Hdf5 1 12 merges (#1528)

* Use internal version of H5Eprint2 to avoid possible stack overflow (#661)

* Add support for parallel filters to h5repack (#832)

* Allow parallel filters feature for comm size of 1 (#840)

* Avoid popping API context when one wasn't pushed (#848)

* Fix several warnings (#720)

* Don't allow H5Pset(get)_all_coll_metadata_ops for DXPLs (#1201)

* Fix free list tracking and cleanup cast alignment warnings (#1288)

* Fix free list tracking and cleanup cast alignment warnings

* Add free list tracking code to H5FL 'arr' routines

* Fix usage of several HDfprintf format specifiers after HDfprintf removal (#1324)

* Use appropriate printf format specifiers for haddr_t and hsize_t types directly (#1340)

* Fix H5ACmpio dirty bytes creation debugging (#1357)

* Fix documentation for H5D_space_status_t enum values (#1372)

* Parallel rank0 deadlock fixes (#1183)

* Fix several places where rank 0 can skip past collective MPI operations on failure

* Committing clang-format changes

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Fix a few issues noted by LGTM (#1421)

* Fix cache sanity checking code by moving functions to wider scope (#1435)

* Fix metadata cache bug when resizing a pinned/protected entry (v2) (#1463)

* Disable memory alloc sanity checks by default for Autotools debug builds (#1468)

* Committing clang-format changes

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

10 files changed, 61 insertions, 27 deletions

diff --git a/tools/lib/h5diff_array.c b/tools/lib/h5diff_array.c
index e16a045..1d93df3 100644
--- a/tools/lib/h5diff_array.c
+++ b/tools/lib/h5diff_array.c
@@ -2084,7 +2084,7 @@ diff_ldouble_element(unsigned char *mem1, unsigned char *mem2, hsize_t elem_idx,
             opts->print_percentage = 0;
             print_pos(opts, elem_idx, 0);
             if (print_data(opts)) {
-                parallel_print(F_FORMAT, temp1_double, temp2_double, ABS(temp1_double - temp2_double));
+                parallel_print(LD_FORMAT, temp1_double, temp2_double, ABS(temp1_double - temp2_double));
             }
             nfound++;
         }
@@ -2131,7 +2131,7 @@ diff_ldouble_element(unsigned char *mem1, unsigned char *mem2, hsize_t elem_idx,
             opts->print_percentage = 0;
             print_pos(opts, elem_idx, 0);
             if (print_data(opts)) {
-                parallel_print(F_FORMAT, temp1_double, temp2_double, ABS(temp1_double - temp2_double));
+                parallel_print(LD_FORMAT, temp1_double, temp2_double, ABS(temp1_double - temp2_double));
             }
             nfound++;
         }
@@ -2178,7 +2178,7 @@ diff_ldouble_element(unsigned char *mem1, unsigned char *mem2, hsize_t elem_idx,
             opts->print_percentage = 0;
             print_pos(opts, elem_idx, 0);
             if (print_data(opts)) {
-                parallel_print(F_FORMAT, temp1_double, temp2_double, ABS(temp1_double - temp2_double));
+                parallel_print(LD_FORMAT, temp1_double, temp2_double, ABS(temp1_double - temp2_double));
             }
             nfound++;
         }
diff --git a/tools/lib/h5diff_attr.c b/tools/lib/h5diff_attr.c
index 5c1777a..63b6d8f 100644
--- a/tools/lib/h5diff_attr.c
+++ b/tools/lib/h5diff_attr.c
@@ -292,7 +292,7 @@ build_match_list_attrs(hid_t loc1_id, hid_t loc2_id, table_attrs_t **table_out,
     }
 
     if (opts->mode_verbose_level >= 1)
-        parallel_print("Attributes status:  %d common, %d only in obj1, %d only in obj2\n",
+        parallel_print("Attributes status:  %zu common, %zu only in obj1, %zu only in obj2\n",
                        table_lp->nattrs - table_lp->nattrs_only1 - table_lp->nattrs_only2,
                        table_lp->nattrs_only1, table_lp->nattrs_only2);
 
diff --git a/tools/lib/h5tools.c b/tools/lib/h5tools.c
index eee9c53..3c447a7 100644
--- a/tools/lib/h5tools.c
+++ b/tools/lib/h5tools.c
@@ -903,7 +903,7 @@ h5tools_fopen(const char *fname, unsigned flags, hid_t fapl_id, hbool_t use_spec
      * as TRUE, we should return failure now since the file couldn't be opened with
      * the VFL driver/VOL connector that was set on the FAPL by the caller.
      */
-    if (fid < 0 && use_specific_driver)
+    if (use_specific_driver)
         H5TOOLS_GOTO_ERROR(H5I_INVALID_HID, "failed to open file using specified FAPL");
 
     /*
diff --git a/tools/lib/h5tools_dump.c b/tools/lib/h5tools_dump.c
index 06c4d9f..98f7c0f 100644
--- a/tools/lib/h5tools_dump.c
+++ b/tools/lib/h5tools_dump.c
@@ -2486,7 +2486,7 @@ found_string_type:
                     ctx->need_prefix = TRUE;
 
                     h5tools_str_reset(buffer);
-                    h5tools_str_append(buffer, "OPAQUE_SIZE \"%s\";", size);
+                    h5tools_str_append(buffer, "OPAQUE_SIZE \"%zu\";", size);
                     h5tools_render_element(stream, info, ctx, buffer, &curr_pos, (size_t)ncols, (hsize_t)0,
                                            (hsize_t)0);
                 }
@@ -2996,7 +2996,7 @@ h5tools_dump_oid(FILE *stream, const h5tool_format_t *info, h5tools_context_t *c
     ctx->need_prefix = TRUE;
 
     h5tools_str_reset(&buffer);
-    h5tools_str_append(&buffer, "%s %s %d %s", OBJID, BEGIN, oid, END);
+    h5tools_str_append(&buffer, "%s %s %" PRId64 " %s", OBJID, BEGIN, oid, END);
     h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0, (hsize_t)0);
 
     h5tools_str_close(&buffer);
diff --git a/tools/lib/h5tools_str.c b/tools/lib/h5tools_str.c
index 57e7813..bd14483 100644
--- a/tools/lib/h5tools_str.c
+++ b/tools/lib/h5tools_str.c
@@ -258,7 +258,8 @@ h5tools_str_fmt(h5tools_str_t *str /*in,out*/, size_t start, const char *fmt)
             HDassert(temp);
         }
 
-        HDstrncpy(temp, str->s + start, n);
+        HDstrncpy(temp, str->s + start, n - 1);
+        temp[n - 1] = '\0';
     }
 
     /* Reset the output string and append a formatted version */
diff --git a/tools/src/h5dump/h5dump_ddl.c b/tools/src/h5dump/h5dump_ddl.c
index 1e92057..dd95b3c 100644
--- a/tools/src/h5dump/h5dump_ddl.c
+++ b/tools/src/h5dump/h5dump_ddl.c
@@ -1318,7 +1318,7 @@ attr_search(hid_t oid, const char *attr_name, const H5A_info_t H5_ATTR_UNUSED *a
     j = (int)HDstrlen(op_name) - 1;
     /* find the last / */
     while (j >= 0) {
-        if (op_name[j] == '/' && (j == 0 || (j > 0 && op_name[j - 1] != '\\')))
+        if (op_name[j] == '/' && (j == 0 || (op_name[j - 1] != '\\')))
             break;
         j--;
     }
@@ -1343,13 +1343,21 @@ attr_search(hid_t oid, const char *attr_name, const H5A_info_t H5_ATTR_UNUSED *a
                 ret = FAIL;
             }
             else {
+                size_t buffer_space = w - 1;
+
                 HDmemset(obj_name, '\0', w);
                 if (op_name[0] != '/') {
-                    HDstrncat(obj_name, buf, u + 1);
-                    if (buf[u - 1] != '/')
-                        HDstrncat(obj_name, "/", (size_t)2);
+                    HDstrncat(obj_name, buf, buffer_space);
+                    buffer_space -= MIN(buffer_space, u);
+
+                    if (buf[u - 1] != '/') {
+                        HDstrncat(obj_name, "/", buffer_space);
+                        buffer_space -= MIN(buffer_space, 2);
+                    }
                 }
-                HDstrncat(obj_name, op_name, v + 1);
+
+                HDstrncat(obj_name, op_name, buffer_space);
+                buffer_space -= MIN(buffer_space, v);
 
                 handle_attributes(oid, obj_name, NULL, 0, NULL);
                 HDfree(obj_name);
@@ -1421,10 +1429,10 @@ lnk_search(const char *path, const H5L_info2_t *li, void *_op_data)
     else {
         if (k == 2) {
             HDstrcpy(search_name, "/");
-            HDstrncat(search_name, op_name, search_len + 1);
+            HDstrcat(search_name, op_name);
         }
         else
-            HDstrncpy(search_name, op_name, search_len + 1);
+            HDstrcpy(search_name, op_name);
         search_name[search_len + k - 1] = '\0';
 
         if (HDstrcmp(path, search_name) == 0) {
@@ -1533,7 +1541,7 @@ handle_attributes(hid_t fid, const char *attr, void H5_ATTR_UNUSED *data, int H5
 
     /* find the last / */
     while (j >= 0) {
-        if (attr[j] == '/' && (j == 0 || (j > 0 && attr[j - 1] != '\\')))
+        if (attr[j] == '/' && (j == 0 || (attr[j - 1] != '\\')))
             break;
         j--;
     }
diff --git a/tools/src/h5dump/h5dump_xml.c b/tools/src/h5dump/h5dump_xml.c
index 0e881df..e9006b6 100644
--- a/tools/src/h5dump/h5dump_xml.c
+++ b/tools/src/h5dump/h5dump_xml.c
@@ -591,6 +591,8 @@ xml_name_to_XID(hid_t loc_id, const char *str, char *outstr, int outlen, int gen
     if (outlen < 22)
         return 1;
 
+    H5_CHECK_OVERFLOW(outlen, int, size_t);
+
     lookup_ret = ref_path_table_lookup(str, &obj_token);
     if (lookup_ret < 0) {
         if (HDstrlen(str) == 0) {
@@ -600,7 +602,7 @@ xml_name_to_XID(hid_t loc_id, const char *str, char *outstr, int outlen, int gen
                     ref_path_table_gen_fake(str, &obj_token);
 
                     H5Otoken_to_str(loc_id, &obj_token, &obj_tok_str);
-                    HDsprintf(outstr, "xid_%s", obj_tok_str);
+                    HDsnprintf(outstr, (size_t)outlen, "xid_%s", obj_tok_str);
                     H5free_memory(obj_tok_str);
 
                     return 0;
@@ -615,7 +617,7 @@ xml_name_to_XID(hid_t loc_id, const char *str, char *outstr, int outlen, int gen
                 ref_path_table_gen_fake(str, &obj_token);
 
                 H5Otoken_to_str(loc_id, &obj_token, &obj_tok_str);
-                HDsprintf(outstr, "xid_%s", obj_tok_str);
+                HDsnprintf(outstr, (size_t)outlen, "xid_%s", obj_tok_str);
                 H5free_memory(obj_tok_str);
 
                 return 0;
@@ -627,7 +629,7 @@ xml_name_to_XID(hid_t loc_id, const char *str, char *outstr, int outlen, int gen
     }
 
     H5Otoken_to_str(loc_id, &obj_token, &obj_tok_str);
-    HDsprintf(outstr, "xid_%s", obj_tok_str);
+    HDsnprintf(outstr, (size_t)outlen, "xid_%s", obj_tok_str);
     H5free_memory(obj_tok_str);
 
     return 0;
@@ -3598,7 +3600,10 @@ xml_dump_fill_value(hid_t dcpl, hid_t type)
                 h5tools_str_reset(&buffer);
                 h5tools_str_append(&buffer, "\"");
                 for (i = 0; i < sz; i++) {
-                    h5tools_str_append(&buffer, "%x ", *(unsigned int *)buf + (i * sizeof(unsigned int)));
+                    unsigned long val = *(unsigned int *)buf + (i * sizeof(unsigned int));
+
+                    H5_CHECK_OVERFLOW(val, unsigned long, unsigned);
+                    h5tools_str_append(&buffer, "%x ", (unsigned)val);
                 }
                 h5tools_str_append(&buffer, "\"");
                 h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos,
diff --git a/tools/src/h5import/h5import.c b/tools/src/h5import/h5import.c
index 100eba3..509cc87 100644
--- a/tools/src/h5import/h5import.c
+++ b/tools/src/h5import/h5import.c
@@ -3771,6 +3771,7 @@ getCompressionParameter(struct Input *in, FILE *strm)
 static int
 getExternalFilename(struct Input *in, FILE *strm)
 {
+    size_t      temp_len;
     char        temp[255];
     const char *err1 = "Unable to get 'string' value.\n";
 
@@ -3779,8 +3780,10 @@ getExternalFilename(struct Input *in, FILE *strm)
         return (-1);
     }
 
-    in->externFilename = (char *)HDmalloc((size_t)(HDstrlen(temp) + 1) * sizeof(char));
-    (void)HDstrncpy(in->externFilename, temp, HDstrlen(temp) + 1);
+    temp_len           = HDstrlen(temp);
+    in->externFilename = (char *)HDmalloc((temp_len + 1) * sizeof(char));
+    (void)HDstrcpy(in->externFilename, temp);
+    in->externFilename[temp_len] = '\0';
     return (0);
 }
 
diff --git a/tools/src/h5perf/sio_perf.c b/tools/src/h5perf/sio_perf.c
index c979e7a..b2dd765 100644
--- a/tools/src/h5perf/sio_perf.c
+++ b/tools/src/h5perf/sio_perf.c
@@ -277,7 +277,7 @@ run_test_loop(struct options *opts)
     }
 
     /* print size information */
-    output_report("Transfer Buffer Size (bytes): %d\n", buf_bytes);
+    output_report("Transfer Buffer Size (bytes): %zu\n", buf_bytes);
     output_report("File Size(MB): %.2f\n", ((double)parms.num_bytes) / ONE_MB);
 
     print_indent(0);
diff --git a/tools/src/h5repack/h5repack_copy.c b/tools/src/h5repack/h5repack_copy.c
index 536de69..934b4d1 100644
--- a/tools/src/h5repack/h5repack_copy.c
+++ b/tools/src/h5repack/h5repack_copy.c
@@ -626,6 +626,7 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, pack_opt_t *opti
     hid_t              wtype_id      = H5I_INVALID_HID; /* read/write type ID */
     hid_t              ocpl_id       = H5I_INVALID_HID; /* property to pass copy options */
     hid_t              lcpl_id       = H5I_INVALID_HID; /* link creation property list */
+    hid_t              dxpl_id       = H5I_INVALID_HID; /* dataset transfer property list */
     named_dt_t *       named_dt_head = NULL;            /* Pointer to the stack of named datatypes copied */
     size_t             msize;                           /* size of type */
     hsize_t            nelmts;                          /* number of elements in dataset */
@@ -995,12 +996,27 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, pack_opt_t *opti
                                     if (need < H5TOOLS_MALLOCSIZE)
                                         buf = HDmalloc(need);
 
+                                    /* Set up collective write if using filters in parallel */
+                                    {
+#ifdef H5_HAVE_PARALLEL
+                                        hbool_t parallel = (H5FD_MPIO == H5Pget_driver(options->fout_fapl));
+
+                                        if (parallel && apply_s && apply_f) {
+                                            if ((dxpl_id = H5Pcreate(H5P_DATASET_XFER)) < 0)
+                                                H5TOOLS_GOTO_ERROR((-1), "H5Pcreate failed");
+                                            if (H5Pset_dxpl_mpio(dxpl_id, H5FD_MPIO_COLLECTIVE) < 0)
+                                                H5TOOLS_GOTO_ERROR((-1), "H5Pset_dxpl_mpio failed");
+                                        }
+                                        else
+#endif
+                                            dxpl_id = H5P_DEFAULT;
+                                    }
+
                                     if (buf != NULL) {
                                         if (H5Dread(dset_in, wtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) <
                                             0)
                                             H5TOOLS_GOTO_ERROR((-1), "H5Dread failed");
-                                        if (H5Dwrite(dset_out, wtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) <
-                                            0)
+                                        if (H5Dwrite(dset_out, wtype_id, H5S_ALL, H5S_ALL, dxpl_id, buf) < 0)
                                             H5TOOLS_GOTO_ERROR((-1), "H5Dwrite failed");
 
                                         /* Check if we have VL data in the dataset's
@@ -1102,8 +1118,8 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, pack_opt_t *opti
                                             if (H5Dread(dset_in, wtype_id, hslab_space, f_space_id,
                                                         H5P_DEFAULT, hslab_buf) < 0)
                                                 H5TOOLS_GOTO_ERROR((-1), "H5Dread failed");
-                                            if (H5Dwrite(dset_out, wtype_id, hslab_space, f_space_id,
-                                                         H5P_DEFAULT, hslab_buf) < 0)
+                                            if (H5Dwrite(dset_out, wtype_id, hslab_space, f_space_id, dxpl_id,
+                                                         hslab_buf) < 0)
                                                 H5TOOLS_GOTO_ERROR((-1), "H5Dwrite failed");
 
                                             /* reclaim any VL memory, if necessary */
@@ -1382,6 +1398,7 @@ done:
         H5Pclose(dcpl_in);
         H5Pclose(gcpl_in);
         H5Pclose(gcpl_out);
+        H5Pclose(dxpl_id);
         H5Sclose(f_space_id);
         H5Dclose(dset_in);
         H5Dclose(dset_out);