Add Pixie3D flavor of ADIOS2 (#19272)

* Remove print statements and add expressions for Lat/Lon/Depth for SPECFEM3D data.

* Add Pixie3D ADIOS2 reader.

* Revert changes to avtIsovolumeFilter.

* Compile fixes for avtPixie3DFileFormat.

* Add spaces in debug5 statements (address @brugger1's comments in original PR)

* Change cout statements to debug5.

* whitespace cleanup

* Update Adios2.xml with new file.

* Remove unnecessary comments related to unused functions.

* Update release notes.

* Remove 'std::' from in front of 'debug5'.

---------

Co-authored-by: dpugmire <dpugmire@gmail.com>

src/databases/ADIOS2/ADIOS2.xml

@@ -36,6 +36,7 @@
       avtADIOS2FileFormat.C
       avtMEUMMAPSFileFormat.C
       avtGTCFileFormat.C
+      avtPixie3DFileFormat.C
       avtADIOS2BaseFileFormat.C
       avtADIOS2SSTFileFormat.C
       avtLAMMPSFileFormat.C

src/databases/ADIOS2/CMakeLists.txt

@@ -18,6 +18,7 @@ ${COMMON_SOURCES}
 avtADIOS2FileFormat.C
 avtMEUMMAPSFileFormat.C
 avtGTCFileFormat.C
+avtPixie3DFileFormat.C
 avtADIOS2BaseFileFormat.C
 avtADIOS2SSTFileFormat.C
 avtLAMMPSFileFormat.C
@@ -31,6 +32,7 @@ ${COMMON_SOURCES}
 avtADIOS2FileFormat.C
 avtMEUMMAPSFileFormat.C
 avtGTCFileFormat.C
+avtPixie3DFileFormat.C
 avtADIOS2BaseFileFormat.C
 avtADIOS2SSTFileFormat.C
 avtLAMMPSFileFormat.C

src/databases/ADIOS2/avtADIOS2BaseFileFormat.C

@@ -3,7 +3,7 @@
 // details.  No copyright assignment is required to contribute to VisIt.
 
 // ************************************************************************* //
-//                            avtADIOS2BaseFileFormat.C                           //
+//                       avtADIOS2BaseFileFormat.C                           //
 // ************************************************************************* //
 
 #include <avtMTSDFileFormatInterface.h>
@@ -25,6 +25,7 @@
 
 #include <InvalidVariableException.h>
 #include <VisItStreamUtil.h>
+#include <DebugStream.h>
 
 using namespace std;
 
@@ -86,7 +87,7 @@ avtADIOS2BaseFileFormat::CreateInterfaceADIOS2(
         int nList,
         int nBlock,
         std::shared_ptr<adios2::ADIOS> adios,
-        adios2::Engine &reader, 
+        adios2::Engine &reader,
         adios2::IO &io,
         std::map<std::string, adios2::Params> &variables,
         std::map<std::string, adios2::Params> &attributes
@@ -99,11 +100,11 @@ avtADIOS2BaseFileFormat::CreateInterfaceADIOS2(
         ffl[i] =  new avtMTSDFileFormat*[nBlock];
         for (int j = 0; j < nBlock; j++)
         {
-        cout << "----------- ADIOS Base create interface for  " 
-             << list[i*nBlock +j] 
+        debug5 << "----------- ADIOS Base create interface for  "
+             << list[i*nBlock +j]
              << " -----------------" << endl;
 
-            if (!i && !j) 
+            if (!i && !j)
             {
                 ffl[i][j] =  new avtADIOS2BaseFileFormat(adios, reader, io, variables, attributes, list[i*nBlock +j]);
             }
@@ -113,7 +114,7 @@ avtADIOS2BaseFileFormat::CreateInterfaceADIOS2(
             }
         }
     }
-    cout << "----------- ADIOS Base return MTSD interface " << endl;
+    debug5 << "----------- ADIOS Base return MTSD interface " << endl;
     return new avtMTSDFileFormatInterface(ffl, nTimestepGroups, nBlock);
 }
 
@@ -123,10 +124,10 @@ avtADIOS2BaseFileFormat::CreateInterfaceADIOS2(
 //
 //  Programmer: pugmire -- generated by xml2avt
 //  Creation:   Thu Apr 12 08:39:47 PDT 2018
-// 
+//
 //  Modifications:
 //    Justin Privitera, Thu Jan 18 09:56:51 PST 2024
-//    Removed adios2::DebugON since it is not present in newer versions of 
+//    Removed adios2::DebugON since it is not present in newer versions of
 //    adios2.
 //
 // ****************************************************************************
@@ -149,7 +150,7 @@ avtADIOS2BaseFileFormat::avtADIOS2BaseFileFormat(const char *filename)
     {
         numTimeSteps = 100000;
     }
-    else 
+    else
     {
         map<string, adios2::Params> vars = io.AvailableVariables();
         for (auto &v : vars)
@@ -166,9 +167,9 @@ avtADIOS2BaseFileFormat::avtADIOS2BaseFileFormat(const char *filename)
 
 avtADIOS2BaseFileFormat::avtADIOS2BaseFileFormat(std::shared_ptr<adios2::ADIOS> adios,
         adios2::Engine &reader,
-        adios2::IO &io, 
+        adios2::IO &io,
         std::map<std::string, adios2::Params> &variables,
-        std::map<std::string, adios2::Params> &attributes, 
+        std::map<std::string, adios2::Params> &attributes,
         const char *filename)
     : adios(adios),
       numTimeSteps(1),
@@ -185,7 +186,7 @@ avtADIOS2BaseFileFormat::avtADIOS2BaseFileFormat(std::shared_ptr<adios2::ADIOS>
     {
         numTimeSteps = 100000;
     }
-    else 
+    else
     {
         for (auto &v : variables)
         {
@@ -197,21 +198,21 @@ avtADIOS2BaseFileFormat::avtADIOS2BaseFileFormat(std::shared_ptr<adios2::ADIOS>
             }
         }
     }
-    cout << "----------- ADIOS Base reader for " 
-         << filename << " with " << numTimeSteps 
+    debug5 << "----------- ADIOS Base reader for "
+         << filename << " with " << numTimeSteps
          << "steps -----------------" << endl;
 }
 
 avtADIOS2BaseFileFormat::~avtADIOS2BaseFileFormat()
 {
 #if MDSERVER
-    cout << "-----------\nADIOS destructor called in MDSERVER \n-----------------\n" << endl;
+    debug5 << "-----------\nADIOS destructor called in MDSERVER \n-----------------\n" << endl;
 #else
-    cout << "-----------\nADIOS destructor called in ENGINE \n-----------------\n" << endl;
+    debug5 << "-----------\nADIOS destructor called in ENGINE \n-----------------\n" << endl;
 #endif
     if (!isClosed)
     {
-        cout << "-----------\nADIOS reader closes down stream \n-----------------\n" << endl;
+        debug5 << "-----------\nADIOS reader closes down stream \n-----------------\n" << endl;
         reader.Close();
     }
     isClosed = true;
@@ -278,17 +279,17 @@ avtADIOS2BaseFileFormat::PopulateDatabaseMetaData(avtDatabaseMetaData *md, int t
         if (status != adios2::StepStatus::OK)
             return;
 #if MDSERVER
-        cout<<" MDSERVER received streaming step = "<<reader.CurrentStep()<<endl;
+        debug5<<" MDSERVER received streaming step = "<<reader.CurrentStep()<<endl;
 #else
-        cout<<" Server populates metadata from streaming step = "<<reader.CurrentStep()<<endl;
+        debug5<<" Server populates metadata from streaming step = "<<reader.CurrentStep()<<endl;
 #endif
         */
     }
 
     meshInfo.clear();
     variables = io.AvailableVariables();
 
-    cout<<" Server populates metadata with "<<variables.size() <<" variables."<<endl;
+    debug5<<" Server populates metadata with "<<variables.size() <<" variables."<<endl;
 
 #if MDSERVER
     if (stagingMode)
@@ -337,7 +338,7 @@ avtADIOS2BaseFileFormat::PopulateDatabaseMetaData(avtDatabaseMetaData *md, int t
 #if MDSERVER
     if (!isClosed)
     {
-        cout << "-----------\nADIOS reader closes down stream in MDSERVER \n-----------------\n" << endl;
+        debug5 << "-----------\nADIOS reader closes down stream in MDSERVER \n-----------------\n" << endl;
         reader.Close();
     }
     isClosed = true;
@@ -384,7 +385,7 @@ avtADIOS2BaseFileFormat::GetMesh(int timestate, const char *meshname)
     if (shape.size() == 2)
         shape.push_back(1);
 
-    //cout<<"********** SWAP DIMS"<<endl;
+    //debug5<<"********** SWAP DIMS"<<endl;
     std::swap(shape[0], shape[1]);
 
     int dims[3] = {shape[0], shape[1], shape[2]};
@@ -433,7 +434,7 @@ vtkDataArray *
 avtADIOS2BaseFileFormat::GetVar(int timestate, const char *varname)
 {
     static int prev_timestate = 0;
-    cout<<"GetVar: "<<varname<<" ts= "<<timestate<<endl;
+    debug5<<"GetVar: "<<varname<<" ts= "<<timestate<<endl;
 
     if (variables.find(varname) == variables.end())
         return NULL;
@@ -445,14 +446,14 @@ avtADIOS2BaseFileFormat::GetVar(int timestate, const char *varname)
     {
         if (timestate != prev_timestate)
         {
-            cout<<" release step = "<<reader.CurrentStep()<<endl;
+            debug5<<" release step = "<<reader.CurrentStep()<<endl;
             reader.EndStep(); // release previous step
             prev_timestate = timestate;
             adios2::StepStatus status = adios2::StepStatus::NotReady;
-            while (status == adios2::StepStatus::NotReady) 
+            while (status == adios2::StepStatus::NotReady)
             {
                 status = reader.BeginStep(adios2::StepMode::Read, 10.0f);
-                if (status == adios2::StepStatus::EndOfStream || 
+                if (status == adios2::StepStatus::EndOfStream ||
                     status == adios2::StepStatus::OtherError)
                 {
                     reader.Close();
@@ -461,17 +462,17 @@ avtADIOS2BaseFileFormat::GetVar(int timestate, const char *varname)
                 }
                 else if (status == adios2::StepStatus::NotReady)
                 {
-                    cout<<" still waiting for next step = "
+                    debug5<<" still waiting for next step = "
                         <<reader.CurrentStep()<<endl;
                 }
             }
-            cout<<" received streaming step = "<<reader.CurrentStep()<<endl;
+            debug5<<" received streaming step = "<<reader.CurrentStep()<<endl;
         }
     }
 
 
     adios2::Variable<double> v = io.InquireVariable<double>(varname);
-    //cout<<"DIMS= "<<v.Shape()<<endl;
+    //debug5<<"DIMS= "<<v.Shape()<<endl;
     if (!stagingMode)
         v.SetStepSelection({timestate, 1});
 

src/databases/ADIOS2/avtADIOS2FileFormat.C

@@ -3,7 +3,7 @@
 // details.  No copyright assignment is required to contribute to VisIt.
 
 // ************************************************************************* //
-//                            avtADIOSFileFormat.C                           //
+//                           avtADIOS2FileFormat.C                           //
 // ************************************************************************* //
 
 #include <avtFileFormatInterface.h>
@@ -13,6 +13,7 @@
 
 #include <avtADIOS2BaseFileFormat.h>
 #include <avtGTCFileFormat.h>
+#include <avtPixie3DFileFormat.h>
 #include <avtLAMMPSFileFormat.h>
 #include <avtSpecFEMFileFormat.h>
 #include <avtMEUMMAPSFileFormat.h>
@@ -47,9 +48,9 @@
 //
 //   Dave Pugmire, Thu Oct 30 11:59:40 EDT 2014
 //   Added a LAMMPS reader. Modified the flavor flag to an enum for clarity.
-// 
+//
 //   Justin Privitera, Thu Jan 18 09:56:51 PST 2024
-//   Removed adios2::DebugON since it is not present in newer versions of 
+//   Removed adios2::DebugON since it is not present in newer versions of
 //   adios2.
 //   Added special logic for BP5 files.
 //
@@ -59,15 +60,15 @@ avtFileFormatInterface *
 ADIOS2_CreateFileFormatInterface(const char * const *list, int nList, int nBlock)
 {
     avtFileFormatInterface *ffi = NULL;
-    enum Flavor {GTC, BASIC, MEUMMAPS, LAMMPS, SPECFEM, FAIL};
+    enum Flavor {GTC, BASIC, MEUMMAPS, LAMMPS, SPECFEM, PIXIE3D, FAIL};
     bool isSST = (std::string(list[0]).find(".sst") != std::string::npos);
     bool isHDF5 = (std::string(list[0]).find(".h5") != std::string::npos);
     bool isWDM = (std::string(list[0]).find(".ssc") != std::string::npos);
     bool stagingMode = isSST || isWDM;
 
-    cout<<__FILE__<<" "<<__LINE__<<" isSST "<<isSST<<endl;
-    cout<<__FILE__<<" "<<__LINE__<<" isWDM "<<isWDM<<endl;
-    cout<<__FILE__<<" "<<__LINE__<<" isHDF5 "<<isHDF5<<endl;
+    debug5 << __FILE__ << " " << __LINE__ << " isSST " << isSST << endl;
+    debug5 << __FILE__ << " " << __LINE__ << " isWDM " << isWDM << endl;
+    debug5 << __FILE__ << " " << __LINE__ << " isHDF5 " << isHDF5 << endl;
     Flavor flavor = FAIL;
     if (list != NULL || nList > 0)
     {
@@ -85,22 +86,22 @@ ADIOS2_CreateFileFormatInterface(const char * const *list, int nList, int nBlock
             bool stagingMode  = ADIOS2Helper_IsStagingEngine(engineName);
 
             io.SetEngine(engineName);
-            //cout<<__FILE__<<" "<<__LINE__<<" Connect to stream "<<fileName<<" ..."
-            //   <<" engine "<<engineName<<" ..."<<endl;
+            //debug5 << __FILE__ << " " << __LINE__ << " Connect to stream " << fileName << " ..."
+            //   << " engine " << engineName << " ..." << endl;
             if (engineName == "BP5")
                 reader = io.Open(fileName, adios2::Mode::ReadRandomAccess);
             else
                 reader = io.Open(fileName, adios2::Mode::Read);
 
             if (stagingMode)
             {
-                cout<<__FILE__<<" "<<__LINE__<<" Get first step "<<endl;
+                debug5 << __FILE__ << " " << __LINE__ << " Get first step " << endl;
                 adios2::StepStatus status =
                     reader.BeginStep(adios2::StepMode::Read, -1.0f);
                 if (status == adios2::StepStatus::OK)
                 {
-                    std::cout<<" Identifier received streaming step = "
-                        <<reader.CurrentStep()<<endl;
+                    debug5 << " Identifier received streaming step = "
+                        << reader.CurrentStep() << endl;
                     variables = io.AvailableVariables();
                     attributes = io.AvailableAttributes();
 
@@ -113,6 +114,8 @@ ADIOS2_CreateFileFormatInterface(const char * const *list, int nList, int nBlock
                         flavor = LAMMPS;
                     else if (avtMEUMMAPSFileFormat::IdentifyADIOS2(variables,attributes))
                         flavor = MEUMMAPS;
+                    else if (avtPixie3DFileFormat::IdentifyADIOS2(variables,attributes))
+                        flavor = PIXIE3D;
 
                     // generic with staging engines
                     else
@@ -126,9 +129,9 @@ ADIOS2_CreateFileFormatInterface(const char * const *list, int nList, int nBlock
                 variables = io.AvailableVariables();
                 attributes = io.AvailableAttributes();
 #if MDSERVER
-                std::cout<<" MDSERVER Identifier has " << variables.size() << " variables"<<endl;
+                debug5 << " MDSERVER Identifier has " << variables.size() << " variables" << endl;
 #else
-                std::cout<<" Identifier has " << variables.size() << " variables"<<endl;
+                debug5 << " Identifier has " << variables.size() << " variables" << endl;
 #endif
                 // add formats here that support reading from HDF5
                 if (avtGTCFileFormat::Identify(fileName.c_str()))
@@ -139,6 +142,8 @@ ADIOS2_CreateFileFormatInterface(const char * const *list, int nList, int nBlock
                     flavor = MEUMMAPS;
                 else if (avtSpecFEMFileFormat::Identify(fileName.c_str()))
                     flavor = SPECFEM;
+                else if (avtPixie3DFileFormat::Identify(fileName.c_str()))
+                    flavor = PIXIE3D;
 
                 // generic with HDF5 file
                 else if (isHDF5)
@@ -157,9 +162,13 @@ ADIOS2_CreateFileFormatInterface(const char * const *list, int nList, int nBlock
         }
         ENDTRY
 
-        cout<<"FLAVOR= "<<flavor<<endl;
+        debug5 << "FLAVOR= " << flavor << endl;
         switch(flavor)
         {
+          case PIXIE3D:
+            ffi = avtPixie3DFileFormat::CreateInterfaceADIOS2(
+                    list, nList, nBlock, adios, reader, io, variables, attributes);
+            break;
           case GTC:
             ffi = avtGTCFileFormat::CreateInterfaceADIOS2(
                     list, nList, nBlock, adios, reader, io, variables, attributes);
@@ -178,7 +187,6 @@ ADIOS2_CreateFileFormatInterface(const char * const *list, int nList, int nBlock
                     list, nList, nBlock);
             break;
           case BASIC:
-              cout<<"OPEN A BASIC READER"<<endl;
             ffi = avtADIOS2BaseFileFormat::CreateInterfaceADIOS2(
                     list, nList, nBlock, adios, reader, io, variables, attributes);
             break;
@@ -187,6 +195,5 @@ ADIOS2_CreateFileFormatInterface(const char * const *list, int nList, int nBlock
         }
     }
 
-    //cout<<"RETURN ADIOS READER"<<endl;
     return ffi;
 }