[svn-r25295] Add support for FastBit index plugin

9 files changed, 443 insertions, 6 deletions

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 61f760c..70d1b22 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -719,12 +719,20 @@ IF (HDF5_ENABLE_PARALLEL)
     OPTION (HDF5_ENABLE_INDEXING "Enable support for Indexing." OFF)
     IF (HDF5_ENABLE_INDEXING)
       SET (H5_HAVE_INDEXING 1)
+      # ALACRITY
       FIND_PACKAGE (ALACRITY)
       IF (ALACRITY_FOUND)
         SET (H5_HAVE_ALACRITY 1)
         INCLUDE_DIRECTORIES (${ALACRITY_INCLUDE_DIR})
         SET (LINK_LIBS ${LINK_LIBS} ${ALACRITY_LIBRARIES})
       ENDIF (ALACRITY_FOUND)
+      # FastBit
+      FIND_PACKAGE (FASTBIT)
+      IF (FASTBIT_FOUND)
+        SET (H5_HAVE_FASTBIT 1)
+        INCLUDE_DIRECTORIES (${FASTBIT_INCLUDE_DIR})
+        SET (LINK_LIBS ${LINK_LIBS} ${FASTBIT_LIBRARIES})
+      ENDIF (FASTBIT_FOUND)
     ENDIF (HDF5_ENABLE_INDEXING)
   ENDIF (HDF5_ENABLE_EFF)
 ENDIF (HDF5_ENABLE_PARALLEL)
diff --git a/config/cmake/FindFASTBIT.cmake b/config/cmake/FindFASTBIT.cmake
new file mode 100644
index 0000000..2d95f45
--- /dev/null
+++ b/config/cmake/FindFASTBIT.cmake
@@ -0,0 +1,22 @@
+# - Try to find FastBit
+# Once done this will define
+#  FASTBIT_FOUND - System has FastBit
+#  FASTBIT_INCLUDE_DIRS - The FastBit include directories
+#  FASTBIT_LIBRARIES - The libraries needed to use FastBit
+
+find_path(FASTBIT_INCLUDE_DIR iapi.h
+  HINTS /usr/local/include /usr/include)
+
+find_library(FASTBIT_LIBRARY NAMES fastbit
+  PATHS /usr/local/lib /usr/lib)
+
+set(FASTBIT_INCLUDE_DIRS ${FASTBIT_INCLUDE_DIR})
+set(FASTBIT_LIBRARIES ${FASTBIT_LIBRARY})
+
+include(FindPackageHandleStandardArgs)
+# handle the QUIETLY and REQUIRED arguments and set FASTBIT_FOUND to TRUE
+# if all listed variables are TRUE
+find_package_handle_standard_args(FASTBIT DEFAULT_MSG
+                                  FASTBIT_INCLUDE_DIR FASTBIT_LIBRARY)
+
+mark_as_advanced(FASTBIT_INCLUDE_DIR FASTBIT_LIBRARY)
diff --git a/config/cmake/H5pubconf.h.in b/config/cmake/H5pubconf.h.in
index daf6b0d..f94505c 100644
--- a/config/cmake/H5pubconf.h.in
+++ b/config/cmake/H5pubconf.h.in
@@ -317,9 +317,12 @@
 /* Define if we have Indexing support */
 #cmakedefine H5_HAVE_INDEXING @H5_HAVE_INDEXING@
 
-/* Define if we have support for Alacrity */
+/* Define if we have support for ALACRITY */
 #cmakedefine H5_HAVE_ALACRITY @H5_HAVE_ALACRITY@
 
+/* Define if we have support for FastBit */
+#cmakedefine H5_HAVE_FASTBIT @H5_HAVE_FASTBIT@
+
 /* Define to 1 if you have the <pthread.h> header file. */
 #cmakedefine H5_HAVE_PTHREAD_H @H5_HAVE_PTHREAD_H@
 
diff --git a/configure.ac b/configure.ac
index fc73e7f..f3186f5 100644
--- a/configure.ac
+++ b/configure.ac
@@ -3179,6 +3179,83 @@ case $withval in
 esac
 
 ## ----------------------------------------------------------------------
+## Check for FastBit
+##
+AC_ARG_WITH([fastbit],
+            [AS_HELP_STRING([--with-fastbit=DIR],
+                            [Use FastBit [default=no]])],,
+            [withval=no])
+
+case $withval in
+  yes)
+    HAVE_ALACRITY="yes"
+    AC_CHECK_HEADERS([iapi.h])
+    AC_CHECK_LIB([fastbit], [fastbit_selection_create],[MYFASTBIT_LIBS="-lfastbit"], [unset HAVE_FASTBIT])
+    AC_SUBST([MYFASTBIT_LIBS])
+    if test -z "$HAVE_FASTBIT" -a -n "$HDF5_CONFIG_ABORT"; then
+      AC_MSG_ERROR([couldn't find FastBit library])
+    fi
+    ;;
+  no)
+    HAVE_FASTBIT="no"
+    AC_MSG_CHECKING([for FastBit library])
+    AC_MSG_RESULT([suppressed])
+    ;;
+  *)
+    HAVE_FASTBIT="yes"
+    case "$withval" in
+      *,*)
+        fastbit_inc="`echo $withval |cut -f1 -d,`"
+        fastbit_lib="`echo $withval |cut -f2 -d, -s`"
+        ;;
+      *)
+        if test -n "$withval"; then
+          fastbit_inc="$withval/include"
+          fastbit_lib="$withval/lib"
+        fi
+        ;;
+    esac
+
+    ## Trying to include -I/usr/include and -L/usr/lib is redundant and
+    ## can mess some compilers up.
+    if test "X$fastbit_inc" = "X/usr/include"; then
+      fastbit_inc=""
+    fi
+    if test "X$fastbit_lib" = "X/usr/lib"; then
+      fastbit_lib=""
+    fi
+
+    saved_CPPFLAGS="$CPPFLAGS"
+    saved_AM_CPPFLAGS="$AM_CPPFLAGS"
+    saved_LDFLAGS="$LDFLAGS"
+    saved_AM_LDFLAGS="$AM_LDFLAGS"
+
+    if test -n "$fastbit_inc"; then
+      CPPFLAGS="$CPPFLAGS -I$fastbit_inc"
+      AM_CPPFLAGS="$AM_CPPFLAGS -I$fastbit_inc"
+    fi
+
+    AC_CHECK_HEADERS([iapi.h],,[CPPFLAGS="$saved_CPPFLAGS"; AM_CPPFLAGS="$saved_AM_CPPFLAGS"])
+
+    if test -n "$fastbit_lib"; then
+      LDFLAGS="$LDFLAGS -L$fastbit_lib"
+      AM_LDFLAGS="$AM_LDFLAGS -L$fastbit_lib"
+    fi
+
+    AC_CHECK_LIB([fastbit], [fastbit_selection_create],, 
+        [LDFLAGS="$saved_LDFLAGS"; AM_LDFLAGS="$saved_AM_LDFLAGS"; unset HAVE_FASTBIT],
+        )
+
+    if test -z "$HAVE_FASTBIT" -a -n "$HDF5_CONFIG_ABORT"; then
+      AC_MSG_ERROR([couldn't find FastBit library])
+    fi
+
+    AC_DEFINE([HAVE_FASTBIT], [1],
+            [Define if FastBit indexing is supported.])
+    ;;
+esac
+
+## ----------------------------------------------------------------------
 ## Check for python devel
 ##
 AC_MSG_CHECKING([whether to enable the python scripting environment])
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 776df04..4abcb3b 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -662,6 +662,12 @@ IF (HDF5_ENABLE_EFF)
           ${HDF5_SRC_DIR}/H5Xalacrity.c
         )
       ENDIF (ALACRITY_FOUND)
+      IF (FASTBIT_FOUND)
+        set (H5FF_SRCS
+          ${H5FF_SRCS}
+          ${HDF5_SRC_DIR}/H5Xfastbit.c
+        )
+      ENDIF (FASTBIT_FOUND)      
     ENDIF (HDF5_ENABLE_INDEXING)
     set (H5FF_HDRS
         ${HDF5_SRC_DIR}/H5ASpublic.h
diff --git a/src/H5X.c b/src/H5X.c
index 788ff8f..ece543c 100644
--- a/src/H5X.c
+++ b/src/H5X.c
@@ -129,13 +129,15 @@ H5X_init_interface(void)
 
     FUNC_ENTER_NOAPI_NOINIT
 
-//#ifdef H5_HAVE_INDEX_PLUGIN_DUMMY
     if (H5X_register(H5X_DUMMY) < 0)
         HGOTO_ERROR (H5E_PLINE, H5E_CANTINIT, FAIL, "unable to register dummy index plugin");
-//#endif /* H5_HAVE_INDEX_PLUGIN_DUMMY */
 #ifdef H5_HAVE_ALACRITY
     if (H5X_register(H5X_ALACRITY) < 0)
-        HGOTO_ERROR (H5E_PLINE, H5E_CANTINIT, FAIL, "unable to register alacrity index plugin");
+        HGOTO_ERROR (H5E_PLINE, H5E_CANTINIT, FAIL, "unable to register ALACRITY index plugin");
+#endif
+#ifdef H5_HAVE_FASTBIT
+    if (H5X_register(H5X_FASTBIT) < 0)
+        HGOTO_ERROR (H5E_PLINE, H5E_CANTINIT, FAIL, "unable to register FastBit index plugin");
 #endif
 
 done:
diff --git a/src/H5Xfastbit.c b/src/H5Xfastbit.c
new file mode 100644
index 0000000..8fdbad9
--- /dev/null
+++ b/src/H5Xfastbit.c
@@ -0,0 +1,312 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * Copyright by The HDF Group.                                               *
+ * All rights reserved.                                                      *
+ *                                                                           *
+ * This file is part of HDF5.  The full HDF5 copyright notice, including     *
+ * terms governing use, modification, and redistribution, is contained in    *
+ * the files COPYING and Copyright.html.  COPYING can be found at the root   *
+ * of the source code distribution tree; Copyright.html can be found at the  *
+ * root level of an installed copy of the electronic HDF5 document set and   *
+ * is linked from the top-level documents page.  It can also be found at     *
+ * http://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have          *
+ * access to either file, you may request a copy from help@hdfgroup.org.     *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+/*
+ * Purpose:	Alacrity index routines.
+ */
+
+/****************/
+/* Module Setup */
+/****************/
+
+/***********/
+/* Headers */
+/***********/
+#include "H5private.h"		/* Generic Functions */
+#include "H5Xprivate.h"     /* Index */
+#include "H5Eprivate.h"		/* Error handling */
+#include "H5Iprivate.h"		/* IDs */
+#include "H5MMprivate.h"	/* Memory management */
+#include "H5Pprivate.h"
+#include "H5FFprivate.h"
+#include "H5RCprivate.h"
+#include "H5TRprivate.h"
+#include "H5Qprivate.h"
+#include "H5VMprivate.h"
+#include "H5Sprivate.h"
+/* TODO using private headers but could use public ones */
+
+#ifdef H5_HAVE_FASTBIT
+/**
+ * Header file that defines an in-memory C API for accessing the querying
+ * functionality of FastBit IBIS implementation.  It is primarily for
+ * in memory data.
+ */
+#include <iapi.h>
+
+/****************/
+/* Local Macros */
+/****************/
+#define H5X_FASTBIT_DEBUG
+
+#ifdef H5X_FASTBIT_DEBUG
+#define H5X_FASTBIT_LOG_DEBUG(...) do {                        \
+      fprintf(stdout, " # %s(): ", __func__);                   \
+      fprintf(stdout, __VA_ARGS__);                             \
+      fprintf(stdout, "\n");                                    \
+      fflush(stdout);                                           \
+  } while (0)
+#else
+#define H5X_FASTBIT_LOG_DEBUG
+#endif
+
+/******************/
+/* Local Typedefs */
+/******************/
+typedef struct H5X_fastbit_t {
+    void *private_metadata;     /* Internal metadata */
+
+    hid_t opaque_type_id;       /* Datatype used for index datasets */
+    hid_t metadata_id;          /* Array for metadata */
+    hid_t index_id;             /* Array for index data */
+} H5X_fastbit_t;
+
+/********************/
+/* Local Prototypes */
+/********************/
+
+static void *
+H5X_fastbit_create(hid_t file_id, hid_t dataset_id, hid_t xcpl_id,
+        hid_t xapl_id, size_t *metadata_size, void **metadata);
+
+static herr_t
+H5X_fastbit_remove(hid_t file_id, hid_t dataset_id, size_t metadata_size,
+        void *metadata);
+
+static void *
+H5X_fastbit_open(hid_t file_id, hid_t dataset_id, hid_t xapl_id,
+        size_t metadata_size, void *metadata);
+
+static herr_t
+H5X_fastbit_close(void *idx_handle);
+
+static herr_t
+H5X_fastbit_pre_update(void *idx_handle, hid_t dataspace_id, hid_t xxpl_id);
+
+static herr_t
+H5X_fastbit_post_update(void *idx_handle, const void *buf, hid_t dataspace_id,
+        hid_t xxpl_id);
+
+static herr_t
+H5X_fastbit_query(void *idx_handle, hid_t query_id, hid_t xxpl_id,
+        hid_t *dataspace_id);
+
+/*********************/
+/* Package Variables */
+/*********************/
+
+/*****************************/
+/* Library Private Variables */
+/*****************************/
+
+
+/*******************/
+/* Local Variables */
+/*******************/
+
+/* Alacrity index class */
+const H5X_class_t H5X_FASTBIT[1] = {{
+    H5X_CLASS_T_VERS,          /* (From the H5Xpublic.h header file) */
+    H5X_PLUGIN_FASTBIT,        /* (Or whatever number is assigned) */
+    "FASTBIT index plugin",    /* Whatever name desired */
+    H5X_TYPE_DATA_ELEM,        /* This plugin operates on dataset elements */
+    H5X_fastbit_create,        /* create */
+    H5X_fastbit_remove,        /* remove */
+    H5X_fastbit_open,          /* open */
+    H5X_fastbit_close,         /* close */
+    H5X_fastbit_pre_update,    /* pre_update */
+    H5X_fastbit_post_update,   /* post_update */
+    H5X_fastbit_query          /* query */
+}};
+
+
+/*-------------------------------------------------------------------------
+ * Function:    H5X_fastbit_create
+ *
+ * Purpose: This function creates a new instance of a FASTBIT plugin index.
+ *
+ * Return:  Success:    Pointer to the new index
+ *          Failure:    NULL
+ *
+ *------------------------------------------------------------------------
+ */
+static void *
+H5X_fastbit_create(hid_t file_id, hid_t dataset_id, hid_t UNUSED xcpl_id,
+        hid_t xapl_id, size_t *metadata_size, void **metadata)
+{
+    H5X_fastbit_t *fastbit = NULL;
+    void *ret_value = NULL; /* Return value */
+
+    FUNC_ENTER_NOAPI_NOINIT
+    H5X_FASTBIT_LOG_DEBUG("Enter");
+
+done:
+    H5X_FASTBIT_LOG_DEBUG("Leave");
+    FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5X_fastbit_create() */
+
+/*-------------------------------------------------------------------------
+ * Function:    H5X_fastbit_remove
+ *
+ * Purpose: This function removes the FASTBIT plugin index from the file.
+ *
+ * Return:  Non-negative on success/Negative on failure
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5X_fastbit_remove(hid_t UNUSED file_id, hid_t UNUSED dataset_id,
+        size_t UNUSED metadata_size, void UNUSED *metadata)
+{
+    herr_t ret_value = SUCCEED; /* Return value */
+
+    FUNC_ENTER_NOAPI_NOINIT_NOERR
+    H5X_FASTBIT_LOG_DEBUG("Enter");
+
+    H5X_FASTBIT_LOG_DEBUG("Leave");
+    FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5X_fastbit_remove() */
+
+/*-------------------------------------------------------------------------
+ * Function:    H5X_fastbit_open
+ *
+ * Purpose: This function opens an already existing FASTBIT index from a file.
+ *
+ * Return:  Success:    Pointer to the index
+ *          Failure:    NULL
+ *
+ *-------------------------------------------------------------------------
+ */
+static void *
+H5X_fastbit_open(hid_t file_id, hid_t dataset_id, hid_t xapl_id,
+        size_t metadata_size, void *metadata)
+{
+    H5X_fastbit_t *fastbit = NULL;
+    void *ret_value = NULL; /* Return value */
+
+    FUNC_ENTER_NOAPI_NOINIT
+    H5X_FASTBIT_LOG_DEBUG("Enter");
+
+done:
+    H5X_FASTBIT_LOG_DEBUG("Leave");
+    FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5X_fastbit_open() */
+
+/*-------------------------------------------------------------------------
+ * Function:    H5X_fastbit_close
+ *
+ * Purpose: This function closes an FASTBIT index.
+ *
+ * Return:  Non-negative on success/Negative on failure
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5X_fastbit_close(void *idx_handle)
+{
+    H5X_fastbit_t *fastbit = (H5X_fastbit_t *) idx_handle;
+    herr_t ret_value = SUCCEED; /* Return value */
+
+    FUNC_ENTER_NOAPI_NOINIT
+    H5X_FASTBIT_LOG_DEBUG("Enter");
+
+    if (NULL == fastbit)
+        HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "NULL index handle");
+
+done:
+    H5X_FASTBIT_LOG_DEBUG("Leave");
+    FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5X_fastbit_close() */
+
+/*-------------------------------------------------------------------------
+ * Function:    H5X_fastbit_pre_update
+ *
+ * Purpose: This function does a pre_update of indexing information.
+ *
+ * Return:  Non-negative on success/Negative on failure
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5X_fastbit_pre_update(void *idx_handle, hid_t UNUSED dataspace_id, hid_t UNUSED xxpl_id)
+{
+    H5X_fastbit_t *fastbit = (H5X_fastbit_t *) idx_handle;
+    herr_t ret_value = SUCCEED; /* Return value */
+
+    FUNC_ENTER_NOAPI_NOINIT
+    H5X_FASTBIT_LOG_DEBUG("Enter");
+
+    if (NULL == fastbit)
+        HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "NULL index handle");
+
+done:
+    H5X_FASTBIT_LOG_DEBUG("Leave");
+    FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5X_fastbit_pre_update() */
+
+/*-------------------------------------------------------------------------
+ * Function:    H5X_fastbit_post_update
+ *
+ * Purpose: This function does a post_update of indexing information.
+ *
+ * Return:  Non-negative on success/Negative on failure
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5X_fastbit_post_update(void *idx_handle, const void UNUSED *buf,
+        hid_t UNUSED dataspace_id, hid_t UNUSED xxpl_id)
+{
+    H5X_fastbit_t *fastbit = (H5X_fastbit_t *) idx_handle;
+    herr_t ret_value = SUCCEED; /* Return value */
+
+    FUNC_ENTER_NOAPI_NOINIT
+
+    H5X_FASTBIT_LOG_DEBUG("Calling H5X_fastbit_post_update");
+
+    if (NULL == fastbit)
+        HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "NULL index handle");
+
+done:
+    H5X_FASTBIT_LOG_DEBUG("Leave");
+    FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5X_fastbit_post_update() */
+
+/*-------------------------------------------------------------------------
+ * Function:    H5X_fastbit_query
+ *
+ * Purpose: This function retrieves indexing information that matches
+ * the query and returns results under the form of a dataspace ID.
+ *
+ * Return:  Non-negative on success/Negative on failure
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5X_fastbit_query(void *idx_handle, hid_t query_id, hid_t xxpl_id,
+        hid_t *dataspace_id)
+{
+    H5X_fastbit_t *fastbit = (H5X_fastbit_t *) idx_handle;
+    herr_t ret_value = SUCCEED; /* Return value */
+
+    FUNC_ENTER_NOAPI_NOINIT
+    H5X_FASTBIT_LOG_DEBUG("Enter");
+
+
+done:
+    H5X_FASTBIT_LOG_DEBUG("Leave");
+    FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5X_fastbit_query() */
+
+#endif /* H5_HAVE_FASTBIT */
diff --git a/src/H5Xpkg.h b/src/H5Xpkg.h
index fc3cfc8..04f7385 100644
--- a/src/H5Xpkg.h
+++ b/src/H5Xpkg.h
@@ -28,10 +28,17 @@
 H5_DLLVAR const H5X_class_t H5X_DUMMY[1];
 
 /*
- * Alacrity plugin
+ * ALACRITY plugin
  */
 #ifdef H5_HAVE_ALACRITY
 H5_DLLVAR const H5X_class_t H5X_ALACRITY[1];
 #endif
 
+/*
+ * FastBit plugin
+ */
+#ifdef H5_HAVE_FASTBIT
+H5_DLLVAR const H5X_class_t H5X_FASTBIT[1];
+#endif
+
 #endif /* _H5Xpkg_H */
diff --git a/src/Makefile.am b/src/Makefile.am
index feb9518..051ba37 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -90,7 +90,7 @@ libhdf5_la_SOURCES= H5.c H5checksum.c H5dbg.c H5system.c H5timer.c H5trace.c \
         H5Osdspace.c H5Oshared.c H5Ostab.c \
         H5Oshmesg.c H5Otest.c H5Ounknown.c \
         H5P.c H5Pacpl.c H5Pdapl.c H5Pdcpl.c \
-        H5Pxapl.c H5Pxcpl.c H5Pxxpl.c H5X.c H5Xdummy.c H5Xalacrity.c \
+        H5Pxapl.c H5Pxcpl.c H5Pxxpl.c H5X.c H5Xdummy.c H5Xalacrity.c H5Xfastbit.c \
         H5Pdeprec.c H5Pdxpl.c H5Pencdec.c \
         H5Pfapl.c H5Pfcpl.c H5Pfmpl.c \
         H5Pgcpl.c H5Pvcpl.c H5Pmcpl.c H5Pmapl.c H5Pint.c H5Prcapl.c H5Ptrspl.c H5Ptrfpl.c \