Merge pull request #1296 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:1.10/master to 1.10/master

* commit 'f3f29dc7df5f3cc41a5e9462d8c415e540cda3d6': (42 commits)
  Commit version string changes for HDF5 1.10.4 release.
  Merge hdf5_1_10 changes to hdf5_1_10_4.
  Merge in changes from hdf5_1_10.
  Commit release date change.
  Update RELEASE.txt for HDF5 1.10.4 release.
  Add notes about unsupported options
  Add contents of HDF5 1.10.3 RELEASE.txt to HISTORY-1_10.txt and update RELEASE.txt for continuing development.
  Switch maintainer mode to disable, build mode to production, version to 1.10.4, and commit files generated by autogen.sh for release branch hdf5_1_10_4.
  HDFFV-10568 fix hdf5_java library dependency
  Fix Java library location for testing
  Java groups example fix
  Update system commands with HD prefix and whitespace
  Merge pull request #1224 in HDFFV/hdf5 from ~JHENDERSON/hdf5:develop to develop
  Disable failing tests because of execution issue
  Add testfiles to data copy
  Same changes needed for examples as test
  Correct name of test jar
  Only remove test jars
  Remove obsolete var
  Change prefix in example scripts to relative path to bin. This was done for 1.8, and works wherever installed without the need to replace the original prefix.
  ...

16 files changed, 106 insertions, 84 deletions

diff --git a/java/src/jni/CMakeLists.txt b/java/src/jni/CMakeLists.txt
index a0228e1..7b95e0b 100644
--- a/java/src/jni/CMakeLists.txt
+++ b/java/src/jni/CMakeLists.txt
@@ -50,22 +50,10 @@ set (CMAKE_INCLUDE_CURRENT_DIR_IN_INTERFACE ON)
 add_library (${HDF5_JAVA_JNI_LIB_TARGET} SHARED ${HDF5_JAVA_JNI_CSRCS} ${HDF5_JAVA_JNI_CHDRS})
 target_include_directories(${HDF5_JAVA_JNI_LIB_TARGET} PRIVATE ${HDF5_BINARY_DIR} ${HDF5_JAVA_JNI_SOURCE_DIR})
 TARGET_C_PROPERTIES (${HDF5_JAVA_JNI_LIB_TARGET} SHARED)
-target_link_libraries (${HDF5_JAVA_JNI_LIB_TARGET} PUBLIC ${HDF5_LIB_TARGET})
+target_link_libraries (${HDF5_JAVA_JNI_LIB_TARGET} PUBLIC ${HDF5_LIBSH_TARGET})
 set_target_properties (${HDF5_JAVA_JNI_LIB_TARGET} PROPERTIES FOLDER libraries/jni)
 SET_GLOBAL_VARIABLE (HDF5_LIBRARIES_TO_EXPORT "${HDF5_LIBRARIES_TO_EXPORT};${HDF5_JAVA_JNI_LIB_TARGET}")
 H5_SET_LIB_OPTIONS (${HDF5_JAVA_JNI_LIB_TARGET} ${HDF5_JAVA_JNI_LIB_NAME} SHARED "JAVA")
-if (WIN32)
-  get_filename_component (HDF5_JAVA_JNI_DLL_NAME ${HDF5_JAVA_JNI_LIB_TARGET} NAME_WE)
-  set (HDF5_JAVA_JNI_DLL_NAME "${HDF5_JAVA_JNI_DLL_NAME}$<$<CONFIG:Debug>:_D>")
-  # message (STATUS "HDF5_JAVA_JNI_DLL_NAME: ${HDF5_JAVA_JNI_DLL_NAME}")
-  if (BUILD_TESTING)
-    add_custom_target (HDF5_JAVA_JNI-Test-Copy ALL
-        COMMAND ${CMAKE_COMMAND} -E copy_if_different ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${CMAKE_CFG_INTDIR}/${HDF5_JAVA_JNI_DLL_NAME}${CMAKE_SHARED_LIBRARY_SUFFIX} ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${HDF5_JAVA_JNI_DLL_NAME}${CMAKE_SHARED_LIBRARY_SUFFIX}
-        COMMENT "Copying ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${CMAKE_CFG_INTDIR}/${HDF5_JAVA_JNI_DLL_NAME}${CMAKE_SHARED_LIBRARY_SUFFIX} to ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/"
-    )
-    add_dependencies (HDF5_JAVA_JNI-Test-Copy ${HDF5_JAVA_JNI_LIB_TARGET})
-  endif ()
-endif ()
 
 #-----------------------------------------------------------------------------
 # Add Target(s) to CMake Install for import into other projects
diff --git a/java/src/jni/h5Imp.c b/java/src/jni/h5Imp.c
index 2eeb075..1ad6b17 100644
--- a/java/src/jni/h5Imp.c
+++ b/java/src/jni/h5Imp.c
@@ -36,7 +36,6 @@ extern "C" {
 #include "h5Imp.h"
 
 extern JavaVM *jvm;
-extern jobject visit_callback;
 
 /*
  * Class:     hdf_hdf5lib_H5
diff --git a/java/src/jni/h5aImp.c b/java/src/jni/h5aImp.c
index c0dc182..aba2240 100644
--- a/java/src/jni/h5aImp.c
+++ b/java/src/jni/h5aImp.c
@@ -29,7 +29,11 @@ extern "C" {
 #include "h5aImp.h"
 
 extern JavaVM *jvm;
-extern jobject visit_callback;
+
+typedef struct _cb_wrapper {
+    jobject visit_callback;
+    jobject op_data;
+} cb_wrapper;
 
 #ifdef __cplusplus
 #define CBENVPTR (cbenv)
@@ -53,7 +57,8 @@ static herr_t H5AwriteVL_asstr (JNIEnv *env, hid_t attr_id, hid_t mem_id, jobjec
 static herr_t H5AwriteVL_str (JNIEnv *env, hid_t attr_id, hid_t mem_id, jobjectArray buf);
 static herr_t H5AreadVL_asstr (JNIEnv *env, hid_t attr_id, hid_t mem_id, jobjectArray buf);
 static herr_t H5AreadVL_str (JNIEnv *env, hid_t attr_id, hid_t mem_id, jobjectArray buf);
-static herr_t H5A_iterate_cb(hid_t g_id, const char *name, const H5A_info_t *info, void *op_data);
+
+static herr_t H5A_iterate_cb(hid_t g_id, const char *name, const H5A_info_t *info, void *cb_data);
 
 
 /*
@@ -1138,7 +1143,7 @@ Java_hdf_hdf5lib_H5__1H5Aget_1create_1plist
 
 static herr_t
 H5A_iterate_cb
-    (hid_t g_id, const char *name, const H5A_info_t *info, void *op_data) {
+    (hid_t g_id, const char *name, const H5A_info_t *info, void *cb_data) {
     JNIEnv    *cbenv;
     jint       status = -1;
     jclass     cls;
@@ -1147,6 +1152,9 @@ H5A_iterate_cb
     jmethodID  constructor;
     jvalue     args[4];
     jobject    cb_info_t = NULL;
+    cb_wrapper *wrapper = (cb_wrapper *)cb_data;
+    void *op_data = (void *)wrapper->op_data;
+    jobject visit_callback = wrapper->visit_callback;
 
     if(JVMPTR->AttachCurrentThread(JVMPAR2 (void**)&cbenv, NULL) == 0) {
         cls = CBENVPTR->GetObjectClass(CBENVPAR visit_callback);
@@ -1195,14 +1203,14 @@ Java_hdf_hdf5lib_H5_H5Aiterate
     hsize_t       start_idx = (hsize_t)idx;
     herr_t        status = -1;
 
+    cb_wrapper wrapper = {callback_op, op_data};
     ENVPTR->GetJavaVM(ENVPAR &jvm);
-    visit_callback = callback_op;
 
     if ((op_data == NULL) || (callback_op == NULL)) {
         h5nullArgument(env,  "H5Literate_by_name:  op_data or callback_op is NULL");
     } /* end if */
     else {
-        status = H5Aiterate2((hid_t)grp_id, (H5_index_t)idx_type, (H5_iter_order_t)order, (hsize_t*)&start_idx, (H5A_operator2_t)H5A_iterate_cb, (void*)op_data);
+        status = H5Aiterate2((hid_t)grp_id, (H5_index_t)idx_type, (H5_iter_order_t)order, (hsize_t*)&start_idx, (H5A_operator2_t)H5A_iterate_cb, (void*)&wrapper);
 
         if (status < 0)
             h5libraryError(env);
@@ -1224,9 +1232,9 @@ Java_hdf_hdf5lib_H5_H5Aiterate_1by_1name
     const char   *lName;
     hsize_t       start_idx = (hsize_t)idx;
     herr_t        status = -1;
+    cb_wrapper wrapper = {callback_op, op_data};
 
     ENVPTR->GetJavaVM(ENVPAR &jvm);
-    visit_callback = callback_op;
 
     if ((op_data == NULL) || (callback_op == NULL)) {
         h5nullArgument(env,  "H5Literate_by_name:  op_data or callback_op is NULL");
@@ -1234,7 +1242,7 @@ Java_hdf_hdf5lib_H5_H5Aiterate_1by_1name
     else {
         PIN_JAVA_STRING(name, lName);
         if (lName != NULL) {
-            status = H5Aiterate_by_name((hid_t)grp_id, lName, (H5_index_t)idx_type, (H5_iter_order_t)order, (hsize_t*)&start_idx, (H5A_operator2_t)H5A_iterate_cb, (void*)op_data, (hid_t)access_id);
+            status = H5Aiterate_by_name((hid_t)grp_id, lName, (H5_index_t)idx_type, (H5_iter_order_t)order, (hsize_t*)&start_idx, (H5A_operator2_t)H5A_iterate_cb, (void*)&wrapper, (hid_t)access_id);
 
             UNPIN_JAVA_STRING(name, lName);
 
diff --git a/java/src/jni/h5dImp.c b/java/src/jni/h5dImp.c
index 205e9fb..652c873 100644
--- a/java/src/jni/h5dImp.c
+++ b/java/src/jni/h5dImp.c
@@ -30,7 +30,11 @@ extern "C" {
 #include "h5dImp.h"
 
 extern JavaVM *jvm;
-extern jobject visit_callback;
+
+typedef struct _cb_wrapper {
+    jobject visit_callback;
+    jobject op_data;
+} cb_wrapper;
 
 #ifdef __cplusplus
   #ifdef _WINDOWS
@@ -1105,7 +1109,7 @@ Java_hdf_hdf5lib_H5_H5Dwrite_1string
                     const char *utf8 = ENVPTR->GetStringUTFChars(ENVPAR obj, 0);
 
                     if (utf8) {
-                        strncpy(&c_buf[i * str_len], utf8, str_len);
+                        HDstrncpy(&c_buf[i * str_len], utf8, str_len);
                     } /* end if */
 
                     ENVPTR->ReleaseStringUTFChars(ENVPAR obj, utf8);
@@ -1362,13 +1366,9 @@ Java_hdf_hdf5lib_H5_H5DwriteVL
             isVlenStr = 1; /* strings created by H5Tvlen_create(H5T_C_S1) */
         }
         if (isStr == 0 || isComplex>0 || isVlenStr) {
-            h5unimplemented(env, "H5DwriteVL: VL types, which are not string type, not implemented");
-            status = -1;
-#ifdef notdef
             status = H5DwriteVL_asstr(env, (hid_t)dataset_id, (hid_t)mem_type_id,
                                         (hid_t)mem_space_id, (hid_t)file_space_id,
                                         (hid_t)xfer_plist_id, buf);
-#endif
         }
         else if (isStr > 0) {
             status = H5DwriteVL_str(env, (hid_t)dataset_id, (hid_t)mem_type_id,
@@ -1892,7 +1892,7 @@ Java_hdf_hdf5lib_H5_H5Dset_1extent
 
 static herr_t
 H5D_iterate_cb
-    (void* elem, hid_t elem_id, unsigned ndim, const hsize_t *point, void *op_data) {
+    (void* elem, hid_t elem_id, unsigned ndim, const hsize_t *point, void *cb_data) {
     JNIEnv    *cbenv;
     jint       status;
     jclass     cls;
@@ -1900,6 +1900,9 @@ H5D_iterate_cb
     jbyteArray elemArray;
     jlongArray pointArray;
     jsize      size;
+    cb_wrapper *wrapper = (cb_wrapper *)cb_data;
+    void *op_data = (void *)wrapper->op_data;
+    jobject visit_callback = wrapper->visit_callback;
 
     if(JVMPTR->AttachCurrentThread(JVMPAR2 (void**)&cbenv, NULL) != 0) {
         JVMPTR->DetachCurrentThread(JVMPAR);
@@ -1962,9 +1965,9 @@ Java_hdf_hdf5lib_H5_H5Diterate
     herr_t        status = -1;
     jboolean      isCopy;
     jbyte        *buffP;
+    cb_wrapper wrapper = {callback_op, op_data};
 
     ENVPTR->GetJavaVM(ENVPAR &jvm);
-    visit_callback = callback_op;
 
     if (op_data == NULL) {
         h5nullArgument(env,  "H5Diterate:  op_data is NULL");
@@ -1981,7 +1984,7 @@ Java_hdf_hdf5lib_H5_H5Diterate
             h5JNIFatalError(env, "H5Diterate:  buf not pinned");
         } /* end if */
         else {
-            status = H5Diterate((void*)buffP, (hid_t)buf_type, (hid_t)space, (H5D_operator_t)H5D_iterate_cb, (void*)op_data);
+            status = H5Diterate((void*)buffP, (hid_t)buf_type, (hid_t)space, (H5D_operator_t)H5D_iterate_cb, (void*)&wrapper);
 
             if (status < 0) {
             ENVPTR->ReleaseByteArrayElements(ENVPAR buf, buffP, JNI_ABORT);
diff --git a/java/src/jni/h5eImp.c b/java/src/jni/h5eImp.c
index 10a02b0..9c80461 100644
--- a/java/src/jni/h5eImp.c
+++ b/java/src/jni/h5eImp.c
@@ -40,7 +40,11 @@ extern "C" {
 #include "h5eImp.h"
 
 extern JavaVM *jvm;
-extern jobject visit_callback;
+
+typedef struct _cb_wrapper {
+    jobject visit_callback;
+    jobject op_data;
+} cb_wrapper;
 
 #ifdef __cplusplus
   #define CBENVPTR (cbenv)
@@ -60,7 +64,7 @@ extern jobject visit_callback;
 /* Local Prototypes */
 /********************/
 
-static herr_t H5E_walk_cb(int nindx, const H5E_error2_t *info, void *op_data);
+static herr_t H5E_walk_cb(int nindx, const H5E_error2_t *info, void *cb_data);
 
 /*
  * Class:     hdf_hdf5lib_H5
@@ -475,7 +479,7 @@ Java_hdf_hdf5lib_H5_H5Eget_1num
 
 static herr_t
 H5E_walk_cb
-    (int nindx, const H5E_error2_t *info, void *op_data)
+    (int nindx, const H5E_error2_t *info, void *cb_data)
 {
     JNIEnv    *cbenv;
     jint       status = -1;
@@ -485,6 +489,9 @@ H5E_walk_cb
     jmethodID  constructor;
     jvalue     args[7];
     jobject    cb_info_t = NULL;
+    cb_wrapper *wrapper = (cb_wrapper *)cb_data;
+    void *op_data = (void *)wrapper->op_data;
+    jobject visit_callback = wrapper->visit_callback;
 
     if(JVMPTR->AttachCurrentThread(JVMPAR2 (void**)&cbenv, NULL) == 0) {
         cls = CBENVPTR->GetObjectClass(CBENVPAR visit_callback);
@@ -532,13 +539,14 @@ JNIEXPORT void JNICALL
 Java_hdf_hdf5lib_H5_H5Ewalk2
     (JNIEnv *env, jclass cls, jlong stk_id, jlong direction, jobject callback_op, jobject op_data)
 {
+    cb_wrapper wrapper = {callback_op, op_data};
+
     ENVPTR->GetJavaVM(ENVPAR &jvm);
-    visit_callback = callback_op;
 
     if ((op_data == NULL) || (callback_op == NULL)) {
         h5nullArgument(env,  "H5Ewalk2:  op_data or callback_op is NULL");
     } /* end if */
-    else if (H5Ewalk2(stk_id, (H5E_direction_t)direction, (H5E_walk2_t)H5E_walk_cb, (void*)op_data) < 0)
+    else if (H5Ewalk2(stk_id, (H5E_direction_t)direction, (H5E_walk2_t)H5E_walk_cb, (void*)&wrapper) < 0)
             h5libraryError(env);
 } /* end iJava_hdf_hdf5lib_H5_H5Ewalk2f */
 
diff --git a/java/src/jni/h5fImp.c b/java/src/jni/h5fImp.c
index 8cf5252..9d68290 100644
--- a/java/src/jni/h5fImp.c
+++ b/java/src/jni/h5fImp.c
@@ -29,7 +29,6 @@ extern "C" {
 #include "h5util.h"
 
 extern JavaVM *jvm;
-extern jobject visit_callback;
 
 /*
  * Class:     hdf_hdf5lib_H5
@@ -541,7 +540,7 @@ Java_hdf_hdf5lib_H5_H5Fclear_1elink_1file_1cache
  */
 JNIEXPORT void JNICALL
 Java_hdf_hdf5lib_H5_H5Fstart_1swmr_1write
-	(JNIEnv *env, jclass cls, jlong file_id)
+    (JNIEnv *env, jclass cls, jlong file_id)
 {
     if (H5Fstart_swmr_write((hid_t)file_id) < 0)
         h5libraryError(env);
@@ -554,7 +553,7 @@ Java_hdf_hdf5lib_H5_H5Fstart_1swmr_1write
  */
 JNIEXPORT void JNICALL
 Java_hdf_hdf5lib_H5_H5Fstart_1mdc_1logging
-	(JNIEnv *env, jclass cls, jlong file_id)
+    (JNIEnv *env, jclass cls, jlong file_id)
 {
     if (H5Fstart_mdc_logging((hid_t)file_id) < 0)
         h5libraryError(env);
@@ -580,7 +579,7 @@ Java_hdf_hdf5lib_H5_H5Fstop_1mdc_1logging
  */
 JNIEXPORT void JNICALL
 Java_hdf_hdf5lib_H5_H5Fget_1mdc_1logging_1status
-	(JNIEnv *env, jclass cls, jlong file_id, jbooleanArray mdc_logging_status)
+    (JNIEnv *env, jclass cls, jlong file_id, jbooleanArray mdc_logging_status)
 {
     hbool_t    is_enabled;
     hbool_t    is_currently_logging;
diff --git a/java/src/jni/h5gImp.c b/java/src/jni/h5gImp.c
index 41ec382..42c042a 100644
--- a/java/src/jni/h5gImp.c
+++ b/java/src/jni/h5gImp.c
@@ -30,7 +30,6 @@ extern "C" {
 #include "h5gImp.h"
 
 extern JavaVM *jvm;
-extern jobject visit_callback;
 
 /*
  * Class:     hdf_hdf5lib_H5
diff --git a/java/src/jni/h5iImp.c b/java/src/jni/h5iImp.c
index 47574ca..b8bd1cd 100644
--- a/java/src/jni/h5iImp.c
+++ b/java/src/jni/h5iImp.c
@@ -28,7 +28,6 @@ extern "C" {
 #include "h5iImp.h"
 
 extern JavaVM *jvm;
-extern jobject visit_callback;
 
 /*
  * Class:     hdf_hdf5lib_H5
diff --git a/java/src/jni/h5lImp.c b/java/src/jni/h5lImp.c
index f1734fd..e1ec3bd 100644
--- a/java/src/jni/h5lImp.c
+++ b/java/src/jni/h5lImp.c
@@ -28,13 +28,17 @@ extern "C" {
 #include "h5lImp.h"
 
 extern JavaVM *jvm;
-extern jobject visit_callback;
+
+typedef struct _cb_wrapper {
+    jobject visit_callback;
+    jobject op_data;
+} cb_wrapper;
 
 /********************/
 /* Local Prototypes */
 /********************/
 
-static herr_t H5L_iterate_cb(hid_t g_id, const char *name, const H5L_info_t *info, void *op_data);
+static herr_t H5L_iterate_cb(hid_t g_id, const char *name, const H5L_info_t *info, void *cb_data);
 
 /*
  * Class:     hdf_hdf5lib_H5
@@ -541,7 +545,7 @@ Java_hdf_hdf5lib_H5_H5Lmove
 
 static herr_t
 H5L_iterate_cb
-    (hid_t g_id, const char *name, const H5L_info_t *info, void *op_data)
+    (hid_t g_id, const char *name, const H5L_info_t *info, void *cb_data)
 {
     JNIEnv    *cbenv;
     jint       status;
@@ -551,6 +555,9 @@ H5L_iterate_cb
     jmethodID  constructor;
     jvalue     args[5];
     jobject    cb_info_t = NULL;
+    cb_wrapper *wrapper = (cb_wrapper *)cb_data;
+    void *op_data = (void *)wrapper->op_data;
+    jobject visit_callback = wrapper->visit_callback;
 
     if(JVMPTR->AttachCurrentThread(JVMPAR2 (void**)&cbenv, NULL) == 0) {
         cls = CBENVPTR->GetObjectClass(CBENVPAR visit_callback);
@@ -600,15 +607,15 @@ Java_hdf_hdf5lib_H5_H5Lvisit
         jobject callback_op, jobject op_data)
 {
     herr_t status = -1;
+    cb_wrapper wrapper = {callback_op, op_data};
 
     ENVPTR->GetJavaVM(ENVPAR &jvm);
-    visit_callback = callback_op;
 
     if ((op_data == NULL) || (callback_op == NULL)) {
         h5nullArgument(env,  "H5Lvisit:  op_data or callback_op is NULL");
     } /* end if */
     else {
-        status = H5Lvisit((hid_t)grp_id, (H5_index_t)idx_type, (H5_iter_order_t)order, (H5L_iterate_t)H5L_iterate_cb, (void*)op_data);
+        status = H5Lvisit((hid_t)grp_id, (H5_index_t)idx_type, (H5_iter_order_t)order, (H5L_iterate_t)H5L_iterate_cb, (void*)&wrapper);
         if (status < 0)
             h5libraryError(env);
     } /* end else */
@@ -628,9 +635,9 @@ Java_hdf_hdf5lib_H5_H5Lvisit_1by_1name
 {
     herr_t        status = -1;
     const char   *lName;
+    cb_wrapper wrapper = {callback_op, op_data};
 
     ENVPTR->GetJavaVM(ENVPAR &jvm);
-    visit_callback = callback_op;
 
     if ((op_data == NULL) || (callback_op == NULL)) {
         h5nullArgument(env,  "H5Lvisit_by_name:  op_data or callback_op is NULL");
@@ -638,7 +645,7 @@ Java_hdf_hdf5lib_H5_H5Lvisit_1by_1name
     else {
         PIN_JAVA_STRING(name, lName);
         if (lName != NULL) {
-            status = H5Lvisit_by_name((hid_t)grp_id, lName, (H5_index_t)idx_type, (H5_iter_order_t)order, (H5L_iterate_t)H5L_iterate_cb, (void*)op_data, (hid_t)access_id);
+            status = H5Lvisit_by_name((hid_t)grp_id, lName, (H5_index_t)idx_type, (H5_iter_order_t)order, (H5L_iterate_t)H5L_iterate_cb, (void*)&wrapper, (hid_t)access_id);
 
             UNPIN_JAVA_STRING(name, lName);
 
@@ -662,15 +669,15 @@ Java_hdf_hdf5lib_H5_H5Literate
 {
     hsize_t       start_idx = (hsize_t)idx;
     herr_t        status = -1;
+    cb_wrapper wrapper = {callback_op, op_data};
 
     ENVPTR->GetJavaVM(ENVPAR &jvm);
-    visit_callback = callback_op;
 
     if ((op_data == NULL) || (callback_op == NULL)) {
         h5nullArgument(env,  "H5Literate:  op_data or callback_op is NULL");
     } /* end if */
     else {
-        status = H5Literate((hid_t)grp_id, (H5_index_t)idx_type, (H5_iter_order_t)order, (hsize_t*)&start_idx, (H5L_iterate_t)H5L_iterate_cb, (void*)op_data);
+        status = H5Literate((hid_t)grp_id, (H5_index_t)idx_type, (H5_iter_order_t)order, (hsize_t*)&start_idx, (H5L_iterate_t)H5L_iterate_cb, (void*)&wrapper);
 
         if (status < 0)
             h5libraryError(env);
@@ -694,7 +701,7 @@ Java_hdf_hdf5lib_H5_H5Literate_1by_1name
     const char   *lName;
 
     ENVPTR->GetJavaVM(ENVPAR &jvm);
-    visit_callback = callback_op;
+    cb_wrapper wrapper = {callback_op, op_data};
 
     if ((op_data == NULL) || (callback_op == NULL)) {
         h5nullArgument(env,  "H5Literate_by_name:  op_data or callback_op is NULL");
@@ -702,7 +709,7 @@ Java_hdf_hdf5lib_H5_H5Literate_1by_1name
     else {
         PIN_JAVA_STRING(name, lName);
         if (lName != NULL) {
-            status = H5Literate_by_name((hid_t)grp_id, lName, (H5_index_t)idx_type, (H5_iter_order_t)order, (hsize_t*)&start_idx, (H5L_iterate_t)H5L_iterate_cb, (void*)op_data, (hid_t)access_id);
+            status = H5Literate_by_name((hid_t)grp_id, lName, (H5_index_t)idx_type, (H5_iter_order_t)order, (hsize_t*)&start_idx, (H5L_iterate_t)H5L_iterate_cb, (void*)&wrapper, (hid_t)access_id);
 
             UNPIN_JAVA_STRING(name, lName);
 
diff --git a/java/src/jni/h5oImp.c b/java/src/jni/h5oImp.c
index 6093e46..1de505a 100644
--- a/java/src/jni/h5oImp.c
+++ b/java/src/jni/h5oImp.c
@@ -27,13 +27,17 @@ extern "C" {
 #include "h5oImp.h"
 
 extern JavaVM *jvm;
-extern jobject visit_callback;
+
+typedef struct _cb_wrapper {
+    jobject visit_callback;
+    jobject op_data;
+} cb_wrapper;
 
 /********************/
 /* Local Prototypes */
 /********************/
 
-static herr_t H5O_iterate_cb(hid_t g_id, const char *name, const H5O_info_t *info, void *op_data);
+static herr_t H5O_iterate_cb(hid_t g_id, const char *name, const H5O_info_t *info, void *cb_data);
 
 /*
  * Class:     hdf_hdf5lib_H5
@@ -330,7 +334,7 @@ Java_hdf_hdf5lib_H5_H5Olink
 
 static herr_t
 H5O_iterate_cb
-    (hid_t g_id, const char *name, const H5O_info_t *info, void *op_data)
+    (hid_t g_id, const char *name, const H5O_info_t *info, void *cb_data)
 {
     JNIEnv    *cbenv;
     jint       status = -1;
@@ -343,6 +347,9 @@ H5O_iterate_cb
     jobject    ihinfobuf1;
     jobject    ihinfobuf2;
     jobject    cb_info_t = NULL;
+    cb_wrapper *wrapper = (cb_wrapper *)cb_data;
+    void *op_data = (void *)wrapper->op_data;
+    jobject visit_callback = wrapper->visit_callback;
 
     if(JVMPTR->AttachCurrentThread(JVMPAR2 (void**)&cbenv, NULL) != 0) {
         /* printf("JNI H5O_iterate_cb error: AttachCurrentThread failed\n"); */
@@ -448,9 +455,9 @@ Java_hdf_hdf5lib_H5_H5Ovisit
         jobject callback_op, jobject op_data, jint fields)
 {
     herr_t   status = -1;
+    cb_wrapper wrapper = {callback_op, op_data};
 
     ENVPTR->GetJavaVM(ENVPAR &jvm);
-    visit_callback = callback_op;
 
     if (op_data == NULL) {
         h5nullArgument(env, "H5Ovisit:  op_data is NULL");
@@ -459,7 +466,7 @@ Java_hdf_hdf5lib_H5_H5Ovisit
         h5nullArgument(env, "H5Ovisit:  callback_op is NULL");
     } /* end if */
     else {
-        status = H5Ovisit2((hid_t)grp_id, (H5_index_t)idx_type, (H5_iter_order_t)order, (H5O_iterate_t)H5O_iterate_cb, (void*)op_data, (unsigned)fields);
+        status = H5Ovisit2((hid_t)grp_id, (H5_index_t)idx_type, (H5_iter_order_t)order, (H5O_iterate_t)H5O_iterate_cb, (void*)&wrapper, (unsigned)fields);
 
         if (status < 0)
             h5libraryError(env);
@@ -480,9 +487,9 @@ Java_hdf_hdf5lib_H5_H5Ovisit_1by_1name
 {
     herr_t        status = -1;
     const char   *lName;
+    cb_wrapper wrapper = {callback_op, op_data};
 
     ENVPTR->GetJavaVM(ENVPAR &jvm);
-    visit_callback = callback_op;
 
     if (op_data == NULL) {
         h5nullArgument(env, "H5Ovisit_by_name:  op_data is NULL");
@@ -495,7 +502,7 @@ Java_hdf_hdf5lib_H5_H5Ovisit_1by_1name
     else {
         PIN_JAVA_STRING(name, lName);
         if (lName != NULL) {
-            status = H5Ovisit_by_name2((hid_t)grp_id, lName, (H5_index_t)idx_type, (H5_iter_order_t)order, (H5O_iterate_t)H5O_iterate_cb, (void*)op_data, (unsigned)fields, (hid_t)access_id);
+            status = H5Ovisit_by_name2((hid_t)grp_id, lName, (H5_index_t)idx_type, (H5_iter_order_t)order, (H5O_iterate_t)H5O_iterate_cb, (void*)&wrapper, (unsigned)fields, (hid_t)access_id);
 
             UNPIN_JAVA_STRING(name, lName);
 
diff --git a/java/src/jni/h5pImp.c b/java/src/jni/h5pImp.c
index 3ff7436..52008ce 100644
--- a/java/src/jni/h5pImp.c
+++ b/java/src/jni/h5pImp.c
@@ -27,7 +27,6 @@ extern "C" {
 #include "h5pImp.h"
 
 extern JavaVM *jvm;
-extern jobject visit_callback;
 extern jobject copy_callback;
 extern jobject close_callback;
 extern jobject create_callback;
@@ -36,6 +35,11 @@ extern jobject get_callback;
 extern jobject set_callback;
 extern jobject delete_callback;
 
+typedef struct _cb_wrapper {
+    jobject visit_callback;
+    jobject op_data;
+} cb_wrapper;
+
 /********************/
 /* Local Prototypes */
 /********************/
@@ -52,7 +56,7 @@ static herr_t H5P_prp_get_func_cb(hid_t prop_id, const char *name, size_t size,
 static herr_t H5P_prp_set_func_cb(hid_t prop_id, const char *name, size_t size, void *value);
 static herr_t H5P_prp_delete_func_cb(hid_t prop_id, const char *name, size_t size, void *value);
 
-static herr_t H5P_iterate_cb(hid_t prop_id, const char *name, void *op_data);
+static herr_t H5P_iterate_cb(hid_t prop_id, const char *name, void *cb_data);
 
 /*
  * Class:     hdf_hdf5lib_H5
@@ -3877,7 +3881,7 @@ Java_hdf_hdf5lib_H5_H5Pset_1fapl_1multi
                 const char *utf8 = ENVPTR->GetStringUTFChars(ENVPAR obj, 0);
 
                 if (utf8) {
-                    member_name[i] = (char*)HDmalloc(strlen(utf8) + 1);
+                    member_name[i] = (char*)HDmalloc(HDstrlen(utf8) + 1);
                     if (member_name[i]) {
                         strcpy(member_name[i], utf8);
                     } /* end if */
@@ -4185,7 +4189,7 @@ Java_hdf_hdf5lib_H5_H5Pset_1mdc_1config
         h5JNIFatalError(env, "H5Pset_mdc_config: out of memory trace_file_name");
         return;
     } /* end if */
-    strncpy(cacheinfo.trace_file_name, str, 1025);
+    HDstrncpy(cacheinfo.trace_file_name, str, 1025);
     ENVPTR->ReleaseStringUTFChars(ENVPAR j_str, str);
     if(ENVPTR->ExceptionOccurred(ENVONLY)) {
         h5JNIFatalError(env, "H5Pset_mdc_config: loading trace_file_name failed");
@@ -5042,7 +5046,7 @@ H5P_cls_copy_cb
     } /* end if */
     JVMPTR->DetachCurrentThread(JVMPAR);
     return (herr_t)status;
-} /* end H5P_cls_ccopy_cb */
+} /* end H5P_cls_copy_cb */
 
 static herr_t
 H5P_cls_close_cb
@@ -5158,13 +5162,16 @@ Java_hdf_hdf5lib_H5_H5Pget_1mdc_1log_1options
 
 static herr_t
 H5D_append_cb
-    (hid_t dataset_id, hsize_t *cur_dims, void *op_data)
+    (hid_t dataset_id, hsize_t *cur_dims, void *cb_data)
 {
     JNIEnv    *cbenv;
     jint       status = -1;
     jclass     cls;
     jmethodID  mid;
     jlongArray cur_dimsArray;
+    cb_wrapper *wrapper = (cb_wrapper *)cb_data;
+    void *op_data = (void *)wrapper->op_data;
+    jobject visit_callback = wrapper->visit_callback;
 
     if(JVMPTR->AttachCurrentThread(JVMPAR2 (void**)&cbenv, NULL) != 0) {
         JVMPTR->DetachCurrentThread(JVMPAR);
@@ -5199,9 +5206,9 @@ Java_hdf_hdf5lib_H5_H5Pset_1append_1flush
     (JNIEnv *env, jclass clss, jlong plist_id, jint ndims, jlongArray boundary, jobject callback_op, jobject op_data)
 {
     herr_t   status = -1;
+    cb_wrapper wrapper = {callback_op, op_data};
 
     ENVPTR->GetJavaVM(ENVPAR &jvm);
-    visit_callback = callback_op;
 
     if (op_data == NULL) {
         h5nullArgument(env, "H5Pset_append_flush:  op_data is NULL");
@@ -5210,7 +5217,7 @@ Java_hdf_hdf5lib_H5_H5Pset_1append_1flush
         h5nullArgument(env, "H5Pset_append_flush:  callback_op is NULL");
     } /* end if */
     else {
-        status = H5Pset_append_flush((hid_t)plist_id, (unsigned)ndims, (const hsize_t*)boundary, (H5D_append_cb_t)H5D_append_cb, (void*)op_data);
+        status = H5Pset_append_flush((hid_t)plist_id, (unsigned)ndims, (const hsize_t*)boundary, (H5D_append_cb_t)H5D_append_cb, (void*)&wrapper);
 
         if (status < 0)
             h5libraryError(env);
@@ -5603,13 +5610,16 @@ Java_hdf_hdf5lib_H5_H5Pinsert2
 
 static herr_t
 H5P_iterate_cb
-    (hid_t prop_id, const char *name, void *op_data)
+    (hid_t prop_id, const char *name, void *cb_data)
 {
     JNIEnv    *cbenv;
     jint       status = -1;
     jclass     cls;
     jmethodID  mid;
     jstring    str;
+    cb_wrapper *wrapper = (cb_wrapper *)cb_data;
+    void *op_data = (void *)wrapper->op_data;
+    jobject visit_callback = wrapper->visit_callback;
 
     /* fprintf(stderr, "\nJNI H5P_iterate_cb entered\n"); fflush(stderr); */
     if(JVMPTR->AttachCurrentThread(JVMPAR2 (void**)&cbenv, NULL) != 0) {
@@ -5656,9 +5666,9 @@ Java_hdf_hdf5lib_H5_H5Piterate
     herr_t   status = -1;
     jint    *theArray = NULL;
     jboolean isCopy;
+    cb_wrapper wrapper = {callback_op, op_data};
 
     ENVPTR->GetJavaVM(ENVPAR &jvm);
-    visit_callback = callback_op;
 
     if (op_data == NULL) {
         h5nullArgument(env, "H5Piterate:  op_data is NULL");
@@ -5668,7 +5678,7 @@ Java_hdf_hdf5lib_H5_H5Piterate
     } /* end else if */
     else {
         if (idx == NULL) {
-            status = H5Piterate((hid_t)prop_id, NULL, (H5P_iterate_t)H5P_iterate_cb, (void*)op_data);
+            status = H5Piterate((hid_t)prop_id, NULL, (H5P_iterate_t)H5P_iterate_cb, (void*)&wrapper);
         } /* end if */
         else {
             theArray = (jint *)ENVPTR->GetIntArrayElements(ENVPAR idx, &isCopy);
@@ -5676,7 +5686,7 @@ Java_hdf_hdf5lib_H5_H5Piterate
                 h5JNIFatalError(env, "H5Piterate:  idx not pinned");
             } /* end if */
             else
-                status = H5Piterate((hid_t)prop_id, (int*)&theArray[0], (H5P_iterate_t)H5P_iterate_cb, (void*)op_data);
+                status = H5Piterate((hid_t)prop_id, (int*)&theArray[0], (H5P_iterate_t)H5P_iterate_cb, (void*)&wrapper);
         } /* end else */
 
         if (status < 0) {
diff --git a/java/src/jni/h5plImp.c b/java/src/jni/h5plImp.c
index ffd5b7a..d551120 100644
--- a/java/src/jni/h5plImp.c
+++ b/java/src/jni/h5plImp.c
@@ -27,7 +27,6 @@ extern "C" {
 #include "h5plImp.h"
 
 extern JavaVM *jvm;
-extern jobject visit_callback;
 
 /*
  * Class:     hdf_hdf5lib_H5
diff --git a/java/src/jni/h5rImp.c b/java/src/jni/h5rImp.c
index b250550..5f2b86d 100644
--- a/java/src/jni/h5rImp.c
+++ b/java/src/jni/h5rImp.c
@@ -27,7 +27,6 @@ extern "C" {
 #include "h5rImp.h"
 
 extern JavaVM *jvm;
-extern jobject visit_callback;
 
 
 /*
diff --git a/java/src/jni/h5sImp.c b/java/src/jni/h5sImp.c
index 10f69eb..65cdd7b 100644
--- a/java/src/jni/h5sImp.c
+++ b/java/src/jni/h5sImp.c
@@ -27,7 +27,6 @@ extern "C" {
 #include "h5sImp.h"
 
 extern JavaVM *jvm;
-extern jobject visit_callback;
 
 /*
  * Class:     hdf_hdf5lib_H5
@@ -572,7 +571,7 @@ Java_hdf_hdf5lib_H5_H5Sset_1extent_1simple
         h5JNIFatalError(env, "H5Pset_simple_extent:  dims not pinned");
         return -1;
     } /* end if */
-    sa = lp = (hsize_t *) malloc((size_t)rank * sizeof(hsize_t));
+    sa = lp = (hsize_t *) HDmalloc((size_t)rank * sizeof(hsize_t));
     if (sa == NULL) {
         ENVPTR->ReleaseLongArrayElements(ENVPAR dims, dimsP, JNI_ABORT);
         h5JNIFatalError(env, "H5Sset_simple_extent:  dims not converted to hsize_t");
@@ -1018,7 +1017,7 @@ Java_hdf_hdf5lib_H5_H5Sget_1select_1hyper_1blocklist
                 h5JNIFatalError(env, "H5Sget_select_hyper_blocklist:  buf not pinned");
             } /* end if */
             else {
-                ba = (hsize_t *) malloc((size_t)nb * 2 * (size_t)rank * sizeof(hsize_t));
+                ba = (hsize_t *) HDmalloc((size_t)nb * 2 * (size_t)rank * sizeof(hsize_t));
                 if (ba == NULL) {
                     ENVPTR->ReleaseLongArrayElements(ENVPAR buf, bufP, JNI_ABORT);
                     h5JNIFatalError(env, "H5Screate-simple:  buffer not converted to hsize_t");
@@ -1136,7 +1135,7 @@ Java_hdf_hdf5lib_H5_H5Sget_1select_1bounds
             return -1;
         } /* end if */
         rank = (int) ENVPTR->GetArrayLength(ENVPAR start);
-        strt = (hsize_t *)malloc((size_t)rank * sizeof(hsize_t));
+        strt = (hsize_t *)HDmalloc((size_t)rank * sizeof(hsize_t));
         if (strt == NULL) {
             ENVPTR->ReleaseLongArrayElements(ENVPAR start, startP, JNI_ABORT);
             h5JNIFatalError(env, "H5Sget_select_bounds:  start not converted to hsize_t");
diff --git a/java/src/jni/h5tImp.c b/java/src/jni/h5tImp.c
index 7b4af56..307f1a5 100644
--- a/java/src/jni/h5tImp.c
+++ b/java/src/jni/h5tImp.c
@@ -30,7 +30,6 @@ extern "C" {
 #include "h5tImp.h"
 
 extern JavaVM *jvm;
-extern jobject visit_callback;
 
 /*
  * Class:     hdf_hdf5lib_H5
diff --git a/java/src/jni/h5util.c b/java/src/jni/h5util.c
index 33dca7f..fd34ba1 100644
--- a/java/src/jni/h5util.c
+++ b/java/src/jni/h5util.c
@@ -33,7 +33,6 @@ hsize_t H5TOOLS_BUFSIZE = (32 * 1024 * 1024);  /* 32 MB */
 int     H5TOOLS_TEXT_BLOCK = 16;  /* Number of elements on a line in a text export file */
 
 JavaVM *jvm;
-jobject visit_callback;
 jobject copy_callback;
 jobject close_callback;
 jobject create_callback;
@@ -1769,7 +1768,7 @@ h5str_render_bin_output
                         if (H5Tis_variable_str(tid)) {
                             s = *(char**) mem;
                             if (s != NULL)
-                                size = strlen(s);
+                                size = HDstrlen(s);
                         }
                         else {
                             s = (char *) mem;
@@ -2130,11 +2129,11 @@ render_bin_output_region_data_points
                     ret_value = -1;
 
                 HDfree(dims1);
-            } /* end if((dims1 = (hsize_t *) malloc(sizeof(hsize_t) * ndims)) != NULL) */
+            } /* end if((dims1 = (hsize_t *) HDmalloc(sizeof(hsize_t) * ndims)) != NULL) */
             else
                 ret_value = -1;
             HDfree(region_buf);
-        } /* end if((region_buf = malloc(type_size * (size_t)npoints)) != NULL) */
+        } /* end if((region_buf = HDmalloc(type_size * (size_t)npoints)) != NULL) */
         else
             ret_value = -1;
 
@@ -2437,7 +2436,7 @@ Java_hdf_hdf5lib_H5_H5AreadComplex
     H5Tclose(p_type);
 
     n = ENVPTR->GetArrayLength(ENVPAR buf);
-    rdata = (char *)malloc((size_t)n * size);
+    rdata = (char *)HDmalloc((size_t)n * size);
     if (rdata == NULL) {
         h5JNIFatalError(env, "H5AreadComplex:  failed to allocate buff for read");
     } /* end if */
@@ -2953,7 +2952,7 @@ obj_info_all
     if (retVal < 0) {
         *(datainfo->otype+datainfo->count) = -1;
         *(datainfo->ltype+datainfo->count) = -1;
-        *(datainfo->objname+datainfo->count) = (char *)HDmalloc(strlen(name)+1);
+        *(datainfo->objname+datainfo->count) = (char *)HDmalloc(HDstrlen(name)+1);
         HDstrcpy(*(datainfo->objname+datainfo->count), name);
         *(datainfo->objno+datainfo->count) = (unsigned long)-1;
     } /* end if */