Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into develop

config/cmake_ext_mod/runTest.cmake

@@ -144,7 +144,7 @@ if (TEST_MASK_ERROR)
     # the error stack remains in the .err file
     file (READ ${TEST_FOLDER}/${TEST_OUTPUT}.err TEST_STREAM)
   endif ()
-  string (REGEX REPLACE "[.]*_pmi_alps[.]*\n" "" TEST_STREAM "${TEST_STREAM}")
+  string (REGEX REPLACE "^.*_pmi_alps[^\n]+\n" "" TEST_STREAM "${TEST_STREAM}")
   string (REGEX REPLACE "thread [0-9]*:" "thread (IDs):" TEST_STREAM "${TEST_STREAM}")
   string (REGEX REPLACE ": ([^\n]*)[.]c " ": (file name) " TEST_STREAM "${TEST_STREAM}")
   string (REGEX REPLACE " line [0-9]*" " line (number)" TEST_STREAM "${TEST_STREAM}")

java/src/hdf/hdf5lib/H5.java

@@ -1175,7 +1175,6 @@ public class H5 implements java.io.Serializable {
 
     public synchronized static native int H5Aread_reg_ref(long attr_id, long mem_type_id, String[] buf)
             throws HDF5LibraryException, NullPointerException;
-            throws HDF5LibraryException, NullPointerException;
 
     public synchronized static native int H5Aread_short(long attr_id, long mem_type_id, short[] buf, boolean isCriticalPinning)
             throws HDF5LibraryException, NullPointerException;

java/src/jni/CMakeLists.txt

@@ -48,7 +48,9 @@ set (CMAKE_INCLUDE_CURRENT_DIR_IN_INTERFACE ON)
 
 ########### JNI libraries always must be built shared  ###############
 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} ${HDF5_JAVA_JNI_SOURCE_DIR})
+target_include_directories(${HDF5_JAVA_JNI_LIB_TARGET}
+    PRIVATE "${HDF5_BINARY_DIR};${HDF5_JAVA_JNI_SOURCE_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>"
+)
 TARGET_C_PROPERTIES (${HDF5_JAVA_JNI_LIB_TARGET} SHARED)
 target_link_libraries (${HDF5_JAVA_JNI_LIB_TARGET} PUBLIC ${HDF5_LIBSH_TARGET})
 set_target_properties (${HDF5_JAVA_JNI_LIB_TARGET} PROPERTIES FOLDER libraries/jni)

src/CMakeLists.txt

@@ -950,6 +950,7 @@ if (NOT EXISTS ${HDF5_GENERATED_SOURCE_DIR}/H5Tinit.c)
     )
     add_custom_command (
         OUTPUT ${HDF5_GENERATED_SOURCE_DIR}/H5Tinit.c
+               ${HDF5_GENERATED_SOURCE_DIR}/gen_SRCS.stamp1
         COMMAND ${HDF5_BATCH_CMD}
         ARGS ${HDF5_BINARY_DIR}/${HDF5_BATCH_H5DETECT_SCRIPT}
         COMMAND ${CMAKE_COMMAND}
@@ -965,6 +966,7 @@ if (NOT EXISTS ${HDF5_GENERATED_SOURCE_DIR}/H5Tinit.c)
     if (BUILD_SHARED_LIBS)
       add_custom_command (
           OUTPUT     ${HDF5_GENERATED_SOURCE_DIR}/shared/H5Tinit.c
+                     ${HDF5_GENERATED_SOURCE_DIR}/shared/shared_gen_SRCS.stamp1
           COMMAND    ${CMAKE_COMMAND}
           ARGS       -E copy_if_different "${HDF5_GENERATED_SOURCE_DIR}/H5Tinit.c" "${HDF5_GENERATED_SOURCE_DIR}/shared/H5Tinit.c"
           COMMAND    ${CMAKE_COMMAND}
@@ -977,6 +979,7 @@ if (NOT EXISTS ${HDF5_GENERATED_SOURCE_DIR}/H5Tinit.c)
   else ()
     add_custom_command (
         OUTPUT ${HDF5_GENERATED_SOURCE_DIR}/H5Tinit.c
+               ${HDF5_GENERATED_SOURCE_DIR}/gen_SRCS.stamp1
         COMMAND ${CMAKE_CROSSCOMPILING_EMULATOR}$<TARGET_FILE:H5detect>
         ARGS ${HDF5_GENERATED_SOURCE_DIR}/H5Tinit.c
         COMMAND    ${CMAKE_COMMAND}
@@ -987,6 +990,7 @@ if (NOT EXISTS ${HDF5_GENERATED_SOURCE_DIR}/H5Tinit.c)
     if (BUILD_SHARED_LIBS)
       add_custom_command (
           OUTPUT     ${HDF5_GENERATED_SOURCE_DIR}/shared/H5Tinit.c
+                     ${HDF5_GENERATED_SOURCE_DIR}/shared/shared_gen_SRCS.stamp1
           COMMAND    ${CMAKE_COMMAND}
           ARGS       -E copy_if_different "${HDF5_GENERATED_SOURCE_DIR}/H5Tinit.c" "${HDF5_GENERATED_SOURCE_DIR}/shared/H5Tinit.c"
           COMMAND    ${CMAKE_COMMAND}
@@ -998,6 +1002,26 @@ if (NOT EXISTS ${HDF5_GENERATED_SOURCE_DIR}/H5Tinit.c)
     endif ()
   endif ()
   set_source_files_properties (${HDF5_GENERATED_SOURCE_DIR}/H5Tinit.c PROPERTIES GENERATED TRUE)
+else ()
+  add_custom_command (
+      OUTPUT ${HDF5_GENERATED_SOURCE_DIR}/gen_SRCS.stamp1
+      COMMAND    ${CMAKE_COMMAND}
+      ARGS       -E touch ${HDF5_GENERATED_SOURCE_DIR}/gen_SRCS.stamp1
+      DEPENDS    ${HDF5_GENERATED_SOURCE_DIR}/H5Tinit.c
+      WORKING_DIRECTORY ${HDF5_GENERATED_SOURCE_DIR}
+  )
+  if (BUILD_SHARED_LIBS)
+    add_custom_command (
+        OUTPUT     ${HDF5_GENERATED_SOURCE_DIR}/shared/shared_gen_SRCS.stamp1
+        COMMAND    ${CMAKE_COMMAND}
+        ARGS       -E copy_if_different "${HDF5_GENERATED_SOURCE_DIR}/H5Tinit.c" "${HDF5_GENERATED_SOURCE_DIR}/shared/H5Tinit.c"
+        COMMAND    ${CMAKE_COMMAND}
+        ARGS       -E touch ${HDF5_GENERATED_SOURCE_DIR}/shared/shared_gen_SRCS.stamp1
+        DEPENDS    ${HDF5_GENERATED_SOURCE_DIR}/H5Tinit.c
+        WORKING_DIRECTORY ${HDF5_GENERATED_SOURCE_DIR}
+    )
+    set_source_files_properties (${HDF5_GENERATED_SOURCE_DIR}/shared/H5Tinit.c PROPERTIES GENERATED TRUE)
+  endif ()
 endif ()
 
 add_executable (H5make_libsettings ${HDF5_SRC_DIR}/H5make_libsettings.c)
@@ -1011,6 +1035,7 @@ target_link_libraries (H5make_libsettings
 
 add_custom_command (
     OUTPUT ${HDF5_BINARY_DIR}/H5lib_settings.c
+           ${HDF5_BINARY_DIR}/gen_SRCS.stamp2
     COMMAND ${CMAKE_CROSSCOMPILING_EMULATOR}$<TARGET_FILE:H5make_libsettings>
     ARGS ${HDF5_BINARY_DIR}/H5lib_settings.c
     COMMAND    ${CMAKE_COMMAND}
@@ -1022,6 +1047,7 @@ set_source_files_properties (${HDF5_BINARY_DIR}/H5lib_settings.c PROPERTIES GENE
 if (BUILD_SHARED_LIBS)
   add_custom_command (
       OUTPUT ${HDF5_BINARY_DIR}/shared/H5lib_settings.c
+             ${HDF5_BINARY_DIR}/shared/shared_gen_SRCS.stamp2
       COMMAND    ${CMAKE_COMMAND}
       ARGS       -E copy_if_different "${HDF5_BINARY_DIR}/H5lib_settings.c" "${HDF5_BINARY_DIR}/shared/H5lib_settings.c"
       COMMAND    ${CMAKE_COMMAND}

src/H5A.c

@@ -1046,6 +1046,8 @@ H5Aget_info(hid_t attr_id, H5A_info_t *ainfo)
     /* Check arguments */
     if(NULL == (vol_obj = (H5VL_object_t *)H5I_object_verify(attr_id, H5I_ATTR)))
         HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not an attribute")
+    if(!ainfo)
+        HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "attribute_info parameter cannot be NULL")
 
     loc_params.type = H5VL_OBJECT_BY_SELF;
     loc_params.obj_type = H5I_get_type(attr_id);

test/tattr.c

@@ -143,6 +143,10 @@ float attr_data5=-5.123F;        /* Test data for 5th attribute */
 #define DIM1 100
 #define RANK 2
 
+/* Used by test_attr_info_null_info_pointer() */
+#define GET_INFO_NULL_POINTER_ATTR_NAME "NullInfoPointerAttr"
+
+
 /* Attribute iteration struct */
 typedef struct {
     H5_iter_order_t order;      /* Direction of iteration */
@@ -5874,6 +5878,65 @@ test_attr_info_by_idx(hbool_t new_format, hid_t fcpl, hid_t fapl)
     CHECK(ret, FAIL, "H5Sclose");
 }   /* test_attr_info_by_idx() */
 
+
+/***************************************************************
+**
+**  test_attr_info_null_info_pointer(): A test to ensure that
+**      passing a NULL attribute info pointer to H5Aget_info
+**      (_by_name/_by_idx) doesn't cause bad behavior.
+**
+****************************************************************/
+static void
+test_attr_info_null_info_pointer(hid_t fcpl, hid_t fapl)
+{
+    herr_t err_ret = -1;
+    hid_t  fid;
+    hid_t  attr;
+    hid_t  sid;
+
+    /* Create dataspace for dataset & attributes */
+    sid = H5Screate(H5S_SCALAR);
+    CHECK(sid, FAIL, "H5Screate");
+
+    /* Create file */
+    fid = H5Fcreate(FILENAME, H5F_ACC_TRUNC, fcpl, fapl);
+    CHECK(fid, FAIL, "H5Fcreate");
+
+    /* Create attribute */
+    attr = H5Acreate2(fid, GET_INFO_NULL_POINTER_ATTR_NAME, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT);
+    CHECK(attr, FAIL, "H5Acreate2");
+
+    H5E_BEGIN_TRY {
+        err_ret = H5Aget_info(attr, NULL);
+    } H5E_END_TRY;
+
+    CHECK(err_ret, SUCCEED, "H5Aget_info");
+
+    H5E_BEGIN_TRY {
+        err_ret = H5Aget_info_by_name(fid, ".", GET_INFO_NULL_POINTER_ATTR_NAME, NULL, H5P_DEFAULT);
+    } H5E_END_TRY;
+
+    CHECK(err_ret, SUCCEED, "H5Aget_info_by_name");
+
+    H5E_BEGIN_TRY {
+        err_ret = H5Aget_info_by_idx(fid, ".", H5_INDEX_NAME, H5_ITER_INC, 0, NULL, H5P_DEFAULT);
+    } H5E_END_TRY;
+
+    CHECK(err_ret, SUCCEED, "H5Aget_info_by_idx");
+
+    /* Close dataspace */
+    err_ret = H5Sclose(sid);
+    CHECK(err_ret, FAIL, "H5Sclose");
+
+    /* Close attribute */
+    err_ret = H5Aclose(attr);
+    CHECK(err_ret, FAIL, "H5Aclose");
+
+    /* Close file */
+    err_ret = H5Fclose(fid);
+    CHECK(err_ret, FAIL, "H5Fclose");
+}
+
 
 /****************************************************************
 **
@@ -10875,6 +10938,7 @@ test_attr(void)
                 test_attr_null_space(my_fcpl, my_fapl);         /* Test storing attribute with NULL dataspace */
                 test_attr_deprec(fcpl, my_fapl);                /* Test deprecated API routines */
                 test_attr_many(new_format, my_fcpl, my_fapl);               /* Test storing lots of attributes */
+                test_attr_info_null_info_pointer(my_fcpl, my_fapl); /* Test passing a NULL attribute info pointer to H5Aget_info(_by_name/_by_idx) */
 
                 /* Attribute creation order tests */
                 test_attr_corder_create_basic(my_fcpl, my_fapl);/* Test creating an object w/attribute creation order info */
@@ -10919,6 +10983,7 @@ test_attr(void)
             test_attr_null_space(fcpl, my_fapl);                /* Test storing attribute with NULL dataspace */
             test_attr_deprec(fcpl, my_fapl);                    /* Test deprecated API routines */
             test_attr_many(new_format, fcpl, my_fapl);               /* Test storing lots of attributes */
+            test_attr_info_null_info_pointer(fcpl, my_fapl); /* Test passing a NULL attribute info pointer to H5Aget_info(_by_name/_by_idx) */
 
             /* New attribute API routine tests, on old-format storage */
             test_attr_info_by_idx(new_format, fcpl, my_fapl);   /* Test querying attribute info by index */