Fix 'open an HDF5 file without H5F_CLOSE_SEMI' warning for Chombo and Enzo

databases/AvtAlgorithms/CMakeLists.txt

 set(Kit_SRCS
-vtkAvtFileFormatAlgorithm.h
-vtkAvtFileFormatAlgorithm.cxx
-vtkAvtMTSDFileFormatAlgorithm.h
-vtkAvtMTSDFileFormatAlgorithm.cxx
-vtkAvtMTMDFileFormatAlgorithm.h
-vtkAvtMTMDFileFormatAlgorithm.cxx
-vtkAvtSTSDFileFormatAlgorithm.h
-vtkAvtSTSDFileFormatAlgorithm.cxx
-vtkAvtSTMDFileFormatAlgorithm.h
-vtkAvtSTMDFileFormatAlgorithm.cxx
+  vtkAvtFileFormatAlgorithm.cxx
+  vtkAvtMTSDFileFormatAlgorithm.cxx
+  vtkAvtMTMDFileFormatAlgorithm.cxx
+  vtkAvtSTSDFileFormatAlgorithm.cxx
+  vtkAvtSTMDFileFormatAlgorithm.cxx
 )
 
 set(FullPath_SRCS)

databases/AvtAlgorithms/vtkAvtFileFormatAlgorithm.cxx

@@ -956,5 +956,3 @@ void vtkAvtFileFormatAlgorithm::PrintSelf(ostream& os, vtkIndent indent)
   this->Superclass::PrintSelf(os, indent);
    os << indent << "Output Type: " << this->OutputType << "\n";
 }
-
-

databases/AvtAlgorithms/vtkAvtFileFormatAlgorithm.h

@@ -30,8 +30,8 @@ SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 ========================================================================*/
 
-#ifndef _vtkVisItReader_h
-#define _vtkVisItReader_h
+#ifndef _vtkAvtFileFormatAlgorithm_h
+#define _vtkAvtFileFormatAlgorithm_h
 
 #include "vtkIOVisItBridgeModule.h" //for export macro
 
@@ -74,7 +74,7 @@ public:
   static vtkAvtFileFormatAlgorithm *New();
   vtkTypeMacro(vtkAvtFileFormatAlgorithm,vtkCompositeDataSetAlgorithm);
   void PrintSelf(ostream& os, vtkIndent indent);
-  
+
   // Description:
   // Get the number of point or cell arrays available in the input.
   int GetNumberOfPointArrays();
@@ -147,7 +147,7 @@ protected:
   // see algorithm for more info
   virtual int FillOutputPortInformation(int port, vtkInformation* info);
 
-  //methods that setup selection arrays that the client will interact with  
+  //methods that setup selection arrays that the client will interact with
   void SetupDataArraySelections();
   void SetupMeshSelections();
   void SetupMaterialSelections();
@@ -155,8 +155,8 @@ protected:
   //method to setup the proper block bounds for the data.
   //this method is needed to support dynamic block loading
   //for certain streaming pipelines
-  virtual void SetupBlockBoundsInformation(vtkInformation *outInfo);  
-  
+  virtual void SetupBlockBoundsInformation(vtkInformation *outInfo);
+
   //method setups the number of timesteps that the file has
   void SetupTemporalInformation(vtkInformation *outInfo);
 

databases/AvtAlgorithms/vtkFileCloseSemiProperty.h

+#ifndef _vtkFileCloseSemiProperty_h
+#define _vtkFileCloseSemiProperty_h
+
+/*
+ * Needs <hdf5.h>, so include this header only after you include the
+ * hdf5 header. Because you might need to select the right API for hdf5 (such
+ * as with H5_USE_16_API) the hdf5 header is not included here.
+ */
+
+class vtkFileCloseSemiProperty
+{
+public:
+  vtkFileCloseSemiProperty ()
+  {
+    this->Fapl = H5Pcreate(H5P_FILE_ACCESS);
+    H5Pset_fclose_degree(this->Fapl, H5F_CLOSE_SEMI);
+  }
+  ~vtkFileCloseSemiProperty ()
+  {
+    H5Pclose(this->Fapl);
+  }
+  operator hid_t() const
+  {
+    return this->Fapl;
+  }
+
+
+private:
+  hid_t Fapl;
+};
+
+#endif

databases/Chombo/avtChomboFileFormat.C

@@ -95,6 +95,7 @@
 #define H5_USE_16_API
 #include <hdf5.h>
 #include <visit-hdf5.h>
+#include "vtkFileCloseSemiProperty.h"
 #include <boost/cstdint.hpp>
 // using     boost::boost::int32_t; // This conflicts with Visual Studio 10
 using     std::string;
@@ -448,7 +449,8 @@ avtChomboFileFormat::InitializeReader(void)
     //
     // Open file
     //
-    file_handle = H5Fopen(filenames[0], H5F_ACC_RDONLY, H5P_DEFAULT);
+    file_handle = H5Fopen(filenames[0], H5F_ACC_RDONLY, 
+                          vtkFileCloseSemiProperty ());
     if (file_handle < 0)
     {
         EXCEPTION1(InvalidDBTypeException, "Cannot be a Chombo file, since "
@@ -1344,7 +1346,7 @@ avtChomboFileFormat::InitializeReader(void)
             VisItStat_t fs;
             if (VisItStat(mappingFilename.c_str(), &fs) == 0)
             {
-                hid_t mapping_file_handle = H5Fopen(mappingFilename.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT);
+                hid_t mapping_file_handle = H5Fopen(mappingFilename.c_str(), H5F_ACC_RDONLY, vtkFileCloseSemiProperty ());
                 if (mapping_file_handle > 0)
                 {
                     hid_t slash = H5Gopen(mapping_file_handle, "/");
@@ -2620,7 +2622,8 @@ avtChomboFileFormat::GetMesh(int patch, const char *meshname)
 
         if (file_handle < 0)
         {
-            file_handle = H5Fopen(filenames[0], H5F_ACC_RDONLY, H5P_DEFAULT);
+            file_handle = H5Fopen(filenames[0], H5F_ACC_RDONLY, 
+                                  vtkFileCloseSemiProperty ());
             if (file_handle < 0)
             {
                 EXCEPTION1(InvalidDBTypeException, "Cannot be a Chombo file, since "
@@ -3084,7 +3087,8 @@ avtChomboFileFormat::GetVar(int patch, const char *varname)
         SNPRINTF(name, 1024, "level_%d", level);
         if (file_handle < 0)
         {
-            file_handle = H5Fopen(filenames[0], H5F_ACC_RDONLY, H5P_DEFAULT);
+            file_handle = H5Fopen(filenames[0], H5F_ACC_RDONLY,
+                                  vtkFileCloseSemiProperty ());
             if (file_handle < 0)
             {
                 EXCEPTION1(InvalidDBTypeException, "Cannot be a Chombo file, since "
@@ -3189,7 +3193,8 @@ avtChomboFileFormat::GetVar(int patch, const char *varname)
         {
             if (file_handle < 0)
             {
-                file_handle = H5Fopen(filenames[0], H5F_ACC_RDONLY, H5P_DEFAULT);
+                file_handle = H5Fopen(filenames[0], H5F_ACC_RDONLY, 
+                                      vtkFileCloseSemiProperty ());
                 if (file_handle < 0)
                 {
                     EXCEPTION1(InvalidDBTypeException, "Cannot be a Chombo file, since "
@@ -3425,7 +3430,8 @@ avtChomboFileFormat::GetVectorVar(int patch, const char *varname)
             SNPRINTF(name, 1024, "level_%d", level);
             if (file_handle < 0)
             {
-                file_handle = H5Fopen(filenames[0], H5F_ACC_RDONLY, H5P_DEFAULT);
+                file_handle = H5Fopen(filenames[0], H5F_ACC_RDONLY, 
+                                      vtkFileCloseSemiProperty ());
                 if (file_handle < 0)
                 {
                     EXCEPTION1(InvalidDBTypeException, "Cannot be a Chombo file, since "

databases/Enzo/avtEnzoFileFormat.C

@@ -80,6 +80,7 @@
 #define H5_USE_16_API
 #include <hdf5.h>
 #include <visit-hdf5.h>
+#include "vtkFileCloseSemiProperty.h"
 #endif
 
 using std::string;
@@ -629,7 +630,8 @@ avtEnzoFileFormat::DetermineVariablesFromGridFile()
 #endif
     {
 #ifdef HAVE_LIBHDF5
-        hid_t fileId = H5Fopen(gridFileName.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT);
+        hid_t fileId = H5Fopen(gridFileName.c_str(), H5F_ACC_RDONLY, 
+                               vtkFileCloseSemiProperty ());
         if (fileId < 0)
         {
 #ifdef HAVE_LIBHDF4
@@ -1434,7 +1436,8 @@ avtEnzoFileFormat::GetMesh(int domain, const char *meshname)
             return NULL;
         }
 
-        hid_t fileId = H5Fopen(particleFileName.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT);
+        hid_t fileId = H5Fopen(particleFileName.c_str(), H5F_ACC_RDONLY, 
+                               vtkFileCloseSemiProperty ());
         if (fileId < 0)
         {
             EXCEPTION1(InvalidFilesException, particleFileName.c_str());
@@ -1870,7 +1873,8 @@ avtEnzoFileFormat::GetVar(int domain, const char *varname)
         // HDF5 STUFF
         string gridFileName = grids[domain+1].gridFileName;
 
-        hid_t fileId = H5Fopen(gridFileName.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT);
+        hid_t fileId = H5Fopen(gridFileName.c_str(), H5F_ACC_RDONLY, 
+                               vtkFileCloseSemiProperty ());
         if (fileId < 0)
         {
             EXCEPTION1(InvalidFilesException, gridFileName.c_str());

databases/LAMMPS/avtLAMMPSDumpFileFormat.h

@@ -34,7 +34,92 @@
 
 class avtLAMMPSDumpFileFormat : public avtMTSDFileFormat
 {
-  public:
+private:
+  struct AtomInfo
+  {
+    AtomInfo():vars(),names(),types(),ids(),
+              enableType(false),enableIds(false),numVars(0){}
+
+    void Clear()
+        { vars.resize(0); names.resize(0); types.resize(0); ids.resize(0);
+          enableType = false; enableIds = false; numVars = 0;
+        };
+
+    void AddVariable(const std::string& name)
+        {
+        //if it is id or type we don't push back since it is stored separately
+        if(name == "id")
+            {
+            enableIds = true;
+            }
+        if(name == "type")
+            {
+            enableType = true;
+            }
+        else
+            {
+            names.push_back(name);
+            vars.resize(names.size());
+            }
+        ++numVars;
+        }
+    int GetNumberOfVariables() const
+        {
+        return numVars;
+        }
+
+    void SetNumberOfAtoms(std::size_t size)
+    {
+        if(HasIds())    { ids.resize(size);   }
+        if(HasTypes())  { types.resize(size); }
+        for(std::size_t i=0; i < vars.size(); ++i) { vars[i].resize(size); }
+    }
+
+
+    //helper methods to get the variable names
+    typedef std::vector<std::string>::const_iterator name_iterator;
+    name_iterator GetVariableNamesBegin() const { return names.begin(); }
+    name_iterator GetVariableNamesEnd() const { return names.end(); }
+    int GetVarIndex(const std::string& n) const
+    {
+    for(int i=0; i < names.size(); ++i)
+        {
+        if(names[i] == n)
+          { return i; }
+        }
+        return -1;
+    }
+
+    //helper methods for types
+    bool SetHasTypes(bool b) { enableType = b; }
+    bool HasTypes() const { return enableType; }
+    const std::vector<int>& GetTypes() const { return types; }
+    void SetType(std::size_t pos, int t) { types[pos]=t; }
+
+    //helper methods for ids
+    bool SetHasIds(bool b) { enableIds = b; }
+    bool HasIds() const { return enableIds; }
+    const std::vector<int>& GetIds() const { return ids; }
+    void SetId(std::size_t pos, int i) { ids[pos]=i; }
+
+
+    //operators to make this like you can access the vars easily
+    const std::vector<float> &operator[](std::size_t idx) const
+        { return vars[idx]; }
+    std::vector<float>& operator[](std::size_t idx)
+        { return vars[idx]; }
+
+
+    private:
+        std::vector < std::vector<float> > vars;
+        std::vector < std::string > names;
+        std::vector < int > types;
+        std::vector < int > ids;
+        bool enableType, enableIds;
+        int numVars;
+  };
+
+public:
     static bool        FileExtensionIdentify(const std::string&);
     static bool        FileContentsIdentify(const std::string&);
     static avtFileFormatInterface *CreateInterface(
@@ -46,7 +131,7 @@ class avtLAMMPSDumpFileFormat : public avtMTSDFileFormat
     virtual int            GetNTimesteps(void);
 
     virtual const char    *GetType(void)   { return "LAMMPS"; };
-    virtual void           FreeUpResources(void); 
+    virtual void           FreeUpResources(void);
 
     virtual vtkDataSet    *GetMesh(int, const char *);
     virtual vtkDataArray  *GetVar(int, const char *);
@@ -59,8 +144,7 @@ class avtLAMMPSDumpFileFormat : public avtMTSDFileFormat
     std::string                    filename;
     bool                           metaDataRead;
     int                            nTimeSteps;
-    int                            nVars;
-    std::vector<int>               nAtoms;
+
     double                         xMin, xMax;
     double                         yMin, yMax;
     double                         zMin, zMax;
@@ -69,9 +153,9 @@ class avtLAMMPSDumpFileFormat : public avtMTSDFileFormat
     bool                     xScaled,yScaled,zScaled;
     int                      xIndex, yIndex, zIndex;
     int                      speciesIndex, idIndex;
-    std::vector< std::vector<float> >  vars;
-    std::vector<int>              speciesVar;
-    std::vector< std::string >         varNames;
+
+    std::vector<int>               nAtoms;
+    AtomInfo                       atomVars;
 
     virtual void    PopulateDatabaseMetaData(avtDatabaseMetaData *, int);
     void            OpenFileAtBeginning();