Merge pull request #35 from uiuc-hpc/hdf5-pnetcdf-new-funcs

Automatic tracing wrapper generation

.gitignore

@@ -102,5 +102,9 @@ install
 /build/
 .cache
 
+# IDE-specific
+.idea/
+/cmake-build-debug/
+
 # clangd database
 compile_commands.json

CMakeLists.txt

@@ -4,9 +4,9 @@ include_directories(${PROJECT_BINARY_DIR})
 #------------------------------------------------------------------------------
 # Version information
 #------------------------------------------------------------------------------
-set(RECORDER_VERSION_MAJOR "2")
-set(RECORDER_VERSION_MINOR "5")
-set(RECORDER_VERSION_PATCH "2")
+set(RECORDER_VERSION_MAJOR "3")
+set(RECORDER_VERSION_MINOR "0")
+set(RECORDER_VERSION_PATCH "0")
 set(RECORDER_PACKAGE "recorder")
 set(RECORDER_PACKAGE_NAME "RECORDER")
 set(RECORDER_PACKAGE_VERSION "${RECORDER_VERSION_MAJOR}.${RECORDER_VERSION_MINOR}.${RECORDER_VERSION_PATCH}")
@@ -15,6 +15,13 @@ set(RECORDER_PACKAGE_VERSION_MINOR "${RECORDER_VERSION_PATCH}")
 set(RECORDER_PACKAGE_STRING "${RECORDER_PACKAGE_NAME} ${RECORDER_PACKAGE_VERSION}")
 set(RECORDER_PACKAGE_TARNAME "${RECORDER_PACKAGE}")
 
+
+# ignore warning message
+if(POLICY CMP0074)
+    cmake_policy(SET CMP0074 OLD)
+endif()
+
+
 #------------------------------------------------------------------------------
 # Setup install and output Directories
 #------------------------------------------------------------------------------
@@ -124,6 +131,10 @@ option(RECORDER_ENABLE_CUDA_TRACE "Enable tracing of CUDA kernels." OFF)
 option(RECORDER_ENABLE_FCNTL_TRACE "Enable tracing of fcntl()." ON)
 option(RECORDER_INSTALL_TESTS "Enable installation of tests." OFF)
 
+
+set(PNETCDF_INSTALL_PATH "/usr" CACHE STRING "Build Recorder with PnetCDF")
+
+
 #mark_as_advanced(RECORDER_ENABLE_CUDA_TRACE)
 #mark_as_advanced(RECORDER_ENABLE_FCNTL_TRACE)
 

docs/source/build.rst

@@ -12,9 +12,11 @@ is currently under active development.
 
 -  MPI
 -  HDF5
+-  PnetCDF (optional) - Needed for PnetCDF tracing
 -  Arrow (optional) > 5.0.0 - Needed for building Parquet convertor.
 -  CUDA (optional) - Needed for CUDA kernels interception.
 
+
 *Note that Recorder and the applications you intend to trace must be
 compiled with the same version of HDF5 and MPI.*
 
@@ -44,6 +46,9 @@ need to use ``-DCMAKE_PREFIX_PATH`` to indicate their locations:
          -DCMAKE_INSTALL_PREFIX=[install location]                   \
          -DCMAKE_PREFIX_PATH=[semicolon separated depedencies dir]
 
+Recorder can also be built with PnetCDF to trace PnetCDF calls, use `-DRECORDER_WITH_PNETCDF=/path/to/pnetcdf/install`
+to build Recorder with the specified PnetCDF.
+
 (2) Intercepting ``fcntl()`` call:
 
 Since v2.1.7, ``fcntl(int fd, int cmd, ...)`` is intercepted. The

include/recorder-utils.h

@@ -16,10 +16,11 @@ double recorder_wtime(void);                    // return the timestamp
 char* itoa(off64_t val);                        // convert an integer to string
 char* ftoa(double val);                         // convert a float to string
 char* ptoa(const void* ptr);                    // convert a pointer to string
+char* strtoa(const char* ptr);                  // convert a char* to string (safer strdup)
 char* arrtoa(size_t arr[], int count);          // convert an array of size_t to a string
 char** assemble_args_list(int arg_count, ...);
 const char* get_function_name_by_id(int id);
-unsigned char get_function_id_by_name(const char* name);
+int get_function_id_by_name(const char* name);
 char* realrealpath(const char* path);           // return the absolute path (mapped to id in string)
 int mkpath(char* file_path, mode_t mode);       // recursive mkdir()
 

include/recorder.h

@@ -32,6 +32,8 @@
 #define RECORDER_MPIIO_TRACING              "RECORDER_MPIIO_TRACING"
 #define RECORDER_MPI_TRACING                "RECORDER_MPI_TRACING"
 #define RECORDER_HDF5_TRACING               "RECORDER_HDF5_TRACING"
+#define RECORDER_PNETCDF_TRACING            "RECORDER_PNETCDF_TRACING"
+#define RECORDER_NETCDF_TRACING             "RECORDER_NETCDF_TRACING"
 
 
 /**
@@ -49,6 +51,8 @@
  *
  */
 #define RECORDER_INTERCEPTOR_PROLOGUE_CORE(ret, func, real_args)                    \
+    /*printf("chen intercept %s\n", #func);*/\
+    /*fflush(stdout);*/\
     Record *record = recorder_malloc(sizeof(Record));                               \
     record->func_id = get_function_id_by_name(#func);                               \
     record->tid = recorder_gettid();                                                \
@@ -61,7 +65,7 @@
     if (sizeof(ret)) {                                                              \
         record->res = malloc(sizeof(ret));                                          \
         memcpy(record->res, &res, sizeof(ret));                                     \
-    } 
+    }
 
 // Fortran wrappers call this
 // ierr is of type MPI_Fint*, set only for fortran calls

lib/CMakeLists.txt

@@ -45,6 +45,47 @@ else()
     message(STATUS, "HDF5 not found")
 endif()
 
+# PnetCDF is not a CMAKE project, we use find_path() to locate it
+# this requires users to set -DRECORDER_WITH_PNETCDF=/xx/xx/
+find_path(PNETCDF_INCLUDE_DIRS pnetcdf.h ${RECORDER_WITH_PNETCDF}/include)
+find_path(PNETCDF_LIBRARY_FOUND libpnetcdf.so ${RECORDER_WITH_PNETCDF}/lib)
+if(PNETCDF_INCLUDE_DIRS AND PNETCDF_LIBRARY_FOUND)
+    message("-- " "Found PnetCDF:" ${RECORDER_WITH_PNETCDF})
+    set(RECORDER_SRCS
+        ${CMAKE_CURRENT_SOURCE_DIR}/recorder-pnetcdf.c
+        ${RECORDER_SRCS}
+    )
+    include_directories(${PNETCDF_INCLUDE_DIRS})
+    set(PNETCDF_LIBRARIES ${RECORDER_WITH_PNETCDF}/lib/libpnetcdf.so)
+    set(RECORDER_EXT_INCLUDE_DEPENDENCIES ${PNETCDF_INCLUDE_DIRS}
+            ${RECORDER_EXT_INCLUDE_DEPENDENCIES})
+    set(RECORDER_EXT_LIB_DEPENDENCIES
+            ${PNETCDF_LIBRARIES} ${RECORDER_EXT_LIB_DEPENDENCIES})
+else()
+    message("-- " "PnetCDF not found. Will build Recorder without it.")
+endif()
+
+# Look for NetCDF
+# -DRECORDER_WITH_NETCDF=/xx/xx/
+find_path(NETCDF_INCLUDE_DIRS netcdf.h ${RECORDER_WITH_NETCDF}/include)
+find_path(NETCDF_LIBRARY_FOUND libnetcdf.so ${RECORDER_WITH_NETCDF}/lib)
+if(NETCDF_INCLUDE_DIRS AND NETCDF_LIBRARY_FOUND)
+    message("-- " "Found NetCDF:" ${RECORDER_WITH_NETCDF})
+    set(RECORDER_SRCS
+        ${CMAKE_CURRENT_SOURCE_DIR}/recorder-netcdf.c
+        ${RECORDER_SRCS}
+    )
+    include_directories(${NETCDF_INCLUDE_DIRS})
+    set(NETCDF_LIBRARIES ${RECORDER_WITH_NETCDF}/lib/libnetcdf.so)
+    set(RECORDER_EXT_INCLUDE_DEPENDENCIES ${NETCDF_INCLUDE_DIRS}
+            ${RECORDER_EXT_INCLUDE_DEPENDENCIES})
+    set(RECORDER_EXT_LIB_DEPENDENCIES
+            ${NETCDF_LIBRARIES} ${RECORDER_EXT_LIB_DEPENDENCIES})
+else()
+    message("-- " "NetCDF not found. Will build Recorder without it.")
+endif()
+
+
 find_package(MPI REQUIRED)
 if(MPI_FOUND)
     include_directories(${MPI_CXX_INCLUDE_DIRS})
@@ -129,6 +170,8 @@ target_compile_definitions(recorder
         PRIVATE $<$<BOOL:${HAVE___LXSTAT64}>:HAVE___LXSTAT64>
         PRIVATE $<$<BOOL:${HAVE___FXSTAT}>:HAVE___FXSTAT>
         PRIVATE $<$<BOOL:${HAVE___FXSTAT64}>:HAVE___FXSTAT64>
+        PRIVATE $<$<AND:$<BOOL:${PNETCDF_INCLUDE_DIRS}>,$<BOOL:${PNETCDF_LIBRARY_FOUND}>>:RECORDER_WITH_PNETCDF>
+        PRIVATE $<$<AND:$<BOOL:${NETCDF_INCLUDE_DIRS}>,$<BOOL:${NETCDF_LIBRARY_FOUND}>>:RECORDER_WITH_NETCDF>
         PRIVATE $<$<BOOL:${RECORDER_ENABLE_FCNTL_TRACE}>:RECORDER_ENABLE_FCNTL_TRACE>
         PRIVATE $<$<BOOL:${RECORDER_ENABLE_CUDA_TRACE}>:RECORDER_ENABLE_CUDA_TRACE>
         )