Add adios2 dependency and showcase

Author: pgrete

CMakeLists.txt

@@ -15,7 +15,7 @@ else()
     "For further directions open an issue on GitLab.")
 endif()
 
-project(athenaPK LANGUAGES CXX)
+project(athenaPK LANGUAGES C CXX)
 
 set(CMAKE_CXX_EXTENSIONS OFF)
 set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
@@ -63,6 +63,13 @@ if (NOT PARTHENON_DISABLE_MPI)
   endif()
 endif()
 
+if (NOT ATHENAPK_DISABLE_ADIOS2)
+  find_package(ADIOS2 REQUIRED)
+  if (NOT ADIOS2_FOUND)
+    message(FATAL_ERROR "ADIOS2 requested but couldn't be found. Either set ADIOS2_DIR to the install prefix as hint or disable by setting ATHENAPK_DISABLE_ADIOS2=ON")
+  endif()
+endif()
+
 option(AthenaPK_ENABLE_TESTING "Enable AthenaPK test" ON)
 set(PARTHENON_ENABLE_PYTHON_MODULE_CHECK ${AthenaPK_ENABLE_TESTING} CACHE BOOL "Check if local python version contains all modules required for running tests.")
 

scripts/write_bp.py

@@ -0,0 +1,13 @@
+import numpy as np
+from adios2 import Stream
+myvar = np.arange(16, dtype=np.float64).reshape(4,4)
+nsteps = 1
+
+shape = myvar.shape # .tolist()
+start = np.zeros_like(shape).tolist()
+count = myvar.shape #.tolist()
+
+with Stream("test.bp", "w") as s:
+   for _ in s.steps(nsteps):
+      s.write("myvarname", myvar, shape, start, count)
+

src/CMakeLists.txt

@@ -26,4 +26,8 @@ add_executable(
 
 add_subdirectory(pgen)
 
-target_link_libraries(athenaPK PRIVATE parthenon)
+if (ADIOS2_FOUND)
+  target_link_libraries(athenaPK PRIVATE parthenon adios2::cxx11_mpi MPI::MPI_C)
+else()
+  target_link_libraries(athenaPK PRIVATE parthenon)
+endif()

src/pgen/kh.cpp

@@ -24,8 +24,12 @@
 #include <cmath>     // log
 #include <cstring>   // strcmp()
 
+#include <adios2.h>
+
 // Parthenon headers
+#include "globals.hpp"
 #include "mesh/mesh.hpp"
+#include <iostream>
 #include <parthenon/driver.hpp>
 #include <parthenon/package.hpp>
 #include <random>
@@ -57,6 +61,27 @@ void ProblemGenerator(Mesh *pmesh, ParameterInput *pin, MeshData<Real> *md) {
   const auto &cons = md->PackVariables(std::vector<std::string>{"cons"});
   const auto num_blocks = md->NumBlocks();
 
+  // Silly ADIOS2 test
+
+  adios2::fstream iStream("test.bp", adios2::fstream::in, MPI_COMM_WORLD);
+  adios2::fstep iStep;
+  // There's only a single step in the input file, so there's no issue using the while
+  // logic here.
+  while (adios2::getstep(iStream, iStep)) {
+    // only read row of current rank
+    const adios2::Dims start{static_cast<unsigned long>(parthenon::Globals::my_rank), 0};
+    const adios2::Dims count{1, 4};
+    auto mydata = iStream.read<double>("myvarname", start, count);
+    std::cerr << "[" << parthenon::Globals::my_rank << "] ";
+    for (auto var : mydata) {
+      std::cerr << var << " ";
+    }
+    std::cerr << "\n";
+    // Just to be sure we break (to not read any other steps if present in the bp file)
+    break;
+  }
+  iStream.close();
+
   //--- iprob=1. This was the classic, unresolved K-H test.
 
   //--- iprob=2. Uniform density medium moving at +/-vflow seperated by a single shear