Merge pull request #2256 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to develop

* commit '1385457eb2874b75fd7b9fa0c470e9e4225a104e':
  Added JIRA note
  io_timer.c uses a parallel lib function
  Fix standalone compile issues

6 files changed, 186 insertions, 51 deletions

diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt
index 055229b..9ebc231 100644
--- a/release_docs/RELEASE.txt
+++ b/release_docs/RELEASE.txt
@@ -368,6 +368,14 @@ New Features
 
     Java Library:
     ----------------
+    - Tests fail for non-English locale.
+
+      In the JUnit tests with a non-English locale, only the part before
+      the decimal comma is replaced by XXXX and this leads to a comparison
+      error. Changed the regex for the Time substitution.
+
+      (ADB - 2020/01/09, HDFFV-10995)
+
     - Fix a failure in JUnit-TestH5P on 32-bit architectures
 
       (JTH - 2019/04/30)
diff --git a/tools/lib/io_timer.c b/tools/lib/io_timer.c
index cb89019..472824b 100644
--- a/tools/lib/io_timer.c
+++ b/tools/lib/io_timer.c
@@ -138,43 +138,43 @@ io_time_set(io_time_t *pt, timer_type t, int start_stop)
     switch(pt->type){
 #ifdef H5_HAVE_PARALLEL
     case MPI_CLOCK:
-	if (start_stop == TSTART) {
-	    pt->mpi_timer[t] = MPI_Wtime();
-
-	    /* When we start the timer for HDF5_FINE_WRITE_FIXED_DIMS or HDF5_FINE_READ_FIXED_DIMS
-	     * we compute the time it took to only open the file */
-	    if(t == HDF5_FINE_WRITE_FIXED_DIMS)
-		pt->total_time[HDF5_FILE_WRITE_OPEN] += pt->mpi_timer[t] - pt->mpi_timer[HDF5_GROSS_WRITE_FIXED_DIMS];
-	    else if(t == HDF5_FINE_READ_FIXED_DIMS)
-		pt->total_time[HDF5_FILE_READ_OPEN] += pt->mpi_timer[t] - pt->mpi_timer[HDF5_GROSS_READ_FIXED_DIMS];
-
-	} else {
-	    pt->total_time[t] += MPI_Wtime() - pt->mpi_timer[t];
-	    pt->mpi_timer[t] = MPI_Wtime();
-
-	    /* When we stop the timer for HDF5_GROSS_WRITE_FIXED_DIMS or HDF5_GROSS_READ_FIXED_DIMS
-	     * we compute the time it took to close the file after the last read/write finished */
-	    if(t == HDF5_GROSS_WRITE_FIXED_DIMS)
-		pt->total_time[HDF5_FILE_WRITE_CLOSE] += pt->mpi_timer[t] - pt->mpi_timer[HDF5_FINE_WRITE_FIXED_DIMS];
-	    else if(t == HDF5_GROSS_READ_FIXED_DIMS)
-		pt->total_time[HDF5_FILE_READ_CLOSE] += pt->mpi_timer[t] - pt->mpi_timer[HDF5_FINE_READ_FIXED_DIMS];
-	}
-	break;
+    if (start_stop == TSTART) {
+        pt->mpi_timer[t] = MPI_Wtime();
+
+        /* When we start the timer for HDF5_FINE_WRITE_FIXED_DIMS or HDF5_FINE_READ_FIXED_DIMS
+        * we compute the time it took to only open the file */
+        if(t == HDF5_FINE_WRITE_FIXED_DIMS)
+        pt->total_time[HDF5_FILE_WRITE_OPEN] += pt->mpi_timer[t] - pt->mpi_timer[HDF5_GROSS_WRITE_FIXED_DIMS];
+        else if(t == HDF5_FINE_READ_FIXED_DIMS)
+        pt->total_time[HDF5_FILE_READ_OPEN] += pt->mpi_timer[t] - pt->mpi_timer[HDF5_GROSS_READ_FIXED_DIMS];
+
+    } else {
+        pt->total_time[t] += MPI_Wtime() - pt->mpi_timer[t];
+        pt->mpi_timer[t] = MPI_Wtime();
+
+        /* When we stop the timer for HDF5_GROSS_WRITE_FIXED_DIMS or HDF5_GROSS_READ_FIXED_DIMS
+        * we compute the time it took to close the file after the last read/write finished */
+        if(t == HDF5_GROSS_WRITE_FIXED_DIMS)
+        pt->total_time[HDF5_FILE_WRITE_CLOSE] += pt->mpi_timer[t] - pt->mpi_timer[HDF5_FINE_WRITE_FIXED_DIMS];
+        else if(t == HDF5_GROSS_READ_FIXED_DIMS)
+        pt->total_time[HDF5_FILE_READ_CLOSE] += pt->mpi_timer[t] - pt->mpi_timer[HDF5_FINE_READ_FIXED_DIMS];
+    }
+    break;
 #else
     case MPI_CLOCK:
-	    HDfprintf(stderr, "MPI clock set in serial library\n");
-	    return NULL;
+        HDfprintf(stderr, "MPI clock set in serial library\n");
+        return NULL;
 #endif /* H5_HAVE_PARALLEL */
     case SYS_CLOCK:
             if (start_stop == TSTART) {
                 HDgettimeofday(&pt->sys_timer[t], NULL);
 
-		/* When we start the timer for HDF5_FINE_WRITE_FIXED_DIMS or HDF5_FINE_READ_FIXED_DIMS
-		 * we compute the time it took to only open the file */
-		if(t == HDF5_FINE_WRITE_FIXED_DIMS)
-		    pt->total_time[HDF5_FILE_WRITE_OPEN] += sub_time(&(pt->sys_timer[t]), &(pt->sys_timer[HDF5_GROSS_WRITE_FIXED_DIMS]));
-		else if(t == HDF5_FINE_READ_FIXED_DIMS)
-		    pt->total_time[HDF5_FILE_READ_OPEN] += sub_time(&(pt->sys_timer[t]), &(pt->sys_timer[HDF5_GROSS_READ_FIXED_DIMS]));
+        /* When we start the timer for HDF5_FINE_WRITE_FIXED_DIMS or HDF5_FINE_READ_FIXED_DIMS
+        * we compute the time it took to only open the file */
+        if(t == HDF5_FINE_WRITE_FIXED_DIMS)
+            pt->total_time[HDF5_FILE_WRITE_OPEN] += sub_time(&(pt->sys_timer[t]), &(pt->sys_timer[HDF5_GROSS_WRITE_FIXED_DIMS]));
+        else if(t == HDF5_FINE_READ_FIXED_DIMS)
+            pt->total_time[HDF5_FILE_READ_OPEN] += sub_time(&(pt->sys_timer[t]), &(pt->sys_timer[HDF5_GROSS_READ_FIXED_DIMS]));
 
 
             } else {
@@ -183,19 +183,19 @@ io_time_set(io_time_t *pt, timer_type t, int start_stop)
                 HDgettimeofday(&sys_t, NULL);
                 pt->total_time[t] += sub_time(&sys_t, &(pt->sys_timer[t]));
 
-		/* When we stop the timer for HDF5_GROSS_WRITE_FIXED_DIMS or HDF5_GROSS_READ_FIXED_DIMS
-		 * we compute the time it took to close the file after the last read/write finished */
-		if(t == HDF5_GROSS_WRITE_FIXED_DIMS)
-		    pt->total_time[HDF5_FILE_WRITE_CLOSE] += sub_time(&(pt->sys_timer[t]), &(pt->sys_timer[HDF5_FINE_WRITE_FIXED_DIMS]));
-		else if(t == HDF5_GROSS_READ_FIXED_DIMS)
-		    pt->total_time[HDF5_FILE_READ_CLOSE] += sub_time(&(pt->sys_timer[t]), &(pt->sys_timer[HDF5_FINE_READ_FIXED_DIMS]));
+        /* When we stop the timer for HDF5_GROSS_WRITE_FIXED_DIMS or HDF5_GROSS_READ_FIXED_DIMS
+        * we compute the time it took to close the file after the last read/write finished */
+        if(t == HDF5_GROSS_WRITE_FIXED_DIMS)
+            pt->total_time[HDF5_FILE_WRITE_CLOSE] += sub_time(&(pt->sys_timer[t]), &(pt->sys_timer[HDF5_FINE_WRITE_FIXED_DIMS]));
+        else if(t == HDF5_GROSS_READ_FIXED_DIMS)
+            pt->total_time[HDF5_FILE_READ_CLOSE] += sub_time(&(pt->sys_timer[t]), &(pt->sys_timer[HDF5_FINE_READ_FIXED_DIMS]));
 
             }
-	break;
+    break;
 
     default:
-	    HDfprintf(stderr, "Unknown time clock type (%d)\n", pt->type);
-	    return NULL;
+        HDfprintf(stderr, "Unknown time clock type (%d)\n", pt->type);
+        return NULL;
     } /* end switch */
 
 #if 0
@@ -221,10 +221,3 @@ io_time_get(io_time_t *pt, timer_type t)
 
     return pt->total_time[t];
 }
-
-#if 0
-/* standalone is not working yet. Need fix later. -AKC- */
-#ifdef STANDALONE
-#include "pio_standalone.c"
-#endif
-#endif
diff --git a/tools/test/perform/CMakeLists.txt b/tools/test/perform/CMakeLists.txt
index f250065..a01a88f 100644
--- a/tools/test/perform/CMakeLists.txt
+++ b/tools/test/perform/CMakeLists.txt
@@ -21,7 +21,7 @@ endif ()
 set_target_properties (h5perf_serial PROPERTIES FOLDER perform)
 
 if (HDF5_BUILD_PERFORM_STANDALONE)
-  #-- Adding test for h5perf_serial_alone
+  #-- Adding test for h5perf_serial_alone - io_timer.c includes
   set (h5perf_serial_alone_SOURCES
       ${HDF5_TOOLS_DIR}/lib/io_timer.c
       ${HDF5_TOOLS_TEST_PERFORM_SOURCE_DIR}/sio_perf.c
@@ -32,10 +32,10 @@ if (HDF5_BUILD_PERFORM_STANDALONE)
   target_include_directories (h5perf_serial_alone PRIVATE "${HDF5_SRC_DIR};${HDF5_BINARY_DIR};${HDF5_TOOLS_DIR}/lib;$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
   if (NOT BUILD_SHARED_LIBS)
     TARGET_C_PROPERTIES (h5perf_serial_alone STATIC)
-    target_link_libraries (h5perf_serial_alone PRIVATE ${HDF5_LIB_TARGET})
+    target_link_libraries (h5perf_serial_alone PRIVATE ${HDF5_LIB_TARGET} "$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_LIBRARIES}>")
   else ()
     TARGET_C_PROPERTIES (h5perf_serial_alone SHARED)
-    target_link_libraries (h5perf_serial_alone PRIVATE ${HDF5_LIBSH_TARGET})
+    target_link_libraries (h5perf_serial_alone PRIVATE ${HDF5_LIBSH_TARGET} "$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_LIBRARIES}>")
   endif ()
   set_target_properties (h5perf_serial_alone PROPERTIES FOLDER perform)
   set_property (TARGET h5perf_serial_alone
diff --git a/tools/test/perform/pio_perf.h b/tools/test/perform/pio_perf.h
index 7605f20..55d721e 100644
--- a/tools/test/perform/pio_perf.h
+++ b/tools/test/perform/pio_perf.h
@@ -13,12 +13,13 @@
 #ifndef PIO_PERF_H__
 #define PIO_PERF_H__
 
-#include "io_timer.h"
 #ifndef STANDALONE
+#include "io_timer.h"
 #include "h5test.h"
 #include "h5tools.h"
 #include "h5tools_utils.h"
 #else
+#include "io_timer.h"
 #include "pio_standalone.h"
 #endif
 
diff --git a/tools/test/perform/pio_standalone.c b/tools/test/perform/pio_standalone.c
index 0fba904..8cdca85 100644
--- a/tools/test/perform/pio_standalone.c
+++ b/tools/test/perform/pio_standalone.c
@@ -164,3 +164,135 @@ print_version(const char *progname)
            progname, H5_VERS_MAJOR, H5_VERS_MINOR, H5_VERS_RELEASE,
            H5_VERS_SUBRELEASE[0] ? "-" : "", H5_VERS_SUBRELEASE);
 }
+
+#ifdef STANDALONE
+/*
+ * Function:    h5_set_info_object
+ * Purpose:     Process environment variables setting to set up MPI Info
+ *              object.
+ * Return:      0 if all is fine; otherwise non-zero.
+ * Programmer:  Albert Cheng, 2002/05/21.
+ * Modifications:
+ *          Bill Wendling, 2002/05/31
+ *          Modified so that the HDF5_MPI_INFO environment variable can
+ *          be a semicolon separated list of "key=value" pairings. Most
+ *          of the code is to remove any whitespaces which might be
+ *          surrounding the "key=value" pairs.
+ */
+int
+h5_set_info_object(void)
+{
+    char  *envp;      /* environment pointer */
+    int    ret_value=0;
+
+    /* handle any MPI INFO hints via $HDF5_MPI_INFO */
+    if ((envp = HDgetenv("HDF5_MPI_INFO")) != NULL){
+        char *next, *valp;
+
+        valp = envp = next = HDstrdup(envp);
+
+        if (!valp) return 0;
+
+        /* create an INFO object if not created yet */
+        if (h5_io_info_g == MPI_INFO_NULL)
+            MPI_Info_create(&h5_io_info_g);
+
+        do {
+            size_t len;
+            char *key_val, *endp, *namep;
+
+            if (*valp == ';')
+                valp++;
+
+            /* copy key/value pair into temporary buffer */
+            len = strcspn(valp, ";");
+            next = &valp[len];
+            key_val = (char *)HDcalloc(1, len + 1);
+
+            /* increment the next pointer past the terminating semicolon */
+            if (*next == ';')
+                ++next;
+
+            namep = HDstrncpy(key_val, valp, len);
+
+            /* pass up any beginning whitespaces */
+            while (*namep && (*namep == ' ' || *namep == '\t'))
+                namep++;
+
+            if (!*namep) continue; /* was all white space, so move to next k/v pair */
+
+            /* eat up any ending white spaces */
+            endp = &namep[HDstrlen(namep) - 1];
+
+            while (endp && (*endp == ' ' || *endp == '\t'))
+                *endp-- = '\0';
+
+            /* find the '=' */
+            valp = HDstrchr(namep, '=');
+
+            if (valp != NULL) {     /* it's a valid key/value pairing */
+                char *tmp_val = valp + 1;
+
+                /* change '=' to \0, move valp down one */
+                *valp-- = '\0';
+
+                /* eat up ending whitespace on the "key" part */
+                while (*valp == ' ' || *valp == '\t')
+                    *valp-- = '\0';
+
+                valp = tmp_val;
+
+                /* eat up beginning whitespace on the "value" part */
+                while (*valp == ' ' || *valp == '\t')
+                    *valp++ = '\0';
+
+                /* actually set the darned thing */
+                if (MPI_SUCCESS != MPI_Info_set(h5_io_info_g, namep, valp)) {
+                    HDprintf("MPI_Info_set failed\n");
+                    ret_value = -1;
+                }
+            }
+
+            valp = next;
+            HDfree(key_val);
+        } while (next && *next);
+
+        HDfree(envp);
+    }
+
+    return ret_value;
+}
+
+
+/*
+ * Function:    h5_dump_info_object
+ * Purpose:     Display content of an MPI Info object
+ * Return:      void
+ * Programmer:  Albert Cheng 2002/05/21
+ * Modifications:
+ */
+void
+h5_dump_info_object(MPI_Info info)
+{
+    char  key[MPI_MAX_INFO_KEY+1];
+    char  value[MPI_MAX_INFO_VAL+1];
+    int    flag;
+    int    i, nkeys;
+
+    HDprintf("Dumping MPI Info Object (up to %d bytes per item):\n", MPI_MAX_INFO_VAL);
+    if (info==MPI_INFO_NULL){
+  HDprintf("object is MPI_INFO_NULL\n");
+    }
+    else {
+  MPI_Info_get_nkeys(info, &nkeys);
+  HDprintf("object has %d items\n", nkeys);
+  for (i=0; i<nkeys; i++){
+      MPI_Info_get_nthkey(info, i, key);
+      MPI_Info_get(info, key, MPI_MAX_INFO_VAL, value, &flag);
+      HDprintf("%s=%s\n", key, value);
+  }
+
+    }
+}
+#endif  /* STANDALONE */
+
diff --git a/tools/test/perform/sio_perf.h b/tools/test/perform/sio_perf.h
index 83caf54..d26c78b 100644
--- a/tools/test/perform/sio_perf.h
+++ b/tools/test/perform/sio_perf.h
@@ -13,12 +13,13 @@
 #ifndef SIO_PERF_H__
 #define SIO_PERF_H__
 
-#include "io_timer.h"
 #ifndef STANDALONE
+#include "io_timer.h"
 #include "h5test.h"
 #include "h5tools.h"
 #include "h5tools_utils.h"
 #else
+#include "io_timer.h"
 #include "sio_standalone.h"
 #endif