Adapt examles

Author: franzpoeschel

examples/11_particle_dataframe.py

@@ -35,8 +35,11 @@
 
 # This "if" is important for distributed dask runs
 if __name__ == "__main__":
-    s = io.Series("../samples/git-sample/data%T.h5", io.Access.read_only)
-    electrons = s.snapshots()[400].particles["electrons"]
+    s = io.Series("../samples/git-sample/data%T.h5", io.Access.read_only, {
+        "defer_iteration_parsing": True
+    })
+    # with defer_iteration_parsing, open() must be called explicitly
+    electrons = s.snapshots()[400].open().particles["electrons"]
 
     # all particles
     df = electrons.to_df()

examples/2_read_serial.cpp

@@ -29,8 +29,10 @@ using namespace openPMD;
 
 int main()
 {
-    Series series =
-        Series("../samples/git-sample/data%T.h5", Access::READ_ONLY);
+    Series series = Series(
+        "../samples/git-sample/data%T.h5",
+        Access::READ_ONLY,
+        R"({"defer_iteration_parsing": true})");
     cout << "Read a Series with openPMD standard version " << series.openPMD()
          << '\n';
 
@@ -40,7 +42,8 @@ int main()
         cout << "\n\t" << i.first;
     cout << '\n';
 
-    Iteration i = series.snapshots()[100];
+    // with defer_iteration_parsing, open() must be called explicitly
+    Iteration i = series.snapshots()[100].open();
     cout << "Iteration 100 contains " << i.meshes.size() << " meshes:";
     for (auto const &m : i.meshes)
         cout << "\n\t" << m.first;

examples/2_read_serial.py

@@ -10,7 +10,9 @@
 
 if __name__ == "__main__":
     series = io.Series("../samples/git-sample/data%T.h5",
-                       io.Access.read_only)
+                       io.Access.read_only, {
+                           "defer_iteration_parsing": True
+                       })
     print("Read a Series with openPMD standard version %s" %
           series.openPMD)
 
@@ -20,7 +22,8 @@
         print("\t {0}".format(i))
     print("")
 
-    i = series.snapshots()[100]
+    # with defer_iteration_parsing, open() must be called explicitly
+    i = series.snapshots()[100].open()
     print("Iteration 100 contains {0} meshes:".format(len(i.meshes)))
     for m in i.meshes:
         print("\t {0}".format(m))

examples/2a_read_thetaMode_serial.cpp

@@ -31,10 +31,13 @@ int main()
 {
     /* The pattern %E instructs the openPMD-api to determine the file ending
      * automatically. It can also be given explicitly, e.g. `data%T.h5`. */
-    Series series =
-        Series("../samples/git-sample/thetaMode/data%T.h5", Access::READ_ONLY);
+    Series series = Series(
+        "../samples/git-sample/thetaMode/data%T.h5",
+        Access::READ_ONLY,
+        R"({"defer_iteration_parsing": true})");
 
-    Iteration i = series.snapshots()[500];
+    // defer_iteration_parsing implies that open() must be called explicitly
+    Iteration i = series.snapshots()[500].open();
     MeshRecordComponent E_z_modes = i.meshes["E"]["z"];
     Extent extent = E_z_modes.getExtent(); // (modal components, r, z)
 

examples/2a_read_thetaMode_serial.py

@@ -12,9 +12,12 @@
     # The pattern %E instructs the openPMD-api to determine the file ending
     # automatically. It can also be given explicitly, e.g. `data%T.h5`.
     series = io.Series("../samples/git-sample/thetaMode/data%T.h5",
-                       io.Access.read_only)
+                       io.Access.read_only, {
+                           "defer_iteration_parsing": True
+                       })
 
-    i = series.snapshots()[500]
+    # with defer_iteration_parsing, open() must be called explicitly
+    i = series.snapshots()[500].open()
     E_z_modes = i.meshes["E"]["z"]
     shape = E_z_modes.shape  # (modal components, r, z)
 

examples/4_read_parallel.cpp

@@ -40,11 +40,17 @@ int main(int argc, char *argv[])
     MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
 
     Series series = Series(
-        "../samples/git-sample/data%T.h5", Access::READ_ONLY, MPI_COMM_WORLD);
+        "../samples/git-sample/data%T.h5",
+        Access::READ_ONLY,
+        MPI_COMM_WORLD,
+        R"({"defer_iteration_parsing": true})");
     if (0 == mpi_rank)
         cout << "Read a series in parallel with " << mpi_size << " MPI ranks\n";
 
-    MeshRecordComponent E_x = series.snapshots()[100].meshes["E"]["x"];
+    // with defer_iteration_parsing, open() must be called explicitly
+    // explicit Iteration opening is recommended in general for parallel
+    // applications
+    MeshRecordComponent E_x = series.snapshots()[100].open().meshes["E"]["x"];
 
     Offset chunk_offset = {static_cast<long unsigned int>(mpi_rank) + 1, 1, 1};
     Extent chunk_extent = {2, 2, 1};

examples/4_read_parallel.py

@@ -20,13 +20,17 @@
     series = io.Series(
         "../samples/git-sample/data%T.h5",
         io.Access.read_only,
-        comm
+        comm, {
+            "defer_iteration_parsing": True
+        }
     )
     if 0 == comm.rank:
         print("Read a series in parallel with {} MPI ranks".format(
               comm.size))
 
-    E_x = series.snapshots()[100].meshes["E"]["x"]
+    # with defer_iteration_parsing, open() must be called explicitly
+    # explicit use of open() is recommended for parallel applications
+    E_x = series.snapshots()[100].open().meshes["E"]["x"]
 
     chunk_offset = [comm.rank + 1, 1, 1]
     chunk_extent = [2, 2, 1]

examples/6_dump_filebased_series.cpp

@@ -7,8 +7,10 @@ using namespace openPMD;
 
 int main()
 {
-    Series o =
-        Series("../samples/git-sample/data%T.h5", Access::READ_RANDOM_ACCESS);
+    Series o = Series(
+        "../samples/git-sample/data%T.h5",
+        Access::READ_RANDOM_ACCESS,
+        R"({"defer_iteration_parsing": true})");
 
     std::cout << "Read iterations ";
     for (auto const &val : o.snapshots())
@@ -39,6 +41,8 @@ int main()
 
     for (auto &[index, i] : o.snapshots())
     {
+        // with defer_iteration_parsing, open() must be called explicitly
+        i.open();
         std::cout << "Read attributes in iteration " << index << ":\n";
         for (auto const &val : i.attributes())
             std::cout << '\t' << val << '\n';