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authorLarry Knox <lrknox@hdfgroup.org>2017-04-13 18:07:56 (GMT)
committerLarry Knox <lrknox@hdfgroup.org>2017-04-13 18:07:56 (GMT)
commitae32f505e08060e41e619a52dda979072b31af55 (patch)
tree1fb96d63d689ad331ffc19f00478d8eab8726508
parentfca6ea1fc4e3646f0431d1974b797c10b87b61d9 (diff)
parent32e706e2cc1cb73cc6cacf78e9174b7afa5e5430 (diff)
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Merge pull request #423 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10_1 to hdf5_1_10_1
* commit '32e706e2cc1cb73cc6cacf78e9174b7afa5e5430': Add new files in release_docs to MANIFEST. Cimmit changes to Makefile.in(s) and H5PL.c that resulted from running autogen.sh. Skip tests for page buffering in test/fheap.c for parallel build Skip the two tests for page buffering in test/fheap.c because this feature is disabled in parallel. Activate full testing when this feature is re-enabled in the future for parallel build. Due to HDFVIEW-19 add read VL as string function
-rw-r--r--MANIFEST4
-rw-r--r--README.txt2
-rw-r--r--c++/src/Makefile.in16
-rw-r--r--fortran/src/Makefile.in16
-rw-r--r--hl/c++/src/Makefile.in16
-rw-r--r--hl/fortran/src/Makefile.in16
-rw-r--r--hl/src/Makefile.in16
-rw-r--r--java/src/hdf/hdf5lib/H5.java3
-rw-r--r--java/src/jni/Makefile.in16
-rw-r--r--java/src/jni/h5dImp.c91
-rw-r--r--java/src/jni/h5dImp.h9
-rw-r--r--release_docs/RELEASE.txt2
-rw-r--r--src/H5PL.c2
-rw-r--r--src/Makefile.in16
-rw-r--r--test/fheap.c13
15 files changed, 121 insertions, 117 deletions
diff --git a/MANIFEST b/MANIFEST
index a573567..4b9c45e 100644
--- a/MANIFEST
+++ b/MANIFEST
@@ -431,7 +431,9 @@
./release_docs/COPYING
./release_docs/HISTORY-1_0-1_8_0_rc3.txt
-./release_docs/HISTORY-1_9.txt
+./release_docs/HISTORY-1_8.txt
+./release_docs/HISTORY-1_10.txt
+./release_docs/HISTORY-1_8_0-1_10_0.txt
./release_docs/INSTALL
./release_docs/INSTALL_CMake.txt
./release_docs/INSTALL_Cygwin.txt
diff --git a/README.txt b/README.txt
index d0d2ba5..632e380 100644
--- a/README.txt
+++ b/README.txt
@@ -1,4 +1,4 @@
-HDF5 version 1.10.1-pre2 currently under development
+HDF5 version 1.10.1-pre2 released on 2017-04-12
Please refer to the release_docs/INSTALL file for installation instructions.
------------------------------------------------------------------------------
diff --git a/c++/src/Makefile.in b/c++/src/Makefile.in
index ae63898..6dde879 100644
--- a/c++/src/Makefile.in
+++ b/c++/src/Makefile.in
@@ -740,11 +740,6 @@ TRACE = perl $(top_srcdir)/bin/trace
# .chklog files are output from those tests.
# *.clog and *.clog2 are from the MPE option.
CHECK_CLEANFILES = *.chkexe *.chklog *.clog *.clog2
-
-# Add libtool shared library version numbers to the HDF5 library
-# See libtool versioning documentation online.
-# After making changes, run bin/reconfigure to update other configure related
-# files like Makefile.in.
LT_VERS_INTERFACE = 101
LT_VERS_REVISION = 0
LT_VERS_AGE = 0
@@ -1401,17 +1396,6 @@ uninstall-am: uninstall-binSCRIPTS uninstall-includeHEADERS \
help:
@$(top_srcdir)/bin/makehelp
-# 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.
-
# Some C++ compilers/linkers (PGI?) create a directory named "ii_files" that
# holds *.ii files, which are template entity instantiations.
# This entire directory should be cleaned.
diff --git a/fortran/src/Makefile.in b/fortran/src/Makefile.in
index 3f12add..b94ba58 100644
--- a/fortran/src/Makefile.in
+++ b/fortran/src/Makefile.in
@@ -768,11 +768,6 @@ TRACE = perl $(top_srcdir)/bin/trace
# .chklog files are output from those tests.
# *.clog and *.clog2 are from the MPE option.
CHECK_CLEANFILES = *.chkexe *.chklog *.clog *.clog2
-
-# Add libtool shared library version numbers to the HDF5 library
-# See libtool versioning documentation online.
-# After making changes, run bin/reconfigure to update other configure related
-# files like Makefile.in.
LT_VERS_INTERFACE = 101
LT_VERS_REVISION = 0
LT_VERS_AGE = 0
@@ -1407,17 +1402,6 @@ uninstall-am: uninstall-libLTLIBRARIES uninstall-local
help:
@$(top_srcdir)/bin/makehelp
-# 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.
-
# Fortran module files can have different extensions and different names
# (e.g., different capitalizations) on different platforms. Write rules
# for them explicitly rather than trying to teach automake about them.
diff --git a/hl/c++/src/Makefile.in b/hl/c++/src/Makefile.in
index a50b6ff..597c9ca 100644
--- a/hl/c++/src/Makefile.in
+++ b/hl/c++/src/Makefile.in
@@ -730,11 +730,6 @@ TRACE = perl $(top_srcdir)/bin/trace
# .chklog files are output from those tests.
# *.clog and *.clog2 are from the MPE option.
CHECK_CLEANFILES = *.chkexe *.chklog *.clog *.clog2
-
-# Add libtool shared library version numbers to the HDF5 library
-# See libtool versioning documentation online.
-# After making changes, run bin/reconfigure to update other configure related
-# files like Makefile.in.
LT_VERS_INTERFACE = 101
LT_VERS_REVISION = 0
LT_VERS_AGE = 0
@@ -1298,17 +1293,6 @@ uninstall-am: uninstall-includeHEADERS uninstall-libLTLIBRARIES
help:
@$(top_srcdir)/bin/makehelp
-# 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.
-
# lib/progs/tests targets recurse into subdirectories. build-* targets
# build files in this directory.
build-lib: $(LIB)
diff --git a/hl/fortran/src/Makefile.in b/hl/fortran/src/Makefile.in
index 4f22961..507f609 100644
--- a/hl/fortran/src/Makefile.in
+++ b/hl/fortran/src/Makefile.in
@@ -758,11 +758,6 @@ TRACE = perl $(top_srcdir)/bin/trace
# .chklog files are output from those tests.
# *.clog and *.clog2 are from the MPE option.
CHECK_CLEANFILES = *.chkexe *.chklog *.clog *.clog2
-
-# Add libtool shared library version numbers to the HDF5 library
-# See libtool versioning documentation online.
-# After making changes, run bin/reconfigure to update other configure related
-# files like Makefile.in.
LT_VERS_INTERFACE = 101
LT_VERS_REVISION = 0
LT_VERS_AGE = 0
@@ -1340,17 +1335,6 @@ uninstall-am: uninstall-libLTLIBRARIES uninstall-local
help:
@$(top_srcdir)/bin/makehelp
-# 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.
-
# Fortran module files can have different extensions and different names
# (e.g., different capitalizations) on different platforms. Write rules
# for them explicitly rather than trying to teach automake about them.
diff --git a/hl/src/Makefile.in b/hl/src/Makefile.in
index 48ddcd7..d53c363 100644
--- a/hl/src/Makefile.in
+++ b/hl/src/Makefile.in
@@ -729,11 +729,6 @@ TRACE = perl $(top_srcdir)/bin/trace
# .chklog files are output from those tests.
# *.clog and *.clog2 are from the MPE option.
CHECK_CLEANFILES = *.chkexe *.chklog *.clog *.clog2
-
-# Add libtool shared library version numbers to the HDF5 library
-# See libtool versioning documentation online.
-# After making changes, run bin/reconfigure to update other configure related
-# files like Makefile.in.
LT_VERS_INTERFACE = 101
LT_VERS_REVISION = 0
LT_VERS_AGE = 0
@@ -1304,17 +1299,6 @@ uninstall-am: uninstall-includeHEADERS uninstall-libLTLIBRARIES
help:
@$(top_srcdir)/bin/makehelp
-# 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.
-
# lib/progs/tests targets recurse into subdirectories. build-* targets
# build files in this directory.
build-lib: $(LIB)
diff --git a/java/src/hdf/hdf5lib/H5.java b/java/src/hdf/hdf5lib/H5.java
index 03d7b6b..1f0dd3a 100644
--- a/java/src/hdf/hdf5lib/H5.java
+++ b/java/src/hdf/hdf5lib/H5.java
@@ -1796,6 +1796,9 @@ public class H5 implements java.io.Serializable {
return H5Dread_short(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true);
}
+ public synchronized static native int H5DreadVL(long dataset_id, long mem_type_id, long mem_space_id,
+ long file_space_id, long xfer_plist_id, Object[] buf) throws HDF5LibraryException, NullPointerException;
+
public synchronized static native int H5Dread_string(long dataset_id, long mem_type_id, long mem_space_id,
long file_space_id, long xfer_plist_id, String[] buf) throws HDF5LibraryException, NullPointerException;
diff --git a/java/src/jni/Makefile.in b/java/src/jni/Makefile.in
index 62b8da4..d29e539 100644
--- a/java/src/jni/Makefile.in
+++ b/java/src/jni/Makefile.in
@@ -730,11 +730,6 @@ TRACE = perl $(top_srcdir)/bin/trace
# .chklog files are output from those tests.
# *.clog and *.clog2 are from the MPE option.
CHECK_CLEANFILES = *.chkexe *.chklog *.clog *.clog2
-
-# Add libtool shared library version numbers to the HDF5 library
-# See libtool versioning documentation online.
-# After making changes, run bin/reconfigure to update other configure related
-# files like Makefile.in.
LT_VERS_INTERFACE = 101
LT_VERS_REVISION = 0
LT_VERS_AGE = 0
@@ -1297,17 +1292,6 @@ uninstall-am: uninstall-libLTLIBRARIES
help:
@$(top_srcdir)/bin/makehelp
-# 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.
-
# lib/progs/tests targets recurse into subdirectories. build-* targets
# build files in this directory.
build-lib: $(LIB)
diff --git a/java/src/jni/h5dImp.c b/java/src/jni/h5dImp.c
index d869601..66efed0 100644
--- a/java/src/jni/h5dImp.c
+++ b/java/src/jni/h5dImp.c
@@ -53,6 +53,7 @@ extern jobject visit_callback;
/* Local Prototypes */
/********************/
+static herr_t H5DreadVL_asstr (JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t file_sid, hid_t xfer_plist_id, jobjectArray buf);
static herr_t H5DreadVL_str (JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t file_sid, hid_t xfer_plist_id, jobjectArray buf);
static herr_t H5DreadVL_array (JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t file_sid, hid_t xfer_plist_id, jobjectArray buf);
static herr_t H5DwriteVL_str (JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t file_sid, hid_t xfer_plist_id, jobjectArray buf);
@@ -992,6 +993,96 @@ Java_hdf_hdf5lib_H5_H5Dwrite_1double
/*
* Class: hdf_hdf5lib_H5
+ * Method: H5DreadVL
+ * Signature: (JJJJJ[Ljava/lang/String;)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5DreadVL
+ (JNIEnv *env, jclass clss, jlong dataset_id, jlong mem_type_id, jlong mem_space_id,
+ jlong file_space_id, jlong xfer_plist_id, jobjectArray buf)
+{
+ herr_t status = -1;
+ htri_t isVlenStr=0;
+
+ if (buf == NULL) {
+ h5nullArgument(env, "H5DreadVL: buf is NULL");
+ } /* end if */
+ else {
+ isVlenStr = H5Tdetect_class((hid_t)mem_type_id, H5T_STRING);
+
+ if (isVlenStr)
+ h5badArgument(env, "H5DreadVL: type is not variable length non-string");
+ else
+ status = H5DreadVL_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);
+ } /* end else */
+
+ return (jint)status;
+} /* end Java_hdf_hdf5lib_H5_H5Dread_1VLStrings */
+
+herr_t
+H5DreadVL_asstr
+ (JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t file_sid, hid_t xfer_plist_id, jobjectArray buf)
+{
+ jint i;
+ jint n;
+ jstring jstr;
+ h5str_t h5str;
+ hvl_t *rdata;
+ size_t size;
+ size_t max_len = 0;
+ herr_t status = -1;
+
+ n = ENVPTR->GetArrayLength(ENVPAR buf);
+ rdata = (hvl_t*)HDcalloc((size_t)n, sizeof(hvl_t));
+ if (rdata == NULL) {
+ h5JNIFatalError(env, "H5DreadVL_notstr: failed to allocate buff for read");
+ } /* end if */
+ else {
+ status = H5Dread(did, tid, mem_sid, file_sid, xfer_plist_id, rdata);
+
+ if (status < 0) {
+ H5Dvlen_reclaim(tid, mem_sid, xfer_plist_id, rdata);
+ HDfree(rdata);
+ h5JNIFatalError(env, "H5DreadVL_notstr: failed to read data");
+ } /* end if */
+ else {
+ max_len = 1;
+ for (i=0; i < n; i++) {
+ if ((rdata + i)->len > max_len)
+ max_len = (rdata + i)->len;
+ }
+
+ size = H5Tget_size(tid) * max_len;
+ HDmemset(&h5str, 0, sizeof(h5str_t));
+ h5str_new(&h5str, 4 * size);
+
+ if (h5str.s == NULL) {
+ H5Dvlen_reclaim(tid, mem_sid, xfer_plist_id, rdata);
+ HDfree(rdata);
+ h5JNIFatalError(env, "H5DreadVL_notstr: failed to allocate buf");
+ } /* end if */
+ else {
+ for (i=0; i < n; i++) {
+ h5str.s[0] = '\0';
+ h5str_sprintf(&h5str, did, tid, rdata+i, 0);
+ jstr = ENVPTR->NewStringUTF(ENVPAR h5str.s);
+ ENVPTR->SetObjectArrayElement(ENVPAR buf, i, jstr);
+ } /* end for */
+ h5str_free(&h5str);
+
+ H5Dvlen_reclaim(tid, mem_sid, xfer_plist_id, rdata);
+ HDfree(rdata);
+ } /* end else */
+ } /* end else */
+ } /* end else */
+
+ return status;
+}
+
+/*
+ * Class: hdf_hdf5lib_H5
* Method: H5Dread_string
* Signature: (JJJJJ[Ljava/lang/String;)I
*/
diff --git a/java/src/jni/h5dImp.h b/java/src/jni/h5dImp.h
index 22b8f63..3cf24fe 100644
--- a/java/src/jni/h5dImp.h
+++ b/java/src/jni/h5dImp.h
@@ -204,6 +204,15 @@ Java_hdf_hdf5lib_H5_H5Dwrite_1double
/*
* Class: hdf_hdf5lib_H5
+ * Method: H5DreadVL
+ * Signature: (JJJJJ[Ljava/lang/String;)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5DreadVL
+(JNIEnv*, jclass, jlong, jlong, jlong, jlong, jlong, jobjectArray);
+
+/*
+ * Class: hdf_hdf5lib_H5
* Method: H5Dread_string
* Signature: (JJJJJ[Ljava/lang/String;)I
*/
diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt
index 3ab04d3..c5788b2 100644
--- a/release_docs/RELEASE.txt
+++ b/release_docs/RELEASE.txt
@@ -1,4 +1,4 @@
-HDF5 version 1.10.1-pre2 currently under development
+HDF5 version 1.10.1-pre2 released on 2017-04-12
================================================================================
INTRODUCTION
diff --git a/src/H5PL.c b/src/H5PL.c
index 512b00b..481368c 100644
--- a/src/H5PL.c
+++ b/src/H5PL.c
@@ -562,6 +562,7 @@ H5PLremove(unsigned int index)
unsigned int plindex;
FUNC_ENTER_API(FAIL)
+ H5TRACE1("e", "Iu", index);
if(H5PL_num_paths_g == 0)
HGOTO_ERROR(H5E_PLUGIN, H5E_NOSPACE, FAIL, "no directories in table")
if(index >= H5PL_MAX_PATH_NUM)
@@ -606,6 +607,7 @@ H5PLget(unsigned int index, char *pathname/*out*/, size_t size)
char *dl_path = NULL;
FUNC_ENTER_API(FAIL)
+ H5TRACE3("Zs", "Iuxz", index, pathname, size);
if(H5PL_num_paths_g == 0)
HGOTO_ERROR(H5E_PLUGIN, H5E_NOSPACE, FAIL, "no directories in table")
if(index >= H5PL_MAX_PATH_NUM)
diff --git a/src/Makefile.in b/src/Makefile.in
index 63be7e6..8c6029d 100644
--- a/src/Makefile.in
+++ b/src/Makefile.in
@@ -861,11 +861,6 @@ TRACE = perl $(top_srcdir)/bin/trace
# .chklog files are output from those tests.
# *.clog and *.clog2 are from the MPE option.
CHECK_CLEANFILES = *.chkexe *.chklog *.clog *.clog2
-
-# Add libtool shared library version numbers to the HDF5 library
-# See libtool versioning documentation online.
-# After making changes, run bin/reconfigure to update other configure related
-# files like Makefile.in.
LT_VERS_INTERFACE = 101
LT_VERS_REVISION = 0
LT_VERS_AGE = 0
@@ -1853,17 +1848,6 @@ uninstall-am: uninstall-includeHEADERS uninstall-libLTLIBRARIES \
help:
@$(top_srcdir)/bin/makehelp
-# 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.
-
# Number format detection
# The LD_LIBRARY_PATH setting is a kludge.
# Things should have been all set during H5detect making.
diff --git a/test/fheap.c b/test/fheap.c
index 11ee760..4be6cb9 100644
--- a/test/fheap.c
+++ b/test/fheap.c
@@ -16386,14 +16386,23 @@ main(void)
/*
* Caution when turning on ExpressMode 0:
- * It will activate testing with different combinations of
+ * It will activate testing with different combinations of
* page buffering and file space strategy and the
* running time will be long.
+ * For parallel build, the last two tests for page buffering
+ * are skipped because this feature is disabled in parallel.
+ * Activate full testing when this feature is re-enabled
+ * in the future for parallel build.
*/
if(ExpressMode > 1)
HDprintf("***Express test mode on. Some tests may be skipped\n");
- else if(ExpressMode == 0)
+ else if(ExpressMode == 0) {
+#ifdef H5_HAVE_PARALLEL
+ num_pb_fs = NUM_PB_FS - 2;
+#else
num_pb_fs = NUM_PB_FS;
+#endif
+ }
/* Initialize heap creation parameters */
init_small_cparam(&small_cparam);