Merge branch 'use_openpmd-api' of github.com:guj/amrex into use_openp…

…md-api
guj · Mar 28, 2024 · 13f7ff5 · 13f7ff5
2 parents a129a8f + 6d206ca
commit 13f7ff5
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Showing 18 changed files with 27 additions and 59 deletions.
diff --git a/.github/workflows/clang.yml b/.github/workflows/clang.yml
@@ -195,7 +195,12 @@ jobs:
         cd openPMD-api-0.15.2
         mkdir build
         cd build
-        cmake .. -DopenPMD_USE_PYTHON=OFF -DCMAKE_CXX_COMPILER_LAUNCHER=ccache
+        cmake ..  \
+          -DCMAKE_CXX_COMPILER_LAUNCHER=ccache  \
+          -DopenPMD_BUILD_EXAMPLES=OFF  \
+          -DopenPMD_BUILD_CLI_TOOLS=OFF  \
+          -DopenPMD_BUILD_TESTING=OFF  \
+          -DopenPMD_USE_PYTHON=OFF  \
         make -j4
         sudo make install
     - name: Build & Test
@@ -211,7 +216,7 @@ jobs:
         mkdir build
         cd build
         cmake ..                                      \
-            -DAMReX_OPENPMD_API=ON                    \
+            -DAMReX_OPENPMD=ON                        \
             -DCMAKE_VERBOSE_MAKEFILE=ON               \
             -DAMReX_ENABLE_TESTS=ON                   \
             -DAMReX_SPACEDIM=3                        \

diff --git a/Src/Base/AMReX_PlotFileUtil.H b/Src/Base/AMReX_PlotFileUtil.H
@@ -12,7 +12,7 @@
 #include <AMReX_PlotFileUtilHDF5.H>
 #endif
 
-#ifdef AMREX_USE_OPENPMD_API
+#ifdef AMREX_USE_OPENPMD
 #include <AMReX_PlotFileUtilOPENPMD.H>
 #endif
 

diff --git a/Src/CMakeLists.txt b/Src/CMakeLists.txt
@@ -200,7 +200,7 @@ if (AMReX_HDF5)
    add_subdirectory(Extern/HDF5)
 endif ()
 
-if (AMReX_OPENPMD_API)
+if (AMReX_OPENPMD)
    add_subdirectory(Extern/openPMD-api)
 endif()
 

diff --git a/Src/Extern/openPMD-api/AMReX_ParticlesOPENPMD.H b/Src/Extern/openPMD-api/AMReX_ParticlesOPENPMD.H
@@ -1,8 +1,7 @@
 #ifndef AMREX_PTL_OPENPMD_API_H
 #define AMREX_PTL_OPENPMD_API_H
 
-/**
-*   This file is included from AMReX_ParticleCounter.H
+/** @file This file is included from AMReX_ParticleCounter.H
 *   and belongs to the class ParticleContainer_impl.
 *   The namespace amrex was already declared.
 *

diff --git a/Src/Extern/openPMD-api/AMReX_PlotFileOPENPMD.cpp b/Src/Extern/openPMD-api/AMReX_PlotFileOPENPMD.cpp
@@ -594,8 +594,6 @@ namespace amrex::openpmd_api {
       mesh.setAttribute("fieldSmoothing", "none");
       mesh_comp.resetDataset(dataset);
 
-      helper::setOpenPMDUnit( mesh, varName.m_FieldName );
-
       auto relative_cell_pos = helper::getRelativeCellPosition(mf);     // AMReX Fortran index order
       std::reverse( relative_cell_pos.begin(), relative_cell_pos.end() ); // now in C order
       mesh_comp.setPosition( relative_cell_pos );

diff --git a/Src/Extern/openPMD-api/AMReX_PlotFileUtilOPENPMD.H b/Src/Extern/openPMD-api/AMReX_PlotFileUtilOPENPMD.H
@@ -12,7 +12,7 @@
 #include <AMReX_Particles.H>
 #endif
 
-#ifdef AMREX_USE_OPENPMD_API
+#ifdef AMREX_USE_OPENPMD
 #include <openPMD/openPMD.hpp>
 #endif
 
@@ -23,36 +23,6 @@ namespace amrex::openpmd_api
 {
     namespace helper
     {
-      inline void
-      setOpenPMDUnit ( openPMD::Mesh mesh, std::string const& field_name )
-      {
-        if (field_name[0] == 'E'){
-          mesh.setUnitDimension({
-              {openPMD::UnitDimension::L,  1},
-              {openPMD::UnitDimension::M,  1},
-              {openPMD::UnitDimension::T, -3},
-              {openPMD::UnitDimension::I, -1},
-            });
-        } else if (field_name[0] == 'B'){
-          mesh.setUnitDimension({
-              {openPMD::UnitDimension::M,  1},
-              {openPMD::UnitDimension::I, -1},
-              {openPMD::UnitDimension::T, -2}
-              });
-        }else if (field_name[0] == 'j'){ // current
-          mesh.setUnitDimension({
-              {openPMD::UnitDimension::L, -2},
-              {openPMD::UnitDimension::I,  1},
-            });
-        } else if (field_name.substr(0,3) == "rho"){ // charge density
-          mesh.setUnitDimension({
-              {openPMD::UnitDimension::L, -3},
-              {openPMD::UnitDimension::I,  1},
-              {openPMD::UnitDimension::T,  1},
-            });
-        }
-      } // name space helper
-
       // from warpx Utils/RelativeCellPosition.cpp
       inline std::vector< double >
       getRelativeCellPosition(amrex::MultiFab const& mf)

diff --git a/Src/Extern/openPMD-api/AMReX_PlotFileUtilOPENPMD_PTLImpl.H b/Src/Extern/openPMD-api/AMReX_PlotFileUtilOPENPMD_PTLImpl.H
@@ -1,7 +1,6 @@
 #ifndef AMREX_PLOTFILE_OPENPMD_PTLS_API_H
 #define AMREX_PLOTFILE_OPENPMD_PTLS_API_H
 
-//extern  std::unique_ptr< amrex::openpmd_api::AMReX_openPMDHandler > amrex::openpmd_api::m_OpenPMDHandler;
 namespace amrex::openpmd_api
 {
     extern  std::unique_ptr< amrex::openpmd_api::AMReX_openPMDHandler > m_OpenPMDHandler;
@@ -26,9 +25,6 @@ namespace amrex::openpmd_api
     {
       BL_PROFILE("amrex::openpmd_api::WriteParticles()");
 
-      amrex::Print()<<"   Real: "<<pc.NStructReal<<" "<<pc.NumRealComps()<<"\n";
-      amrex::Print()<<"   Int:  "<<pc.NStructInt<<" "<<pc.NumIntComps()<<"\n";
-
       if ((m_OpenPMDHandler == nullptr) || (m_OpenPMDHandler->m_Writer == nullptr)) {
         return;
       }
@@ -658,4 +654,4 @@ namespace amrex::openpmd_api
 
 } // namespace amrex::openpmd_api
 
-#endif // AMREX_PLOTFILE_OPENPMD_API_H
+#endif // AMREX_PLOTFILE_OPENPMD_PTLS_API_H
diff --git a/Src/Extern/openPMD-api/CMakeLists.txt b/Src/Extern/openPMD-api/CMakeLists.txt
@@ -1,4 +1,4 @@
-add_amrex_define(AMREX_USE_OPENPMD_API NO_LEGACY IF AMReX_OPENPMD_API)
+add_amrex_define(AMREX_USE_OPENPMD NO_LEGACY IF AMReX_OPENPMD)
 
 foreach(D IN LISTS AMReX_SPACEDIM)
 

diff --git a/Src/Particle/AMReX_ParticleContainer.H b/Src/Particle/AMReX_ParticleContainer.H
@@ -1355,7 +1355,7 @@ public:
 #include "AMReX_ParticlesHDF5.H"
 #endif
 
-#ifdef AMREX_USE_OPENPMD_API
+#ifdef AMREX_USE_OPENPMD
 #include "AMReX_ParticlesOPENPMD.H"
 #endif
 

diff --git a/Tests/CMakeLists.txt b/Tests/CMakeLists.txt
@@ -135,7 +135,7 @@ else()
       list(APPEND AMREX_TESTS_SUBDIRS HDF5Benchmark)
    endif ()
 
-   if (AMReX_OPENPMD_API)
+   if (AMReX_OPENPMD)
       list(APPEND AMREX_TESTS_SUBDIRS openPMDTests)
    endif ()
 

diff --git a/Tests/openPMDTests/fields/main.cpp b/Tests/openPMDTests/fields/main.cpp
@@ -106,7 +106,7 @@ struct TestField
 
 void saveFile(char const* fname, const InputParams& inputs, const TestField& testField)
 {
-#ifdef AMREX_USE_OPENPMD_API
+#ifdef AMREX_USE_OPENPMD
   openpmd_api::InitHandler(fname);
 
   for (int ts = 0; ts < inputs.nplotfile; ts++)

diff --git a/Tests/openPMDTests/ptls/warpxWriter.H b/Tests/openPMDTests/ptls/warpxWriter.H
@@ -94,7 +94,7 @@ void AMReX_warpxWriter::SetupMeshComp (openPMD::Mesh& mesh,
   mesh.setAttribute("fieldSmoothing", "none");
   mesh_comp.resetDataset(dataset);
 
-  amrex::openpmd_api::helper::setOpenPMDUnit( mesh, varName.m_FieldName );
+  //amrex::openpmd_api::helper::setOpenPMDUnit( mesh, varName.m_FieldName ); // removed this function. define in app if needed
 
   auto relative_cell_pos = amrex::openpmd_api::helper::getRelativeCellPosition(mf);     // AMReX Fortran index order
   std::reverse( relative_cell_pos.begin(), relative_cell_pos.end() ); // now in C order

diff --git a/Tools/CMake/AMReXConfig.cmake.in b/Tools/CMake/AMReXConfig.cmake.in
@@ -85,7 +85,7 @@ set(AMReX_PETSC_FOUND               @AMReX_PETSC@)
 set(AMReX_SUNDIALS_FOUND            @AMReX_SUNDIALS@)
 set(AMReX_HDF5_FOUND                @AMReX_HDF5@)
 set(AMReX_HDF5_ZFP_FOUND            @AMReX_HDF5_ZFP@)
-set(AMReX_OPENPMD_API_FOUND         @AMReX_OPENPMD_API@)
+set(AMReX_OPENPMD_FOUND             @AMReX_OPENPMD@)
 
 # Compilation options
 set(AMReX_FPE_FOUND                 @AMReX_FPE@)
@@ -138,7 +138,7 @@ set(AMReX_HYPRE                     @AMReX_HYPRE@)
 set(AMReX_PETSC                     @AMReX_PETSC@)
 set(AMReX_HDF5                      @AMReX_HDF5@)
 set(AMReX_HDF5_ZFP                  @AMReX_HDF5_ZFP@)
-set(AMReX_OPENPMD_API               @AMReX_OPENPMD_API@)
+set(AMReX_OPENPMD                   @AMReX_OPENPMD@)
 
 # Compilation options
 set(AMReX_FPE                       @AMReX_FPE@)
@@ -217,7 +217,7 @@ if (@AMReX_HYPRE@)
    find_dependency(HYPRE 2.20.0 REQUIRED)
 endif ()
 
-if (@AMReX_OPENPMD_API@)
+if (@AMReX_OPENPMD@)
     find_dependency(openpmd REQUIRED)
 endif ()
 

diff --git a/Tools/CMake/AMReXOptions.cmake b/Tools/CMake/AMReXOptions.cmake
@@ -353,8 +353,8 @@ cmake_dependent_option(AMReX_HDF5_ZFP "Enable ZFP compression in HDF5-based IO"
 print_option(AMReX_HDF5_ZFP)
 
 # openPMD-api
-option(AMReX_OPENPMD_API "Enable I/O through openPMD-api" OFF)
-print_option(AMReX_OPENPMD_API)
+option(AMReX_OPENPMD "Enable I/O through openPMD-api" OFF)
+print_option(AMReX_OPENPMD)
 
 # SUNDIALS
 option( AMReX_SUNDIALS "Enable SUNDIALS interfaces" OFF )

diff --git a/Tools/CMake/AMReXSetDefines.cmake b/Tools/CMake/AMReXSetDefines.cmake
@@ -173,7 +173,7 @@ add_amrex_define(AMREX_USE_HDF5_ZFP NO_LEGACY IF AMReX_HDF5_ZFP)
 #
 # openPMD-api
 #
-add_amrex_define(AMREX_USE_OPENPMD_API NO_LEGACY IF AMReX_OPENPMD_API)
+add_amrex_define(AMREX_USE_OPENPMD NO_LEGACY IF AMReX_OPENPMD)
 
 
 #

diff --git a/Tools/CMake/AMReXThirdPartyLibraries.cmake b/Tools/CMake/AMReXThirdPartyLibraries.cmake
@@ -1,7 +1,7 @@
 #
-# openPMD_api related targets
+# openPMD-api related targets
 #
-if (AMReX_OPENPMD_API)
+if (AMReX_OPENPMD)
     if (AMReX_MPI)
        find_package(openPMD 0.14.2 CONFIG REQUIRED COMPONENTS MPI)
     else ()

diff --git a/Tools/CMake/AMReX_Config_ND.H.in b/Tools/CMake/AMReX_Config_ND.H.in
@@ -59,7 +59,7 @@
 #cmakedefine AMREX_USE_HDF5
 #cmakedefine AMREX_USE_HDF5_ASYNC
 #cmakedefine AMREX_USE_HDF5_ZFP
-#cmakedefine AMREX_USE_OPENPMD_API
+#cmakedefine AMREX_USE_OPENPMD
 #cmakedefine AMREX_USE_HYPRE
 #cmakedefine AMREX_USE_PETSC
 #cmakedefine AMREX_USE_SUNDIALS

diff --git a/Tools/GNUMake/packages/Make.openpmd b/Tools/GNUMake/packages/Make.openpmd
@@ -1,4 +1,4 @@
-CPPFLAGS += -DAMREX_USE_OPENPMD_API
+CPPFLAGS += -DAMREX_USE_OPENPMD
 include $(AMREX_HOME)/Src/Extern/openPMD-api/Make.package
 
 ifndef AMREX_OPENPMD_HOME