Use Blosc2 filter

not yet integrated into CI

Author: franzpoeschel

examples/7_extended_write_serial.cpp

@@ -1,12 +1,40 @@
 #include <openPMD/openPMD.hpp>
 
-#include <algorithm>
+#if __has_include(<blosc2_filter.h>)
+#include <blosc2_filter.h>
+#define OPENPMD_USE_BLOSC2_FILTER 1
+#else
+#define OPENPMD_USE_BLOSC2_FILTER 0
+#endif
+
 #include <iostream>
+#include <numeric>
+#include <stdexcept>
 
 int main()
 {
     namespace io = openPMD;
 
+#if OPENPMD_USE_BLOSC2_FILTER
+    /*
+     * This registers the Blosc2 plugin from
+     * https://github.com/Blosc/HDF5-Blosc2 as a demonstration on how to
+     * activate and configure dynamic HDF5 filter plugins through openPMD.
+     */
+
+    char *version, *date;
+    int r = register_blosc2(&version, &date);
+    if (r < 1)
+    {
+        throw std::runtime_error("Unable to register Blosc2 plugin with HDF5.");
+    }
+    else
+    {
+        std::cout << "Blosc2 plugin registered in version " << version
+                  << " and date " << date << "." << std::endl;
+    }
+#endif
+
     {
         auto f = io::Series(
             "working/directory/2D_simData.h5",
@@ -91,7 +119,7 @@ int main()
         }
 
         io::Mesh mesh = cur_it.meshes["lowRez_2D_field"];
-        mesh.setAxisLabels({"x", "y"});
+        mesh.setAxisLabels({"x", "y", "z"});
 
         // data is assumed to reside behind a pointer as a contiguous
         // column-major array shared data ownership during IO is indicated with
@@ -134,6 +162,49 @@ int main()
         d.options = datasetConfig;
         mesh["x"].resetDataset(d);
 
+#if OPENPMD_USE_BLOSC2_FILTER
+        /*
+         * FILTER_BLOSC2 resolves to 32026, the permanent plugin ID registered
+         * with the HDF Group. Plugin-specific options are given via c_values,
+         * refer to the specific plugin's documentation. For the Blosc2 plugin,
+         * parameters 0, 1, 2 and 3 are reserved. Parameter 4 is the compression
+         * level, parameter 5 is a boolean for activating shuffling and
+         * parameter 6 denotes the compression method.
+         */
+        d.options = R"END(
+{
+  "adios2": {
+    "dataset": {
+      "operators": [
+        {
+          "type": "zlib",
+          "parameters": {
+            "clevel": 9
+          }
+        }
+      ]
+    }
+  },
+  "hdf5": {
+    "dataset": {
+      "chunks": "auto",
+      "permanent_filters": {
+        "id": )END" +
+            std::to_string(FILTER_BLOSC2) + R"END(,
+        "flags": "mandatory",
+        "c_values": [0, 0, 0, 0, 4, 1, )END" +
+            std::to_string(BLOSC_ZSTD) + R"END(]
+      }
+    }
+  }
+})END";
+#endif
+        d.extent = {500, 500};
+        mesh["z"].resetDataset(d);
+        auto span = mesh["z"].storeChunk<double>({0, 0}, {500, 500});
+        auto span_data = span.currentBuffer();
+        std::iota(span_data.begin(), span_data.end(), 41.);
+
         io::ParticleSpecies electrons = cur_it.particles["electrons"];
 
         io::Extent mpiDims{4};