Merge 1.12.1RC to the trunk, picking up VizSchema plugin reader and also

changes to the build notes.


git-svn-id: http://visit.ilight.com/svn/visit/trunk/src@8834 18c085ea-50e0-402c-830e-de6fd14e8384

BUILD_NOTES

@@ -16,7 +16,6 @@ shell prompt.
     Mesa     5.0       3-D Graphics Library   http://www.mesa3d.org/
     Python   2.5       Scripting Language     http://www.python.org
     Qt       4.4.3     GUI Toolkit            http://www.trolltech.com
-    Silo     4.5.1     File I/O library       http://silo.llnl.gov
     VTK      5.0.0c    Visualization Toolkit  http://www.kitware.com
 
 
@@ -36,6 +35,7 @@ build and install those libraries prior to building VisIt.
 
     Library  Version  Description            For More Information
     =======  =======  ===========            ====================
+    Silo     4.7      File I/O library       http://silo.llnl.gov
     Boxlib   ???      An AMR I/O library     ???
     ExodusII 4.46     File I/O library       http://www.sourceforge.net/projects/exodusII
     H5Part   1.3.3    Fili I/O library       https://codeforge.lbl.gov/projects/h5part/
@@ -501,8 +501,8 @@ Silo, read the BUILD_NOTES file in the Silo distribution for more information.
 #
 # Build Silo
 #
-sh silo060605.sh
-cd silo060605
+gunzip < silo-4.7.tar.gz | tar xvf -
+cd silo-4.7
 
 #
 #
@@ -521,21 +521,21 @@ cd silo060605
 # which is described later in this document.  The hdf5 library you use must
 # be a serial version.  VisIt will not work with a parallel version.
 #
-# env CFLAGS=-O2 ./configure --without-readline -with-hdf5=$VISITDIR/hdf5/1.6.5/$VISITARCH/include,$VISITDIR/hdf5/1.6.5/$VISITARCH/lib --without-exodus
+# env CFLAGS=-O2 ./configure --without-readline -with-hdf5=$VISITDIR/hdf5/1.6.5/$VISITARCH/include,$VISITDIR/hdf5/1.6.5/$VISITARCH/lib
 #
-env CFLAGS=-O2 ./configure --without-readline --without-hdf5 --without-exodus
+env CFLAGS=-O2 ./configure --without-readline --without-hdf5
 make
 
 #
 # Install it in the visit directory under the silo directory.
 #
 mkdir $VISITDIR/silo
-mkdir $VISITDIR/silo/4.5.1
-mkdir $VISITDIR/silo/4.5.1/$VISITARCH
-mkdir $VISITDIR/silo/4.5.1/$VISITARCH/{include,lib}
-cp silo/silo/silo.{h,inc}   $VISITDIR/silo/4.5.1/$VISITARCH/include
-cp silo/sdx/sdx.{h,inc}     $VISITDIR/silo/4.5.1/$VISITARCH/include
-cp lib/libsilo.a            $VISITDIR/silo/4.5.1/$VISITARCH/lib
+mkdir $VISITDIR/silo/4.7
+mkdir $VISITDIR/silo/4.7/$VISITARCH
+mkdir $VISITDIR/silo/4.7/$VISITARCH/{include,lib}
+cp silo/silo/silo.{h,inc}   $VISITDIR/silo/4.7/$VISITARCH/include
+cp lib/libsilo.a            $VISITDIR/silo/4.7/$VISITARCH/lib
+cp lib/libsiloh5.a          $VISITDIR/silo/4.7/$VISITARCH/lib
 cd ..
 
 

BUILD_NOTES_MacOSX

@@ -83,11 +83,11 @@ Build Notes (if you still want to do it by hand)
                    http://www.llnl.gov/visit/3rd_party/vtk-5.0.0c.tar.gz
     cmake    2.4.5    Make file generation  http://www.cmake.org
                    http://www.llnl.gov/visit/3rd_party/cmake-2.4.5.tar.gz
-    Silo     4.5.1    File I/O library       
-                   http://www.llnl.gov/visit/3rd_party/silo060605.sh
     
     Optional Version  Description           For More Information
     ======== =======  ===========           ====================
+    Silo     4.7      File I/O library       
+                   https://wci.llnl.gov/codes/silo/silo-4.7/silo-4.7.tar.gz
     Boxlib   2.5      An AMR I/O library    
                    http://www.llnl.gov/visit/3rd_party/boxlib.tar.rz
     CFITSIO  3006     File I/O library       
@@ -1231,8 +1231,8 @@ for HDF5. I needed to do a machine merge in order to get a universal binary,
 because the endianness and word size is determined in configure.
 
 # Build silo source into an archive library
-sh silo060605.sh
-cd silo060605
+gunzip < silo-4.7.tar.gz | tar xvf -
+cd silo-4.7
 #
 
 # Need to fake-out dependency tracking.
@@ -1253,8 +1253,8 @@ chmod +x configure
 ./configure --prefix=$VISITPATH/silo CFLAGS="-O2 -fno-common" \
 CXXFLAGS="-O2 -fno-common" \
 LDFLAGS="-Wl,-headerpad_max_install_names,-undefined,dynamic_lookup" \
---disable-sdx --disable-browser --without-readline \
---without-exodus --without-python --with-hdf5=$HDF5INCLUDE,$HDF5LIB
+--disable-browser --without-readline \
+--without-python --with-hdf5=$HDF5INCLUDE,$HDF5LIB
 
 # Compile the needed subroutines. Force make to ignore errors from
 # archive creation, it should get us to where we want to be.
@@ -1263,7 +1263,7 @@ make -i
 gcc -dynamiclib -o libsilo.dylib silo/*/*.o \
 -Wl,-headerpad_max_install_names,\
 -install_name,@executable_path/../lib/libsilo.dylib,\
--compatibility_version,4.5,-current_version,4.5.1 \
+-compatibility_version,4.7,-current_version,4.7 \
 -L$HDF5LIB -lhdf5 -lsz -lz
 
 # Install headers. Ignore archive creation errors.

databases/Makefile.in

@@ -373,6 +373,10 @@
 #   Brad Whitlock, Mon Sep 14 15:45:59 PDT 2009
 #   I added the Adventure reader.
 #
+#   Hank Childs, Wed Nov  4 11:19:20 PST 2009
+#   Added Vs (VizSchema) plugin on behalf of Marc Durant and Sveta
+#   Shesharina of Tech-X.
+#
 ##############################################################################
 
 @SET_MAKE@
@@ -400,6 +404,7 @@ HDF5_TARGET= \
 	SAMRAI \
 	Tetrad \
 	UNIC \
+	Vs \
 	XDMF
 
 MILI=Mili

databases/Vs/README

+VizSchema Database Reader Plugin for VisIt
+
+VizSchema is a specification for markup added to hdf5 files
+to describe the data contained within.  Properly marked-up
+files can be opened using this database reader, and thus
+displayed in VisIt.  VizSchema also allows users to specify
+run information and other miscellaneous data in a standardized
+manner.  VizSchema is designed to be versatile and can be 
+added to data files after the fact.
+
+VizSchema requires VisIt to be compiled with support for HDF5
+
+For details about VizSchema, and contact information for developers,
+please visit the development website at:
+https://ice.txcorp.com/trac/vizschema/wiki
+
+Tech-X Corporation
+5621 Arapaho Ave, Suite A
+Boulder, CO
+USA
\ No newline at end of file

databases/Vs/Vs.xml

+<?xml version="@VERSION@"?>
+  <Plugin name="Vs" type="database" label="Vs Files" version="@VERSION@" enabled="true" mdspecificcode="false" engspecificcode="false" onlyengine="false" noengine="false" dbtype="STMD" haswriter="false" hasoptions="false">
+    <Files components="M">
+      avtVsFileFormat.C
+      VsFilter.C
+      VsH5Reader.C
+      VsSchema.C
+      VsUtils.C
+    </Files>
+
+    <Files components="E">
+      avtVsFileFormat.C
+      VsFilter.C
+      VsH5Reader.C
+      VsSchema.C
+      VsUtils.C
+    </Files>
+
+    <CXXFLAGS>
+      $(HDF5_INCLUDE)
+    </CXXFLAGS>
+    <LIBS>
+      $(HDF5_LIB) $(SZIP_LIB)
+    </LIBS>
+    <Extensions>
+      vsh5
+      h5
+    </Extensions>
+    <Attribute name="" purpose="" persistent="true" keyframe="true" exportAPI="" exportInclude="">
+    </Attribute>
+  </Plugin>

databases/Vs/VsCommonPluginInfo.C

+/*****************************************************************************
+*
+* Copyright (c) 2000 - 2008, Lawrence Livermore National Security, LLC
+* Produced at the Lawrence Livermore National Laboratory
+* LLNL-CODE-400142
+* All rights reserved.
+*
+* This file is  part of VisIt. For  details, see https://visit.llnl.gov/.  The
+* 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
+*    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
+*    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
+* 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
+* 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.
+*
+*****************************************************************************/
+
+#include <VsPluginInfo.h>
+#include <avtVsFileFormat.h>
+#include <avtSTMDFileFormatInterface.h>
+#include <avtGenericDatabase.h>
+#include <DBOptionsAttributes.h>
+#include <DebugStream.h>
+// definition of VISIT_VERSION
+#include <visit-config.h>
+#include <visit-hdf5.h>
+#include <hdf5.h>
+
+//by default we load 100% of data
+const int VsCommonPluginInfo::defaultStride = 1;
+std::string VsCommonPluginInfo::strideSettingAxis1_Name ="Stride for loading data - Axis 1:";
+std::string VsCommonPluginInfo::strideSettingAxis2_Name ="Stride for loading data - Axis 2:";
+std::string VsCommonPluginInfo::strideSettingAxis3_Name ="Stride for loading data - Axis 3:";
+
+// ****************************************************************************
+//  Method:  VsCommonPluginInfo::VsCommonPluginInfo
+//
+//  Purpose:
+//    Constructs a VsCommonPluginInfo with default values
+//
+//  Programmer:  Marc Durant
+//  Creation:    omitted
+//
+// ****************************************************************************
+VsCommonPluginInfo::VsCommonPluginInfo() {
+       settings.resize(3);
+       settings[0] = defaultStride;
+       settings[1] = defaultStride;
+       settings[2] = defaultStride;
+}
+
+// ****************************************************************************
+//  Method:  VsCommonPluginInfo::GetDatabaseType
+//
+//  Purpose:
+//    Returns the type of a Vs database.
+//
+//  Programmer:  generated by xml2info
+//  Creation:    omitted
+//
+// ****************************************************************************
+DatabaseType
+VsCommonPluginInfo::GetDatabaseType()
+{
+    return DB_TYPE_STSD;
+}
+
+// ****************************************************************************
+//  Method: VsCommonPluginInfo::SetupDatabase
+//
+//  Purpose:
+//      Sets up a Vs database.
+//
+//  Arguments:
+//      list    A list of file names.
+//      nList   The number of timesteps in list.
+//      nBlocks The number of blocks in the list.
+//
+//  Returns:    A Vs database from list.
+//
+//  Programmer: generated by xml2info
+//  Creation:   omitted
+//
+// ****************************************************************************
+avtDatabase *
+VsCommonPluginInfo::SetupDatabase(const char *const *list,
+                                   int nList, int nBlock)
+{
+#if HDF5_VERSION_GE(1,8,1)
+    avtSTMDFileFormat **ffl = new avtSTMDFileFormat*[nList];
+    for (int i = 0 ; i < nList ; i++)
+    {
+        ffl[i] = new avtVsFileFormat(list[i], settings);
+    }
+    avtSTMDFileFormatInterface *inter
+           = new avtSTMDFileFormatInterface(ffl, nList);
+    return new avtGenericDatabase(inter);
+#else
+                     #ifdef VISIT_VERSION //Visit 2.0.0 and later use VISIT_VERSION instead of VERSION, and require a different debugstream accessor as well
+                            DebugStream::Stream3() <<"VsCommonPluginInfo::SetupDatabase() - Vizschema database plugin requires hdf5 1.8.1 or later." <<std::endl;
+                            DebugStream::Stream3() <<"VsCommonPluginInfo::SetupDatabase() - Plugin is disabled and will not open files." <<std::endl;
+                #else
+                            debug3 <<"VsCommonPluginInfo::SetupDatabase() - Vizschema database plugin requires hdf5 1.8.1 or later." <<std::endl;
+                            debug3 <<"VsCommonPluginInfo::SetupDatabase() - Plugin is disabled and will not open files." <<std::endl;
+                #endif
+
+    return NULL;
+#endif
+}
+
+// ****************************************************************************
+//  Method: VsCommonPluginInfo::GetReadOptions
+//
+//  Purpose:
+//      Returns a list of available plugin settings and their defaults
+//
+//  Arguments:
+//
+//  Returns:    A DBOptionsAttributes object populated with setting names & defaults
+//
+//  Programmer: Marc Durant
+//  Creation:   omitted
+//
+// ****************************************************************************
+DBOptionsAttributes *
+VsCommonPluginInfo::GetReadOptions() const
+{
+    /* This code is from the SILO plugin and is here as reference
+    DBOptionsAttributes *rv = new DBOptionsAttributes;
+    vector<string> ignoreOpts;
+    ignoreOpts.push_back("Always"); // 0
+    ignoreOpts.push_back("Auto");   // 1
+    ignoreOpts.push_back("Never");  // 2
+    ignoreOpts.push_back("Undef");  // 3
+    rv->SetEnum(SILO_RDOPT_IGNORE_SEXTS, 3); // Undef
+    rv->SetEnumStrings(SILO_RDOPT_IGNORE_SEXTS, ignoreOpts);
+    rv->SetEnum(SILO_RDOPT_IGNORE_DEXTS, 3); // Undef
+    rv->SetEnumStrings(SILO_RDOPT_IGNORE_DEXTS, ignoreOpts);
+    rv->SetBool(SILO_RDOPT_FORCE_SINGLE, true);
+    rv->SetBool(SILO_RDOPT_SEARCH_ANNOTINT, false);
+
+    // Specify obsolete options and their default values
+    rv->SetObsolete(SILO_RDOPT_IGNORE_SEXTS2);
+    rv->SetObsolete(SILO_RDOPT_IGNORE_DEXTS2);
+
+    return rv;*/
+
+    DBOptionsAttributes *rv = new DBOptionsAttributes;
+    rv->SetInt(VsCommonPluginInfo::strideSettingAxis1_Name.c_str(), defaultStride);
+    rv->SetInt(VsCommonPluginInfo::strideSettingAxis2_Name.c_str(), defaultStride);
+    rv->SetInt(VsCommonPluginInfo::strideSettingAxis3_Name.c_str(), defaultStride);
+
+    return rv;
+
+}
+
+// ****************************************************************************
+//  Method: VsCommonPluginInfo::SetReadOptions
+//
+//  Purpose:
+//      Accepts a list of settings and values, stores those values for the plugin
+//
+//  Arguments:
+//      opts    A DBOptionsAttributes object containing settings
+//
+//  Returns:
+//
+//  Programmer: Marc Durant
+//  Creation:   omitted
+//
+// ****************************************************************************
+void VsCommonPluginInfo::SetReadOptions(DBOptionsAttributes *opts) {
+
+       for (int i = 0; i < opts->GetNumberOfOptions(); i++)
+    {
+        string optname = opts->GetName(i);
+        if (optname == VsCommonPluginInfo::strideSettingAxis1_Name.c_str()) {
+               settings[0] = opts->GetInt(VsCommonPluginInfo::strideSettingAxis1_Name.c_str());
+               if (settings[0] < 0)
+                      settings[0] = defaultStride;
+        }
+
+        if (optname == VsCommonPluginInfo::strideSettingAxis2_Name.c_str()) {
+               settings[1] = opts->GetInt(VsCommonPluginInfo::strideSettingAxis2_Name.c_str());
+                if (settings[1] < 0)
+                       settings[1] = defaultStride;
+        }
+
+        if (optname == VsCommonPluginInfo::strideSettingAxis3_Name.c_str()) {
+               settings[2] = opts->GetInt(VsCommonPluginInfo::strideSettingAxis3_Name.c_str());
+                if (settings[2] < 0)
+                       settings[2] = defaultStride;
+         }
+    }
+}

databases/Vs/VsEnginePluginInfo.C

+/*****************************************************************************
+*
+* Copyright (c) 2000 - 2008, Lawrence Livermore National Security, LLC
+* Produced at the Lawrence Livermore National Laboratory
+* LLNL-CODE-400142
+* All rights reserved.
+*
+* This file is  part of VisIt. For  details, see https://visit.llnl.gov/.  The
+* 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
+*    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
+*    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
+* 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
+* 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.
+*
+*****************************************************************************/
+
+#include <VsPluginInfo.h>
+
+#if defined(__APPLE__)
+#define GetEngineInfo Vs_GetEngineInfo
+#endif
+
+// ****************************************************************************
+//  Function:  GetEngineInfo
+//
+//  Purpose:
+//    Return a new EnginePluginInfo for the Vs database.
+//
+//  Programmer: generated by xml2info
+//  Creation:   omitted
+//
+// ****************************************************************************
+extern "C" EngineDatabasePluginInfo* GetEngineInfo()
+{
+    return new VsEnginePluginInfo;
+}
+
+// ****************************************************************************
+//  Method: VsEnginePluginInfo::GetWriter
+//
+//  Purpose:
+//      Sets up a Vs writer.
+//
+//  Returns:    A Vs writer.
+//
+//  Programmer: generated by xml2info
+//  Creation:   omitted
+//
+// ****************************************************************************
+avtDatabaseWriter *
+VsEnginePluginInfo::GetWriter(void)
+{
+    return NULL;
+}
+

databases/Vs/VsFilter.C

+#include <hdf5.h>
+#include <visit-hdf5.h>
+#if HDF5_VERSION_GE(1,8,1)
+/**
+ *
+ * @file        VsFilter.cpp
+ *
+ * @brief       Implementation for inspecting an HDF5 file
+ *
+ * @version $Id: VsFilter.C 496 2009-08-05 22:57:22Z mdurant $
+ *
+ * Copyright &copy; 2007-2008, Tech-X Corporation
+ * See LICENSE file for conditions of use.
+ *
+ */
+
+// vsh5
+#include <VsFilter.h>
+#include <VsSchema.h>
+#include <VsUtils.h>
+#include <hdf5.h>
+
+struct RECURSION_DATA {
+  VsH5Meta* meta;
+  std::ostream* debugStream;
+  int depth;
+  std::string path;
+};
+
+VsFilter::VsFilter(std::ostream& dbgstrm) : debugStrmRef(dbgstrm) {
+}
+
+VsFilter::VsFilter(hid_t fId, std::ostream& dbgstrm) :
+        debugStrmRef(dbgstrm), fileId(fId) {
+  makeH5Meta();
+}
+
+void VsFilter::makeH5Meta() {
+  h5meta.ptr = 0;
+// Create the list of vs datasets and groups
+// corresponding to variables, variables with mesh and meshes.
+  RECURSION_DATA data;
+  data.debugStream = &debugStrmRef;
+  data.meta = &h5meta;
+  data.depth = 0;
+  data.path = "";
+
+  H5Giterate(fileId, "/", NULL, visitIfc, &data);
+}
+
+herr_t VsFilter::visitIfc(hid_t locId, const char* name, void* opdata) {
+  RECURSION_DATA* data = static_cast< RECURSION_DATA* >(opdata);
+  VsH5Meta* metaPtr = data->meta;
+  std::ostream& osRef = *(data->debugStream);
+
+//cerr <<"working with interface " << endl;
+  herr_t ret = 0;
+  H5G_stat_t statbuf;
+  H5Gget_objinfo (locId, name, false, &statbuf);
+
+  //the fully qualified name of this object
+  std::string fullName = makeCanonicalName(data->path, name);//data->path + "/" + name;
+
+  switch (statbuf.type) {
+
+    case H5G_GROUP: {
+      osRef << "VsFilter::visitIfc: node '" << name << "' is a group." << std::endl;
+      hid_t groupId = H5Gopen(locId, name, H5P_DEFAULT);
+// Metadata for this group
+      VsGMeta* gm = new VsGMeta();
+      gm->name = name;
+      gm->depth = data->depth + 1;
+      gm->path = data->path;
+      gm->iid = groupId;
+// Collect attributes of the group
+      std::pair<VsIMeta*, std::ostream*> gpd(gm, &osRef);
+      H5Aiterate(groupId, H5_INDEX_NAME, H5_ITER_INC, NULL, visitAttrib, &gpd);
+// Check is gm's isMesh is true and add to meshes
+// Check if the group is a mesh and register.  Move the ptr to the mesh
+      if (gm->isMesh) {
+        osRef << "VsFilter::visitIfc: node '" << name << "' is a mesh."
+              << std::endl;
+        std::pair<std::string, VsGMeta*> el(fullName, gm);
+        metaPtr->gMeshes2.insert(el);
+        metaPtr->ptr = gm;
+      }
+      else if (gm->isVsVars) {
+        osRef << "VsFilter::visitIfc: node '" << name << "' is vsVars." <<
+                std::endl;
+        std::pair<std::string, VsGMeta*> el(fullName, gm);
+        metaPtr->vsVars2.insert(el);
+        metaPtr->ptr = gm;
+      }
+      else {
+// If group is not a mesh - delete it - needs to be changed to work with groups
+// which are variables
+        osRef << "VsFilter::visitIfc: node '" << name << "' is not a mesh."
+              << "  Deleting." << std::endl;
+        delete gm;
+      }
+
+      // recurse to examine child groups
+      RECURSION_DATA nextLevelData;
+      nextLevelData.debugStream = data->debugStream;
+      nextLevelData.depth = data->depth + 1;
+      nextLevelData.path = fullName;
+      nextLevelData.meta = data->meta;
+      osRef <<"VsFilter::visitIfc(...): Recursing with path " <<fullName <<" and depth " <<nextLevelData.depth <<"." <<std::endl;
+      H5Giterate(locId, name, NULL, visitIfc, &nextLevelData);
+      osRef <<"VsFilter::visitIfc(...): Returned from recursion" <<std::endl;
+
+      break;
+    }
+
+    case H5G_DATASET: {
+      osRef << "VsFilter::visitIfc: node '" << name <<
+        "' is a dataset." << std::endl;
+      hid_t datasetId = H5Dopen(locId, name, H5P_DEFAULT);
+      osRef << "VsFilter::visitIfc: node '" << name <<
+        "' opened." << std::endl;
+
+// Metadata for this dataset
+      VsDMeta* vm = new VsDMeta();
+      std::string sname = name;
+      vm->name = sname;
+      vm->path = data->path;
+      vm->depth = data->depth + 1;
+      vm->type = H5Tget_native_type(H5Dget_type(datasetId), H5T_DIR_DEFAULT);
+      vm->iid = datasetId;
+      getDims(vm->iid, true, vm->dims);
+// Collect attributes of this dataset
+      std::pair<VsIMeta*, std::ostream*> gpd(vm, &osRef);
+      H5Aiterate(datasetId, H5_INDEX_NAME, H5_ITER_INC, NULL, visitAttrib,
+        &gpd);
+
+      //all datasets get registered in a general list
+      std::pair<std::string, VsDMeta*> el(fullName, vm);
+      metaPtr->datasets.insert(el);
+
+// Test isVariable etc and add register
+      if (vm->isVariable) {
+              std::pair<std::string, VsDMeta*> el2(fullName, vm);
+        metaPtr->vars2.insert(el2);
+        osRef <<"VsFilter::visitIfc: node '" <<name <<
+          "' is a Variable." <<std::endl;
+      }
+      if (vm->isVariableWithMesh) {
+              std::pair<std::string, VsDMeta*> el2(fullName, vm);
+        metaPtr->varsWithMesh2.insert(el2);
+        osRef <<"VsFilter::visitIfc: node '" <<name <<
+          "' is a variable with mesh." <<std::endl;
+      }
+      if (vm->isMesh) {
+              std::pair<std::string, VsDMeta*> el2(fullName, vm);
+        metaPtr->dMeshes2.insert(el2);
+        osRef <<"VsFilter::visitIfc: node '" <<name <<
+          "' is a dataset mesh." <<std::endl;
+      }
+// If this dataset is not a var, mesh or varWith mesh, and its parent is a
+// mesh group, attach to this mesh and do not change the ptr.  Otherwise delete it.
+      if (metaPtr->ptr) {
+        if ((!vm->isVariable) && (!vm->isVariableWithMesh)&&(!vm->isMesh) &&
+            (static_cast<VsGMeta*>(metaPtr->ptr)->isMesh)) {
+          (static_cast<VsGMeta*>(metaPtr->ptr))->datasets.push_back(vm);
+        }
+        if ((!vm->isVariable) && (!vm->isVariableWithMesh)&&(!vm->isMesh) &&
+            (!static_cast<VsGMeta*>(metaPtr->ptr)->isMesh) &&
+            (metaPtr->ptr)) {
+          delete vm;
+        }
+      }
+    }
+    default:
+      break;
+  }
+  return ret;
+}
+
+herr_t VsFilter::visitAttrib(hid_t dId, const char* name,
+       const H5A_info_t* ai, void* opdata) {
+
+  std::pair<VsIMeta*, std::ostream*>* gpdPtr =
+        static_cast<std::pair<VsIMeta*, std::ostream*>*>(opdata);
+  // VsIMeta* iMetaPtr = static_cast<VsIMeta*>(opdata);
+  VsIMeta* iMetaPtr = gpdPtr->first;
+  std::ostream& osRef = *gpdPtr->second;
+
+  osRef << "VsFilter::visitAttrib(...): getting attribute '" <<
+        name << "'." << std::endl;
+
+  hid_t attId = H5Aopen_name(dId, name);
+// Metadata for this attribute
+  VsAMeta* am = new VsAMeta();
+  am->type = H5Tget_native_type(H5Aget_type(attId), H5T_DIR_DEFAULT);
+  am->aid = attId;
+  am->name = name;
+// 0 shows that it is attribute
+  getDims(am->aid, false, am->dims);
+
+// add attrib metadata
+  am->depth = iMetaPtr->depth+1;
+  iMetaPtr->attribs.push_back(am);
+// check for type attribute
+  std::string aname = name;
+  if (aname.compare(VsSchema::typeAtt) == 0) {
+    std::string attValue;
+    herr_t err = getAttributeHelper(attId, &attValue, 0, 0);
+    if (err == 0) {
+     osRef << "VsFilter::visitAttrib(...): attribute '" << name <<
+        "' is '" << attValue << "'." << std::endl;
+// See if this dataset or group is a mesh
+      if (attValue.compare(VsSchema::meshKey) == 0) {
+        iMetaPtr->isMesh = true;
+      }
+// See if this group is derived vars
+      if ( (iMetaPtr->isGroup) && (attValue.compare(VsSchema::vsVarsKey) == 0)) {
+        (static_cast<VsGMeta*>(iMetaPtr))->isVsVars = true;
+      }
+      if (!iMetaPtr->isGroup) {
+// See if this dataset is a variable or variableWithMesh
+        if(attValue.compare(VsSchema::varKey) == 0) {
+          iMetaPtr->isVariable = true;
+        }
+        if(attValue.compare(VsSchema::varWithMeshKey) == 0) {
+          iMetaPtr->isVariableWithMesh = true;
+        }
+      }
+    }
+    else {
+     osRef << "VsFilter::visitAttrib(...): error getting attribute '" <<
+        name << "'.  Is this of type H5T_STR_NULLTERM and a SCALAR?" << std::endl;
+    }
+  }
+  else {
+     osRef << "VsFilter::visitAttrib(...): attribute '" << name <<
+        "' is not '" << VsSchema::typeAtt << "'." << std::endl;
+  }
+  return 0;
+}
+
+void VsFilter::write() const {
+  h5meta.write(debugStrmRef);
+}
+
+void VsFilter::setFile(hid_t fId) {
+  fileId = fId;
+  h5meta.clear();
+  makeH5Meta();
+}
+
+#endif

databases/Vs/VsFilter.h

+#include <hdf5.h>
+#include <visit-hdf5.h>
+#if HDF5_VERSION_GE(1,8,1)
+/**