tue Jun 24 15:26:07 PDT 2008
//
// Modifications:
//   
// ****************************************************************************

OperatorPluginManager *
NetworkManager::GetOperatorPluginManager() const
{
    return operatorPlugins;
}

// ****************************************************************************
// Method: NetworkManager::GetPlotPluginManager
//
// Purpose: 
//   Return the plot plugin manager.
//
// Returns:    the plot plugin manager.
//
// Programmer: Brad Whitlock
// Creation:   Tue Jun 24 15:26:28 PDT 2008
//
// Modifications:
//   
// ****************************************************************************

PlotPluginManager *
NetworkManager::GetPlotPluginManager() const
{
    return plotPlugins;
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}

// ****************************************************************************
//  Method: NetworkManager::ClearAllNetworks
//
//  Purpose:
//      Clears out the caches.  Really only used for checking for memory leaks.
//
//  Programmer: Hank Childs
//  Creation:   January 7, 2001
//
//  Modifications:
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//    Sean Ahern, Tue May 14 14:35:42 PDT 2002
//    Retrofitted for my new network management techniques.
//
//    Sean Ahern, Tue May 21 16:09:56 PDT 2002
//    Told the underlying objects to free their data.
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//
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//    Hank Childs, Mon Jan  5 16:30:04 PST 2004
//    Don't clear out the vectors, so this can be consistent with how the
//    ClearNetworksWithDatabase works.
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//
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//    Brad Whitlock, Thu Feb 26 11:58:58 PDT 2004
//    I replaced the commented out cerr with debug3.
//
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//    Hank Childs, Sun Mar  7 16:05:03 PST 2004
//    Delete the networks before the databases, since the networks have
//    references to the databases (and the previous ordering yielded dangling
//    pointers).
//
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//    Mark C. Miller, Wed Sep  8 17:06:25 PDT 2004
//    Added code to clear the vis window and the list of plots currently in
//    the window.
//
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//    Mark C. Miller, Mon Sep 13 18:30:26 PDT 2004
//    Protected call to clear viswin and plotsCurrentlyInWindow with test
//    for emptiness
//
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//    Mark C. Miller, Tue Jan  4 10:23:19 PST 2005
//    Added code to delete VisWindow objects
//
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//    Hank Childs, Thu Mar  2 10:06:33 PST 2006
//    Added support for image based plots.
//
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// ****************************************************************************
void
NetworkManager::ClearAllNetworks(void)
{
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    debug3 << "NetworkManager::ClearAllNetworks(void)" << endl;
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    for (size_t i = 0; i < networkCache.size(); i++)
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    {
        if (networkCache[i] != NULL)
            delete networkCache[i];
        networkCache[i] = NULL;
    }

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    for (size_t i = 0; i < databaseCache.size(); i++)
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    {
        if (databaseCache[i] != NULL)
            delete databaseCache[i];
        databaseCache[i] = NULL;
    }

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    for (size_t i = 0 ; i < globalCellCounts.size() ; i++)
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    {
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        globalCellCounts[i] = -1;
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    }
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    std::map<int, EngineVisWinInfo>::iterator it;
    for (it = viswinMap.begin(); it != viswinMap.end(); it++)
    {
        it->second.viswin->ClearPlots();
        it->second.plotsCurrentlyInWindow.clear();
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        it->second.imageBasedPlots.clear();
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        delete it->second.viswin;
    }
    viswinMap.clear();
    NewVisWindow(0);
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}

// ****************************************************************************
//  Method: NetworkManager::ClearNetworksWithDatabase
//
//  Purpose:
//      Clears out the caches that reference a specific database.
//
//  Arguments:
//      db      The name of a database.
//
//  Programmer: Hank Childs
//  Creation:   January 5, 2004
//
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//  Modifications:
//    Brad Whitlock, Thu Feb 26 11:58:58 PDT 2004
//    I replaced the commented out cerr with debug3.
//
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//    Mark C. Miller, Wed Sep  8 17:06:25 PDT 2004
//    Added code to clear the vis window and the list of plots currently in
//    the window for the first plot id it encounters in this db
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//
//    Mark C. Miller, Mon Sep 13 18:30:26 PDT 2004
//    Moved code to delete the networkCache entry to after the clearning
//    of the viswin.
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//
//    Mark C. Miller, Tue Jan  4 10:23:19 PST 2005
//    Modified for viswinMap object
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// ****************************************************************************
void
NetworkManager::ClearNetworksWithDatabase(const std::string &db)
{
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    debug3 << "NetworkManager::ClearNetworksWithDatabase()" << endl;
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    //
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    // Clear out the networks before the databases.  This is because if we
    // delete the databases first, the networks will have dangling pointers.
    //
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    for (size_t i = 0; i < networkCache.size(); i++)
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    {
        if (networkCache[i] != NULL)
        {
            NetnodeDB *ndb = networkCache[i]->GetNetDB();
            if (ndb != NULL)
            {
                if (ndb->GetFilename() == db)
                {
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                    DoneWithNetwork(i);
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                }
            }
        }
    }
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    for (size_t i = 0; i < databaseCache.size(); i++)
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    {
        if (databaseCache[i] != NULL)
        {
            if (databaseCache[i]->GetFilename() == db)
            {
                delete databaseCache[i];
                databaseCache[i] = NULL;
            }
        }
    }
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}

// ****************************************************************************
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//  Method: NetworkManager::GetDBFromCache
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//
//  Purpose:
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//      Get a DB from the cache.  If it's not there already, create it and
//      return it.
//
//  Programmer: Sean Ahern
//  Creation:   Mon Dec 23 12:28:30 PST 2002
//
//  Modifications:
//
//    Brad Whitlock, Wed May 14 12:56:16 PDT 2003
//    I made it get the metadata and the SIL if the time is greater than 0.
//    This ensures that we pick up the metadata and SIL for the time state
//    that we're intersted in.
//
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//    Brad Whitlock, Mon Aug 25 16:51:35 PST 2003
//    Changed the return statement to CATCH_RETURN2 so bad things don't happen
//    when we use fake exceptions.
//
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//    Mark C. Miller Thu Oct  9 10:59:27 PDT 2003
//    I modified to force GetMetaData and GetSIL if they're invariant 
//
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//    Hank Childs, Tue Nov  4 14:19:05 PST 2003
//    Checked in work-around (HACK) to avoid apparent compiler bug on AIX.
//
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//    Hank Childs, Mon Jan  5 16:49:28 PST 2004
//    Do not assume that all of the cached databases are non-NULL.
//
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//    Hank Childs, Mon Mar  1 08:48:26 PST 2004
//    Send the time to the database factory as well.
//
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//    Hank Childs, Mon Mar 22 11:10:43 PST 2004
//    Allow for the DB type to be explicitly specified.
//
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//    Mark C. Miller, Tue Sep 28 19:57:42 PDT 2004
//    Added code to pass avtDatabaseMetaData to LoadBalancer->AddDatabase
//
//    Hank Childs, Sun Feb 27 12:30:17 PST 2005
//    Added avtDatabase argument to AddDatabase.
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//
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//    Hank Childs, Tue Sep 20 13:03:00 PDT 2005
//    Don't assume that filename lengths are bigger than 6 characters ['6616].
//
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//    Hank Childs, Fri Oct  7 17:22:01 PDT 2005
//    Tell database what it's full name is.  Also, remove some antiquated code
//    that the variable name in the DB info to the empty string.  I believe
//    the code was no longer doing anything useful, besides torpedoing SR
//    and CMFE when used in combination.  The test suite passes without it
//    and there is really no explanation for why we were doing it.
//
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//    Mark C. Miller, Wed Nov 16 10:46:36 PST 2005
//    Changed interface to lb->AddDatabase 
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//
//    Hank Childs, Thu Jan 11 16:10:12 PST 2007
//    Added argument to DatabaseFactory calls.
//
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//    Mark C. Miller, Thu Jun 14 10:26:37 PDT 2007
//    Added support to treat all databases as time varying
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//
//    Mark C. Miller, Wed Aug 22 20:16:59 PDT 2007
//    Added treatAllDBsAsTimeVarying to GetSIL call
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//
//    Hank Childs, Fri Feb  1 15:45:28 PST 2008
//    Added argument for loading database plugins.
//
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//    Mark C. Miller, Tue Jun 10 22:36:25 PDT 2008
//    Added support for ignoring bad extents from dbs.
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//
//    Brad Whitlock, Tue Jun 24 15:45:43 PDT 2008
//    Pass the database plugin manager to the factory.
//
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// ****************************************************************************
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NetnodeDB *
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NetworkManager::GetDBFromCache(const string &filename, int time,
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    const char *format, bool treatAllDBsAsTimeVarying, 
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    bool fileMayHaveUnloadedPlugin, bool ignoreExtents)
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{
    // If we don't have a load balancer, we're dead.
    if (loadBalancer == NULL)
    {
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        debug1 << "Internal error: A load balancer was never registered." 
               << endl;
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        EXCEPTION0(ImproperUseException);
    }

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    // Find a matching database 
    NetnodeDB* cachedDB = NULL;
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    for (size_t i = 0; i < databaseCache.size(); i++)
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    {
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        if (databaseCache[i] == NULL)
            continue;
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        if (databaseCache[i]->GetFilename() == filename)
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        {
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            cachedDB = databaseCache[i];
            break;
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        }
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    }

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    // use of these makes calls to GetMetaData a little clearer
    const bool forceReadAllCyclesAndTimes = false;
    const bool forceReadThisCycleAndTime  = false;

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    // got a match
    if (cachedDB != NULL)
    {
        // even if we found the DB in the cache,
        // we need to update the metadata if its time-varying
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        if (treatAllDBsAsTimeVarying ||
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            !cachedDB->GetDB()->MetaDataIsInvariant() ||
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            !cachedDB->GetDB()->SILIsInvariant())
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        {
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            cachedDB->GetDB()->GetMetaData(time,
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                                           forceReadAllCyclesAndTimes,
                                           forceReadThisCycleAndTime,
                                           treatAllDBsAsTimeVarying);
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            cachedDB->GetDB()->GetSIL(time, treatAllDBsAsTimeVarying);
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        }
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        return cachedDB;
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    }

    // No match.  Load a new DB.
    debug3 << "Loading new database" << endl;
    TRY
    {
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        if (fileMayHaveUnloadedPlugin)
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             GetDatabasePluginManager()->LoadPluginsNow();

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        avtDatabase *db = NULL;
        NetnodeDB *netDB = NULL;
        const char *filename_c = filename.c_str();
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        std::vector<std::string> plugins;  // unused
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        if (filename.length() >= 6 &&
            filename.substr(filename.length() - 6) == ".visit")
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        {
            db = avtDatabaseFactory::VisitFile(
                GetDatabasePluginManager(),
                filename_c,
                time,
                plugins,
                format);
        }
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        else
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        {
            db = avtDatabaseFactory::FileList(
                GetDatabasePluginManager(),
                &filename_c,
                1,
                time,
                plugins, 
                format);
        }

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        db->SetFullDBName(filename);
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        db->SetIgnoreExtents(ignoreExtents);
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        // If we want to open the file at a later timestep, get the
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        // SIL so that it contains the right data.
        if ((time > 0) ||
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            treatAllDBsAsTimeVarying ||
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            (!db->MetaDataIsInvariant()) ||
            (!db->SILIsInvariant()))
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        {
            debug2 << "NetworkManager::AddDB: We were instructed to open "
                   << filename.c_str() << " at timestate=" << time
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                   << " so we're reading the SIL early."
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                   << endl;
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            db->GetMetaData(time,
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                            forceReadAllCyclesAndTimes,
                            forceReadThisCycleAndTime,
                            treatAllDBsAsTimeVarying);
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            db->GetSIL(time, treatAllDBsAsTimeVarying);
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        }

        netDB = new NetnodeDB(db);
        databaseCache.push_back(netDB);

        netDB->SetDBInfo(filename, "", time);
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        loadBalancer->AddDatabase(filename, db, time);
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        // The code here should be:
        // CATCH_RETURN2(1, netDB);
        //
        // However: this is crashing on AIX when you do a re-open (see '3984).
        // After investigating this bug, I have determined the following:
        // (1) A valid pointer is being returned from this function.  However
        // the calling function receives NULL (leading to a seg fault).
        // (2) When compiling with fake exceptions and running under purify
        // on the Suns, there are no warnings.
        // (3) The catch return unwinds into 3 calls.  If you put a print
        // statement right before the last one (the return), everything is
        // returned correctly and there is no seg fault.
        //
        // I'm always very leery to call something a compiler bug.  However,
        // on different platforms there is no problem.  I think it is even
        // more fishy that things work if there is a print statement and don't
        // if there is not.  It certainly sounds like a compiler bug.
        //
        // Below is code that "makes this work".  It is essentially a
        // CATCH_RETURN2 with a print statement in the middle.  If CATCH_RETURN
        // were to ever change, this coding would have to change as well
        // (thus, I have introduced a maintenance problem).  As such, I put
        // a comment in VisItException.h referencing this comment.  If the
        // coding below can ever be replaced with an everyday CATCH_RETURN,
        // the comment in VisItException.h should be removed.
        //
#ifdef FAKE_EXCEPTIONS
           exception_delete(exception_caught); 
           jump_stack_top -= (1); 
           debug5 << "This debug statement (from the NetworkManager) is "
                  << "being issued to get around a compiler bug." << endl;
           return (netDB); 
#else
           return netDB;
#endif
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    }
    CATCH(DatabaseException)
    {
        debug1 << "ERROR - could not create database " << filename.c_str()
            << endl;
        RETHROW;
    }
    ENDTRY
}

// ****************************************************************************
//  Method: NetworkManager::StartNetwork
//
//  Purpose:
//      Start building the pipeline.
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//
//  Programmer: Jeremy Meredith
//  Creation:   September 29, 2000
//
//  Modifications:
//
//    Jeremy Meredith, Thu Nov  2 14:07:34 PST 2000
//    Changed the file initialization.  Apparently substr() may not portably 
//    be a const method of strings....
//
//    Hank Childs, Tue Jun 12 20:01:55 PDT 2001
//    Incorporate data specifications and the load balancer.
//
//    Jeremy Meredith, Thu Jul 26 12:08:42 PDT 2001
//    Fixed a bug passing the data file name to the load balancer.
//
//    Hank Childs, Thu Jul 26 20:17:56 PDT 2001
//    Re-enable caching by checking data specifications.
//
//    Brad Whitlock, Mon Oct 22 18:33:37 PST 2001
//    Changed the exception keywords to macros.
//
//    Jeremy Meredith, Fri Nov  9 10:24:23 PST 2001
//    Replaced netPool with netMRU, and simply made it release its
//    data, not delete the whole network. Made is only set the data
//    specification, not the pipeline specification yet.
//
//    Hank Childs, Fri Dec 14 17:39:36 PST 2001
//    Add support for using a more compact version of sil attributes.
//
//    Sean Ahern, Mon May 13 17:24:25 PDT 2002
//    Refactored to start support for a tree-based network scheme.
//
//    Sean Ahern, Tue May 28 09:47:21 PDT 2002
//    Added tree-based networks.
//
//    Brad Whitlock, Fri Jun 28 14:03:49 PST 2002
//    I renamed Network to DataNetwork to make the Windows compiler happy.
//
//    Hank Childs, Thu Sep 12 11:11:16 PDT 2002
//    There was an issue with multiple networks sharing NetnodeDBs, so I
//    made them all have their own reference.
//
//    Jeremy Meredith, Thu Oct 24 16:03:39 PDT 2002
//    Added material options.
//
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//    Sean Ahern, Mon Dec 23 12:38:17 PST 2002
//    Changed this dramatically.  Broke out a good portion of the logic
//    into GetDBFromCache.
//
//    Sean Ahern, Sat Mar  8 00:59:16 America/Los_Angeles 2003
//    Cleaned up unnecessarily complicated code.
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//
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//    Jeremy Meredith, Wed Jul 30 10:45:45 PDT 2003
//    Added the check for requiring full connectivity.
//
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//    Jeremy Meredith, Fri Sep  5 15:23:13 PDT 2003
//    Added a flag for the new MIR algorithm.
//
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//    Jeremy Meredith, Thu Oct 30 16:09:32 PST 2003
//    Added code to make sure varLeaves was non-empty before accessing it.
//
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//    Jeremy Meredith, Fri Oct 31 13:05:26 PST 2003
//    Made the error message for no-real-variables more informative.
//
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//    Hank Childs, Sun Mar  7 16:05:03 PST 2004
//    Do not make the database be a node for the network.  Also add the EEF
//    as a node.
//
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//    Jeremy Meredith, Tue Mar 23 14:40:20 PST 2004
//    Added the file format as an argument.  Made use of it in GetDBFromCache.
//
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//    Mark C. Miller, Thu Aug 19 10:28:45 PDT 2004
//    Removed #ifdef 0 code block
//
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//    Jeremy Meredith, Tue Dec 14 14:02:35 PST 2004
//    The code to get the real variable name was a duplicate of two
//    other spots in VisIt, but this one was out of date.  I
//    refactored the best one into ParsingExprList::GetRealVariable
//    and made this one point to it.
//
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//    Brad Whitlock, Tue Feb 22 12:13:44 PDT 2005
//    Made format argument come first. I also made it possible for an empty
//    format string to make the code behave as through no format was specified.
//
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//    Hank Childs, Wed Jul 13 10:38:02 PDT 2005
//    Added call to SetTime to prevent UMR when exporting databases.
//
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//    Hank Childs, Wed Aug 17 21:55:55 PDT 2005
//    Pass along the material options to simplify the interface reconstruction.
//
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//    Jeremy Meredith, Thu Aug 18 17:54:51 PDT 2005
//    Added a new isovolume algorithm, with adjustable VF cutoff.
//
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//    Mark C. Miller, Wed Nov 16 10:46:36 PST 2005
//    Added mesh management attributes 
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//
//    Mark C. Miller, Sun Dec  3 12:20:11 PST 2006
//    Added setting of flatness tolerance to data spec for CSG stuff
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//
//    Hank Childs, Wed Jan 17 10:42:21 PST 2007
//    Tell the output of the expression evaluator filter that it is *not*
//    transient, since picks sometimes like to look at these.
//
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//    Added support to treat all databases as time varying
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//
//    Mark C. Miller, Wed Aug 22 20:16:59 PDT 2007
//    Added treatAllDBsAsTimeVarying to GetSIL call.
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//
//    Hank Childs, Fri Feb  1 15:48:01 PST 2008
//    Add new Boolean argument to GetDBFromCache. 
//
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//    Added support for ignoring bad extents from dbs.
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//
//    Hank Childs, Fri Jan 16 15:30:15 PST 2009
//    Store the variable with the working network.
//
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//    Jeremy Meredith, Fri Feb 13 11:22:39 EST 2009
//    Added MIR iteration capability.
//
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// ****************************************************************************
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void
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NetworkManager::StartNetwork(const string &format,
                             const string &filename,
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                             const string &var,
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                             int time,
                             const CompactSILRestrictionAttributes &atts,
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                             const MaterialAttributes &matopts,
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                             const MeshManagementAttributes &meshopts,
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                             bool treatAllDBsAsTimeVarying,
                             bool ignoreExtents)
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{
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    // If the variable is an expression, we need to find a "real" variable
    // name to work with.
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    string leaf = ParsingExprList::GetRealVariable(var);
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    // Make empty strings behave as though no format was specified.
    const char *defaultFormat = 0;
    if(format.size() > 0)
        defaultFormat = format.c_str();

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    // Start up the DataNetwork and add the database to it.
    workingNet = new DataNetwork;
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    bool fileMayHaveUnloadedPlugin = false;
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    NetnodeDB *netDB = GetDBFromCache(filename, time, defaultFormat,
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                                      treatAllDBsAsTimeVarying, 
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                                      fileMayHaveUnloadedPlugin,
                                      ignoreExtents);
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    workingNet->SetNetDB(netDB);
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    workingNet->SetVariable(leaf);
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    netDB->SetDBInfo(filename, leaf, time);
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    // Put an ExpressionEvaluatorFilter right after the netDB to handle
    // expressions that come up the pipe.
    avtExpressionEvaluatorFilter *f = new avtExpressionEvaluatorFilter();
    NetnodeFilter *filt = new NetnodeFilter(f, "ExpressionEvaluator");
    filt->GetInputNodes().push_back(netDB);
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    f->GetOutput()->SetTransientStatus(false);
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    // Push the ExpressionEvaluator onto the working list.
    workingNetnodeList.push_back(filt);
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    workingNet->AddNode(filt);
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    // Push the variable name onto the name stack.
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    nameStack.push_back(var);
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    debug4 << "NetworkManager::AddDB: Adding " << var.c_str()
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           << " to the name stack" << endl;

    // Set up the data spec.
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    avtSILRestriction_p silr =
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        new avtSILRestriction(workingNet->GetNetDB()->GetDB()->
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            GetSIL(time, treatAllDBsAsTimeVarying), atts);
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    avtDataRequest *dataRequest = new avtDataRequest(var.c_str(), time, silr);
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    // Set up some options from the data specification
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    dataRequest->SetNeedMixedVariableReconstruction(matopts.GetForceMIR());
    dataRequest->SetNeedSmoothMaterialInterfaces(matopts.GetSmoothing());
    dataRequest->SetNeedCleanZonesOnly(matopts.GetCleanZonesOnly());
    dataRequest->SetNeedValidFaceConnectivity(matopts.GetNeedValidConnectivity());
    dataRequest->SetMIRAlgorithm(matopts.GetAlgorithm());
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    dataRequest->SetMIRNumIterations(matopts.GetIterationEnabled() ?
                                     matopts.GetNumIterations() : 0);
    dataRequest->SetMIRIterationDamping(matopts.GetIterationDamping());
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    dataRequest->SetSimplifyHeavilyMixedZones(matopts.GetSimplifyHeavilyMixedZones());
    dataRequest->SetMaxMaterialsPerZone(matopts.GetMaxMaterialsPerZone());
    dataRequest->SetIsovolumeMIRVF(matopts.GetIsoVolumeFraction());
    dataRequest->SetDiscTol(meshopts.GetDiscretizationTolerance()[0]);
    dataRequest->SetFlatTol(meshopts.GetDiscretizationTolerance()[1]);
    dataRequest->SetDiscMode(meshopts.GetDiscretizationMode());
    dataRequest->SetDiscBoundaryOnly(meshopts.GetDiscretizeBoundaryOnly());
    dataRequest->SetPassNativeCSG(meshopts.GetPassNativeCSG());
    workingNet->SetDataSpec(dataRequest);
    workingNet->SetTime(dataRequest->GetTimestep());
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    // The plot starts out as NULL.
    workingNet->SetPlot(NULL);
}

// ****************************************************************************
// Method: NetworkManager::DefineDB
//
// Purpose: 
//   Defines a new database with the specified name and list of files.
//
// Arguments:
//    dbName   : The database name.
//    files    : The list of files that make up the database.
//    time     : The timestep that we want to examine.
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//    format   : The file format type of the DB.
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//   
// Programmer: Brad Whitlock
// Creation:   Tue Mar 25 13:41:08 PST 2003
//
// Modifications:
//   Brad Whitlock, Wed May 14 12:56:16 PDT 2003
//   I made it get the metadata and the SIL if the time is greater than 0.
//   This ensures that we pick up the metadata and SIL for the time state
//   that we're intersted in.
//
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//   Hank Childs, Mon Jan  5 16:49:28 PST 2004
//   Account for databases in the cached lists that have been cleared.
//
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//   Hank Childs, Mon Mar  1 08:48:26 PST 2004
//   Send the time to the database factory as well.
//
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//   Hank Childs, Mon Mar 22 11:10:43 PST 2004
//   Send the file format type to the database factory.
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//
//   Mark C. Miller, Tue Sep 28 19:57:42 PDT 2004
//   Added code to pass avtDatabaseMetaData to LoadBalancer->AddDatabase
//
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//   Brad Whitlock, Tue Feb 22 12:17:27 PDT 2005
//   I changed the code so it an empty format string behaves as though no
//   format was specified.
//
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//   Hank Childs, Sun Feb 27 12:30:17 PST 2005
//   Added avtDatabase argument to AddDatabase.
//
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//   Hank Childs, Fri Oct  7 09:30:57 PDT 2005
//   Tell the database what its full name is.
//
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//   Mark C. Miller, Wed Nov 16 10:46:36 PST 2005
//   Changed interface to lb->AddDatabase 
//
//   Hank Childs, Thu Jan 11 16:10:12 PST 2007
//   Added argument to DatabaseFactory calls.
//
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//   Brad Whitlock, Tue Jun 24 15:48:27 PDT 2008
//   Pass the database plugin manager to the database factory.
//
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// ****************************************************************************
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void
NetworkManager::DefineDB(const string &dbName, const string &dbPath,
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    const stringVector &files, int time, const string &format)
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{
    //
    // We gotta have a load balancer
    //
    if (loadBalancer == NULL)
    {
        debug1 << "Internal error: A load balancer was never registered."
               << endl;
        EXCEPTION0(ImproperUseException);
    }

    // Prepend the path to the files.
    stringVector filesWithPath;
    filesWithPath.reserve(files.size());
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    for(size_t i = 0; i < files.size(); ++i)
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        filesWithPath.push_back(dbPath + files[i]);

    //
    // If the database is in the virtualDatabases map, then check the
    // new list of files against the old list of files.
    //
    StringVectorMap::const_iterator it = virtualDatabases.find(dbName);
    if(it != virtualDatabases.end())
    {
        // If the list of files is the same, return because we don't
        // need to change the list of files. If the list of files differ
        // then replace the list of files.
        if(filesWithPath == it->second)
        {
            debug3 << "NetworkManager::DefineDB: No need to change "
                   << "virtual database definition for "
                   << dbName.c_str() << endl;

            // The definition is the same so we don't need to change it
            // but we have to make sure that it exists in the database
            // cache or else we'll have to define it. It's possible that
            // a clear cache rpc could have purged it from the database
            // cache.
            bool found = false;
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            for(size_t i = 0; i < databaseCache.size() && !found; ++i)
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            {
                if (databaseCache[i] == NULL)
                    continue;
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                found = (databaseCache[i]->GetFilename() == dbName);
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            }
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            // If the database was in the database cache, we can return.
            if(found)
                return;
        }
        else
        {
            debug3 << "NetworkManager::DefineDB: Changed "
                   << "virtual database definition for "
                   << dbName.c_str() << endl;
            virtualDatabases[dbName] = filesWithPath;
        }
    }

    //
    // Remove from the database cache databases that have the same name.
    //
    std::vector<NetnodeDB*> databaseBadMatches;
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    for (size_t i = 0; i < databaseCache.size(); i++)
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    {
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        if (databaseCache[i] == NULL)
            continue;
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        if (databaseCache[i]->GetFilename() != dbName)
            databaseBadMatches.push_back(databaseCache[i]);
    }
    databaseCache = databaseBadMatches;

    const char **names = 0;
    TRY
    {
        // Open the database
        avtDatabase *db = NULL;
        const char *dbName_c = dbName.c_str();

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        // Make empty strings behave as though no format was specified.
        const char *defaultFormat = 0;
        if(format.size() > 0)
            defaultFormat = format.c_str();

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        std::vector<std::string> plugins;  // unused
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        if (filesWithPath.size() > 0)
        {
            // Make an array of pointers that we can pass to the database
            // factory so we can create a database based on a virtual
            // file.
            names = new const char *[filesWithPath.size()];
            for(int i = 0; i < filesWithPath.size(); ++i)
                names[i] = filesWithPath[i].c_str();
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            db = avtDatabaseFactory::FileList(GetDatabasePluginManager(),
                  names, filesWithPath.size(), time, plugins, defaultFormat);
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            delete [] names;
            names = 0;

            // Add the virtual database to the virtual database map.
            virtualDatabases[dbName] = filesWithPath;
            debug3 << "NetworkManager::DefineDB: Added new virtual database "
                   << "definition for " << dbName.c_str() << endl;
        }
        else if (dbName.substr(dbName.length() - 6) == ".visit")
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        {
            db = avtDatabaseFactory::VisitFile(GetDatabasePluginManager(),
                dbName_c, time, plugins, defaultFormat);
        }
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        else
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        {
            db = avtDatabaseFactory::FileList(GetDatabasePluginManager(),
                &dbName_c, 1, time, plugins, defaultFormat);
        }
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        db->SetFullDBName(dbName);
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        // If we want to open the file at a later timestep, get the
        // metadata and the SIL so that it contains the right data.
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        if ((time > 0) ||
            (!db->MetaDataIsInvariant()) || 
            (!db->SILIsInvariant()))
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        {
            debug2 << "NetworkManager::DefineDB: We were instructed to define "
                       << dbName.c_str() << " at timestate=" << time
                       << " so we're reading the MetaData and SIL early."
                       << endl;
            db->GetMetaData(time);
            db->GetSIL(time);
        }

        // Create a netnode using the opened database and stick it in
        // the database cache.
        NetnodeDB *netDB = new NetnodeDB(db);
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        netDB->SetDBInfo(dbName, "", time);
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        databaseCache.push_back(netDB);

        // Add the database to the load balancer.
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