[svn-r16184] Several Items:

1) In H5F.c, modified several metadata cache related routines to
   talk to the new cache, not the pre-journaling cache.

2) Enabled the API smoke check in cache2_journal.

3) Wrote a example of use of the journaling API and included
   it as a test in cache2_journal.c.  Some re-factoring of the
   cache2 test code to move supporting macros and functions
   out of cache2_api.c and into cache2_common.c & .h.

4) Modified tools/h5recover/trecover to include a new verify
   option, which is intended to verify that a file has been
   correctly recovered via h5recover.

   The basic idea of this feature is to look at the data sets
   in the architype and recovered files, and verify that the metadata
   in the versions in the recovered file (if they appear at all), agree
   with the architype versions where it must, and contain plausible
   values where it is possible that changes were lost.

   The test also looks at the raw data, and dumps the architype and
   recovered versions to stdout if anything looks "odd".

   At present, my addition only works with the integer chunked
   data set -- not with the other data set types that can be
   created by trecover.

   The code for the verify function is in the new file
   trecover_verifier.c.  Updated Makefile.am and the manifest
   accordingly.

5) Modified the synchronous crash test in tools/h5recover to
   to function when return codes are not passed back to the
   calling script, and to use the above modifications to trecover
   to examine the recovered file, instead of comparing the output
   of dumps of the architype and recovered files.

6) Commented out the asynchronous crash test in tools/h5recover,
   as the functionality of that test is now handled in the
   "walking crash" test.

7) Modified the "walking crash" test to use the trecover modifications
   to verify each recovery.

8) Modified the journaling file marking tests to function when the
   the return code is not passed back to the calling script.

9) Commented out the "tgroup-1.ls 1 -w80 -r -g tgroup.h5" in
   tools/h5ls.  I am given to understand that this test was
   failing on redstorm due to yod's failure to pass back return
   codes.  I have not investigated this personally.

10) Updated bin/reconfigure to deal with recent changes in the file
   system structure on jam.

Testing:

  Tested (serial) on Phoenix, Linew, and RSQ -- all pass.  Note that 
  on the "walking crash" test in tools/h5recover, I was unable to 
  set the asynchronous crash delay small enough to get the crash to 
  occur before trecover completed (I got down to 1 usec).  This 
  was not a problem on on redstorm the last time we tried testing 
  there, so I'm not too worried about it.

  I also did a parallel test on jam -- this test failed with an assertion
  failure in dtypes -- output follows:

============================
 dtypes  Test Log
============================
Testing non-aligned conversions (ALIGNMENT=1)....
Testing H5Tget_class()                                                 PASSED
Testing H5Tcopy()                                                      PASSED
Testing H5Tdetect_class()                                              PASSED
Testing compound datatypes                                             PASSED
Testing query functions of compound and enumeration types              PASSED
Testing transient datatypes                                            PASSED
Testing named datatypes                                                PASSED
Testing functions of encoding and decoding datatypes                   PASSED
Testing encoding datatypes with the 'use the latest format' flag       PASSED
Testing exceptions for int <-> float conversions                       PASSED
Testing deprected API routines for datatypes                           PASSED
Testing string conversions                                             PASSED
Testing random string conversion speed                                 PASSED
Testing some type functions for string                                 PASSED
Testing compound element reordering                                    PASSED
Testing compound subset conversions                                    PASSED
Testing compound element shrinking & reordering                        PASSED
Testing optimized struct converter                                     PASSED
Testing compound element growing                                       PASSED
Testing compound element insertion                                     PASSED
Testing packing compound datatypes                                     PASSED
Testing compound datatype with VL string                              dtypes: H5FD.c:2150: H5FD_write: Assertion `1==H5P_isa_class(dxpl_id,(H5P_CLS_DATASET_XFER_g))' failed.
Command terminated by signal 6
0.20user 0.10system 0:00.39elapsed 75%CPU (0avgtext+0avgdata 0maxresident)k
0inputs+0outputs (4major+10263minor)pagefaults 0swaps

   I'm checking in anyway, as this looks unrelated to any of my recent 
   changes.  Quincey and I should get together about this one.

1 files changed, 6 insertions, 2 deletions

diff --git a/tools/h5recover/Makefile.in b/tools/h5recover/Makefile.in
index 852813d..8ba4ab2 100644
--- a/tools/h5recover/Makefile.in
+++ b/tools/h5recover/Makefile.in
@@ -77,7 +77,8 @@ h5recover_OBJECTS = h5recover.$(OBJEXT)
 h5recover_LDADD = $(LDADD)
 h5recover_DEPENDENCIES = $(LIBH5TOOLS) $(LIBHDF5)
 am_trecover_OBJECTS = trecover_main.$(OBJEXT) \
-	trecover_writer.$(OBJEXT) trecover_crasher.$(OBJEXT)
+	trecover_writer.$(OBJEXT) trecover_crasher.$(OBJEXT) \
+	trecover_verifier.$(OBJEXT)
 trecover_OBJECTS = $(am_trecover_OBJECTS)
 trecover_LDADD = $(LDADD)
 trecover_DEPENDENCIES = $(LIBH5TOOLS) $(LIBHDF5)
@@ -361,7 +362,9 @@ check_SCRIPTS = $(TEST_SCRIPT)
 SCRIPT_DEPEND = trecover$(EXEEXT)
 
 # Source files for the program
-trecover_SOURCES = trecover_main.c trecover_writer.c trecover_crasher.c
+trecover_SOURCES = trecover_main.c trecover_writer.c trecover_crasher.c \
+                 trecover_verifier.c
+
 
 # All the programs depend on the hdf5 and h5tools libraries
 LDADD = $(LIBH5TOOLS) $(LIBHDF5)
@@ -472,6 +475,7 @@ distclean-compile:
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/h5recover.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/trecover_crasher.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/trecover_main.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/trecover_verifier.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/trecover_writer.Po@am__quote@
 
 .c.o: