Bring async branch to develop (#166)

* Add H5Fwait, H5Dwait, and other changes for async vol connector

* Revert temporary testing changes

* Add H5Fwait to header file

* Add H5VLreset_lib_state() routine.

* Correct VOL wrap context when retrieving library state for file open & create.

* Manage the API context's VOL connector state as part of the library state.

* Set the 'VOL connector property valid' flag when restoring the library state.

* Don't push new API context on stack when retrieving "current" one.

* Check for NULL VOL wrap context before decrementing refcount on it, when
freeing the API context state.

* Manage recount of underlying connector for VOL wrap context.

* Add H5TSmutex_acquire() and H5TSmutex_release() routines to acquire and
release the global lock on the HDF5 library.

* Update library with new functions related to library global lock

* Add asynchronous token API

* Add new lightweight FUNC_ENTER / LEAVE macros for helping to structure the
threadsafety (H5TS*) routines.

* Sync w/develop

* Initial event set code framework.

* Elaborate on the H5ES routines, starting to add API routines.

Update the "close ID" callbacks to allow asynchronous request tokens to be
passed in from an asynchronous close API call.

Refactor current asynchronous API routines (H5Fopen/H5Fclose and
H5Dread/H5Dread) to use event sets instead of directly working with request
tokens from the application.

Clean up a few other minor warnings & code style issues.

* Implement H5EScreate, H5ESget_count, and H5ESclose.

It should be possible to write a simple application that creates an event
set and uses it with H5Fopen_async, H5Dread_async, H5Dwrite_async, and
H5Fclose_async, then calls H5ESclose (which waits for all async events to
complete).

* Add source file for event set test.

* Refactor sync & async API routines to call common routine.

Move dataset API read / write routines to src/H5D.c, along with all the other
API routines.

Progress on "fake" async VOL connector, for testing.

* Modify async implementation to wrap async requests in a H5VL_object_t
struct so the VOL layer can find the connector when accessing the
request at a later point.

* Free the requests is H5ESclose.  Remove comments implying that request
wait, notify, and cancel callbacks should free the request.

* Fix bug in error handling in H5Fclose.

* Fix bugs in async file routines.  Rename H5VL_create_object_generic to
H5VL_create_object.

* Add explicit async version of H5Fcreate.

* Add more _async routines

* Correct typo for return value from H5Awrite changes

* Add H5EStest and H5ESwait routines

* Updated with API tracing info

* Fix NULL pointer dereference in H5ES__wait

* Add H5is_library_terminating() routine, so that VOL connectors can detect
when the library is shutting down.

* Fix typo

* Remove event from event set's linked list

* Move block of code so that vol_obj is valid

* Avoid setting properties in the DXPL when reseting the library state (and in
the test code).

* Refactor argument tracing to implement new capability for tracing arguments
of non-API routines, with the H5ARG_TRACE macro.   This macro is updated
automatically with the bin/trace script that runs as part of the autogen.sh
process.   Major changes were in src/H5trace.c and bin/trace, with the other
changes being cleanups to the argument lists, to improve their presentation
in the tracing output.

Also - added the "managed string" routines, which can dynamically allocate
strings, appending printf-formatted output to the string efficiently.

* Release memory for managed strings

* Fix printf() formats.

* More printf() format fixes.

* Add H5Eappend_stack routine and regression tests

* Clean up a few missed merge conflicts and update the error stacks.

* Remove unnecessary fork() operations and ten second sleep().

* Restore commented out attribute out, to better enable tracking down the previous failure

* Allow multiple H5ARG_TRACE macros within a routine to be updated

* Switch to using "new" H5ES_insert (which takes the arguments for the caller routine) for all event set operations.  Renames H5ES_insert_new to H5ES_insert and removes the previous H5ES_insert.

* Merge "managed" string routines into "ref-counted" strings, and refactor code to use them.

* Add missing file.

* Add caller's name and arguments to event, for error reporting

* Refactor event set setup for "API common" internal routines

* Checkin async API routines for H5A* and H5G* modules as listed in ID-283.
Fix couple h5dump expected output files due to the changes.

* Add some of the error query routines needed for event sets.

* Refactor to make async setup / teardown and "common" routines cleaner

* (1) Add async APIs to H5L, H5F, and H5D modules
(2) Fix errors in previous checkins of async APIs in H5A and H5G modules
(3) h5dump expected output changes

* Enhance event info, for better error handling

* Change name of temporary vol_obj variable, to help reduce coding errors

* Fix oversight with vol_obj pointer

* Minor code cleanup

* Add missing \'valid\' flag for VOL wrapper context, when restoring the library\'s state

* Run source formatter

* Change H5TSmutex lock and release to include a lock count

* Update error reporting ideas

* Minor updates to improve sanity checking for retrieving / restoring library state

* Updated with feedback from h5py team members

* Refactor internal event set list and event handling, add implementation for H5ESget_err_info

* Change the VOL request subclass callbacks that switch from using "H5ES_status_t" to "H5VL_request_status_t", and also add a H5VL_request_status_t* parameter to the 'cancel' callback in the request subclass.  Also more code quality cleanups to add iterator callbacks to internal event set routines.

* Update API tracing for new H5VL_request_status_t typedef

* Finish converting internal event set operations to use list iterator callbacks, instead of directly accessing the list structure

* Add H5VL_REQUEST_GET_ERR_STACK operation to request subclass, for retrieving a copy of the error stack for a failed asynchronous operation

* Remove 'canceled' event status from Java constants

* Be safer about releasing resources when inserting a newly opened/created object or file into an event set

* Remove H5EStest, add H5ES_WAIT_NONE for 0 timeout, and revise parameters to H5ESwait, to make it more "aggregate".

* Remove H5ES_STATUS_CANCELED from Java wrappers also

* (a) Add async APIs for H5O module as listed in jira issue ID-283.
(b) Remove verification of name parameter in async related routines for H55A and H5L modules
    because it is checked in H5VL_setup* routine.
(c) Modify h5dump expected output due to the async changes.

* Corrections based on PR feedback.

* Further changes to make based on PR feedback.

* Fix missed merge marker, and reformatted line

* Clean up some warnings

* Correct level of indirection

* Relocate prototype (and doxygen info) for H5Aclose

* Change non-static function declarations to be static

* Ensure that H5TSpublic.h header gets installed (#129)

* Add 'wrapper' versions of async calls, to allow language wrappers and layers on top of HDF5 to pass in their application information.

* Switch H5Aexists\*_async and H5Lexists\*_async to use flag to return status, instead of return value.  Make the corresponding changes through most of the v1 and v2 B-tree code.  Clean up warnings in H5public.h and cmpd_dtransform.c.

* Add H5Iregister_future routine and tests.

* Correct return value for H5Lexists_async

* Add H5_DLL macro to public H5ES API routines

* Update supported -> flags parameter for introspect_query callback

* Remove my email address.  Update passthrough VOL connector ID.

* Fix comment for post_open_api_common

* Remove unused non-blocking VOL connector

* Minor cleanup in async branch in preparation for merge to develop

* Update CMake and the Autotools to use the new pass-through VOL ID

* Fix for SWMR daily test failures (#160)

The H5I_register_using_existing_id() call did not initialize the future
ID callbacks, causing the library to segfault when it tried to
resolve those function pointers.

* Added selective async APIs (#150)

* Added selective async APIs

Description:
    Added the following APIs:
        H5Ropen_attr_async
        H5Ropen_object_async
        H5Ropen_region_async

        H5Mcreate_async
        H5Mopen_async
        H5Mput_async
        H5Mget_async
        H5Mclose_async

        H5Tcommit_async
        H5Topen_async
        H5Tcopy_async
        H5Tclose_async
    - Updated an expected output file to include a new internal function
      in the error stack for the failure case.

* Updated async APIs per reviews, including removing async version of
H5Tcopy.

* Removed statements that were added by mistake in the previous commit.

* Fix compile issues in H5M and warnings elsewhere

* Reformat code

* Brings VOL_LIST changes from develop. (#163)

Co-authored-by: Houjun Tang <htang4@lbl.gov>
Co-authored-by: Neil Fortner <nfortne2@hdfgroup.org>
Co-authored-by: vchoi <vchoi@jelly.ad.hdfgroup.org>
Co-authored-by: vchoi-hdfgroup <55293060+vchoi-hdfgroup@users.noreply.github.com>
Co-authored-by: jhendersonHDF <jhenderson@hdfgroup.org>
Co-authored-by: Dana Robinson <derobins@hdfgroup.org>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: bmribler <39579120+bmribler@users.noreply.github.com>

MANIFEST

@@ -685,6 +685,13 @@
 ./src/H5EAsblock.c
 ./src/H5EAstat.c
 ./src/H5EAtest.c
+./src/H5ES.c
+./src/H5ESevent.c
+./src/H5ESint.c
+./src/H5ESlist.c
+./src/H5ESmodule.h
+./src/H5ESpkg.h
+./src/H5ESprivate.h
 ./src/H5ESpublic.h
 ./src/H5F.c
 ./src/H5Faccum.c
@@ -1015,6 +1022,7 @@
 ./src/H5Tvlen.c
 ./src/H5TS.c
 ./src/H5TSprivate.h
+./src/H5TSpublic.h
 ./src/H5UC.c
 ./src/H5UCprivate.h
 ./src/H5VL.c
@@ -1115,6 +1123,7 @@
 ./test/enum.c
 ./test/err_compat.c
 ./test/error_test.c
+./test/event_set.c
 ./test/evict_on_close.c
 ./test/extend.c
 ./test/external.c

bin/trace

@@ -79,10 +79,12 @@ $Source = "";
                "H5E_major_t"                => "i",     # H5E_major_t is typedef'd to hid_t
                "H5E_minor_t"                => "i",     # H5E_minor_t is typedef'd to hid_t
                "hid_t"                      => "i",
+               "H5I_future_discard_func_t"  => "ID",
                "H5I_free_t"                 => "If",
                "H5_index_t"                 => "Ii",
                "H5I_iterate_func_t"         => "II",
                "H5_iter_order_t"            => "Io",
+               "H5I_future_realize_func_t"  => "IR",
                "int"                        => "Is",
                "int32_t"                    => "Is",
                "H5I_search_func_t"          => "IS",

c++/test/th5s.cpp

@@ -33,7 +33,7 @@ using namespace H5;
 
 #include "h5test.h"
 #include "h5cpputil.h" // C++ utilility header file
-#include "H5srcdir.h"  // srcdir querying header file
+#include "H5srcdir.h" // srcdir querying header file
 
 const H5std_string TESTFILE("th5s.h5");
 const H5std_string DATAFILE("th5s1.h5");

hl/tools/gif2h5/gifread.c

@@ -354,7 +354,7 @@ ReadDataSubBlocks(GIFBYTE **MemGif2, /* GIF image file input FILE stream
 #ifdef COMMENTED_OUT
         *ptr1++ = dataSize; /* Write the data count */
 #endif                      /* COMMENTED_OUT */
-        while (dataSize--)  /* Read/write the Plain Text data */
+        while (dataSize--) /* Read/write the Plain Text data */
             *ptr1++ = *(*MemGif2)++;
 
         /* Check if there is another data sub-block */

hl/tools/gif2h5/hdfgifwr.c

@@ -73,7 +73,7 @@ static unsigned long cur_accum = 0;
 static int           cur_bits  = 0;
 
 #define MAXCODE(n_bits) ((1 << (n_bits)) - 1)
-#define XV_BITS         12   /* BITS was already defined on some systems */
+#define XV_BITS         12 /* BITS was already defined on some systems */
 #define HSIZE           5003 /* 80% occupancy */
 
 typedef unsigned char char_type;

java/src/hdf/hdf5lib/HDF5Constants.java

@@ -455,7 +455,6 @@ public class HDF5Constants {
     private static final int H5ES_STATUS_IN_PROGRESS = H5ES_STATUS_IN_PROGRESS();
     private static final int H5ES_STATUS_SUCCEED = H5ES_STATUS_SUCCEED();
     private static final int H5ES_STATUS_FAIL = H5ES_STATUS_FAIL();
-    private static final int H5ES_STATUS_CANCELED = H5ES_STATUS_CANCELED();
 
     public static final int H5F_ACC_CREAT = H5F_ACC_CREAT();
     public static final int H5F_ACC_EXCL = H5F_ACC_EXCL();
@@ -1509,8 +1508,6 @@ public class HDF5Constants {
 
     private static native final int H5ES_STATUS_FAIL();
 
-    private static native final int H5ES_STATUS_CANCELED();
-
     private static native final int H5F_ACC_CREAT();
 
     private static native final int H5F_ACC_EXCL();

java/src/jni/h5Constants.c

@@ -1210,11 +1210,6 @@ Java_hdf_hdf5lib_HDF5Constants_H5ES_1STATUS_1FAIL(JNIEnv *env, jclass cls)
 {
     return H5ES_STATUS_FAIL;
 }
-JNIEXPORT jlong JNICALL
-Java_hdf_hdf5lib_HDF5Constants_H5ES_1STATUS_1CANCELED(JNIEnv *env, jclass cls)
-{
-    return H5ES_STATUS_CANCELED;
-}
 
 /* Java does not have unsigned native types */
 H5_GCC_DIAG_OFF("sign-conversion")

src/CMakeLists.txt

@@ -174,13 +174,18 @@ IDE_GENERATED_PROPERTIES ("H5EA" "${H5EA_HDRS}" "${H5EA_SOURCES}" )
 
 
 set (H5ES_SOURCES
+    ${HDF5_SRC_DIR}/H5ES.c
+    ${HDF5_SRC_DIR}/H5ESevent.c
+    ${HDF5_SRC_DIR}/H5ESint.c
+    ${HDF5_SRC_DIR}/H5ESlist.c
 )
 set (H5ES_HDRS
     ${HDF5_SRC_DIR}/H5ESpublic.h
 )
 IDE_GENERATED_PROPERTIES ("H5ES" "${H5ES_HDRS}" "${H5ES_SOURCES}" )
 
 
+
 set (H5F_SOURCES
     ${HDF5_SRC_DIR}/H5F.c
     ${HDF5_SRC_DIR}/H5Faccum.c
@@ -440,6 +445,7 @@ set (H5MP_HDRS
 )
 IDE_GENERATED_PROPERTIES ("H5MP" "${H5MP_HDRS}" "${H5MP_SOURCES}" )
 
+
 set (H5O_SOURCES
     ${HDF5_SRC_DIR}/H5O.c
     ${HDF5_SRC_DIR}/H5Oainfo.c
@@ -640,6 +646,7 @@ set (H5TS_SOURCES
     ${HDF5_SRC_DIR}/H5TS.c
 )
 set (H5TS_HDRS
+    ${HDF5_SRC_DIR}/H5TSpublic.h
 )
 IDE_GENERATED_PROPERTIES ("H5TS" "${H5TS_HDRS}" "${H5TS_SOURCES}" )
 
@@ -726,6 +733,7 @@ set (H5_MODULE_HEADERS
     ${HDF5_SRC_DIR}/H5Dmodule.h
     ${HDF5_SRC_DIR}/H5Emodule.h
     ${HDF5_SRC_DIR}/H5EAmodule.h
+    ${HDF5_SRC_DIR}/H5ESmodule.h
     ${HDF5_SRC_DIR}/H5Fmodule.h
     ${HDF5_SRC_DIR}/H5FAmodule.h
     ${HDF5_SRC_DIR}/H5FDdrvr_module.h
@@ -767,6 +775,7 @@ set (common_SRCS
     ${H5D_SOURCES}
     ${H5E_SOURCES}
     ${H5EA_SOURCES}
+    ${H5ES_SOURCES}
     ${H5F_SOURCES}
     ${H5FA_SOURCES}
     ${H5FD_SOURCES}
@@ -836,6 +845,7 @@ set (H5_PUBLIC_HEADERS
     ${H5S_HDRS}
     ${H5SM_HDRS}
     ${H5T_HDRS}
+    ${H5TS_HDRS}
     ${H5VL_HDRS}
     ${H5Z_HDRS}
 )
@@ -875,6 +885,9 @@ set (H5_PRIVATE_HEADERS
     ${HDF5_SRC_DIR}/H5EApkg.h
     ${HDF5_SRC_DIR}/H5EAprivate.h
 
+    ${HDF5_SRC_DIR}/H5ESpkg.h
+    ${HDF5_SRC_DIR}/H5ESprivate.h
+
     ${HDF5_SRC_DIR}/H5Fpkg.h
     ${HDF5_SRC_DIR}/H5Fprivate.h
 

src/H5.c

@@ -254,6 +254,8 @@ H5_init_library(void)
      *   It might not be initialized during normal file open.
      *   When the application does not close the file, routines in the module might
      *   be called via H5_term_library() when shutting down the file.
+     * The dataspace interface needs to be initialized so that future IDs for
+     *   dataspaces work.
      */
     if (H5E_init() < 0)
         HGOTO_ERROR(H5E_FUNC, H5E_CANTINIT, FAIL, "unable to initialize error interface")
@@ -267,6 +269,8 @@ H5_init_library(void)
         HGOTO_ERROR(H5E_FUNC, H5E_CANTINIT, FAIL, "unable to initialize link interface")
     if (H5FS_init() < 0)
         HGOTO_ERROR(H5E_FUNC, H5E_CANTINIT, FAIL, "unable to initialize FS interface")
+    if (H5S_init() < 0)
+        HGOTO_ERROR(H5E_FUNC, H5E_CANTINIT, FAIL, "unable to initialize dataspace interface")
 
     /* Finish initializing interfaces that depend on the interfaces above */
     if (H5VL_init_phase2() < 0)
@@ -357,21 +361,31 @@ H5_term_library(void)
         /* Try to organize these so the "higher" level components get shut
          * down before "lower" level components that they might rely on. -QAK
          */
-        pending += DOWN(L);
 
-        /* Close the "top" of various interfaces (IDs, etc) but don't shut
-         *  down the whole interface yet, so that the object header messages
-         *  get serialized correctly for entries in the metadata cache and the
-         *  symbol table entry in the superblock gets serialized correctly, etc.
-         *  all of which is performed in the 'F' shutdown.
+        /* Close the event sets first, so that all asynchronous operations
+         *  complete before anything else attempts to shut down.
          */
-        pending += DOWN(A_top);
-        pending += DOWN(D_top);
-        pending += DOWN(G_top);
-        pending += DOWN(M_top);
-        pending += DOWN(R_top);
-        pending += DOWN(S_top);
-        pending += DOWN(T_top);
+        pending += DOWN(ES);
+
+        /* Close down the user-facing interfaces, after the event sets */
+        if (pending == 0) {
+            /* Close the interfaces dependent on others */
+            pending += DOWN(L);
+
+            /* Close the "top" of various interfaces (IDs, etc) but don't shut
+             *  down the whole interface yet, so that the object header messages
+             *  get serialized correctly for entries in the metadata cache and the
+             *  symbol table entry in the superblock gets serialized correctly, etc.
+             *  all of which is performed in the 'F' shutdown.
+             */
+            pending += DOWN(A_top);
+            pending += DOWN(D_top);
+            pending += DOWN(G_top);
+            pending += DOWN(M_top);
+            pending += DOWN(R_top);
+            pending += DOWN(S_top);
+            pending += DOWN(T_top);
+        } /* end if */
 
         /* Don't shut down the file code until objects in files are shut down */
         if (pending == 0)
@@ -1183,12 +1197,12 @@ H5free_memory(void *mem)
 herr_t
 H5is_library_threadsafe(hbool_t *is_ts /*out*/)
 {
-    herr_t ret_value = SUCCEED;         /* Return value */
+    herr_t ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API_NOINIT
     H5TRACE1("e", "x", is_ts);
 
-    if(is_ts) {
+    if (is_ts) {
 #ifdef H5_HAVE_THREADSAFE
         *is_ts = TRUE;
 #else /* H5_HAVE_THREADSAFE */
@@ -1218,14 +1232,14 @@ H5is_library_threadsafe(hbool_t *is_ts /*out*/)
 herr_t
 H5is_library_terminating(hbool_t *is_terminating /*out*/)
 {
-    herr_t ret_value = SUCCEED;         /* Return value */
+    herr_t ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_API_NOINIT
     H5TRACE1("e", "x", is_terminating);
 
     HDassert(is_terminating);
 
-    if(is_terminating)
+    if (is_terminating)
         *is_terminating = H5_TERM_GLOBAL;
     else
         ret_value = FAIL;