Merge pull request #2 from Analytics4MD/dspaces_2_w_ci

Adds DataSpaces 2 support and GitHub CI

.github/basic_test/CMakeLists.txt

@@ -0,0 +1,52 @@
+cmake_minimum_required(VERSION 3.12)
+project(a4md_basic_test_ci)
+
+set(CMAKE_VERBOSE_MAKEFILE ON)
+
+set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR})
+
+set(CMAKE_CXX_STANDARD 11)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+set(CMAKE_CXX_EXTENSIONS OFF)
+
+find_package(MPI REQUIRED)
+
+cmake_policy(SET CMP0094 NEW)
+find_package(Python3 REQUIRED COMPONENTS Interpreter Development)
+if (NOT ${Python3_VERSION_MAJOR} EQUAL 3)
+    message(FATAL_ERROR "FindPython3 somehow found a Python install that wasn't Python 3")
+endif ()
+if (${Python3_VERSION_MINOR} LESS_EQUAL 3)
+    message(FATAL_ERROR "Found Python 3.${Python3_VERSION_MINOR}.${Python3_VERSION_PATCH}, which has a version less than minimum allowed of 3.3")
+endif ()
+
+find_package(Boost 1.59.0 REQUIRED COMPONENTS iostreams serialization)
+
+find_package(A4MD REQUIRED)
+
+add_executable(producer producer.cxx)
+add_executable(consumer consumer.cxx)
+
+target_link_libraries(producer MPI::MPI_CXX Python3::Python Boost::boost Boost::iostreams Boost::serialization ${A4MD_LIBRARIES})
+target_link_libraries(consumer MPI::MPI_CXX Python3::Python Boost::boost Boost::iostreams Boost::serialization ${A4MD_LIBRARIES})
+target_include_directories(producer PRIVATE ${A4MD_INCLUDE_DIRS})
+target_include_directories(consumer PRIVATE ${A4MD_INCLUDE_DIRS})
+
+install(TARGETS producer DESTINATION bin)
+install(TARGETS consumer DESTINATION bin)
+install(FILES flux_prod_cons.sh
+        DESTINATION bin
+        PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE
+                    GROUP_READ GROUP_WRITE GROUP_EXECUTE
+                    WORLD_READ WORLD_WRITE WORLD_EXECUTE
+)
+install(FILES local_prod_cons.sh
+        DESTINATION bin
+        PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE
+        GROUP_READ GROUP_WRITE GROUP_EXECUTE
+        WORLD_READ WORLD_WRITE WORLD_EXECUTE
+)
+install(DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/script/"
+        DESTINATION bin
+        USE_SOURCE_PERMISSIONS
+)

.github/basic_test/FindA4MD.cmake

@@ -0,0 +1,79 @@
+# Copied from
+# https://github.com/Analytics4MD/A4MD-sample-workflow
+
+# Find A4MD include directories and libraries
+# A4MD_INCLUDE_DIRECTORIES - where to find A4MD headers
+# A4MD_LIBRARIES           - list of libraries to link against when using A4MD
+# A4MD_FOUND               - Do not attempt to use A4MD if "no", "0", or undefined.
+
+include(FindPackageHandleStandardArgs)
+
+find_path(A4MD_INCLUDE_DIRS NAMES chunk.h HINTS
+        ${A4MD_PREFIX}/include
+        /usr/include
+        /usr/local/include
+        /opt/local/include
+        /sw/include
+)
+
+find_library(A4MD_INGEST_LIBRARIES NAMES a4md_ingest HINTS
+        ${A4MD_PREFIX}/lib
+        /usr/lib
+        /usr/local/lib
+        /opt/local/lib
+        /sw/lib
+)
+
+find_library(A4MD_RETRIEVE_LIBRARIES NAMES a4md_retrieve HINTS
+        ${A4MD_PREFIX}/lib
+        /usr/lib
+        /usr/local/lib
+        /opt/local/lib
+        /sw/lib
+)
+
+find_library(A4MD_DTL_LIBRARIES NAMES a4md_dtl HINTS
+        ${A4MD_PREFIX}/lib
+        /usr/lib
+        /usr/local/lib
+        /opt/local/lib
+        /sw/lib
+)
+
+find_library(A4MD_COMMON_LIBRARIES NAMES a4md_cmn HINTS
+        ${A4MD_PREFIX}/lib
+        /usr/lib
+        /usr/local/lib
+        /opt/local/lib
+        /sw/lib
+)
+
+set(A4MD_LIBRARIES ${A4MD_INGEST_LIBRARIES} ${A4MD_RETRIEVE_LIBRARIES} ${A4MD_DTL_LIBRARIES} ${A4MD_COMMON_LIBRARIES})
+
+SET(A4MD_TRANSPORT_LIBRARIES "")
+
+find_package(dspaces CONFIG REQUIRED)
+set(A4MD_INCLUDE_DIRS ${A4MD_INCLUDE_DIRS})
+set(A4MD_TRANSPORT_LIBRARIES ${A4MD_TRANSPORT_LIBRARIES} dspaces::dspaces)
+message(STATUS "${A4MD_TRANSPORT_LIBRARIES}")
+list(APPEND A4MD_LIBRARIES ${A4MD_TRANSPORT_LIBRARIES})
+
+find_package_handle_standard_args(A4MD DEFAULT_MSG
+        A4MD_INCLUDE_DIRS
+        A4MD_INGEST_LIBRARIES
+        A4MD_RETRIEVE_LIBRARIES
+        A4MD_DTL_LIBRARIES
+        A4MD_COMMON_LIBRARIES
+        A4MD_TRANSPORT_LIBRARIES
+)
+
+mark_as_advanced(
+        A4MD_INCLUDE_DIRS
+        A4MD_INGEST_LIBRARIES
+        A4MD_RETRIEVE_LIBRARIES
+        A4MD_DTL_LIBRARIES
+        A4MD_COMMON_LIBRARIES
+        A4MD_TRANSPORT_LIBRARIES
+        A4MD_LIBRARIES
+        A4MD_FOUND
+)

.github/basic_test/consumer.cxx

@@ -0,0 +1,156 @@
+// Copied from
+// https://github.com/Analytics4MD/A4MD-sample-workflow
+
+#include <unistd.h>
+#include "mpi.h"
+#ifdef DTL_DECAF
+#include "decaf_reader.h"
+#include <bredala/data_model/boost_macros.h>
+#endif
+#include "dataspaces_reader.h"
+#include "md_stager.h"
+#include "md_analyzer.h"
+#include "md_retriever.h"
+#include "timer.h"
+
+#define DTL_COLOR 0
+#define NON_DTL_COLOR 1
+#define ROOT 0
+
+int main (int argc, const char** argv)
+{
+    MPI_Init(NULL,NULL);
+    int rank, app_rank;
+    MPI_Comm global_comm = MPI_COMM_WORLD;
+    MPI_Comm app_comm, dtl_comm;
+    int color;
+    int *appnum, present;
+    MPI_Comm_rank(global_comm, &rank);
+    MPI_Comm_get_attr(global_comm, MPI_APPNUM, &appnum, &present);
+    MPI_Comm_split(global_comm, *appnum, rank, &app_comm);
+    MPI_Comm_rank(app_comm, &app_rank);
+    MPI_Comm_free(&app_comm);
+    if (app_rank == ROOT)
+    {
+        color = DTL_COLOR;
+    }
+    else
+    {
+        color = NON_DTL_COLOR;
+    }
+    MPI_Comm_split(global_comm, color, rank, &dtl_comm);
+
+    if (app_rank == ROOT)
+    {
+        printf("---======== In Consummer::main()\n");
+        if (argc < 2)
+        {
+            fprintf(stderr, "./consumer decaf json_conf py_path py_func n_frames\n");
+            fprintf(stderr, "./consumer dataspaces client_id group_id py_path py_func n_frames\n");
+            return -1;
+        }
+        std::string dtl_type((char*)argv[1]);
+#ifdef DTL_DECAF
+        if ( (dtl_type.compare("decaf") != 0) && (dtl_type.compare("dataspaces") != 0) )
+        {
+            fprintf(stderr, "ERROR: DTL type must be decaf or dataspaces\n");
+            return -1;
+        }
+#else
+        if (dtl_type.compare("dataspaces") != 0)
+        {
+            fprintf(stderr, "ERROR: DTL type must be dataspaces\n");
+            return -1;
+        }
+#endif
+        std::string json_conf;
+        std::string py_path;
+        std::string py_func;
+        int client_id;
+        int group_id;
+        int n_frames;
+        if (dtl_type.compare("decaf") == 0)
+        {
+            if (argc != 6)
+            {
+                fprintf(stderr, "ERROR: ./consumer decaf json_conf py_path py_func n_frames\n");
+                return -1;
+            }
+            // Input arguments
+            json_conf = (char*)argv[2];
+            py_path = (char*)argv[3];
+            py_func = (char*)argv[4];
+            n_frames = atoi(argv[5]);
+        }
+
+        if (dtl_type.compare("dataspaces") == 0)
+        {
+            if (argc != 7)
+            {
+                fprintf(stderr, "ERROR: ./consumer dataspaces client_id group_id py_path py_func n_frames\n");
+                return -1;
+            }
+            // Input arguments
+            client_id = atoi(argv[2]);
+            group_id = atoi(argv[3]);
+            py_path = (char*)argv[4];
+            py_func = (char*)argv[5];
+            n_frames = atoi(argv[6]);
+        }
+
+        // Number of chunks
+        unsigned long int total_chunks = n_frames;// +1 for the call before simulation starts
+
+        // Preprocess Python path
+        std::size_t module_start = py_path.find_last_of("/");
+        std::size_t module_end = py_path.rfind(".py");
+        if (module_end == std::string::npos)
+        {
+            fprintf(stderr, "ERROR: Expecting a python module in the python script path argument.\n");
+            return -1;
+        }
+        // get directory
+        std::string py_dir = (std::string::npos==module_start)? std::string(".") : py_path.substr(0,module_start);
+        // get file
+        std::string py_name = py_path.substr(module_start+1, module_end-module_start-1);
+        printf("Python directory : %s\n", py_dir.c_str());
+        printf("Python script name : %s\n", py_name.c_str());
+        printf("Python function: %s\n", py_func.c_str());
+
+
+        ChunkReader* chunk_reader;
+#ifdef DTL_DECAF
+        if (dtl_type.compare("decaf") == 0)
+        {
+            chunk_reader = new DecafReader(json_conf, total_chunks, dtl_comm);
+        }
+#endif
+        if (dtl_type.compare("dataspaces") == 0)
+        {
+            chunk_reader = new DataSpacesReader(client_id, group_id, total_chunks, dtl_comm);
+        }
+
+        ChunkWriter *chunk_writer = new MDAnalyzer((char*)py_name.c_str(), (char*)py_func.c_str(), (char*)py_dir.c_str());
+
+        ChunkStager *chunk_stager = new MDStager(chunk_reader, chunk_writer);
+        int n_window_width = 1;
+        Retriever *retriever = new MDRetriever(*chunk_stager, n_frames, n_window_width);
+
+        // Main run
+        TimeVar t_start = timeNow();
+        retriever->run();
+        DurationMilli md_retriever_time_ms = timeNow()-t_start;
+        auto total_md_retriever_time_ms = md_retriever_time_ms.count();
+        printf("total_retriever_time_ms : %f\n",total_md_retriever_time_ms);
+
+        // Free memory
+        delete retriever;
+        delete chunk_stager;
+        delete chunk_writer;
+        delete chunk_reader;
+    }
+
+    MPI_Comm_free(&dtl_comm);
+    MPI_Finalize();
+    return 0;
+}