add more silo blueprint i/o support

LLNL · Jun 15, 2023 · 1ac3851 · 1ac3851
2 parents 0ceaa01 + d06c6c4
commit 1ac3851
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Showing 116 changed files with 7,285 additions and 1,192 deletions.
diff --git a/src/cmake/thirdparty/SetupSilo.cmake b/src/cmake/thirdparty/SetupSilo.cmake
@@ -59,6 +59,13 @@ if(${SILO_JSON_LIBS})
 endif()
 set(SILO_INCLUDE_DIRS ${SILO_INCLUDE_DIR} )
 
+#
+# Add ZLIB to the SILO_LIBRARIES
+#
+if(ZLIB_FOUND)
+    list(APPEND SILO_LIBRARIES ${ZLIB_LIBRARIES})
+endif()
+
 
 include(FindPackageHandleStandardArgs)
 # handle the QUIETLY and REQUIRED arguments and set SILO_FOUND to TRUE

diff --git a/src/libs/blueprint/conduit_blueprint_mesh.cpp b/src/libs/blueprint/conduit_blueprint_mesh.cpp
@@ -7813,6 +7813,21 @@ mesh::flatten(const conduit::Node &mesh,
     do_flatten.execute(mesh, output);
 }
 
+//-----------------------------------------------------------------------------
+void mesh::generate_domain_ids(conduit::Node &domains)
+{
+  int num_domains = (int)domains.number_of_children();
+
+  int domain_offset = 0;
+
+  for(int i = 0; i < num_domains; ++i)
+  {
+    conduit::Node &dom = domains.child(i);
+    dom["state/domain_id"] = domain_offset + i;
+  }
+}
+
+
 }
 //-----------------------------------------------------------------------------
 // -- end conduit::blueprint --

diff --git a/src/libs/blueprint/conduit_blueprint_mesh.hpp b/src/libs/blueprint/conduit_blueprint_mesh.hpp
@@ -216,6 +216,7 @@ void CONDUIT_BLUEPRINT_API flatten(const conduit::Node &mesh,
                                    const conduit::Node &options,
                                    conduit::Node &output);
 
+void CONDUIT_BLUEPRINT_API generate_domain_ids(conduit::Node &domains);
 
 //-----------------------------------------------------------------------------
 /// blueprint mesh transform methods (these work on multi domain meshes)

diff --git a/src/libs/blueprint/conduit_blueprint_mpi_mesh.cpp b/src/libs/blueprint/conduit_blueprint_mpi_mesh.cpp
@@ -2706,6 +2706,40 @@ flatten(const conduit::Node &mesh, const conduit::Node &options,
     do_flatten.execute(mesh, output);
 }
 
+//-------------------------------------------------------------------------
+//
+// recalculate domain ids so that we are consistant.
+// Assumes that domains are valid
+//
+void generate_domain_ids(conduit::Node &domains,
+                         MPI_Comm mpi_comm)
+{
+  int num_domains = (int)domains.number_of_children();
+
+  int domain_offset = 0;
+
+  int comm_size = 1;
+  int rank = 0;
+
+  MPI_Comm_rank(mpi_comm,&rank);
+  MPI_Comm_size(mpi_comm, &comm_size);
+  int *domains_per_rank = new int[comm_size];
+
+  MPI_Allgather(&num_domains, 1, MPI_INT, domains_per_rank, 1, MPI_INT, mpi_comm);
+
+  for(int i = 0; i < rank; ++i)
+  {
+    domain_offset += domains_per_rank[i];
+  }
+  delete[] domains_per_rank;
+
+  for(int i = 0; i < num_domains; ++i)
+  {
+    conduit::Node &dom = domains.child(i);
+    dom["state/domain_id"] = domain_offset + i;
+  }
+}
+
 //-----------------------------------------------------------------------------
 }
 //-----------------------------------------------------------------------------

diff --git a/src/libs/blueprint/conduit_blueprint_mpi_mesh.hpp b/src/libs/blueprint/conduit_blueprint_mpi_mesh.hpp
@@ -247,6 +247,9 @@ void CONDUIT_BLUEPRINT_API flatten(const conduit::Node &mesh,
                                    conduit::Node &output,
                                    MPI_Comm comm);
 
+void CONDUIT_BLUEPRINT_API generate_domain_ids(conduit::Node &domains,
+                                               MPI_Comm mpi_comm);
+
 //-----------------------------------------------------------------------------
 }
 //-----------------------------------------------------------------------------

diff --git a/src/libs/conduit/conduit_utils.hpp b/src/libs/conduit/conduit_utils.hpp
@@ -97,7 +97,7 @@
 //-----------------------------------------------------------------------------
 #define CONDUIT_ASSERT( cond, msg )                                  \
 {                                                                    \
-    if(!cond)                                                        \
+    if(!(cond))                                                      \
     {                                                                \
         std::ostringstream conduit_oss_assert;                       \
         conduit_oss_assert << msg;                                   \
@@ -120,7 +120,7 @@
 //-----------------------------------------------------------------------------
 #define CONDUIT_CHECK( cond, msg )                                   \
 {                                                                    \
-    if(!cond)                                                        \
+    if(!(cond))                                                      \
     {                                                                \
         std::ostringstream conduit_oss_check;                        \
         conduit_oss_check << msg;                                    \

diff --git a/src/libs/relay/CMakeLists.txt b/src/libs/relay/CMakeLists.txt
@@ -377,7 +377,9 @@ set(conduit_relay_mpi_io_headers conduit_relay_mpi_io.hpp)
 set(conduit_relay_mpi_io_deps conduit
                               ${conduit_blt_mpi_deps}
                               conduit_relay_mpi
-                              conduit_relay)
+                              conduit_relay
+                              conduit_blueprint
+                              conduit_blueprint_mpi)
 
 #
 # Specify relay mpi c headers

diff --git a/src/libs/relay/conduit_relay_io.cpp b/src/libs/relay/conduit_relay_io.cpp
@@ -392,15 +392,6 @@ save(const Node &node,
 #else
         CONDUIT_ERROR("conduit_relay lacks Silo support: " <<
                       "Failed to save conduit node to path " << path);
-#endif
-    }
-    else if(protocol == "conduit_silo_mesh")
-    {
-#ifdef CONDUIT_RELAY_IO_SILO_ENABLED
-        silo_mesh_write(node,path);
-#else
-        CONDUIT_ERROR("conduit_relay lacks Silo support: " <<
-                      "Failed to save conduit mesh node to path " << path);
 #endif
     }
     else if( protocol == "adios")
@@ -534,16 +525,6 @@ save_merged(const Node &node,
 #else
         CONDUIT_ERROR("conduit_relay lacks Silo support: " <<
                       "Failed to save conduit node to path " << path);
-#endif
-    }
-    else if(protocol == "conduit_silo_mesh")
-    {
-#ifdef CONDUIT_RELAY_IO_SILO_ENABLED
-        /// TODO .. ?
-        silo_mesh_write(node,path);
-#else
-        CONDUIT_ERROR("conduit_relay lacks Silo support: " <<
-                      "Failed to save conduit mesh node to path " << path);
 #endif
     }
     else if( protocol == "adios")