Merge branch 'develop' into parallel_vds_developinactive/parallel_vds_develop

1 files changed, 505 insertions, 0 deletions

diff --git a/java/src/jni/h5pDXPLImp.c b/java/src/jni/h5pDXPLImp.c
new file mode 100644
index 0000000..323fa8c
--- /dev/null
+++ b/java/src/jni/h5pDXPLImp.c
@@ -0,0 +1,505 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * Copyright by The HDF Group.                                               *
+ * Copyright by the Board of Trustees of the University of Illinois.         *
+ * All rights reserved.                                                      *
+ *                                                                           *
+ * This file is part of HDF5.  The full HDF5 copyright notice, including     *
+ * terms governing use, modification, and redistribution, is contained in    *
+ * the COPYING file, which can be found at the root of the source code       *
+ * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.  *
+ * If you do not have access to either file, you may request a copy from     *
+ * help@hdfgroup.org.                                                        *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+/*
+ *  For details of the HDF libraries, see the HDF Documentation at:
+ *    http://hdfgroup.org/HDF5/doc/
+ *
+ */
+
+#ifdef __cplusplus
+extern "C" {
+#endif /* __cplusplus */
+
+#include <stdlib.h>
+#include "hdf5.h"
+#include "h5jni.h"
+#include "h5pDXPLImp.h"
+
+/*
+ * Pointer to the JNI's Virtual Machine; used for callback functions.
+ */
+/* extern JavaVM *jvm; */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Pset_buffer
+ * Signature: (JJ[B[B)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Pset_1buffer
+    (JNIEnv *env, jclass clss, jlong plist, jlong size, jbyteArray tconv, jbyteArray bkg)
+{
+#ifdef notdef
+    jboolean  isCopy;
+    jbyte    *tconvP = NULL;
+    jbyte    *bkgP = NULL;
+#endif
+    herr_t    status = FAIL;
+
+    UNUSED(clss);
+#ifndef notdef
+    UNUSED(plist);
+    UNUSED(size);
+    UNUSED(tconv);
+    UNUSED(bkg);
+#endif
+
+    H5_UNIMPLEMENTED(ENVONLY, "H5Pset_buffer: not implemented");
+
+    /* NOTE: DON'T IMPLEMENT THIS!!! */
+#ifdef notdef
+    if (NULL != tconv)
+        PIN_BYTE_ARRAY(ENVONLY, tconv, tconvP, &isCopy, "H5Pset_buffer: tconv not pinned");
+    if (NULL != bkg)
+        PIN_BYTE_ARRAY(ENVONLY, bkg, bkgP, &isCopy, "H5Pset_buffer: bkg not pinned");
+
+    if ((status = H5Pset_buffer((hid_t)plist, (size_t)size, tconvP, bkgP)) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+#endif
+
+done:
+#ifdef notdef
+    if (bkgP)
+        UNPIN_BYTE_ARRAY(ENVONLY, bkg, bkgP, (status < 0) ? JNI_ABORT : 0);
+    if (tconvP)
+        UNPIN_BYTE_ARRAY(ENVONLY, tconv, tconvP, (status < 0) ? JNI_ABORT : 0);
+#endif
+
+    return (jint)status;
+} /* end Java_hdf_hdf5lib_H5_H5Pset_1buffer */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Pget_buffer
+ * Signature: (J[B[B)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Pget_1buffer
+    (JNIEnv *env, jclass clss, jlong plist, jbyteArray tconv, jbyteArray bkg)
+{
+#ifdef notdef
+    jboolean  isCopy;
+    jbyte    *tconvP = NULL;
+    jbyte    *bkgP = NULL;
+#endif
+    herr_t    status = FAIL;
+
+    UNUSED(clss);
+#ifndef notdef
+    UNUSED(plist);
+    UNUSED(tconv);
+    UNUSED(bkg);
+#endif
+
+    H5_UNIMPLEMENTED(ENVONLY, "H5Pget_buffer: not implemented");
+
+    /* NOTE: DON'T IMPLEMENT THIS!!! */
+#ifdef notdef
+    if (NULL == tconv)
+        H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Pget_buffer: tconv input array is NULL");
+    if (NULL == bkg)
+        H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Pget_buffer: bkg array is NULL");
+
+    PIN_BYTE_ARRAY(ENVONLY, tconv, tconvP, &isCopy, "H5Pget_buffer: tconv not pinned");
+    PIN_BYTE_ARRAY(ENVONLY, bkg, bkgP, &isCopy, "H5Pget_buffer: bkg not pinned");
+
+    if ((status = H5Pget_buffer((hid_t)plist, tconvP, bkgP)) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+#endif
+
+done:
+#ifdef notdef
+    if (bkgP)
+        UNPIN_BYTE_ARRAY(ENVONLY, bkg, bkgP, (status < 0) ? JNI_ABORT : 0);
+    if (tconvP)
+        UNPIN_BYTE_ARRAY(ENVONLY, tconv, tconvP, (status < 0) ? JNI_ABORT : 0);
+#endif
+
+    return (jint)status;
+} /* end Java_hdf_hdf5lib_H5_H5Pget_1buffer */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Pset_buffer_size
+ * Signature: (JJ)V
+ */
+JNIEXPORT void JNICALL
+Java_hdf_hdf5lib_H5_H5Pset_1buffer_1size
+    (JNIEnv *env, jclass clss, jlong plist, jlong size)
+{
+    UNUSED(clss);
+
+    if (H5Pset_buffer((hid_t)plist, (size_t)size, NULL, NULL) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+
+done:
+    return;
+} /* end Java_hdf_hdf5lib_H5_H5Pset_1buffer_1size */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Pget_buffer_size
+ * Signature: (J)J
+ */
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_H5_H5Pget_1buffer_1size
+    (JNIEnv *env, jclass clss, jlong plist)
+{
+    size_t size = 0;
+
+    UNUSED(clss);
+
+    if (!(size = H5Pget_buffer((hid_t)plist, NULL, NULL)))
+        H5_LIBRARY_ERROR(ENVONLY);
+
+done:
+    return (jlong)size;
+} /* end Java_hdf_hdf5lib_H5_H5Pget_1buffer_1size */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Pset_preserve
+ * Signature: (JZ)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Pset_1preserve
+    (JNIEnv *env, jclass clss, jlong plist, jboolean status)
+{
+    hbool_t st = JNI_FALSE;
+    herr_t  retVal = FAIL;
+
+    UNUSED(clss);
+
+    if (JNI_TRUE == status)
+        st = TRUE;
+    else if (JNI_FALSE == status)
+        st = false;
+    else
+        H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Pset_preserve: status not TRUE or FALSE");
+
+    if ((retVal = H5Pset_preserve((hid_t)plist, st)) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+
+done:
+    return (jint)retVal;
+} /* end Java_hdf_hdf5lib_H5_H5Pset_1preserve */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Pget_preserve
+ * Signature: (J)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Pget_1preserve
+    (JNIEnv *env, jclass clss, jlong plist)
+{
+    herr_t retVal = FAIL;
+
+    UNUSED(clss);
+
+    if ((retVal = H5Pget_preserve((hid_t)plist)) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+
+done:
+    return (jint)retVal;
+} /* end Java_hdf_hdf5lib_H5_H5Pget_1preserve */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Pset_edc_check
+ * Signature: (JI)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Pset_1edc_1check
+    (JNIEnv *env, jclass clss, jlong plist, jint check)
+{
+    herr_t retVal = FAIL;
+
+    UNUSED(clss);
+
+    if ((retVal = H5Pset_edc_check((hid_t)plist, (H5Z_EDC_t)check)) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+
+done:
+    return (jint)retVal;
+} /* end Java_hdf_hdf5lib_H5_H5Pset_1edc_1check */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Pget_edc_check
+ * Signature: (J)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Pget_1edc_1check
+    (JNIEnv *env, jclass clss, jlong plist)
+{
+    H5Z_EDC_t retVal = -1;
+
+    UNUSED(clss);
+
+    if ((retVal = H5Pget_edc_check((hid_t)plist)) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+
+done:
+    return (jint)retVal;
+} /* end Java_hdf_hdf5lib_H5_H5Pget_1edc_1check */
+
+/*
+ * TODO: H5Pset_filter_callback
+ */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Pset_data_transform
+ * Signature: (JLjava/lang/String;)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Pset_1data_1transform
+    (JNIEnv *env, jclass clss, jlong plist_id, jstring expression)
+{
+    const char *express = NULL;
+    herr_t      retVal = FAIL;
+
+    UNUSED(clss);
+
+    if (NULL == expression)
+        H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Pset_data_transform: data transform expression is NULL");
+
+    PIN_JAVA_STRING(ENVONLY, expression, express, NULL, "H5Pset_data_transform: data transform expression not pinned");
+
+    if ((retVal = H5Pset_data_transform((hid_t)plist_id, express)) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+
+done:
+    if (express)
+        UNPIN_JAVA_STRING(ENVONLY, expression, express);
+
+    return (jint)retVal;
+} /* end Java_hdf_hdf5lib_H5_H5Pset_1data_1transform */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Pget_data_transform
+ * Signature: (J[Ljava/lang/String;J)J
+ */
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_H5_H5Pget_1data_1transform
+    (JNIEnv *env, jclass clss, jlong plist_id, jobjectArray expression, jlong size)
+{
+    jstring  str = NULL;
+    char    *express = NULL;
+    ssize_t  express_size = -1;
+
+    UNUSED(clss);
+
+    if (size <= 0)
+        H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Pget_data_transform: size <= 0");
+
+    if ((express_size = H5Pget_data_transform((hid_t)plist_id, (char *)NULL, (size_t)size)) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+
+    if (NULL == (express = (char *) HDmalloc(sizeof(char) * (size_t)express_size + 1)))
+        H5_JNI_FATAL_ERROR(ENVONLY, "H5Pget_data_transform: memory allocation failed");
+
+    if (H5Pget_data_transform((hid_t)plist_id, express, (size_t)express_size + 1) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+    express[express_size] = '\0';
+
+    if (NULL == (str = ENVPTR->NewStringUTF(ENVONLY, express))) {
+        CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
+        H5_JNI_FATAL_ERROR(ENVONLY, "H5Pget_data_transform: out of memory - unable to construct string from UTF characters");
+    }
+
+    ENVPTR->SetObjectArrayElement(ENVONLY, expression, 0, str);
+    CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+
+done:
+    if (express)
+        HDfree(express);
+
+    return (jlong)express_size;
+} /* end Java_hdf_hdf5lib_H5_H5Pget_1data_1transform */
+
+/*
+ * TODO: H5Pset_type_conv_cb
+ */
+
+/*
+ * TODO: H5Pget_type_conv_cb
+ */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Pset_hyper_vector_size
+ * Signature: (JJ)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Pset_1hyper_1vector_1size
+    (JNIEnv *env, jclass clss, jlong plist, jlong vector_size)
+{
+    herr_t retVal = FAIL;
+
+    UNUSED(clss);
+
+    if ((retVal = H5Pset_hyper_vector_size((hid_t)plist, (size_t)vector_size)) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+
+done:
+    return (jint)retVal;
+} /* end Java_hdf_hdf5lib_H5_H5Pset_1hyper_1vector_1size */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Pget_hyper_vector_size
+ * Signature: (J[J)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Pget_1hyper_1vector_1size
+    (JNIEnv *env, jclass clss, jlong plist, jlongArray vector_size)
+{
+    jboolean  isCopy;
+    size_t    size;
+    jlong    *theArray = NULL;
+    herr_t    retVal = FAIL;
+
+    UNUSED(clss);
+
+    if (NULL == vector_size)
+        H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Pget_hyper_vector_size: vector_size is NULL");
+
+    PIN_LONG_ARRAY(ENVONLY, vector_size, theArray, &isCopy, "H5Pget_hyper_vector_size: vector_size not pinned");
+
+    if ((retVal =  H5Pget_hyper_vector_size((hid_t)plist, &size)) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+
+    theArray[0] = (jlong)size;
+
+done:
+    if (theArray)
+        UNPIN_LONG_ARRAY(ENVONLY, vector_size, theArray, (retVal < 0) ? JNI_ABORT : 0);
+
+    return (jint)retVal;
+} /* end Java_hdf_hdf5lib_H5_H5Pget_1hyper_1vector_1size */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Pset_btree_ratios
+ * Signature: (JDDD)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Pset_1btree_1ratios
+    (JNIEnv *env, jclass clss, jlong plist_id, jdouble left, jdouble middle, jdouble right)
+{
+    herr_t status = FAIL;
+
+    UNUSED(clss);
+
+    if ((status = H5Pset_btree_ratios((hid_t)plist_id, (double)left,(double)middle, (double)right)) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+
+done:
+    return (jint)status;
+} /* end Java_hdf_hdf5lib_H5_H5Pset_1btree_1ratios */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Pget_btree_ratios
+ * Signature: (J[D[D[D)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Pget_1btree_1ratios
+    (JNIEnv *env, jclass clss, jlong plist_id, jdoubleArray left,
+        jdoubleArray middle, jdoubleArray right)
+{
+    jboolean  isCopy;
+    jdouble  *leftP = NULL;
+    jdouble  *middleP = NULL;
+    jdouble  *rightP = NULL;
+    herr_t    status = FAIL;
+
+    UNUSED(clss);
+
+    if (NULL == left)
+        H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Pget_btree_ratios: left input array is NULL");
+    if (NULL == middle)
+        H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Pget_btree_ratios: middle input array is NULL");
+    if (NULL == right)
+        H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Pget_btree_ratios: right input array is NULL");
+
+    PIN_DOUBLE_ARRAY(ENVONLY, left, leftP, &isCopy, "H5Pget_btree_ratios: left array not pinned");
+    PIN_DOUBLE_ARRAY(ENVONLY, middle, middleP, &isCopy, "H5Pget_btree_ratios: middle array not pinned");
+    PIN_DOUBLE_ARRAY(ENVONLY, right, rightP, &isCopy, "H5Pget_btree_ratios: right array not pinned");
+
+    if ((status = H5Pget_btree_ratios((hid_t)plist_id, (double *)leftP,
+            (double *)middleP, (double *)rightP)) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+
+done:
+    if (rightP)
+        UNPIN_DOUBLE_ARRAY(ENVONLY, right, rightP, (status < 0) ? JNI_ABORT : 0);
+    if (middleP)
+        UNPIN_DOUBLE_ARRAY(ENVONLY, middle, middleP, (status < 0) ? JNI_ABORT : 0);
+    if (leftP)
+        UNPIN_DOUBLE_ARRAY(ENVONLY, left, leftP, (status < 0) ? JNI_ABORT : 0);
+
+    return (jint)status;
+} /* end Java_hdf_hdf5lib_H5_H5Pget_1btree_1ratios */
+
+/*
+ * TODO: H5Pset_vlen_mem_manager
+ */
+
+/*
+ * TODO: H5Pget_vlen_mem_manager
+ */
+
+/*
+ * TODO: H5Pset_dxpl_mpio
+ */
+
+/*
+ * TODO: H5Pget_dxpl_mpio
+ */
+
+/*
+ * TODO: H5Pset_dxpl_mpio_chunk_opt
+ */
+
+/*
+ * TODO: H5Pset_dxpl_mpio_chunk_opt_num
+ */
+
+/*
+ * TODO: H5Pset_dxpl_mpio_chunk_opt_ratio
+ */
+
+/*
+ * TODO: H5Pset_dxpl_mpio_collective_opt
+ */
+
+/*
+ * TODO: H5Pget_mpio_actual_chunk_opt_mode
+ */
+
+/*
+ * TODO: H5Pget_mpio_actual_io_mode
+ */
+
+/*
+ * TODO: H5Pget_mpio_no_collective_cause
+ */
+
+#ifdef __cplusplus
+} /* end extern "C" */
+#endif /* __cplusplus */