fix build errors with cmake

boutproject · Sep 11, 2023 · 04623d4 · 04623d4
1 parent 704bfa3
commit 04623d4
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Showing 6 changed files with 42 additions and 27 deletions.
diff --git a/include/bout/options_adios.hxx b/include/bout/options_adios.hxx
@@ -18,7 +18,7 @@ namespace bout {
 
 class OptionsADIOS : public OptionsIO {
 public:
-  OptionsADIOS(const std::string& filename, bout::OptionsIO::FileMode mode = bout::OptionsIO::FileMode::replace) {}
+  explicit OptionsADIOS(const std::string& filename, bout::OptionsIO::FileMode mode = bout::OptionsIO::FileMode::replace) {}
   OptionsADIOS(const OptionsADIOS&) = default;
   OptionsADIOS(OptionsADIOS&&) = default;
   OptionsADIOS& operator=(const OptionsADIOS&) = default;
@@ -28,9 +28,15 @@ public:
   Options read() { throw BoutException("OptionsADIOS not available\n"); }
 
   /// Write options to file
-  void write(const Options& options) {
+  void write(const Options& options, const std::string& time_dim) {
     throw BoutException("OptionsADIOS not available\n");
   }
+
+  void verifyTimesteps() const{
+    throw BoutException("OptionsADIOS not available\n");
+  }
+
+
 };
 
 } // namespace bout
@@ -51,7 +57,7 @@ public:
   // Constructors need to be defined in implementation due to forward
   // declaration of ADIOSStream
   OptionsADIOS();
-  explicit OptionsADIOS(std::string filename, bout::OptionsIO::FileMode mode =
+  OptionsADIOS(std::string filename, bout::OptionsIO::FileMode mode =
                                                   bout::OptionsIO::FileMode::replace);
   ~OptionsADIOS();
   OptionsADIOS(const OptionsADIOS&) = delete;

diff --git a/include/bout/options_io.hxx b/include/bout/options_io.hxx
@@ -22,12 +22,8 @@ public:
   };
 
   enum class Library {
-#if BOUT_HAS_ADIOS
     ADIOS,
-#endif
-#if BOUT_HAS_NETCDF
     NetCDF,
-#endif
     Invalid
   };
 
@@ -41,7 +37,7 @@ public:
 #endif
 
   OptionsIO();
-  explicit OptionsIO(std::string filename, FileMode mode = FileMode::replace);
+  OptionsIO(std::string filename, FileMode mode = FileMode::replace);
   ~OptionsIO();
   OptionsIO(const OptionsIO&) = delete;
   OptionsIO(OptionsIO&&) noexcept;

diff --git a/include/bout/options_netcdf.hxx b/include/bout/options_netcdf.hxx
@@ -30,9 +30,13 @@ public:
   Options read() { throw BoutException("OptionsNetCDF not available\n"); }
 
   /// Write options to file
-  void write(const Options& options) {
+  void write(const Options& options, const std::string& time_dim) {
     throw BoutException("OptionsNetCDF not available\n");
   }
+
+  void verifyTimesteps() const{
+    throw BoutException("OptionsADIOS not available\n");
+  }
 };
 
 } // namespace bout
@@ -55,7 +59,7 @@ public:
   // Constructors need to be defined in implementation due to forward
   // declaration of NcFile
   OptionsNetCDF();
-  explicit OptionsNetCDF(std::string filename, FileMode mode = FileMode::replace);
+  OptionsNetCDF(std::string filename, FileMode mode = FileMode::replace);
   ~OptionsNetCDF();
   OptionsNetCDF(const OptionsNetCDF&) = delete;
   OptionsNetCDF(OptionsNetCDF&&) noexcept;

diff --git a/src/sys/options/options_adios.cxx b/src/sys/options/options_adios.cxx
@@ -237,51 +237,64 @@ void ADIOSPutVarVisitor::operator()<std::string>(const std::string& value) {
 template <>
 void ADIOSPutVarVisitor::operator()<Field2D>(const Field2D& value) {
   // Pointer to data. Assumed to be contiguous array
-  adios2::Dims shape = {(size_t)value.getNx(), (size_t)value.getNy()};
-  adios2::Variable<BoutReal> var = stream.io.DefineVariable<BoutReal>(varname, shape);
+  auto mesh = value.getMesh();
+  adios2::Dims shape = {(size_t)BoutComm::size(), (size_t)value.getNx(), (size_t)value.getNy()};
+  adios2::Dims start = {(size_t)BoutComm::rank(), 0, 0};
+  adios2::Dims count = {1, shape[1], shape[2]};
+  adios2::Variable<BoutReal> var = stream.io.DefineVariable<BoutReal>(varname, shape, start, count);
   stream.engine.Put<BoutReal>(var, &value(0, 0));
 }
 
 template <>
 void ADIOSPutVarVisitor::operator()<Field3D>(const Field3D& value) {
   // Pointer to data. Assumed to be contiguous array
-  adios2::Dims shape = {(size_t)value.getNx(), (size_t)value.getNz()};
-  adios2::Variable<BoutReal> var = stream.io.DefineVariable<BoutReal>(varname, shape);
+  adios2::Dims shape = {(size_t)BoutComm::size(), (size_t)value.getNx(), (size_t)value.getNy(), (size_t)value.getNz()};
+  adios2::Dims start = {(size_t)BoutComm::rank(), 0, 0, 0};
+  adios2::Dims count = {1, shape[1], shape[2], shape[3]};
+  adios2::Variable<BoutReal> var = stream.io.DefineVariable<BoutReal>(varname, shape, start, count);
   stream.engine.Put<BoutReal>(var, &value(0, 0, 0));
 }
 
 template <>
 void ADIOSPutVarVisitor::operator()<FieldPerp>(const FieldPerp& value) {
   // Pointer to data. Assumed to be contiguous array
-  adios2::Dims shape = {(size_t)value.getNx(), (size_t)value.getNz()};
-  adios2::Variable<BoutReal> var = stream.io.DefineVariable<BoutReal>(varname, shape);
+  adios2::Dims shape = {(size_t)BoutComm::size(), (size_t)value.getNx(), (size_t)value.getNz()};
+  adios2::Dims start = {(size_t)BoutComm::rank(), 0, 0};
+  adios2::Dims count = {1, shape[1], shape[2]};
+  adios2::Variable<BoutReal> var = stream.io.DefineVariable<BoutReal>(varname, shape, start, count);
   stream.engine.Put<BoutReal>(var, &value(0, 0));
 }
 
 template <>
 void ADIOSPutVarVisitor::operator()<Array<BoutReal>>(const Array<BoutReal>& value) {
   // Pointer to data. Assumed to be contiguous array
-  adios2::Dims shape = {(size_t)value.size()};
-  adios2::Variable<BoutReal> var = stream.io.DefineVariable<BoutReal>(varname, shape);
+  adios2::Dims shape = {(size_t)BoutComm::size(), (size_t)value.size()};
+  adios2::Dims start = {(size_t)BoutComm::rank(), 0};
+  adios2::Dims count = {1, shape[1]};
+  adios2::Variable<BoutReal> var = stream.io.DefineVariable<BoutReal>(varname, shape, start, count);
   stream.engine.Put<BoutReal>(var, value.begin());
 }
 
 template <>
 void ADIOSPutVarVisitor::operator()<Matrix<BoutReal>>(const Matrix<BoutReal>& value) {
   // Pointer to data. Assumed to be contiguous array
   auto s = value.shape();
-  adios2::Dims shape = {(size_t)std::get<0>(s), (size_t)std::get<1>(s)};
-  adios2::Variable<BoutReal> var = stream.io.DefineVariable<BoutReal>(varname, shape);
+  adios2::Dims shape = {(size_t)BoutComm::size(), (size_t)std::get<0>(s), (size_t)std::get<1>(s)};
+  adios2::Dims start = {(size_t)BoutComm::rank(), 0, 0};
+  adios2::Dims count = {1, shape[1], shape[2]};
+  adios2::Variable<BoutReal> var = stream.io.DefineVariable<BoutReal>(varname, shape, start, count);
   stream.engine.Put<BoutReal>(var, value.begin());
 }
 
 template <>
 void ADIOSPutVarVisitor::operator()<Tensor<BoutReal>>(const Tensor<BoutReal>& value) {
   // Pointer to data. Assumed to be contiguous array
   auto s = value.shape();
-  adios2::Dims shape = {(size_t)std::get<0>(s), (size_t)std::get<1>(s),
+  adios2::Dims shape = {(size_t)BoutComm::size(), (size_t)std::get<0>(s), (size_t)std::get<1>(s),
                         (size_t)std::get<2>(s)};
-  adios2::Variable<BoutReal> var = stream.io.DefineVariable<BoutReal>(varname, shape);
+  adios2::Dims start = {(size_t)BoutComm::rank(), 0, 0, 0};
+  adios2::Dims count = {1, shape[1], shape[2], shape[3]};
+  adios2::Variable<BoutReal> var = stream.io.DefineVariable<BoutReal>(varname, shape,  start, count);
   stream.engine.Put<BoutReal>(var, value.begin());
 }
 

diff --git a/src/sys/options/options_io.cxx b/src/sys/options/options_io.cxx
@@ -11,12 +11,8 @@
 #include <iostream>
 #include <vector>
 
-#if BOUT_HAS_ADIOS
 #include "bout/options_adios.hxx"
-#endif
-#if BOUT_HAS_NETCDF
 #include "bout/options_netcdf.hxx"
-#endif
 
 namespace bout {
 

diff --git a/tests/integrated/test-options-adios/test-options-adios.cxx b/tests/integrated/test-options-adios/test-options-adios.cxx
@@ -79,7 +79,7 @@ int main(int argc, char** argv) {
   data["field"] = Field3D(3.0);
 
   // Append data to file
-  OptionsADIOS("time.nc", bout::OptionsIO::FileMode::append).write(data);
+  OptionsADIOS("time.bp", bout::OptionsIO::FileMode::append).write(data);
 
   BoutFinalise();
 };