Upgrade ADIOS2 to 2.10.0-rc1 (#19228) (#19251)

src/CMake/FindADIOS2.cmake

@@ -20,6 +20,9 @@
 #   Justin Privitera, Wed Apr 27 17:46:52 PDT 2022
 #   Updated adios2 to 2.7.1 and added all the libraries it creates to the
 #   installation as well as additional logic for parallel building.
+# 
+#   Justin Privitera, Thu Jan 18 09:56:51 PST 2024
+#   adios2 libs have changed so I removed many of the old ones.
 #
 #****************************************************************************/
 
@@ -28,12 +31,10 @@
 if(NOT WIN32)
     SET_UP_THIRD_PARTY(ADIOS2 LIBS
         adios2_c adios2_atl adios2_dill adios2_evpath adios2_ffs
-        adios2_taustubs adios2_cmenet adios2_cmzplenet adios2_cmepoll
-        adios2_core adios2_cmmulticast adios2_enet adios2_cmselect
-        adios2_cxx11 adios2_cmsockets adios2_cmudp)
+        adios2_perfstubs adios2_cxx11 adios2_core adios2_enet)
 else()
     SET_UP_THIRD_PARTY(ADIOS2 LIBS
-        adios2_c adios2_cxx11 adios2_core adios2_taustubs)
+        adios2_c adios2_cxx11 adios2_core adios2_perfstubs)
 endif()
 
 if(VISIT_PARALLEL)

src/databases/ADIOS2/ADIOS2HelperFuncs.C

@@ -1,4 +1,7 @@
 #include <ADIOS2HelperFuncs.h>
+#include <visit-config.h>
+#include <iostream>
+#include <fstream>
 
 std::string ADIOS2Helper_GetEngineName(const std::string &fname)
 {
@@ -13,8 +16,23 @@ std::string ADIOS2Helper_GetEngineName(const std::string &fname)
     if (fname.find(".bp/md.0") != std::string::npos)
         return "BPFile";
 
-	if (ADIOS2Helper_FileIsDirectory(fname))
-	    return "BP4";
+    if (ADIOS2Helper_FileIsDirectory(fname))
+    {
+        std::string engine_name;
+        std::string bp5_special_file = fname + VISIT_SLASH_STRING + "mmd.0";
+        std::ifstream ifs;
+        ifs.open(bp5_special_file.c_str());
+        if(!ifs.is_open())
+        {
+            engine_name = "BP4";
+        }
+        else
+        {
+            engine_name = "BP5";
+        }
+        ifs.close();
+        return engine_name;
+    }
     else
         return "BPFile";
 }

src/databases/ADIOS2/avtADIOS2BaseFileFormat.C

@@ -123,12 +123,17 @@ 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 
+//    adios2.
 //
 // ****************************************************************************
 
 
 avtADIOS2BaseFileFormat::avtADIOS2BaseFileFormat(const char *filename)
-    : adios(std::make_shared<adios2::ADIOS>(adios2::DebugON)),
+    : adios(std::make_shared<adios2::ADIOS>()),
       numTimeSteps(1),
       isClosed(false),
       avtMTSDFileFormat(&filename, 1)

src/databases/ADIOS2/avtADIOS2FileFormat.C

@@ -47,6 +47,11 @@
 //
 //   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 
+//   adios2.
+//   Added special logic for BP5 files.
 //
 // ****************************************************************************
 
@@ -66,7 +71,7 @@ ADIOS2_CreateFileFormatInterface(const char * const *list, int nList, int nBlock
     Flavor flavor = FAIL;
     if (list != NULL || nList > 0)
     {
-        std::shared_ptr<adios2::ADIOS> adios(std::make_shared<adios2::ADIOS>(adios2::DebugON));
+        std::shared_ptr<adios2::ADIOS> adios(std::make_shared<adios2::ADIOS>());
         adios2::IO io(adios->DeclareIO("ReadBP"));
         adios2::Engine reader;
         std::map<std::string, adios2::Params> variables, attributes;
@@ -81,8 +86,12 @@ ADIOS2_CreateFileFormatInterface(const char * const *list, int nList, int nBlock
 
             io.SetEngine(engineName);
             //cout<<__FILE__<<" "<<__LINE__<<" Connect to stream "<<fileName<<" ..."
-            //    <<" engine "<<engineName<<" ..."<<endl;
-            reader = io.Open(fileName, adios2::Mode::Read);
+            //   <<" 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;

src/databases/ADIOS2/avtADIOS2SSTFileFormat.C

@@ -81,11 +81,16 @@ avtADIOS2SSTFileFormat::CreateInterface(const char *const *list,
 //
 //  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 
+//    adios2.
 //
 // ****************************************************************************
 
 avtADIOS2SSTFileFormat::avtADIOS2SSTFileFormat(const char *filename)
-    : adios(std::make_shared<adios2::ADIOS>(adios2::DebugON)),
+    : adios(std::make_shared<adios2::ADIOS>()),
       io(adios->DeclareIO("sstIO")),
       numTimeSteps(1),
       avtMTSDFileFormat(&filename, 1)

src/databases/ADIOS2/avtGTCFileFormat.C

@@ -125,11 +125,16 @@ avtGTCFileFormat::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 
+//    adios2.
 //
 // ****************************************************************************
 
 avtGTCFileFormat::avtGTCFileFormat(const char *filename)
-    : adios(std::make_shared<adios2::ADIOS>(adios2::DebugON)),
+    : adios(std::make_shared<adios2::ADIOS>()),
       io(adios->DeclareIO("ReadBP")),
       numTimeSteps(1),
       avtMTSDFileFormat(&filename, 1),

src/databases/ADIOS2/avtLAMMPSFileFormat.C

@@ -30,7 +30,7 @@ using namespace std;
 bool
 avtLAMMPSFileFormat::Identify(const char *fname)
 {
-    shared_ptr<adios2::ADIOS> adios = std::make_shared<adios2::ADIOS>(adios2::DebugON);
+    shared_ptr<adios2::ADIOS> adios = std::make_shared<adios2::ADIOS>();
     adios2::IO io = adios2::IO(adios->DeclareIO("ReadBPLAMMPS"));
     io.SetEngine("BP");
     adios2::Engine reader = io.Open(fname, adios2::Mode::Read);
@@ -123,11 +123,16 @@ avtLAMMPSFileFormat::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 
+//    adios2.
 //
 // ****************************************************************************
 
 avtLAMMPSFileFormat::avtLAMMPSFileFormat(const char *filename)
-    : adios(std::make_shared<adios2::ADIOS>(adios2::DebugON)),
+    : adios(std::make_shared<adios2::ADIOS>()),
       numTimeSteps(1),
       currentTimestep(-1),
       numAtoms(-1),

src/databases/ADIOS2/avtMEUMMAPSFileFormat.C

@@ -135,11 +135,16 @@ avtMEUMMAPSFileFormat::CreateInterfaceADIOS2(
 //
 //  Programmer: dpn -- generated by xml2avt
 //  Creation:   Tue Sep 11 13:23:54 PST 2018
+// 
+//  Modifications:
+//    Justin Privitera, Thu Jan 18 09:56:51 PST 2024
+//    Removed adios2::DebugON since it is not present in newer versions of 
+//    adios2.
 //
 // ****************************************************************************
 
 avtMEUMMAPSFileFormat::avtMEUMMAPSFileFormat(const char *filename)
-    :  adios(std::make_shared<adios2::ADIOS>(adios2::DebugON)),
+    :  adios(std::make_shared<adios2::ADIOS>()),
        io(adios->DeclareIO("ReadBP")),
        numTimeSteps(1),
        avtMTMDFileFormat(filename)

src/databases/ADIOS2/avtSpecFEMFileFormat.C

@@ -106,17 +106,22 @@ avtSpecFEMFileFormat::CreateInterface(const char *const *list,
 //
 //  Programmer: Dave Pugmire
 //  Creation:   Wed Mar 17 15:29:24 EDT 2010
+// 
+//  Modifications:
+//    Justin Privitera, Thu Jan 18 09:56:51 PST 2024
+//    Removed adios2::DebugON since it is not present in newer versions of 
+//    adios2.
 //
 // ****************************************************************************
 
 avtSpecFEMFileFormat::avtSpecFEMFileFormat(const char *nm)
     : avtMTMDFileFormat(nm),
 #ifdef PARALLEL
-      adiosMesh(std::make_shared<adios2::ADIOS>((MPI_Comm)VISIT_MPI_COMM, adios2::DebugON)),
-      adiosData(std::make_shared<adios2::ADIOS>((MPI_Comm)VISIT_MPI_COMM, adios2::DebugON))
+      adiosMesh(std::make_shared<adios2::ADIOS>((MPI_Comm)VISIT_MPI_COMM)),
+      adiosData(std::make_shared<adios2::ADIOS>((MPI_Comm)VISIT_MPI_COMM))
 #else
-      adiosMesh(std::make_shared<adios2::ADIOS>(adios2::DebugON)),
-      adiosData(std::make_shared<adios2::ADIOS>(adios2::DebugON))
+      adiosMesh(std::make_shared<adios2::ADIOS>()),
+      adiosData(std::make_shared<adios2::ADIOS>())
 #endif
 {
     string filename(nm), meshNm, dataNm;
@@ -1720,6 +1725,9 @@ avtSpecFEMFileFormat::GenerateFileNames(const std::string &nm,
 // Creation:    April  9, 2014
 //
 // Modifications:
+//    Justin Privitera, Thu Jan 18 09:56:51 PST 2024
+//    Removed adios2::DebugON since it is not present in newer versions of 
+//    adios2.
 //
 //****************************************************************************
 
@@ -1729,7 +1737,7 @@ avtSpecFEMFileFormat::IsMeshFile(const string &fname)
 #if 0
     {
         #ifdef PARALLEL
-        adios2::ADIOS adios((MPI_Comm)VISIT_MPI_COMM, adios2::DebugON);
+        adios2::ADIOS adios((MPI_Comm)VISIT_MPI_COMM);
         adios2::IO io = adios2::IO(adios.DeclareIO("ReadBP"));
         io.SetEngine("BP");
         adios2::Engine reader = io.Open(fname, adios2::Mode::Read);
@@ -1740,7 +1748,7 @@ avtSpecFEMFileFormat::IsMeshFile(const string &fname)
     }
 #endif
 
-    shared_ptr<adios2::ADIOS> adios = std::make_shared<adios2::ADIOS>(adios2::DebugON);
+    shared_ptr<adios2::ADIOS> adios = std::make_shared<adios2::ADIOS>();
     adios2::IO io = adios2::IO(adios->DeclareIO("ReadBP"));
     io.SetEngine("BP");
     adios2::Engine reader = io.Open(fname, adios2::Mode::Read);

src/resources/help/en_US/relnotes3.4.1.html

@@ -42,7 +42,13 @@
   <li>Upgraded MFEM library version to 4.6.0.</li>
   <li>The <i>surface_normal</i> expression now accepts mesh types other than polydata, allowing it to be used more easily as an operator-created variable.</li>
   <li>Added more keywords ("MFA", "2fa", "Autentication", and "OTP") that cause VisIt clients to open a second popup for a password.</li>
-  <li>GetPlotInformation() can now contain entries for multiple-curves when Query-over-time is performed on multiple variables. For example, if a pick-through-time was performed for variables 'u' and 'v', the curve for 'v' would be retrieved via 'GetPlotInformation()['Curves']['v']. Single variable results will still be retrieved via 'GetPlotInformation()['Curve'].
+  <li>Updated the ADIOS2 library version to 2.10.0-rc1, allowing BP5 files to be read by VisIt.</li>
+  <li>Removed the dependency on C-Blosc1.</li>
+  <li>Added a new dependency on C-Blosc2.</li>
+  <li>VisIt's Blueprint reader was enhanced so fields in Blueprint index files can supply a <i>display_name</i> hint that specifies the name used to expose the field in VisIt. This feature enables the index file to group related variables under sub-menus if the names in include slash characters.</li>
+  <li>VisIt's Blueprint reader was enhanced so fields that are low-order but are associated with a high-order mesh can be refined when the mesh is refined, as when the user applies a <i>MultiresControl</i> operator. This enables VisIt to correctly view such fields.</li>
+  <li>VisIt's CLI has a new <i>GetLastMessage()</i> function that returns the last message that VisIt issued, regardless of its type.</li>
+  <li>GetPlotInformation() can now contain entries for multiple-curves when Query-over-time is performed on multiple variables. For example, if a pick-through-time was performed for variables 'u' and 'v', the curve for 'v' would be retrieved via 'GetPlotInformation()['Curves']['v']. Single variable results will still be retrieved via 'GetPlotInformation()['Curve'].</li>
 </ul>
 
 <p>Click the following link to view the release notes for the previous version

src/test/tests/databases/adios2.py

@@ -11,6 +11,8 @@
 #  Date:       Mon May  9 18:05:05 PDT 2022
 #
 #  Modifications:
+#     Justin Privitera, Thu Jan 18 09:40:00 PST 2024
+#     Added BP5 tests.
 #
 # ----------------------------------------------------------------------------
 RequiredDatabasePlugin("ADIOS2")
@@ -20,6 +22,10 @@
 adios2_test_dir = "adios2_v2.7.1_test_data"
 cube_data = data_path(pjoin(adios2_test_dir,"interesting_cube00000000.bp"))
 
+bp5_test_dir = "adios2_v2.10.0-rc1_bp5_test_data"
+plt0 = data_path(pjoin(bp5_test_dir,"plt00000.bp"))
+plt758 = data_path(pjoin(bp5_test_dir,"plt00758.bp"))
+
 def set_3d_view():
     v = View3DAttributes()
     v.viewNormal = (0.844823, 0.290329, 0.449425)
@@ -47,31 +53,32 @@ def set_test_view(tag_name):
     else:
         ResetView()
 
-def test(mesh_name, tag_name):
-    AddPlot("Mesh", mesh_name, 1, 1)
-    AddPlot("Pseudocolor", "/data/0/meshes/admbase_lapse_rl00/admbase_alp", 1, 1)
-    AddOperator("Clip", 1)
-    SetActivePlots(1)
-    SetActivePlots(1)
-    ClipAtts = ClipAttributes()
-    ClipAtts.quality = ClipAtts.Fast  # Fast, Accurate
-    ClipAtts.funcType = ClipAtts.Plane  # Plane, Sphere
-    ClipAtts.plane1Status = 1
-    ClipAtts.plane2Status = 0
-    ClipAtts.plane3Status = 0
-    ClipAtts.plane1Origin = (35, 35, 35)
-    ClipAtts.plane2Origin = (0, 0, 0)
-    ClipAtts.plane3Origin = (0, 0, 0)
-    ClipAtts.plane1Normal = (1, 0, 0)
-    ClipAtts.plane2Normal = (0, 1, 0)
-    ClipAtts.plane3Normal = (0, 0, 1)
-    ClipAtts.planeInverse = 0
-    ClipAtts.planeToolControlledClipPlane = ClipAtts.Plane1  # NONE, Plane1, Plane2, Plane3
-    ClipAtts.center = (0, 0, 0)
-    ClipAtts.radius = 1
-    ClipAtts.sphereInverse = 0
-    ClipAtts.crinkleClip = 0
-    SetOperatorOptions(ClipAtts, 0, 1)
+def test(mesh_name, tag_name, var_name, mesh_plot = False):
+    if mesh_plot:
+        AddPlot("Mesh", mesh_name)
+    AddPlot("Pseudocolor", var_name)
+    if "3d" in tag_name:
+        AddOperator("Clip", 1)
+        SetActivePlots(1)
+        ClipAtts = ClipAttributes()
+        ClipAtts.quality = ClipAtts.Fast  # Fast, Accurate
+        ClipAtts.funcType = ClipAtts.Plane  # Plane, Sphere
+        ClipAtts.plane1Status = 1
+        ClipAtts.plane2Status = 0
+        ClipAtts.plane3Status = 0
+        ClipAtts.plane1Origin = (35, 35, 35)
+        ClipAtts.plane2Origin = (0, 0, 0)
+        ClipAtts.plane3Origin = (0, 0, 0)
+        ClipAtts.plane1Normal = (1, 0, 0)
+        ClipAtts.plane2Normal = (0, 1, 0)
+        ClipAtts.plane3Normal = (0, 0, 1)
+        ClipAtts.planeInverse = 0
+        ClipAtts.planeToolControlledClipPlane = ClipAtts.Plane1  # NONE, Plane1, Plane2, Plane3
+        ClipAtts.center = (0, 0, 0)
+        ClipAtts.radius = 1
+        ClipAtts.sphereInverse = 0
+        ClipAtts.crinkleClip = 0
+        SetOperatorOptions(ClipAtts, 0, 1)
     DrawPlots()
     set_test_view(tag_name)
     Test(tag_name + "_" +  mesh_name + "_mesh")
@@ -82,7 +89,26 @@ def test(mesh_name, tag_name):
 OpenDatabase(cube_data, 0, "ADIOS2_1.0")
 mesh_name = "mesh71x71x71"
 tag_name = "adios2_3d_bp"
-test(mesh_name, tag_name)
+var_name = "/data/0/meshes/admbase_lapse_rl00/admbase_alp"
+do_mesh_plot = True
+test(mesh_name, tag_name, var_name, do_mesh_plot)
 CloseDatabase(cube_data)
 
+# requires adios2 to be built with c-blosc support
+TestSection("Adios2 BP5 Tests")
+
+OpenDatabase(plt0, 0, "ADIOS2_1.0")
+mesh_name = "mesh512x512"
+tag_name = "adios2_2d_bp5_1"
+var_name = "/data/0/meshes/gasDensity"
+test(mesh_name, tag_name, var_name)
+CloseDatabase(plt0)
+
+OpenDatabase(plt758, 0, "ADIOS2_1.0")
+mesh_name = "mesh512x512"
+tag_name = "adios2_2d_bp5_2"
+var_name = "/data/758/meshes/gasDensity"
+test(mesh_name, tag_name, var_name)
+CloseDatabase(plt758)
+
 Exit()