diff options
author | Larry Knox <lrknox@hdfgroup.org> | 2017-04-13 18:07:56 (GMT) |
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committer | Larry Knox <lrknox@hdfgroup.org> | 2017-04-13 18:07:56 (GMT) |
commit | ae32f505e08060e41e619a52dda979072b31af55 (patch) | |
tree | 1fb96d63d689ad331ffc19f00478d8eab8726508 | |
parent | fca6ea1fc4e3646f0431d1974b797c10b87b61d9 (diff) | |
parent | 32e706e2cc1cb73cc6cacf78e9174b7afa5e5430 (diff) | |
download | hdf5-ae32f505e08060e41e619a52dda979072b31af55.zip hdf5-ae32f505e08060e41e619a52dda979072b31af55.tar.gz hdf5-ae32f505e08060e41e619a52dda979072b31af55.tar.bz2 |
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-- | MANIFEST | 4 | ||||
-rw-r--r-- | README.txt | 2 | ||||
-rw-r--r-- | c++/src/Makefile.in | 16 | ||||
-rw-r--r-- | fortran/src/Makefile.in | 16 | ||||
-rw-r--r-- | hl/c++/src/Makefile.in | 16 | ||||
-rw-r--r-- | hl/fortran/src/Makefile.in | 16 | ||||
-rw-r--r-- | hl/src/Makefile.in | 16 | ||||
-rw-r--r-- | java/src/hdf/hdf5lib/H5.java | 3 | ||||
-rw-r--r-- | java/src/jni/Makefile.in | 16 | ||||
-rw-r--r-- | java/src/jni/h5dImp.c | 91 | ||||
-rw-r--r-- | java/src/jni/h5dImp.h | 9 | ||||
-rw-r--r-- | release_docs/RELEASE.txt | 2 | ||||
-rw-r--r-- | src/H5PL.c | 2 | ||||
-rw-r--r-- | src/Makefile.in | 16 | ||||
-rw-r--r-- | test/fheap.c | 13 |
15 files changed, 121 insertions, 117 deletions
@@ -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 @@ -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 @@ -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); |