Merge pull request #826 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to develop

* commit 'e94ed99c5bf7c4ae5df56f75606ef1b486e16bb2':
  Add HD prefix
  HDFFV-9724 Remove VDS file cache functionality
  Removed incorrect MPI text
  Par example needs to link with mpi libs
  Because of MPI requirements in library ALWAYS add include path
  Cleanup comments and if() in TRY blocks
  Skip test if 1.6 API
  HDFFV-9724 Add ENV VAR to vds test
  HDFFV-9724 Copy efc_open search from Lextern_traverse
  Add prefix dir to the clear command
  HDFFV-9724 Add H5LS prefix test with ${ORIGIN}
  Add h5dump VDS prefix tests
  HDFFV-9724 combine efc and vds into one function
  Correct var name
  Fix VDS file cache var names
  Remove return from void functions
  Added java wrappers and tests
  HDFFV-9724 Initial changes and test
  Changed reference from dl to CMake variable
  H5detect and H5make_libsettings need include folder

1 files changed, 366 insertions, 0 deletions

diff --git a/src/H5Pdapl.c b/src/H5Pdapl.c
index 494de3e..da06297 100644
--- a/src/H5Pdapl.c
+++ b/src/H5Pdapl.c
@@ -71,6 +71,17 @@
 #define H5D_ACS_VDS_PRINTF_GAP_DEF              (hsize_t)0
 #define H5D_ACS_VDS_PRINTF_GAP_ENC              H5P__encode_hsize_t
 #define H5D_ACS_VDS_PRINTF_GAP_DEC              H5P__decode_hsize_t
+/* Definitions for VDS file prefix */
+#define H5D_ACS_VDS_PREFIX_SIZE                 sizeof(char *)
+#define H5D_ACS_VDS_PREFIX_DEF                  NULL /*default is no prefix */
+#define H5D_ACS_VDS_PREFIX_SET                  H5P__dapl_vds_file_pref_set
+#define H5D_ACS_VDS_PREFIX_GET                  H5P__dapl_vds_file_pref_get
+#define H5D_ACS_VDS_PREFIX_ENC                  H5P__dapl_vds_file_pref_enc
+#define H5D_ACS_VDS_PREFIX_DEC                  H5P__dapl_vds_file_pref_dec
+#define H5D_ACS_VDS_PREFIX_DEL                  H5P__dapl_vds_file_pref_del
+#define H5D_ACS_VDS_PREFIX_COPY                 H5P__dapl_vds_file_pref_copy
+#define H5D_ACS_VDS_PREFIX_CMP                  H5P__dapl_vds_file_pref_cmp
+#define H5D_ACS_VDS_PREFIX_CLOSE                H5P__dapl_vds_file_pref_close
 /* Definition for append flush */
 #define H5D_ACS_APPEND_FLUSH_SIZE               sizeof(H5D_append_flush_t)
 #define H5D_ACS_APPEND_FLUSH_DEF                {0,{0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0},NULL,NULL}
@@ -112,6 +123,14 @@ static herr_t H5P__decode_chunk_cache_nbytes(const void **_pp, void *_value);
 /* Property list callbacks */
 static herr_t H5P__dacc_vds_view_enc(const void *value, void **pp, size_t *size);
 static herr_t H5P__dacc_vds_view_dec(const void **pp, void *value);
+static herr_t H5P__dapl_vds_file_pref_set(hid_t prop_id, const char* name, size_t size, void* value);
+static herr_t H5P__dapl_vds_file_pref_get(hid_t prop_id, const char* name, size_t size, void* value);
+static herr_t H5P__dapl_vds_file_pref_enc(const void *value, void **_pp, size_t *size);
+static herr_t H5P__dapl_vds_file_pref_dec(const void **_pp, void *value);
+static herr_t H5P__dapl_vds_file_pref_del(hid_t prop_id, const char* name, size_t size, void* value);
+static herr_t H5P__dapl_vds_file_pref_copy(const char* name, size_t size, void* value);
+static int H5P__dapl_vds_file_pref_cmp(const void *value1, const void *value2, size_t size);
+static herr_t H5P__dapl_vds_file_pref_close(const char* name, size_t size, void* value);
 
 /* Property list callbacks */
 static herr_t H5P__dapl_efile_pref_set(hid_t prop_id, const char* name, size_t size, void* value);
@@ -160,6 +179,7 @@ const H5P_libclass_t H5P_CLS_DACC[1] = {{
 /* Property value defaults */
 static const H5D_append_flush_t H5D_def_append_flush_g = H5D_ACS_APPEND_FLUSH_DEF;   /* Default setting for append flush */
 static const char *H5D_def_efile_prefix_g = H5D_ACS_EFILE_PREFIX_DEF;                /* Default external file prefix string */
+static const char *H5D_def_vds_prefix_g = H5D_ACS_VDS_PREFIX_DEF;                    /* Default vds prefix string */
 
 
 /*-------------------------------------------------------------------------
@@ -210,6 +230,12 @@ H5P__dacc_reg_prop(H5P_genclass_t *pclass)
             NULL, NULL, NULL, NULL) < 0)
         HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class")
 
+    /* Register property for vds prefix */
+    if(H5P_register_real(pclass, H5D_ACS_VDS_PREFIX_NAME, H5D_ACS_VDS_PREFIX_SIZE, &H5D_def_vds_prefix_g,
+            NULL, H5D_ACS_VDS_PREFIX_SET, H5D_ACS_VDS_PREFIX_GET, H5D_ACS_VDS_PREFIX_ENC, H5D_ACS_VDS_PREFIX_DEC,
+            H5D_ACS_VDS_PREFIX_DEL, H5D_ACS_VDS_PREFIX_COPY, H5D_ACS_VDS_PREFIX_CMP, H5D_ACS_VDS_PREFIX_CLOSE) < 0)
+         HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class")
+
     /* Register info for append flush */
     /* (Note: this property should not have an encode/decode callback -QAK) */
     if(H5P_register_real(pclass, H5D_ACS_APPEND_FLUSH_NAME, H5D_ACS_APPEND_FLUSH_SIZE, &H5D_def_append_flush_g,
@@ -226,6 +252,254 @@ done:
     FUNC_LEAVE_NOAPI(ret_value)
 } /* end H5P__dacc_reg_prop() */
 
+
+/*-------------------------------------------------------------------------
+ * Function:    H5P__dapl_vds_file_pref_set
+ *
+ * Purpose:     Copies a vds file prefix property when it's set
+ *              for a property list
+ *
+ * Return:      SUCCEED/FAIL
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5P__dapl_vds_file_pref_set(hid_t H5_ATTR_UNUSED prop_id, const char H5_ATTR_UNUSED *name,
+    size_t H5_ATTR_UNUSED size, void *value)
+{
+    FUNC_ENTER_STATIC_NOERR
+
+    /* Sanity check */
+    HDassert(value);
+
+    /* Copy the prefix */
+    *(char **)value = H5MM_xstrdup(*(const char **)value);
+
+    FUNC_LEAVE_NOAPI(SUCCEED)
+} /* end H5P__dapl_vds_file_pref_set() */
+
+
+/*-------------------------------------------------------------------------
+ * Function:    H5P__dapl_vds_file_pref_get
+ *
+ * Purpose:     Copies a vds file prefix property when it's retrieved
+ *              from a property list
+ *
+ * Return:      SUCCEED/FAIL
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5P__dapl_vds_file_pref_get(hid_t H5_ATTR_UNUSED prop_id, const char H5_ATTR_UNUSED *name,
+    size_t H5_ATTR_UNUSED size, void *value)
+{
+    FUNC_ENTER_STATIC_NOERR
+
+    /* Sanity check */
+    HDassert(value);
+
+    /* Copy the prefix */
+    *(char **)value = H5MM_xstrdup(*(const char **)value);
+
+    FUNC_LEAVE_NOAPI(SUCCEED)
+} /* end H5P__dapl_vds_file_pref_get() */
+
+
+/*-------------------------------------------------------------------------
+ * Function:    H5P__dapl_vds_file_pref_enc
+ *
+ * Purpose:     Callback routine which is called whenever the vds file flags
+ *              property in the dataset access property list is
+ *              encoded.
+ *
+ * Return:      SUCCEED/FAIL
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5P__dapl_vds_file_pref_enc(const void *value, void **_pp, size_t *size)
+{
+    const char *vds_file_pref = *(const char * const *)value;
+    uint8_t **pp = (uint8_t **)_pp;
+    size_t len = 0;
+    uint64_t enc_value;
+    unsigned enc_size;
+
+    FUNC_ENTER_NOAPI_NOINIT_NOERR
+
+    HDcompile_assert(sizeof(size_t) <= sizeof(uint64_t));
+
+    /* calculate prefix length */
+    if(NULL != vds_file_pref)
+        len = HDstrlen(vds_file_pref);
+
+    enc_value = (uint64_t)len;
+    enc_size = H5VM_limit_enc_size(enc_value);
+    HDassert(enc_size < 256);
+
+    if(NULL != *pp) {
+        /* encode the length of the prefix */
+        *(*pp)++ = (uint8_t)enc_size;
+        UINT64ENCODE_VAR(*pp, enc_value, enc_size);
+
+        /* encode the prefix */
+        if(NULL != vds_file_pref) {
+            HDmemcpy(*(char **)pp, vds_file_pref, len);
+            *pp += len;
+        } /* end if */
+    } /* end if */
+
+    *size += (1 + enc_size);
+    if(NULL != vds_file_pref)
+        *size += len;
+
+    FUNC_LEAVE_NOAPI(SUCCEED)
+} /* end H5P__dapl_vds_file_pref_enc() */
+
+
+/*-------------------------------------------------------------------------
+ * Function:    H5P__dapl_vds_file_pref_dec
+ *
+ * Purpose:     Callback routine which is called whenever the vds file prefix
+ *              property in the dataset access property list is
+ *              decoded.
+ *
+ * Return:      SUCCEED/FAIL
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5P__dapl_vds_file_pref_dec(const void **_pp, void *_value)
+{
+    char **vds_file_pref = (char **)_value;
+    const uint8_t **pp = (const uint8_t **)_pp;
+    size_t len;
+    uint64_t enc_value;                 /* Decoded property value */
+    unsigned enc_size;                  /* Size of encoded property */
+    herr_t ret_value = SUCCEED;
+
+    FUNC_ENTER_NOAPI_NOINIT
+
+    HDassert(pp);
+    HDassert(*pp);
+    HDassert(vds_file_pref);
+    HDcompile_assert(sizeof(size_t) <= sizeof(uint64_t));
+
+    /* Decode the size */
+    enc_size = *(*pp)++;
+    HDassert(enc_size < 256);
+
+    /* Decode the value */
+    UINT64DECODE_VAR(*pp, enc_value, enc_size);
+    len = (size_t)enc_value;
+
+    if(0 != len) {
+        /* Make a copy of the user's prefix string */
+        if(NULL == (*vds_file_pref = (char *)H5MM_malloc(len + 1)))
+            HGOTO_ERROR(H5E_RESOURCE, H5E_CANTINIT, FAIL, "memory allocation failed for prefix")
+        HDstrncpy(*vds_file_pref, *(const char **)pp, len);
+        (*vds_file_pref)[len] = '\0';
+
+        *pp += len;
+    } /* end if */
+    else
+        *vds_file_pref = NULL;
+
+done:
+    FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5P__dapl_vds_file_pref_dec() */
+
+
+/*-------------------------------------------------------------------------
+ * Function:    H5P__dapl_vds_file_pref_del
+ *
+ * Purpose:     Frees memory used to store the vds file prefix string
+ *
+ * Return:      SUCCEED (Can't fail)
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5P__dapl_vds_file_pref_del(hid_t H5_ATTR_UNUSED prop_id, const char H5_ATTR_UNUSED *name,
+    size_t H5_ATTR_UNUSED size, void *value)
+{
+    FUNC_ENTER_NOAPI_NOINIT_NOERR
+
+    HDassert(value);
+
+    H5MM_xfree(*(void **)value);
+
+    FUNC_LEAVE_NOAPI(SUCCEED)
+} /* end H5P__dapl_vds_file_pref_del() */
+
+
+/*-------------------------------------------------------------------------
+ * Function:    H5P__dapl_vds_file_pref_copy
+ *
+ * Purpose:     Creates a copy of the vds file prefix string
+ *
+ * Return:      SUCCEED/FAIL
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5P__dapl_vds_file_pref_copy(const char H5_ATTR_UNUSED *name, size_t H5_ATTR_UNUSED size, void *value)
+{
+    FUNC_ENTER_NOAPI_NOINIT_NOERR
+
+    HDassert(value);
+
+    *(char **)value = H5MM_xstrdup(*(const char **)value);
+
+    FUNC_LEAVE_NOAPI(SUCCEED)
+} /* end H5P__dapl_vds_file_pref_copy() */
+
+
+/*-------------------------------------------------------------------------
+ * Function:       H5P__dapl_vds_file_pref_cmp
+ *
+ * Purpose:        Callback routine which is called whenever the vds file prefix
+ *                 property in the dataset creation property list is
+ *                 compared.
+ *
+ * Return:         zero if VALUE1 and VALUE2 are equal, non zero otherwise.
+ *-------------------------------------------------------------------------
+ */
+static int
+H5P__dapl_vds_file_pref_cmp(const void *value1, const void *value2, size_t H5_ATTR_UNUSED size)
+{
+    const char *pref1 = *(const char * const *)value1;
+    const char *pref2 = *(const char * const *)value2;
+    int ret_value = 0;
+
+    FUNC_ENTER_NOAPI_NOINIT_NOERR
+
+    if(NULL == pref1 && NULL != pref2)
+        HGOTO_DONE(1);
+    if(NULL != pref1 && NULL == pref2)
+        HGOTO_DONE(-1);
+    if(NULL != pref1 && NULL != pref2)
+        ret_value = HDstrcmp(pref1, pref2);
+
+done:
+    FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5P__dapl_vds_file_pref_cmp() */
+
+
+/*-------------------------------------------------------------------------
+ * Function:    H5P__dapl_vds_file_pref_close
+ *
+ * Purpose:     Frees memory used to store the vds file prefix string
+ *
+ * Return:      SUCCEED/FAIL
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5P__dapl_vds_file_pref_close(const char H5_ATTR_UNUSED *name, size_t H5_ATTR_UNUSED size, void *value)
+{
+    FUNC_ENTER_NOAPI_NOINIT_NOERR
+
+    HDassert(value);
+
+    H5MM_xfree(*(void **)value);
+
+    FUNC_LEAVE_NOAPI(SUCCEED)
+} /* end H5P__dapl_vds_file_pref_close() */
+
 
 /*-------------------------------------------------------------------------
  * Function:    H5P__dapl_efile_pref_set
@@ -1220,3 +1494,95 @@ done:
     FUNC_LEAVE_API(ret_value)
 } /* end H5Pget_efile_prefix() */
 
+
+/*-------------------------------------------------------------------------
+ * Function:    H5Pset_virtual_prefix
+ *
+ * Purpose:     Set a prefix to be applied to the path of any vds files
+ *              traversed.
+  *
+ *              If the prefix starts with ${ORIGIN}, this will be replaced by
+ *              the absolute path of the directory of the HDF5 file containing
+ *              the dataset.
+ *
+ *              If the prefix is ".", no prefix will be applied.
+ *
+ *              This property can be overwritten by the environment variable
+ *              HDF5_VDS_PREFIX.
+ *
+ * Return:    Non-negative on success/Negative on failure
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5Pset_virtual_prefix(hid_t plist_id, const char *prefix)
+{
+    H5P_genplist_t *plist;              /* Property list pointer */
+    herr_t ret_value = SUCCEED;         /* Return value */
+
+    FUNC_ENTER_API(FAIL)
+    H5TRACE2("e", "i*s", plist_id, prefix);
+
+    /* Get the plist structure */
+    if(NULL == (plist = H5P_object_verify(plist_id, H5P_DATASET_ACCESS)))
+        HGOTO_ERROR(H5E_ATOM, H5E_BADATOM, FAIL, "can't find object for ID")
+
+    /* Set prefix */
+    if(H5P_set(plist, H5D_ACS_VDS_PREFIX_NAME, &prefix) < 0)
+        HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set prefix info")
+
+done:
+    FUNC_LEAVE_API(ret_value)
+} /* end H5Pset_virtual_prefix() */
+
+
+/*-------------------------------------------------------------------------
+ * Function:    H5Pget_virtual_prefix
+ *
+ * Purpose:    Gets the prefix to be applied to any vds file
+ *              traversals made using this property list.
+ *
+ *              If the pointer is not NULL, it points to a user-allocated
+ *              buffer.
+ *
+ * Return:    Non-negative on success/Negative on failure
+ *-------------------------------------------------------------------------
+ */
+ssize_t
+H5Pget_virtual_prefix(hid_t plist_id, char *prefix, size_t size)
+{
+    H5P_genplist_t *plist;              /* Property list pointer */
+    char           *my_prefix;          /* Library's copy of the prefix */
+    size_t          len;                /* Length of prefix string */
+    ssize_t         ret_value;          /* Return value */
+
+    FUNC_ENTER_API(FAIL)
+    H5TRACE3("Zs", "i*sz", plist_id, prefix, size);
+
+    /* Get the plist structure */
+    if(NULL == (plist = H5P_object_verify(plist_id, H5P_DATASET_ACCESS)))
+        HGOTO_ERROR(H5E_ATOM, H5E_BADATOM, FAIL, "can't find object for ID")
+
+    /* Get the current prefix */
+    if(H5P_peek(plist, H5D_ACS_VDS_PREFIX_NAME, &my_prefix) < 0)
+        HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't get vds file prefix")
+
+    /* Check for prefix being set */
+    if(my_prefix) {
+        /* Copy to user's buffer, if given */
+        len = HDstrlen(my_prefix);
+        if(prefix) {
+            HDstrncpy(prefix, my_prefix, MIN(len + 1, size));
+            if(len >= size)
+                prefix[size - 1] = '\0';
+        } /* end if */
+    } /* end if */
+    else
+        len = 0;
+
+    /* Set return value */
+    ret_value = (ssize_t)len;
+
+done:
+    FUNC_LEAVE_API(ret_value)
+} /* end H5Pget_virtual_prefix() */
+