refactor(cmake): project structure

CMakeLists.txt

@@ -14,25 +14,6 @@ endif()
 find_package(catalyst 2.0 REQUIRED)
 find_package(ComIn REQUIRED)
 
-add_library(catalyst_adapter MODULE catalyst_adapter.cpp)
-target_link_libraries(catalyst_adapter PRIVATE ComIn::ComIn catalyst::catalyst)
-
-
-if(BUILD_TESTING)
-  comin_add_replay_data(
-    NAME test_nwp_R02B04_R02B05_nest
-    URL "https://gitlab.dkrz.de/api/v4/projects/139706/packages/generic/test_nwp_R02B04_R02B05_nest/1/test_nwp_R02B04_R02B05_nest.tar.gz"
-    MD5HASH 103c0b673fbef0bc07c567b7f3acf975)
-  
-  comin_add_replay_test(NAME catalyst_test
-    REPLAY_DATA "test_nwp_R02B04_R02B05_nest"
-    NUM_PROCS 3
-  )
-
-  comin_test_add_plugin(TEST catalyst_test
-    NAME "catalyst_adapter"
-    PLUGIN_LIBRARY "$<TARGET_FILE:catalyst_adapter>"
-    OPTIONS "/home/nils/projects/comin/catalyst_adaptor/pvExample.py"
-    #   OPTIONS "/home/nils/projects/comin/catalyst_adaptor/gridwriter.py"
-  )
-endif()
+add_subdirectory(src/)
+add_subdirectory(test/)
+add_subdirectory(pipelines/)

pipelines/CMakeLists.txt

+add_subdirectory(live/)
+add_subdirectory(gridwriter/)

pipelines/gridwriter/CMakeLists.txt

+set(REPLAY_DATA_NAME "test_nwp_R02B04_R02B05_nest")
+get_target_property(REPLAY_DATA_PATH "download_replay_data_${REPLAY_DATA_NAME}" DATA_DIRECTORY)
+file(GENERATE OUTPUT master.nml
+  CONTENT "&comin_nml
+  plugin_list(1)%name = \"comin_var_replay_plugin\"
+  plugin_list(1)%plugin_library = \"$<TARGET_FILE:ComIn::comin_var_replay_plugin>\"
+  plugin_list(1)%options = \"${REPLAY_DATA_PATH}/vars_\"
+  plugin_list(2)%name = \"catalyst_adapter\"
+  plugin_list(2)%plugin_library = \"${PROJECT_BINARY_DIR}/src/libcatalyst_adapter.so\"
+  plugin_list(2)%options = \"${CMAKE_CURRENT_SOURCE_DIR}/gridwriter.py\"
+/
+")
+file(GENERATE OUTPUT run.sh
+  CONTENT "#!/bin/sh
+cmake --build . --target \"download_replay_data_${REPLAY_DATA_NAME}\"
+cd ${CMAKE_CURRENT_BINARY_DIR}
+set -e
+${MPIEXEC_EXECUTABLE} ${MPIEXEC_NUMPROC_FLAG} 3  \"$<TARGET_FILE:ComIn::comin_replay>\" \"${REPLAY_DATA_PATH}/\"
+"
+FILE_PERMISSIONS OWNER_EXECUTE OWNER_WRITE OWNER_READ)

gridwriter.py → pipelines/gridwriter/gridwriter.py

@@ -7,7 +7,7 @@
 # Input parameters
 #---------------------------------------------------------
 # Specify the Catalyst channel name
-catalystChannel = "domain1"
+catalystChannel = "2d_domain1"
 
 # Specify the write frequency
 frequency = 1
@@ -54,10 +54,15 @@ def create_extractor(data):
 
 
 # Pipeline
-data = TrivialProducer(registrationName=catalystChannel)
+domain1 = TrivialProducer(registrationName=catalystChannel)
+
+lonlat2sphere = '-1*sin(coordsX)*cos(coordsY)*iHat+cos(coordsX)*cos(coordsY)*jHat+sin(coordsY)*kHat'
+calculator1 = Calculator(registrationName='Calculator1', Input=domain1)
+calculator1.CoordinateResults = 1
+calculator1.Function = lonlat2sphere
 
 # Returns extractor type based on data (or you can manually specify
-extractor = create_extractor(data)
+extractor = create_extractor(calculator1)
 
 # ------------------------------------------------------------------------------
 # Catalyst options

pipelines/live/CMakeLists.txt

+set(REPLAY_DATA_NAME "test_nwp_R02B04_R02B05_nest")
+get_target_property(REPLAY_DATA_PATH "download_replay_data_${REPLAY_DATA_NAME}" DATA_DIRECTORY)
+file(GENERATE OUTPUT master.nml
+  CONTENT "&comin_nml
+  plugin_list(1)%name = \"comin_var_replay_plugin\"
+  plugin_list(1)%plugin_library = \"$<TARGET_FILE:ComIn::comin_var_replay_plugin>\"
+  plugin_list(1)%options = \"${REPLAY_DATA_PATH}/vars_\"
+  plugin_list(2)%name = \"catalyst_adapter\"
+  plugin_list(2)%plugin_library = \"${PROJECT_BINARY_DIR}/src/libcatalyst_adapter.so\"
+  plugin_list(2)%options = \"${CMAKE_CURRENT_SOURCE_DIR}/live.py\"
+/
+")
+file(GENERATE OUTPUT run.sh
+  CONTENT "#!/bin/sh
+cmake --build . --target \"download_replay_data_${REPLAY_DATA_NAME}\"
+cd ${CMAKE_CURRENT_BINARY_DIR}
+set -e
+${MPIEXEC_EXECUTABLE} ${MPIEXEC_NUMPROC_FLAG} 3  \"$<TARGET_FILE:ComIn::comin_replay>\" \"${REPLAY_DATA_PATH}/\"
+"
+FILE_PERMISSIONS OWNER_EXECUTE OWNER_WRITE OWNER_READ)

pvExample.py → pipelines/live/live.py

@@ -12,13 +12,13 @@ options.CatalystLiveTrigger = 'TimeStep'
 
 lonlat2sphere = '-1*sin(coordsX)*cos(coordsY)*iHat+cos(coordsX)*cos(coordsY)*jHat+sin(coordsY)*kHat'
 
-domain1 = TrivialProducer(registrationName='domain1')
+domain1 = TrivialProducer(registrationName='2d_domain1')
 calculator1 = Calculator(registrationName='Calculator1', Input=domain1)
 calculator1.CoordinateResults = 1
 calculator1.Function = lonlat2sphere
 calculator1Display = Show(calculator1)
 
-domain2 = TrivialProducer(registrationName='domain2')
+domain2 = TrivialProducer(registrationName='2d_domain2')
 calculator2 = Calculator(registrationName='Calculator2', Input=domain2)
 calculator2.CoordinateResults = 1
 calculator2.Function = lonlat2sphere

src/CMakeLists.txt

+add_library(catalyst_adapter MODULE catalyst_adapter.cpp)
+target_link_libraries(catalyst_adapter PRIVATE ComIn::ComIn catalyst::catalyst)

catalyst_adapter.cpp → src/catalyst_adapter.cpp

@@ -5,7 +5,6 @@
 #include <comin.h>
 #include <catalyst.hpp>
 
-int ierr = COMIN_SUCCESS;
 void catalyst_adapter_secondary_constructor();
 void catalyst_adapter_execute();
 void catalyst_adapter_destruct();
@@ -19,7 +18,7 @@ extern "C"{ // avoid name-mangling
 
     const char* script_file = NULL;
     int script_file_len;
-    comin_current_get_plugin_options(&script_file, &script_file_len, &ierr);
+    comin_current_get_plugin_options(&script_file, &script_file_len);
     catalyst_init_params["catalyst/scripts/script/filename"] = std::string(script_file, script_file_len);
 
     catalyst_status err = catalyst_initialize(conduit_cpp::c_node(&catalyst_init_params));
@@ -34,9 +33,9 @@ extern "C"{ // avoid name-mangling
     }
     about_node.print();
 
-    comin_callback_register(EP_SECONDARY_CONSTRUCTOR, catalyst_adapter_secondary_constructor, &ierr);
-    comin_callback_register(EP_ATM_WRITE_OUTPUT_BEFORE, catalyst_adapter_execute, &ierr);
-    comin_callback_register(EP_DESTRUCTOR, catalyst_adapter_destruct, &ierr);
+    comin_callback_register(EP_SECONDARY_CONSTRUCTOR, catalyst_adapter_secondary_constructor);
+    comin_callback_register(EP_ATM_WRITE_OUTPUT_BEFORE, catalyst_adapter_execute);
+    comin_callback_register(EP_DESTRUCTOR, catalyst_adapter_destruct);
   }
 }
 
@@ -45,7 +44,7 @@ void catalyst_adapter_secondary_constructor(){
   // prepare the execute node
   for(int jg = 1; jg<=comin_descrdata_get_global_n_dom(); ++jg){
     std::cout << "dom: " << jg << std::endl;
-    auto channel = catalyst_exec_params[std::string("catalyst/channels/domain")+std::to_string(jg)];
+    auto channel = catalyst_exec_params[std::string("catalyst/channels/2d_domain")+std::to_string(jg)];
     // now, create the mesh.
     channel["type"] = "mesh";
 
@@ -84,9 +83,9 @@ void catalyst_adapter_secondary_constructor(){
         it != nullptr;
         it = comin_var_get_descr_list_next(it)){
       t_comin_var_descriptor var_desc;
-      comin_var_get_descr_list_var_desc(it, &var_desc, &ierr);
+      comin_var_get_descr_list_var_desc(it, &var_desc);
       int zaxis_id = -1;
-      comin_metadata_get_integer(var_desc, "zaxis_id", &zaxis_id, &ierr);
+      comin_metadata_get_integer(var_desc, "zaxis_id", &zaxis_id);
       if(var_desc.id == jg &&
          zaxis_id == COMIN_ZAXIS_2D){
         // TODO split tracers in separate arrays

test/CMakeLists.txt

+if(BUILD_TESTING)
+  comin_add_replay_test(NAME catalyst_test
+    REPLAY_DATA "test_nwp_R02B04_R02B05_nest"
+    NUM_PROCS 3
+  )
+
+  comin_test_add_plugin(TEST catalyst_test
+    NAME "catalyst_adapter"
+    PLUGIN_LIBRARY "$<TARGET_FILE:catalyst_adapter>"
+    OPTIONS "/home/nils/projects/comin/catalyst_adaptor/pvExample.py"
+  )
+endif()