Merge pull request #26 in ~VCHOI/my_third_fork from develop to bugfix/develop_seg_fault_sel_compat

* commit '9abbdeaa66c70a00b6a7bedee9c76d2493a8e947': (31 commits)
  Remove system command from valgrind reports
  Whitespace
  Fix incorrect FUNC_LEAVE macro (should match FUNC_ENTER_*_TAG).
  Add semicolons to more PASSED() invocations.
  So that I can use PASSED(); anywhere a statement can go, #define PASSED() with a do-while wrapper.
  revert type cast
  Switch the 'get offset' operation from a dataset 'get' callback to a [native] dataset 'optional' operation.
  Modfy expression to match mpicc build with Intel as intel compiler, not gcc.
  Complete the comment on thread_main(), explaining why the barrier is used.
  Fixed issue building HDF5 with NAG Fortran 7.0.
  The first implementation seemed to allow for the possibility that a thread could block at the barrier, wake and exit the barrier, re-acquire the barrier lock and increase `nentered` before the other blocked threads woke and checked `nentered % count == 0`.  Then the other blocked threads would check `nentered % count == 0` and, finding it false, go back to sleep in the barrier.  This new implementation waits for a looser condition to obtain so that threads don't go back to sleep in the barrier.
  Add java version and reference libsettings
  Test the right condition for the EBUSY return in pthread_barrier_destroy().
  s/exit_failure/EXIT_FAILURE/g
  Implement pthread_barrier(3) for Darwin using a counter, condition variable, and mutex.  Untested.
  Update examples and fix old version references.
  Move MODEL check to before usage in CTestScript.cmake.
  Copy generated files instead creating twice
  Fix standalone link
  Fix Fortran macro use and jni comment
  ...

10 files changed, 71 insertions, 50 deletions

diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 070cf62..f582056 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -1,4 +1,4 @@
-cmake_minimum_required (VERSION 3.10)
+cmake_minimum_required (VERSION 3.12)
 project (HDF5_SRC C)
 
 #-----------------------------------------------------------------------------
diff --git a/src/H5D.c b/src/H5D.c
index 178bb30..61a40df 100644
--- a/src/H5D.c
+++ b/src/H5D.c
@@ -598,7 +598,7 @@ H5Dget_offset(hid_t dset_id)
         HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, HADDR_UNDEF, "invalid dataset identifier")
 
     /* Get the offset */
-    if(H5VL_dataset_get(vol_obj, H5VL_DATASET_GET_OFFSET, H5P_DATASET_XFER_DEFAULT, H5_REQUEST_NULL, &ret_value) < 0)
+    if(H5VL_dataset_optional(vol_obj, H5VL_NATIVE_DATASET_GET_OFFSET, H5P_DATASET_XFER_DEFAULT, H5_REQUEST_NULL, &ret_value) < 0)
         HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, HADDR_UNDEF, "unable to get offset")
 
 done:
diff --git a/src/H5Dchunk.c b/src/H5Dchunk.c
index 556e367..e760f63 100644
--- a/src/H5Dchunk.c
+++ b/src/H5Dchunk.c
@@ -323,6 +323,7 @@ static herr_t H5D__chunk_prune_fill(H5D_chunk_it_ud1_t *udata, hbool_t new_unfil
 #ifdef H5_HAVE_PARALLEL
 static herr_t H5D__chunk_collective_fill(const H5D_t *dset,
     H5D_chunk_coll_info_t *chunk_info, size_t chunk_size, const void *fill_buf);
+static int H5D__chunk_cmp_addr(const void *addr1, const void *addr2);
 #endif /* H5_HAVE_PARALLEL */
 
 static int
@@ -4958,6 +4959,7 @@ H5D__chunk_collective_fill(const H5D_t *dset, H5D_chunk_coll_info_t *chunk_info,
     MPI_Datatype mem_type, file_type;
     H5FD_mpio_xfer_t prev_xfer_mode;    /* Previous data xfer mode */
     hbool_t     have_xfer_mode = FALSE; /* Whether the previous xffer mode has been retrieved */
+    hbool_t     need_addr_sort = FALSE;
     int         i;                  /* Local index variable */
     herr_t ret_value = SUCCEED;     /* Return value */
 
@@ -5006,19 +5008,28 @@ H5D__chunk_collective_fill(const H5D_t *dset, H5D_chunk_coll_info_t *chunk_info,
 
         /* make sure that the addresses in the datatype are
            monotonically non decreasing */
-        if(i)
-            HDassert(chunk_disp_array[i] > chunk_disp_array[i - 1]);
-    } /* end if */
+        if(i && (chunk_disp_array[i] < chunk_disp_array[i - 1]))
+            need_addr_sort = TRUE;
+    } /* end for */
 
     /* calculate if there are any leftover blocks after evenly
        distributing. If there are, then round robin the distribution
        to processes 0 -> leftover. */
     if(leftover && leftover > mpi_rank) {
         chunk_disp_array[blocks] = (MPI_Aint)chunk_info->addr[blocks*mpi_size + mpi_rank];
+        if(blocks && (chunk_disp_array[blocks] < chunk_disp_array[blocks - 1]))
+            need_addr_sort = TRUE;
         block_lens[blocks] = block_len;
         blocks++;
     }
 
+    /*
+     * Ensure that the blocks are sorted in monotonically non-decreasing
+     * order of offset in the file.
+     */
+    if(need_addr_sort)
+        HDqsort(chunk_disp_array, blocks, sizeof(MPI_Aint), H5D__chunk_cmp_addr);
+
     /* MSC - should use this if MPI_type_create_hindexed block is working:
      * mpi_code = MPI_Type_create_hindexed_block(blocks, block_len, chunk_disp_array, MPI_BYTE, &file_type);
      */
@@ -5073,6 +5084,36 @@ done:
 
     FUNC_LEAVE_NOAPI(ret_value)
 } /* end H5D__chunk_collective_fill() */
+
+
+static int
+H5D__chunk_cmp_addr(const void *addr1, const void *addr2)
+{
+    MPI_Aint _addr1 = (MPI_Aint)0, _addr2 = (MPI_Aint)0;
+    int ret_value = 0;
+
+    FUNC_ENTER_STATIC_NOERR
+
+    _addr1 = *((const MPI_Aint *) addr1);
+    _addr2 = *((const MPI_Aint *) addr2);
+
+#if MPI_VERSION >= 3 && MPI_SUBVERSION >= 1
+    {
+        MPI_Aint diff = MPI_Aint_diff(_addr1, _addr2);
+
+        if(diff < (MPI_Aint)0)
+            ret_value = -1;
+        else if(diff > (MPI_Aint)0)
+            ret_value = 1;
+        else
+            ret_value = 0;
+    }
+#else
+    ret_value = (_addr1 > _addr2) - (_addr1 < _addr2);
+#endif
+
+    FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D__chunk_cmp_addr() */
 #endif /* H5_HAVE_PARALLEL */
 
 
@@ -7162,7 +7203,7 @@ H5D__get_num_chunks(const H5D_t *dset, const H5S_t H5_ATTR_UNUSED *space, hsize_
     } /* end else */
 
 done:
-    FUNC_LEAVE_NOAPI(ret_value)
+    FUNC_LEAVE_NOAPI_TAG(ret_value)
 } /* end H5D__get_num_chunks() */
 
 
@@ -7300,7 +7341,7 @@ H5D__get_chunk_info(const H5D_t *dset, const H5S_t H5_ATTR_UNUSED *space, hsize_
     } /* end if H5F_addr_defined */
 
 done:
-    FUNC_LEAVE_NOAPI(ret_value)
+    FUNC_LEAVE_NOAPI_TAG(ret_value)
 } /* end H5D__get_chunk_info() */
 
 
diff --git a/src/H5Ochunk.c b/src/H5Ochunk.c
index 9ce5a46..72402e4 100644
--- a/src/H5Ochunk.c
+++ b/src/H5Ochunk.c
@@ -358,7 +358,7 @@ H5O__chunk_update_idx(H5F_t *f, H5O_t *oh, unsigned idx)
         HGOTO_ERROR(H5E_OHDR, H5E_CANTUNPROTECT, FAIL, "unable to release object header chunk")
 
 done:
-    FUNC_LEAVE_NOAPI(ret_value)
+    FUNC_LEAVE_NOAPI_TAG(ret_value)
 } /* end H5O__chunk_update_idx() */
 
 
diff --git a/src/H5TS.c b/src/H5TS.c
index 9503e05..b0cef7f 100644
--- a/src/H5TS.c
+++ b/src/H5TS.c
@@ -262,7 +262,7 @@ H5TS_mutex_lock(H5TS_mutex_t *mutex)
     if (ret_value)
         return ret_value;
 
-    if(mutex->lock_count && pthread_equal(HDpthread_self(), mutex->owner_thread)) {
+    if(mutex->lock_count && pthread_equal(pthread_self(), mutex->owner_thread)) {
         /* already owned by self - increment count */
         mutex->lock_count++;
     } else {
@@ -271,7 +271,7 @@ H5TS_mutex_lock(H5TS_mutex_t *mutex)
             pthread_cond_wait(&mutex->cond_var, &mutex->atomic_lock);
 
         /* After we've received the signal, take ownership of the mutex */
-        mutex->owner_thread = HDpthread_self();
+        mutex->owner_thread = pthread_self();
         mutex->lock_count = 1;
     }
 
diff --git a/src/H5VLconnector.h b/src/H5VLconnector.h
index baa4cca..39d9b14 100644
--- a/src/H5VLconnector.h
+++ b/src/H5VLconnector.h
@@ -91,7 +91,6 @@ typedef int H5VL_attr_optional_t;
 typedef enum H5VL_dataset_get_t {
     H5VL_DATASET_GET_DAPL,                  /* access property list                */
     H5VL_DATASET_GET_DCPL,                  /* creation property list              */
-    H5VL_DATASET_GET_OFFSET,                /* offset                              */
     H5VL_DATASET_GET_SPACE,                 /* dataspace                           */
     H5VL_DATASET_GET_SPACE_STATUS,          /* space status                        */
     H5VL_DATASET_GET_STORAGE_SIZE,          /* storage size                        */
diff --git a/src/H5VLnative.h b/src/H5VLnative.h
index e1f3f93..b607abc 100644
--- a/src/H5VLnative.h
+++ b/src/H5VLnative.h
@@ -48,6 +48,7 @@
 #define H5VL_NATIVE_DATASET_CHUNK_READ              6   /* H5Dchunk_read                */
 #define H5VL_NATIVE_DATASET_CHUNK_WRITE             7   /* H5Dchunk_write               */
 #define H5VL_NATIVE_DATASET_GET_VLEN_BUF_SIZE       8   /* H5Dvlen_get_buf_size         */
+#define H5VL_NATIVE_DATASET_GET_OFFSET              9   /* H5Dget_offset                */
 
 /* Values for native VOL connector file optional VOL operations */
 #define H5VL_NATIVE_FILE_CLEAR_ELINK_CACHE             0   /* H5Fclear_elink_file_cache            */
diff --git a/src/H5VLnative_dataset.c b/src/H5VLnative_dataset.c
index bea2c50..8660e80 100644
--- a/src/H5VLnative_dataset.c
+++ b/src/H5VLnative_dataset.c
@@ -297,18 +297,6 @@ H5VL__native_dataset_get(void *obj, H5VL_dataset_get_t get_type,
                 break;
             }
 
-        /* H5Dget_offset */
-        case H5VL_DATASET_GET_OFFSET:
-            {
-                haddr_t *ret = HDva_arg(arguments, haddr_t *);
-
-                /* Set return value */
-                *ret = H5D__get_offset(dset);
-                if(!H5F_addr_defined(*ret))
-                    *ret = HADDR_UNDEF;
-                break;
-            }
-
         default:
             HGOTO_ERROR(H5E_VOL, H5E_CANTGET, FAIL, "can't get this type of information from dataset")
     } /* end switch */
@@ -391,16 +379,17 @@ herr_t
 H5VL__native_dataset_optional(void *obj, H5VL_dataset_optional_t optional_type,
     hid_t H5_ATTR_UNUSED dxpl_id, void H5_ATTR_UNUSED **req, va_list arguments)
 {
-    H5D_t *dset = NULL;             /* Dataset */
-    herr_t ret_value = SUCCEED;    /* Return value */
+    H5D_t *dset = (H5D_t *)obj;         /* Dataset */
+    herr_t ret_value = SUCCEED;         /* Return value */
 
     FUNC_ENTER_PACKAGE
 
+    /* Sanity checks */
+    HDassert(dset);
+
     switch(optional_type) {
         case H5VL_NATIVE_DATASET_FORMAT_CONVERT:
             {   /* H5Dformat_convert */
-                dset = (H5D_t *)obj;
-
                 switch(dset->shared->layout.type) {
                     case H5D_CHUNKED:
                         /* Convert the chunk indexing type to version 1 B-tree if not */
@@ -436,8 +425,6 @@ H5VL__native_dataset_optional(void *obj, H5VL_dataset_optional_t optional_type,
             {   /* H5Dget_chunk_index_type */
                 H5D_chunk_index_t *idx_type = HDva_arg(arguments, H5D_chunk_index_t *);
 
-                dset = (H5D_t *)obj;
-
                 /* Make sure the dataset is chunked */
                 if(H5D_CHUNKED != dset->shared->layout.type)
                     HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a chunked dataset")
@@ -453,8 +440,6 @@ H5VL__native_dataset_optional(void *obj, H5VL_dataset_optional_t optional_type,
                 hsize_t *offset = HDva_arg(arguments, hsize_t *);
                 hsize_t *chunk_nbytes = HDva_arg(arguments, hsize_t *);
 
-                dset = (H5D_t *)obj;
-
                 /* Make sure the dataset is chunked */
                 if(H5D_CHUNKED != dset->shared->layout.type)
                     HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a chunked dataset")
@@ -472,8 +457,6 @@ H5VL__native_dataset_optional(void *obj, H5VL_dataset_optional_t optional_type,
                 hid_t        space_id = HDva_arg(arguments, hid_t);
                 hsize_t     *nchunks  = HDva_arg(arguments, hsize_t *);
 
-                dset = (H5D_t *)obj;
-                HDassert(dset);
                 HDassert(dset->shared);
                 HDassert(dset->shared->space);
 
@@ -505,8 +488,6 @@ H5VL__native_dataset_optional(void *obj, H5VL_dataset_optional_t optional_type,
                 haddr_t     *addr        = HDva_arg(arguments, haddr_t *);
                 hsize_t     *size        = HDva_arg(arguments, hsize_t *);
 
-                dset = (H5D_t *)obj;
-                HDassert(dset);
                 HDassert(dset->shared);
                 HDassert(dset->shared->space);
 
@@ -534,8 +515,6 @@ H5VL__native_dataset_optional(void *obj, H5VL_dataset_optional_t optional_type,
                 haddr_t  *addr        = HDva_arg(arguments, haddr_t *);
                 hsize_t  *size        = HDva_arg(arguments, hsize_t *);
 
-                dset = (H5D_t *)obj;
-                HDassert(dset);
                 HDassert(dset->shared);
 
                 /* Make sure the dataset is chunked */
@@ -556,8 +535,6 @@ H5VL__native_dataset_optional(void *obj, H5VL_dataset_optional_t optional_type,
                 void       *buf                 = HDva_arg(arguments, void *);
                 hsize_t     offset_copy[H5O_LAYOUT_NDIMS];  /* Internal copy of chunk offset */
 
-                dset = (H5D_t *)obj;
-
                 /* Check arguments */
                 if(NULL == dset->oloc.file)
                     HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "dataset is not associated with a file")
@@ -585,8 +562,6 @@ H5VL__native_dataset_optional(void *obj, H5VL_dataset_optional_t optional_type,
                 const void     *buf                 = HDva_arg(arguments, const void *);
                 hsize_t         offset_copy[H5O_LAYOUT_NDIMS];  /* Internal copy of chunk offset */
 
-                dset = (H5D_t *)obj;
-
                 /* Check arguments */
                 if(NULL == dset->oloc.file)
                     HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "dataset is not associated with a file")
@@ -612,13 +587,22 @@ H5VL__native_dataset_optional(void *obj, H5VL_dataset_optional_t optional_type,
                 hid_t space_id = HDva_arg(arguments, hid_t);
                 hsize_t *size = HDva_arg(arguments, hsize_t *);
 
-                dset = (H5D_t *)obj;
-
                 if(H5D__vlen_get_buf_size(dset, type_id, space_id, size) < 0)
                     HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get size of vlen buf needed")
                 break;
             }
 
+        /* H5Dget_offset */
+        case H5VL_NATIVE_DATASET_GET_OFFSET:
+            {
+                haddr_t *ret = HDva_arg(arguments, haddr_t *);
+
+                /* Set return value */
+                *ret = H5D__get_offset(dset);
+                if(!H5F_addr_defined(*ret))
+                    *ret = HADDR_UNDEF;
+                break;
+            }
 
         default:
             HGOTO_ERROR(H5E_VOL, H5E_UNSUPPORTED, FAIL, "invalid optional operation")
diff --git a/src/H5private.h b/src/H5private.h
index 3759446..f570723 100644
--- a/src/H5private.h
+++ b/src/H5private.h
@@ -1570,10 +1570,6 @@ extern char *strdup(const char *s);
     #define HDstrdup(S)     strdup(S)
 #endif /* HDstrdup */
 
-#ifndef HDpthread_self
-    #define HDpthread_self()    pthread_self()
-#endif /* HDpthread_self */
-
 /* Macro for "stringizing" an integer in the C preprocessor (use H5_TOSTRING) */
 /* (use H5_TOSTRING, H5_STRINGIZE is just part of the implementation) */
 #define H5_STRINGIZE(x) #x
diff --git a/src/H5trace.c b/src/H5trace.c
index ec5c6a2..7168d5d 100644
--- a/src/H5trace.c
+++ b/src/H5trace.c
@@ -2746,9 +2746,6 @@ H5_trace(const double *returning, const char *func, const char *type, ...)
                                 case H5VL_DATASET_GET_STORAGE_SIZE:
                                     HDfprintf(out, "H5VL_DATASET_GET_STORAGE_SIZE");
                                     break;
-                                case H5VL_DATASET_GET_OFFSET:
-                                    HDfprintf(out, "H5VL_DATASET_GET_OFFSET");
-                                    break;
                                 default:
                                     HDfprintf(out, "%ld", (long)get);
                                     break;
@@ -3276,6 +3273,9 @@ H5_trace(const double *returning, const char *func, const char *type, ...)
                                 case H5VL_NATIVE_DATASET_GET_VLEN_BUF_SIZE:
                                     HDfprintf(out, "H5VL_NATIVE_DATASET_GET_VLEN_BUF_SIZE");
                                     break;
+                                case H5VL_NATIVE_DATASET_GET_OFFSET:
+                                    HDfprintf(out, "H5VL_NATIVE_DATASET_GET_OFFSET");
+                                    break;
                                 default:
                                     HDfprintf(out, "%ld", (long)optional);
                                     break;