IO fixes (tfield; checkpoint)

src/include/OutputFieldsDefault.h

@@ -70,7 +70,6 @@ struct OutputFieldsItemParams
   int pfield_first = 0;
   int tfield_interval = 0;
   int tfield_first = 0;
-  int tfield_average_length = 1000000;
   int tfield_average_every = 1;
   Int3 rn = {};
   Int3 rx = {10000000, 10000000, 10000000};
@@ -114,16 +113,18 @@ class OutputFieldsItem : public OutputFieldsItemParams
       if (timestep != 0) {
         pfield_next_ = timestep + pfield_interval;
         tfield_next_ = timestep + tfield_interval;
+
+        tfield_next_ = timestep / tfield_interval * tfield_interval;
+        if (timestep % tfield_interval > 0)
+          tfield_next_ += tfield_interval;
       }
     }
 
     bool do_pfield = pfield_interval > 0 && timestep >= pfield_next_;
     bool do_tfield = tfield_interval > 0 && timestep >= tfield_next_;
-    bool doaccum_tfield =
-      tfield_interval > 0 &&
-      (((timestep >= (tfield_next_ - tfield_average_length + 1)) &&
-        timestep % tfield_average_every == 0) ||
-       timestep == 0);
+    bool doaccum_tfield = timestep >= (tfield_next_ - tfield_average_every + 1);
+    doaccum_tfield = doaccum_tfield && (tfield_interval > 0);
+    doaccum_tfield = doaccum_tfield || (timestep == 0);
 
     if (do_pfield || doaccum_tfield) {
       prof_start(pr_eval);

src/include/checkpoint.hxx

@@ -7,44 +7,6 @@
 #include "particles_simple.inl"
 #include <kg/io.h>
 
-// ----------------------------------------------------------------------
-// write_checkpoint
-//
-
-template <typename Mparticles, typename MfieldsState>
-void write_checkpoint(const Grid_t& grid, Mparticles& mprts,
-                      MfieldsState& mflds)
-{
-  static int pr, pr_A;
-  if (!pr) {
-    pr = prof_register("cp_write", 1., 0, 0);
-    pr_A = prof_register("cp_write_barier", 1., 0, 0);
-  }
-
-  prof_start(pr);
-  mpi_printf(grid.comm(), "**** Writing checkpoint...\n");
-#if defined(PSC_HAVE_ADIOS2) && !defined(VPIC)
-  prof_start(pr_A);
-  MPI_Barrier(grid.comm()); // not really necessary
-  prof_stop(pr_A);
-
-  std::string filename =
-    "checkpoint_" + std::to_string(grid.timestep()) + ".bp";
-
-  auto io = kg::io::IOAdios2{};
-  auto writer =
-    io.open(filename, kg::io::Mode::Write, grid.comm(), "checkpoint");
-  writer.put("grid", grid);
-  writer.put("mprts", mprts);
-  writer.put("mflds", mflds);
-  writer.close();
-#else
-  std::cerr << "write_checkpoint not available without adios2" << std::endl;
-  std::abort();
-#endif
-  prof_stop(pr);
-}
-
 // ----------------------------------------------------------------------
 // read_checkpoint
 //
@@ -59,13 +21,15 @@ inline void read_checkpoint(const std::string& filename, Grid_t& grid,
 #ifdef PSC_HAVE_ADIOS2
   auto io = kg::io::IOAdios2{};
   auto reader = io.open(filename, kg::io::Mode::Read);
+  reader.beginStep(kg::io::StepMode::Read);
   reader.get("grid", grid);
   mprts.~Mparticles();
   mflds.~MfieldsState();
   new (&mprts) Mparticles(grid);
   new (&mflds) MfieldsState(grid);
   reader.get("mprts", mprts);
   reader.get("mflds", mflds);
+  reader.endStep();
   reader.close();
 
   // FIXME, when we read back a rebalanced grid, other existing fields will
@@ -120,7 +84,46 @@ public:
     write_checkpoint(grid, mprts, mflds);
   }
 
+  template <typename Mparticles, typename MfieldsState>
+  void write_checkpoint(const Grid_t& grid, Mparticles& mprts,
+                        MfieldsState& mflds)
+  {
+    static int pr, pr_A;
+    if (!pr) {
+      pr = prof_register("cp_write", 1., 0, 0);
+      pr_A = prof_register("cp_write_barier", 1., 0, 0);
+    }
+
+    prof_start(pr);
+    mpi_printf(grid.comm(), "**** Writing checkpoint...\n");
+#if defined(PSC_HAVE_ADIOS2) && !defined(VPIC)
+    prof_start(pr_A);
+    MPI_Barrier(grid.comm()); // not really necessary
+    prof_stop(pr_A);
+
+    std::string filename =
+      "checkpoint_" + std::to_string(grid.timestep()) + ".bp";
+
+    mpi_printf(MPI_COMM_WORLD, "??? checkpoint IOAdios2 %p\n", &io);
+    writer = io.open(filename, kg::io::Mode::Write, grid.comm(), "checkpoint");
+    writer.beginStep(kg::io::StepMode::Append);
+    writer.put("grid", grid);
+    writer.put("mprts", mprts);
+    writer.put("mflds", mflds);
+    writer.endStep();
+    writer.close();
+#else
+    std::cerr << "write_checkpoint not available without adios2" << std::endl;
+    std::abort();
+#endif
+    prof_stop(pr);
+  }
+
 private:
   int interval_; // write checkpoint every so many steps
   bool first_time_ = true;
+#ifdef PSC_HAVE_ADIOS2
+  kg::io::IOAdios2 io;
+  kg::io::Engine writer;
+#endif
 };

src/kg/testing/io/TestIO.cxx

@@ -9,14 +9,18 @@ TEST(IO, WriteRead)
 
   {
     auto writer = io.open("test.bp", kg::io::Mode::Write);
+    writer.beginStep(kg::io::StepMode::Append);
     writer.putLocal("var_double", 99.);
+    writer.endStep();
     writer.close();
   }
 
   {
     auto reader = io.open("test.bp", kg::io::Mode::Read);
+    reader.beginStep(kg::io::StepMode::Read);
     double dbl;
     reader.getLocal("var_double", dbl);
+    reader.endStep();
     reader.close();
     EXPECT_EQ(dbl, 99.);
   }
@@ -28,14 +32,18 @@ TEST(IO, WriteReadAttr)
 
   {
     auto writer = io.open("test.bp", kg::io::Mode::Write);
+    writer.beginStep(kg::io::StepMode::Append);
     writer.put("attr_double", 99.);
+    writer.endStep();
     writer.close();
   }
 
   {
     auto reader = io.open("test.bp", kg::io::Mode::Read);
+    reader.beginStep(kg::io::StepMode::Read);
     double dbl;
     reader.get("attr_double", dbl);
+    reader.endStep();
     reader.close();
     EXPECT_EQ(dbl, 99.);
   }
@@ -72,15 +80,19 @@ TEST(IO, WriteReadCustom)
 
   {
     auto writer = io.open("test.bp", kg::io::Mode::Write);
+    writer.beginStep(kg::io::StepMode::Append);
     auto c = Custom{3, 99.};
     writer.put("var_custom", c);
+    writer.endStep();
     writer.close();
   }
 
   {
     auto reader = io.open("test.bp", kg::io::Mode::Read);
+    reader.beginStep(kg::io::StepMode::Read);
     auto c = Custom{};
     reader.get("var_custom", c);
+    reader.endStep();
     reader.close();
     EXPECT_EQ(c.i, 3);
     EXPECT_EQ(c.d, 99.);

src/kg/testing/io/TestIOAdios2.cxx

@@ -22,7 +22,7 @@ TEST(IOAdios2, OpenWriteThenRead)
 {
   auto io = kg::io::IOAdios2{};
   {
-    auto file = io.openFile("test2", kg::io::Mode::Write);
+    auto file = io.openFile("test2.bp", kg::io::Mode::Write);
   }
   {
     auto file = io.openFile("test2.bp", kg::io::Mode::Read);
@@ -33,7 +33,8 @@ TEST(IOAdios2, FilePutGetVariable)
 {
   auto io = kg::io::IOAdios2{};
   {
-    auto file = io.openFile("test3", kg::io::Mode::Write);
+    auto file = io.openFile("test3.bp", kg::io::Mode::Write);
+    file.beginStep(kg::io::StepMode::Append);
     auto dbl = std::vector<double>{1., 2., 3., 4., 5.};
     file.putVariable("dbl", dbl.data(), kg::io::Mode::NonBlocking, {5},
                      {{0}, {5}}, {});
@@ -42,9 +43,11 @@ TEST(IOAdios2, FilePutGetVariable)
     file.putVariable("dbl2", dbl.data() + 3, kg::io::Mode::NonBlocking, {5},
                      {{3}, {2}}, {});
     file.performPuts();
+    file.endStep();
   }
   {
     auto file = io.openFile("test3.bp", kg::io::Mode::Read);
+    file.beginStep(kg::io::StepMode::Read);
 
     auto shape = file.shapeVariable("dbl");
     EXPECT_EQ(shape, kg::io::Dims{5});
@@ -58,6 +61,7 @@ TEST(IOAdios2, FilePutGetVariable)
     file.getVariable("dbl2", dbl2.data(), kg::io::Mode::NonBlocking, {{0}, {5}},
                      {});
     file.performGets();
+    file.endStep();
 
     EXPECT_EQ(dbl, (std::vector<double>{1., 2., 3., 4., 5.}));
     EXPECT_EQ(dbl2, (std::vector<double>{1., 2., 0., 4., 5.}));
@@ -68,16 +72,20 @@ TEST(IOAdios2, FilePutGetAttribute)
 {
   auto io = kg::io::IOAdios2{};
   {
-    auto file = io.openFile("test4", kg::io::Mode::Write);
+    auto file = io.openFile("test4.bp", kg::io::Mode::Write);
+    file.beginStep(kg::io::StepMode::Append);
     auto dbl = std::vector<double>{1., 2., 3., 4., 5.};
     file.putAttribute("attr_dbl", dbl.data(), dbl.size());
+    file.endStep();
   }
   {
     auto file = io.openFile("test4.bp", kg::io::Mode::Read);
+    file.beginStep(kg::io::StepMode::Read);
     auto size = file.sizeAttribute("attr_dbl");
     auto dbl = std::vector<double>(size);
     file.getAttribute("attr_dbl", dbl.data());
     EXPECT_EQ(dbl, (std::vector<double>{1., 2., 3., 4., 5.}));
+    file.endStep();
   }
 }