From 53132d8864dc5733aaf9d19d2d4b7675f52f2eff Mon Sep 17 00:00:00 2001 From: Allen Byrne Date: Wed, 12 Apr 2017 17:21:43 -0500 Subject: Due to HDFVIEW-19 add read VL as string function --- java/src/hdf/hdf5lib/H5.java | 3 ++ java/src/jni/h5dImp.c | 91 ++++++++++++++++++++++++++++++++++++++++++++ java/src/jni/h5dImp.h | 9 +++++ 3 files changed, 103 insertions(+) diff --git a/java/src/hdf/hdf5lib/H5.java b/java/src/hdf/hdf5lib/H5.java index e47ba76..48b2402 100644 --- a/java/src/hdf/hdf5lib/H5.java +++ b/java/src/hdf/hdf5lib/H5.java @@ -1798,6 +1798,9 @@ 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/h5dImp.c b/java/src/jni/h5dImp.c index 9765dc8..0bb015e 100644 --- a/java/src/jni/h5dImp.c +++ b/java/src/jni/h5dImp.c @@ -55,6 +55,7 @@ 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); @@ -994,6 +995,96 @@ 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 eb26265..e79c590 100644 --- a/java/src/jni/h5dImp.h +++ b/java/src/jni/h5dImp.h @@ -206,6 +206,15 @@ 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 */ -- cgit v0.12 From 5f313c0172f9339c7cd69a4fd01c033d89466a8b Mon Sep 17 00:00:00 2001 From: Allen Byrne Date: Mon, 17 Apr 2017 11:32:32 -0500 Subject: HDFFV-10173 fix compile on VS2008 --- src/H5ACpublic.h | 236 +++++++++++++++++++++++++++---------------------------- 1 file changed, 118 insertions(+), 118 deletions(-) diff --git a/src/H5ACpublic.h b/src/H5ACpublic.h index 5fdb3f4..ca0e63f 100644 --- a/src/H5ACpublic.h +++ b/src/H5ACpublic.h @@ -70,65 +70,65 @@ extern "C" { * version number, or an error will be flagged. * * rpt_fcn_enabled: Boolean field used to enable and disable the default - * reporting function. This function is invoked every time the - * automatic cache resize code is run, and reports on its activities. + * reporting function. This function is invoked every time the + * automatic cache resize code is run, and reports on its activities. * - * This is a debugging function, and should normally be turned off. + * This is a debugging function, and should normally be turned off. * * open_trace_file: Boolean field indicating whether the trace_file_name - * field should be used to open a trace file for the cache. + * field should be used to open a trace file for the cache. * * *** DEPRECATED *** Use H5Fstart/stop logging functions instead * - * The trace file is a debuging feature that allow the capture of - * top level metadata cache requests for purposes of debugging and/or - * optimization. This field should normally be set to FALSE, as - * trace file collection imposes considerable overhead. + * The trace file is a debuging feature that allow the capture of + * top level metadata cache requests for purposes of debugging and/or + * optimization. This field should normally be set to FALSE, as + * trace file collection imposes considerable overhead. * - * This field should only be set to TRUE when the trace_file_name - * contains the full path of the desired trace file, and either - * there is no open trace file on the cache, or the close_trace_file - * field is also TRUE. + * This field should only be set to TRUE when the trace_file_name + * contains the full path of the desired trace file, and either + * there is no open trace file on the cache, or the close_trace_file + * field is also TRUE. * * close_trace_file: Boolean field indicating whether the current trace - * file (if any) should be closed. + * file (if any) should be closed. * * *** DEPRECATED *** Use H5Fstart/stop logging functions instead * - * See the above comments on the open_trace_file field. This field - * should be set to FALSE unless there is an open trace file on the - * cache that you wish to close. + * See the above comments on the open_trace_file field. This field + * should be set to FALSE unless there is an open trace file on the + * cache that you wish to close. * * trace_file_name: Full path of the trace file to be opened if the - * open_trace_file field is TRUE. + * open_trace_file field is TRUE. * * *** DEPRECATED *** Use H5Fstart/stop logging functions instead * - * In the parallel case, an ascii representation of the mpi rank of - * the process will be appended to the file name to yield a unique - * trace file name for each process. + * In the parallel case, an ascii representation of the mpi rank of + * the process will be appended to the file name to yield a unique + * trace file name for each process. * - * The length of the path must not exceed H5AC__MAX_TRACE_FILE_NAME_LEN - * characters. + * The length of the path must not exceed H5AC__MAX_TRACE_FILE_NAME_LEN + * characters. * * evictions_enabled: Boolean field used to either report the current - * evictions enabled status of the cache, or to set the cache's - * evictions enabled status. - * - * In general, the metadata cache should always be allowed to - * evict entries. However, in some cases it is advantageous to - * disable evictions briefly, and thereby postpone metadata - * writes. However, this must be done with care, as the cache - * can grow quickly. If you do this, re-enable evictions as - * soon as possible and monitor cache size. - * - * At present, evictions can only be disabled if automatic - * cache resizing is also disabled (that is, ( incr_mode == - * H5C_incr__off ) && ( decr_mode == H5C_decr__off )). There - * is no logical reason why this should be so, but it simplifies - * implementation and testing, and I can't think of any reason - * why it would be desireable. If you can think of one, I'll - * revisit the issue. + * evictions enabled status of the cache, or to set the cache's + * evictions enabled status. + * + * In general, the metadata cache should always be allowed to + * evict entries. However, in some cases it is advantageous to + * disable evictions briefly, and thereby postpone metadata + * writes. However, this must be done with care, as the cache + * can grow quickly. If you do this, re-enable evictions as + * soon as possible and monitor cache size. + * + * At present, evictions can only be disabled if automatic + * cache resizing is also disabled (that is, ( incr_mode == + * H5C_incr__off ) && ( decr_mode == H5C_decr__off )). There + * is no logical reason why this should be so, but it simplifies + * implementation and testing, and I can't think of any reason + * why it would be desireable. If you can think of one, I'll + * revisit the issue. * * set_initial_size: Boolean flag indicating whether the size of the * initial size of the cache is to be set to the value given in @@ -368,80 +368,80 @@ extern "C" { * * PHDF5 uses several strategies to prevent such inconsistencies in metadata, * all of which use the fact that the same stream of dirty metadata is seen - * by all processes for purposes of synchronization. This is done by + * by all processes for purposes of synchronization. This is done by * having each process count the number of bytes of dirty metadata generated, - * and then running a "sync point" whenever this count exceeds a user + * and then running a "sync point" whenever this count exceeds a user * specified threshold (see dirty_bytes_threshold below). * - * The current metadata write strategy is indicated by the + * The current metadata write strategy is indicated by the * metadata_write_strategy field. The possible values of this field, along * with the associated metadata write strategies are discussed below. * * dirty_bytes_threshold: Threshold of dirty byte creation used to - * synchronize updates between caches. (See above for outline and - * motivation.) + * synchronize updates between caches. (See above for outline and + * motivation.) * - * This value MUST be consistant across all processes accessing the - * file. This field is ignored unless HDF5 has been compiled for - * parallel. + * This value MUST be consistant across all processes accessing the + * file. This field is ignored unless HDF5 has been compiled for + * parallel. * * metadata_write_strategy: Integer field containing a code indicating the - * desired metadata write strategy. The valid values of this field - * are enumerated and discussed below: + * desired metadata write strategy. The valid values of this field + * are enumerated and discussed below: * * - * H5AC_METADATA_WRITE_STRATEGY__PROCESS_0_ONLY: + * H5AC_METADATA_WRITE_STRATEGY__PROCESS_0_ONLY: * - * When metadata_write_strategy is set to this value, only process - * zero is allowed to write dirty metadata to disk. All other - * processes must retain dirty metadata until they are informed at - * a sync point that the dirty metadata in question has been written - * to disk. + * When metadata_write_strategy is set to this value, only process + * zero is allowed to write dirty metadata to disk. All other + * processes must retain dirty metadata until they are informed at + * a sync point that the dirty metadata in question has been written + * to disk. * - * When the sync point is reached (or when there is a user generated - * flush), process zero flushes sufficient entries to bring it into - * complience with its min clean size (or flushes all dirty entries in - * the case of a user generated flush), broad casts the list of - * entries just cleaned to all the other processes, and then exits - * the sync point. + * When the sync point is reached (or when there is a user generated + * flush), process zero flushes sufficient entries to bring it into + * complience with its min clean size (or flushes all dirty entries in + * the case of a user generated flush), broad casts the list of + * entries just cleaned to all the other processes, and then exits + * the sync point. * - * Upon receipt of the broadcast, the other processes mark the indicated - * entries as clean, and leave the sync point as well. + * Upon receipt of the broadcast, the other processes mark the indicated + * entries as clean, and leave the sync point as well. * * - * H5AC_METADATA_WRITE_STRATEGY__DISTRIBUTED: + * H5AC_METADATA_WRITE_STRATEGY__DISTRIBUTED: * - * In the distributed metadata write strategy, process zero still makes - * the decisions as to what entries should be flushed, but the actual - * flushes are distributed across the processes in the computation to - * the extent possible. + * In the distributed metadata write strategy, process zero still makes + * the decisions as to what entries should be flushed, but the actual + * flushes are distributed across the processes in the computation to + * the extent possible. * - * In this strategy, when a sync point is triggered (either by dirty - * metadata creation or manual flush), all processes enter a barrier. + * In this strategy, when a sync point is triggered (either by dirty + * metadata creation or manual flush), all processes enter a barrier. * - * On the other side of the barrier, process 0 constructs an ordered - * list of the entries to be flushed, and then broadcasts this list - * to the caches in all the processes. + * On the other side of the barrier, process 0 constructs an ordered + * list of the entries to be flushed, and then broadcasts this list + * to the caches in all the processes. * - * All processes then scan the list of entries to be flushed, flushing - * some, and marking the rest as clean. The algorithm for this purpose - * ensures that each entry in the list is flushed exactly once, and - * all are marked clean in each cache. + * All processes then scan the list of entries to be flushed, flushing + * some, and marking the rest as clean. The algorithm for this purpose + * ensures that each entry in the list is flushed exactly once, and + * all are marked clean in each cache. * - * Note that in the case of a flush of the cache, no message passing - * is necessary, as all processes have the same list of dirty entries, - * and all of these entries must be flushed. Thus in this case it is - * sufficient for each process to sort its list of dirty entries after - * leaving the initial barrier, and use this list as if it had been - * received from process zero. + * Note that in the case of a flush of the cache, no message passing + * is necessary, as all processes have the same list of dirty entries, + * and all of these entries must be flushed. Thus in this case it is + * sufficient for each process to sort its list of dirty entries after + * leaving the initial barrier, and use this list as if it had been + * received from process zero. + * + * To avoid possible messages from the past/future, all caches must + * wait until all caches are done before leaving the sync point. * - * To avoid possible messages from the past/future, all caches must - * wait until all caches are done before leaving the sync point. - * ****************************************************************************/ -#define H5AC__CURR_CACHE_CONFIG_VERSION 1 -#define H5AC__MAX_TRACE_FILE_NAME_LEN 1024 +#define H5AC__CURR_CACHE_CONFIG_VERSION 1 +#define H5AC__MAX_TRACE_FILE_NAME_LEN 1024 #define H5AC_METADATA_WRITE_STRATEGY__PROCESS_0_ONLY 0 #define H5AC_METADATA_WRITE_STRATEGY__DISTRIBUTED 1 @@ -451,9 +451,9 @@ typedef struct H5AC_cache_config_t /* general configuration fields: */ int version; - hbool_t rpt_fcn_enabled; + hbool_t rpt_fcn_enabled; - hbool_t open_trace_file; + hbool_t open_trace_file; hbool_t close_trace_file; char trace_file_name[H5AC__MAX_TRACE_FILE_NAME_LEN + 1]; @@ -512,7 +512,7 @@ typedef struct H5AC_cache_config_t * * structure H5AC_cache_image_config_t * - * H5AC_cache_image_ctl_t is a public structure intended for use in public + * H5AC_cache_image_ctl_t is a public structure intended for use in public * APIs. At least in its initial incarnation, it is a copy of struct * H5C_cache_image_ctl_t. * @@ -526,47 +526,47 @@ typedef struct H5AC_cache_config_t * generate_image: Boolean flag indicating whether a cache image should * be created on file close. * - * save_resize_status: Boolean flag indicating whether the cache image - * should include the adaptive cache resize configuration and status. - * Note that this field is ignored at present. + * save_resize_status: Boolean flag indicating whether the cache image + * should include the adaptive cache resize configuration and status. + * Note that this field is ignored at present. * - * entry_ageout: Integer field indicating the maximum number of - * times a prefetched entry can appear in subsequent cache images. - * This field exists to allow the user to avoid the buildup of - * infrequently used entries in long sequences of cache images. + * entry_ageout: Integer field indicating the maximum number of + * times a prefetched entry can appear in subsequent cache images. + * This field exists to allow the user to avoid the buildup of + * infrequently used entries in long sequences of cache images. * - * The value of this field must lie in the range - * H5AC__CACHE_IMAGE__ENTRY_AGEOUT__NONE (-1) to - * H5AC__CACHE_IMAGE__ENTRY_AGEOUT__MAX (100). + * The value of this field must lie in the range + * H5AC__CACHE_IMAGE__ENTRY_AGEOUT__NONE (-1) to + * H5AC__CACHE_IMAGE__ENTRY_AGEOUT__MAX (100). * - * H5AC__CACHE_IMAGE__ENTRY_AGEOUT__NONE means that no limit - * is imposed on number of times a prefeteched entry can appear - * in subsequent cache images. + * H5AC__CACHE_IMAGE__ENTRY_AGEOUT__NONE means that no limit + * is imposed on number of times a prefeteched entry can appear + * in subsequent cache images. * - * A value of 0 prevents prefetched entries from being included - * in cache images. + * A value of 0 prevents prefetched entries from being included + * in cache images. * - * Positive integers restrict prefetched entries to the specified - * number of appearances. + * Positive integers restrict prefetched entries to the specified + * number of appearances. * - * Note that the number of subsequent cache images that a prefetched - * entry has appeared in is tracked in an 8 bit field. Thus, while - * H5AC__CACHE_IMAGE__ENTRY_AGEOUT__MAX can be increased from its - * current value, any value in excess of 255 will be the functional - * equivalent of H5AC__CACHE_IMAGE__ENTRY_AGEOUT__NONE. + * Note that the number of subsequent cache images that a prefetched + * entry has appeared in is tracked in an 8 bit field. Thus, while + * H5AC__CACHE_IMAGE__ENTRY_AGEOUT__MAX can be increased from its + * current value, any value in excess of 255 will be the functional + * equivalent of H5AC__CACHE_IMAGE__ENTRY_AGEOUT__NONE. * ****************************************************************************/ -#define H5AC__CURR_CACHE_IMAGE_CONFIG_VERSION 1 +#define H5AC__CURR_CACHE_IMAGE_CONFIG_VERSION 1 -#define H5AC__CACHE_IMAGE__ENTRY_AGEOUT__NONE -1 -#define H5AC__CACHE_IMAGE__ENTRY_AGEOUT__MAX 100 +#define H5AC__CACHE_IMAGE__ENTRY_AGEOUT__NONE -1 +#define H5AC__CACHE_IMAGE__ENTRY_AGEOUT__MAX 100 typedef struct H5AC_cache_image_config_t { - int32_t version; + int version; hbool_t generate_image; hbool_t save_resize_status; - int32_t entry_ageout; + int entry_ageout; } H5AC_cache_image_config_t; #ifdef __cplusplus -- cgit v0.12 From a447dd64cc0dcfc7fe17b881103fc76348001dda Mon Sep 17 00:00:00 2001 From: Allen Byrne Date: Mon, 17 Apr 2017 13:58:14 -0500 Subject: HDFFV-10170 fix noinst for test libs --- test/Makefile.am | 2 +- tools/test/h5repack/Makefile.am | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/test/Makefile.am b/test/Makefile.am index a64cd0e..a0774a4 100644 --- a/test/Makefile.am +++ b/test/Makefile.am @@ -106,7 +106,7 @@ if HAVE_SHARED_CONDITIONAL # The libdynlib1, libdynlib2, libdynlib3, and libdynlib4 library for testing plugin module plugin.c. # Build it as shared library if configure is enabled for shared library. - lib_LTLIBRARIES=libdynlib1.la libdynlib2.la libdynlib3.la libdynlib4.la + noinst_LTLIBRARIES+=libdynlib1.la libdynlib2.la libdynlib3.la libdynlib4.la libdynlib1_la_SOURCES=dynlib1.c libdynlib2_la_SOURCES=dynlib2.c libdynlib3_la_SOURCES=dynlib3.c diff --git a/tools/test/h5repack/Makefile.am b/tools/test/h5repack/Makefile.am index 5c284b3..590a7dc 100644 --- a/tools/test/h5repack/Makefile.am +++ b/tools/test/h5repack/Makefile.am @@ -47,7 +47,7 @@ h5repacktst_SOURCES=h5repacktst.c if HAVE_SHARED_CONDITIONAL # Build it as shared library if configure is enabled for shared library. - lib_LTLIBRARIES=libdynlibadd.la libdynlibvers.la + noinst_LTLIBRARIES=libdynlibadd.la libdynlibvers.la libdynlibadd_la_SOURCES=dynlib_rpk.c libdynlibvers_la_SOURCES=dynlib_vrpk.c -- cgit v0.12 From b67e626ba9095f35dd9a8f9e8ca906320f85914c Mon Sep 17 00:00:00 2001 From: Allen Byrne Date: Mon, 17 Apr 2017 16:25:34 -0500 Subject: HDFFV-10173 remove hook for noinst libs --- test/Makefile.am | 3 --- tools/test/h5repack/Makefile.am | 4 ---- 2 files changed, 7 deletions(-) diff --git a/test/Makefile.am b/test/Makefile.am index a0774a4..49b251a 100644 --- a/test/Makefile.am +++ b/test/Makefile.am @@ -112,9 +112,6 @@ if HAVE_SHARED_CONDITIONAL libdynlib3_la_SOURCES=dynlib3.c libdynlib4_la_SOURCES=dynlib4.c -install-exec-hook: - $(RM) $(DESTDIR)$(libdir)/*dynlib* - else # The libh5test library provides common support code for the tests. noinst_LTLIBRARIES=libh5test.la diff --git a/tools/test/h5repack/Makefile.am b/tools/test/h5repack/Makefile.am index 590a7dc..ce403b0 100644 --- a/tools/test/h5repack/Makefile.am +++ b/tools/test/h5repack/Makefile.am @@ -51,10 +51,6 @@ if HAVE_SHARED_CONDITIONAL libdynlibadd_la_SOURCES=dynlib_rpk.c libdynlibvers_la_SOURCES=dynlib_vrpk.c -install-exec-hook: - $(RM) $(DESTDIR)$(libdir)/*dynlib* -endif - # Temporary files. *.h5 are generated by h5repack. They should # copied to the testfiles/ directory if update is required. CHECK_CLEANFILES+=*.h5 *.bin testfiles/h5diff_attr1.h5 testfiles/tfamily*.h5 -- cgit v0.12