mirror of
https://github.com/HDFGroup/hdf5.git
synced 2025-03-31 17:10:47 +08:00
[svn-r11601] Purpose:
Added additional targets to build-all Description: Surveyed files to find out which ones are not built. Added test/space_overflow and perform/benchpar to programs built with --enable-build-all. Discovered that tools/misc/pdb2hdf5 and tools/misc/h5import were obsolete and deleted them. Platforms tested: mir, modi4, sol Misc. update: Update of release file and removal of --enable-pdb2hdf5 to follow.
This commit is contained in:
James Laird
parent
d2f2b5090c
commit
8619af74a4
@ -30,17 +30,19 @@ endif
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# always installed with the tools during make install.
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bin_PROGRAMS=h5perf
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# mpi-perf is not built or run by default, but can be built by hand or by
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# Some programs are not built or run by default, but can be built by hand or by
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# specifying --enable-build-all at configure time.
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# Also, some of these programs should only be built in parallel.
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if BUILD_PARALLEL_CONDITIONAL
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PARA_BUILD_ALL=benchpar mpi-perf
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endif
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if BUILD_ALL_CONDITIONAL
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MPI_PERF=mpi-perf
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else
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MPI_PERF=
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BUILD_ALL_PROGS=$(PARA_BUILD_ALL)
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endif
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# These are the programs that `make all' or `make tests' will build and which
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# `make check' will run. List them in the order they should be run.
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TEST_PROG = iopipe chunk overhead zip_perf perf_meta $(MPI_PERF)
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TEST_PROG = iopipe chunk overhead zip_perf perf_meta $(BUILD_ALL_PROGS)
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check_PROGRAMS=$(TEST_PROG_PARA) $(TEST_PROG) perf
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h5perf_SOURCES=pio_perf.c pio_engine.c pio_timer.c
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@ -30,7 +30,7 @@
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# HDF5 Library Performance Makefile(.in)
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#
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SOURCES = chunk.c $(h5perf_SOURCES) iopipe.c mpi-perf.c overhead.c perf.c perf_meta.c zip_perf.c
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SOURCES = benchpar.c chunk.c $(h5perf_SOURCES) iopipe.c mpi-perf.c overhead.c perf.c perf_meta.c zip_perf.c
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srcdir = @srcdir@
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top_srcdir = @top_srcdir@
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@ -58,7 +58,7 @@ DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
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$(top_srcdir)/config/commence.am \
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$(top_srcdir)/config/conclude.am
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bin_PROGRAMS = h5perf$(EXEEXT)
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check_PROGRAMS = $(am__EXEEXT_1) $(am__EXEEXT_3) perf$(EXEEXT)
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check_PROGRAMS = $(am__EXEEXT_1) $(am__EXEEXT_4) perf$(EXEEXT)
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subdir = perform
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ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
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am__aclocal_m4_deps = $(top_srcdir)/configure.in
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@ -70,14 +70,20 @@ CONFIG_CLEAN_FILES =
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am__installdirs = "$(DESTDIR)$(bindir)"
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binPROGRAMS_INSTALL = $(INSTALL_PROGRAM)
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@BUILD_PARALLEL_CONDITIONAL_TRUE@am__EXEEXT_1 = h5perf$(EXEEXT)
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@BUILD_ALL_CONDITIONAL_TRUE@am__EXEEXT_2 = mpi-perf$(EXEEXT)
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am__EXEEXT_3 = iopipe$(EXEEXT) chunk$(EXEEXT) overhead$(EXEEXT) \
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zip_perf$(EXEEXT) perf_meta$(EXEEXT) $(am__EXEEXT_2)
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@BUILD_PARALLEL_CONDITIONAL_TRUE@am__EXEEXT_2 = benchpar$(EXEEXT) \
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@BUILD_PARALLEL_CONDITIONAL_TRUE@ mpi-perf$(EXEEXT)
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@BUILD_ALL_CONDITIONAL_TRUE@am__EXEEXT_3 = $(am__EXEEXT_2)
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am__EXEEXT_4 = iopipe$(EXEEXT) chunk$(EXEEXT) overhead$(EXEEXT) \
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zip_perf$(EXEEXT) perf_meta$(EXEEXT) $(am__EXEEXT_3)
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PROGRAMS = $(bin_PROGRAMS)
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benchpar_SOURCES = benchpar.c
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benchpar_OBJECTS = benchpar.$(OBJEXT)
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benchpar_LDADD = $(LDADD)
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am__DEPENDENCIES_1 = $(top_builddir)/src/libhdf5.la
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benchpar_DEPENDENCIES = $(am__DEPENDENCIES_1)
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chunk_SOURCES = chunk.c
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chunk_OBJECTS = chunk.$(OBJEXT)
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chunk_LDADD = $(LDADD)
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am__DEPENDENCIES_1 = $(top_builddir)/src/libhdf5.la
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chunk_DEPENDENCIES = $(am__DEPENDENCIES_1)
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am_h5perf_OBJECTS = pio_perf.$(OBJEXT) pio_engine.$(OBJEXT) \
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pio_timer.$(OBJEXT)
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@ -118,10 +124,10 @@ LTCOMPILE = $(LIBTOOL) --tag=CC --mode=compile $(CC) $(DEFS) \
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CCLD = $(CC)
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LINK = $(LIBTOOL) --tag=CC --mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) \
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$(AM_LDFLAGS) $(LDFLAGS) -o $@
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SOURCES = chunk.c $(h5perf_SOURCES) iopipe.c mpi-perf.c overhead.c \
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perf.c perf_meta.c zip_perf.c
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DIST_SOURCES = chunk.c $(h5perf_SOURCES) iopipe.c mpi-perf.c \
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SOURCES = benchpar.c chunk.c $(h5perf_SOURCES) iopipe.c mpi-perf.c \
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overhead.c perf.c perf_meta.c zip_perf.c
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DIST_SOURCES = benchpar.c chunk.c $(h5perf_SOURCES) iopipe.c \
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mpi-perf.c overhead.c perf.c perf_meta.c zip_perf.c
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ETAGS = etags
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CTAGS = ctags
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DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
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@ -353,15 +359,16 @@ H5FC_PP = $(bindir)/h5pfc
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CHECK_CLEANFILES = *.chkexe *.chklog *.clog
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INCLUDES = -I$(top_srcdir)/src -I$(top_srcdir)/test -I$(top_srcdir)/tools/lib
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@BUILD_PARALLEL_CONDITIONAL_TRUE@TEST_PROG_PARA = h5perf
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@BUILD_ALL_CONDITIONAL_FALSE@MPI_PERF =
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# mpi-perf is not built or run by default, but can be built by hand or by
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# Some programs are not built or run by default, but can be built by hand or by
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# specifying --enable-build-all at configure time.
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@BUILD_ALL_CONDITIONAL_TRUE@MPI_PERF = mpi-perf
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# Also, some of these programs should only be built in parallel.
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@BUILD_PARALLEL_CONDITIONAL_TRUE@PARA_BUILD_ALL = benchpar mpi-perf
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@BUILD_ALL_CONDITIONAL_TRUE@BUILD_ALL_PROGS = $(PARA_BUILD_ALL)
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# These are the programs that `make all' or `make tests' will build and which
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# `make check' will run. List them in the order they should be run.
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TEST_PROG = iopipe chunk overhead zip_perf perf_meta $(MPI_PERF)
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TEST_PROG = iopipe chunk overhead zip_perf perf_meta $(BUILD_ALL_PROGS)
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h5perf_SOURCES = pio_perf.c pio_engine.c pio_timer.c
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# These are the files that `make clean' (and derivatives) will remove from
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@ -461,6 +468,9 @@ clean-checkPROGRAMS:
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echo " rm -f $$p $$f"; \
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rm -f $$p $$f ; \
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done
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benchpar$(EXEEXT): $(benchpar_OBJECTS) $(benchpar_DEPENDENCIES)
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@rm -f benchpar$(EXEEXT)
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$(LINK) $(benchpar_LDFLAGS) $(benchpar_OBJECTS) $(benchpar_LDADD) $(LIBS)
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chunk$(EXEEXT): $(chunk_OBJECTS) $(chunk_DEPENDENCIES)
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@rm -f chunk$(EXEEXT)
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$(LINK) $(chunk_LDFLAGS) $(chunk_OBJECTS) $(chunk_LDADD) $(LIBS)
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@ -492,6 +502,7 @@ mostlyclean-compile:
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distclean-compile:
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-rm -f *.tab.c
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@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/benchpar.Po@am__quote@
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@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/chunk.Po@am__quote@
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@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/iopipe.Po@am__quote@
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@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/mpi-perf.Po@am__quote@
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@ -16,11 +16,23 @@
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#include <stdlib.h>
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#include <assert.h>
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#include <math.h>
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#include <float.h>
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#include <string.h>
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#include "hdf5.h"
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/* Local macros */
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/*
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* HDF Boolean type.
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*/
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#ifndef FALSE
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# define FALSE 0
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#endif
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#ifndef TRUE
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# define TRUE 1
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#endif
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/* defines for type of VFL driver to use */
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#define FACC_DEFAULT 0
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#define FACC_MPIO 1
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@ -56,7 +56,8 @@ check_PROGRAMS=$(TEST_PROG) error_test err_compat testmeta
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# so do not appear in this list.
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if BUILD_ALL_CONDITIONAL
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BUILD_ALL_PROGS=gen_deflate gen_filters gen_new_array gen_new_fill \
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gen_new_mtime gen_new_super gen_noencoder gen_nullspace
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gen_new_mtime gen_new_super gen_noencoder gen_nullspace \
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space_overflow
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else
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BUILD_ALL_PROGS=
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endif
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@ -31,7 +31,7 @@
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#
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SOURCES = $(libh5test_la_SOURCES) b+tree.c big.c bittests.c blocktrack.c btree2.c cache.c cmpd_dset.c dangle.c dsets.c dt_arith.c dtransform.c dtypes.c enum.c err_compat.c error_test.c extend.c external.c fillval.c flush1.c flush2.c gen_deflate.c gen_filters.c gen_new_array.c gen_new_fill.c gen_new_mtime.c gen_new_super.c gen_noencoder.c gen_nullspace.c getname.c gheap.c hyperslab.c istore.c lheap.c links.c mount.c mtime.c ntypes.c ohdr.c pool.c reserved.c set_extent.c sheap.c stab.c stream_test.c $(testhdf5_SOURCES) testmeta.c $(ttsafe_SOURCES) unlink.c vfd.c
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SOURCES = $(libh5test_la_SOURCES) b+tree.c big.c bittests.c blocktrack.c btree2.c cache.c cmpd_dset.c dangle.c dsets.c dt_arith.c dtransform.c dtypes.c enum.c err_compat.c error_test.c extend.c external.c fillval.c flush1.c flush2.c gen_deflate.c gen_filters.c gen_new_array.c gen_new_fill.c gen_new_mtime.c gen_new_super.c gen_noencoder.c gen_nullspace.c getname.c gheap.c hyperslab.c istore.c lheap.c links.c mount.c mtime.c ntypes.c ohdr.c pool.c reserved.c set_extent.c sheap.c space_overflow.c stab.c stream_test.c $(testhdf5_SOURCES) testmeta.c $(ttsafe_SOURCES) unlink.c vfd.c
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srcdir = @srcdir@
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top_srcdir = @top_srcdir@
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@ -92,7 +92,8 @@ am__EXEEXT_1 = testhdf5$(EXEEXT) lheap$(EXEEXT) ohdr$(EXEEXT) \
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@BUILD_ALL_CONDITIONAL_TRUE@ gen_new_mtime$(EXEEXT) \
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@BUILD_ALL_CONDITIONAL_TRUE@ gen_new_super$(EXEEXT) \
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@BUILD_ALL_CONDITIONAL_TRUE@ gen_noencoder$(EXEEXT) \
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@BUILD_ALL_CONDITIONAL_TRUE@ gen_nullspace$(EXEEXT)
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@BUILD_ALL_CONDITIONAL_TRUE@ gen_nullspace$(EXEEXT) \
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@BUILD_ALL_CONDITIONAL_TRUE@ space_overflow$(EXEEXT)
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PROGRAMS = $(noinst_PROGRAMS)
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b_tree_SOURCES = b+tree.c
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b_tree_OBJECTS = b+tree.$(OBJEXT)
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@ -263,6 +264,10 @@ sheap_SOURCES = sheap.c
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sheap_OBJECTS = sheap.$(OBJEXT)
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sheap_LDADD = $(LDADD)
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sheap_DEPENDENCIES = libh5test.la $(am__DEPENDENCIES_1)
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space_overflow_SOURCES = space_overflow.c
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space_overflow_OBJECTS = space_overflow.$(OBJEXT)
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space_overflow_LDADD = $(LDADD)
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space_overflow_DEPENDENCIES = libh5test.la $(am__DEPENDENCIES_1)
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stab_SOURCES = stab.c
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stab_OBJECTS = stab.$(OBJEXT)
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stab_LDADD = $(LDADD)
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@ -319,8 +324,9 @@ SOURCES = $(libh5test_la_SOURCES) b+tree.c big.c bittests.c \
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gen_new_mtime.c gen_new_super.c gen_noencoder.c \
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gen_nullspace.c getname.c gheap.c hyperslab.c istore.c lheap.c \
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links.c mount.c mtime.c ntypes.c ohdr.c pool.c reserved.c \
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set_extent.c sheap.c stab.c stream_test.c $(testhdf5_SOURCES) \
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testmeta.c $(ttsafe_SOURCES) unlink.c vfd.c
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set_extent.c sheap.c space_overflow.c stab.c stream_test.c \
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$(testhdf5_SOURCES) testmeta.c $(ttsafe_SOURCES) unlink.c \
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vfd.c
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DIST_SOURCES = $(libh5test_la_SOURCES) b+tree.c big.c bittests.c \
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blocktrack.c btree2.c cache.c cmpd_dset.c dangle.c dsets.c \
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dt_arith.c dtransform.c dtypes.c enum.c err_compat.c \
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@ -329,8 +335,9 @@ DIST_SOURCES = $(libh5test_la_SOURCES) b+tree.c big.c bittests.c \
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gen_new_mtime.c gen_new_super.c gen_noencoder.c \
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gen_nullspace.c getname.c gheap.c hyperslab.c istore.c lheap.c \
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links.c mount.c mtime.c ntypes.c ohdr.c pool.c reserved.c \
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set_extent.c sheap.c stab.c stream_test.c $(testhdf5_SOURCES) \
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testmeta.c $(ttsafe_SOURCES) unlink.c vfd.c
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set_extent.c sheap.c space_overflow.c stab.c stream_test.c \
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$(testhdf5_SOURCES) testmeta.c $(ttsafe_SOURCES) unlink.c \
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vfd.c
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ETAGS = etags
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CTAGS = ctags
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DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
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@ -610,7 +617,8 @@ TEST_PROG = testhdf5 lheap ohdr stab gheap btree2 cache b+tree blocktrack sheap
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# The gen_old_* files can only be compiled with older versions of the library
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# so do not appear in this list.
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@BUILD_ALL_CONDITIONAL_TRUE@BUILD_ALL_PROGS = gen_deflate gen_filters gen_new_array gen_new_fill \
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@BUILD_ALL_CONDITIONAL_TRUE@ gen_new_mtime gen_new_super gen_noencoder gen_nullspace
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@BUILD_ALL_CONDITIONAL_TRUE@ gen_new_mtime gen_new_super gen_noencoder gen_nullspace \
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@BUILD_ALL_CONDITIONAL_TRUE@ space_overflow
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# The libh5test library provides common support code for the tests.
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@ -831,6 +839,9 @@ set_extent$(EXEEXT): $(set_extent_OBJECTS) $(set_extent_DEPENDENCIES)
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sheap$(EXEEXT): $(sheap_OBJECTS) $(sheap_DEPENDENCIES)
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@rm -f sheap$(EXEEXT)
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$(LINK) $(sheap_LDFLAGS) $(sheap_OBJECTS) $(sheap_LDADD) $(LIBS)
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space_overflow$(EXEEXT): $(space_overflow_OBJECTS) $(space_overflow_DEPENDENCIES)
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@rm -f space_overflow$(EXEEXT)
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$(LINK) $(space_overflow_LDFLAGS) $(space_overflow_OBJECTS) $(space_overflow_LDADD) $(LIBS)
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stab$(EXEEXT): $(stab_OBJECTS) $(stab_DEPENDENCIES)
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@rm -f stab$(EXEEXT)
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$(LINK) $(stab_LDFLAGS) $(stab_OBJECTS) $(stab_LDADD) $(LIBS)
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@ -902,6 +913,7 @@ distclean-compile:
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@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/reserved.Po@am__quote@
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@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/set_extent.Po@am__quote@
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@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/sheap.Po@am__quote@
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@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/space_overflow.Po@am__quote@
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@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/stab.Po@am__quote@
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@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/stream_test.Po@am__quote@
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@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/tarray.Po@am__quote@
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@ -1,152 +0,0 @@
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/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
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* Copyright by the Board of Trustees of the University of Illinois. *
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* All rights reserved. *
|
||||
* *
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* This file is part of HDF5. The full HDF5 copyright notice, including *
|
||||
* terms governing use, modification, and redistribution, is contained in *
|
||||
* the files COPYING and Copyright.html. COPYING can be found at the root *
|
||||
* of the source code distribution tree; Copyright.html can be found at the *
|
||||
* root level of an installed copy of the electronic HDF5 document set and *
|
||||
* is linked from the top-level documents page. It can also be found at *
|
||||
* http://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html. If you do not have *
|
||||
* access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. *
|
||||
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
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/*
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* Programmer: Robb Matzke <matzke@llnl.gov>
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* Thursday, June 11, 1998
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*
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* Purpose: Create an hdf5 file with a 1d dataset of uint8.
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*/
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/* See H5private.h for how to include system headers */
|
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#include <hdf5.h>
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#ifdef H5_STDC_HEADERS
|
||||
# include <fcntl.h>
|
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# include <string.h>
|
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# include <stdlib.h>
|
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# include <stdio.h>
|
||||
#endif
|
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|
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#ifdef H5_HAVE_UNISTD_H
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# include <sys/types.h>
|
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# include <unistd.h>
|
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#endif
|
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|
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#ifdef H5_HAVE_SYS_STAT_H
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# include <sys/stat.h>
|
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#endif
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#ifdef WIN32
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# include <io.h>
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#endif
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|
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/*-------------------------------------------------------------------------
|
||||
* Function: usage
|
||||
*
|
||||
* Purpose: Print a usage message and exit with non-zero status
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||||
*
|
||||
* Return: never returns
|
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*
|
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* Programmer: Robb Matzke
|
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* Thursday, June 11, 1998
|
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*
|
||||
* Modifications:
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*
|
||||
*-------------------------------------------------------------------------
|
||||
*/
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static void
|
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usage (const char *argv0)
|
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{
|
||||
fprintf (stderr, "Usage: %s -f HDF5-FILE FILES...\n", argv0);
|
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exit (1);
|
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}
|
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|
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|
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/*-------------------------------------------------------------------------
|
||||
* Function: main
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||||
*
|
||||
* Purpose:
|
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*
|
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* Return: Success: 0
|
||||
*
|
||||
* Failure: 1
|
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*
|
||||
* Programmer: Robb Matzke
|
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* Thursday, June 11, 1998
|
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*
|
||||
* Modifications:
|
||||
*
|
||||
*-------------------------------------------------------------------------
|
||||
*/
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int
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main (int argc, char *argv[])
|
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{
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hid_t file, space=-1, dset=-1;
|
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const char *output_name, *dset_name;
|
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int argno, fd=-1;
|
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hsize_t size[1];
|
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struct stat sb;
|
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|
||||
/* Parse arguments */
|
||||
if (argc<4) usage (argv[0]);
|
||||
if (strcmp (argv[1], "-f")) usage (argv[0]);
|
||||
output_name = argv[2];
|
||||
|
||||
/* create the file */
|
||||
H5E_BEGIN_TRY {
|
||||
if ((file = H5Fcreate (output_name, H5F_ACC_EXCL,
|
||||
H5P_DEFAULT, H5P_DEFAULT))<0 &&
|
||||
(file = H5Fopen (output_name, H5F_ACC_RDWR, H5P_DEFAULT)<0)) {
|
||||
fprintf (stderr, "%s: unable to create or open hdf5 file\n",
|
||||
output_name);
|
||||
exit (1);
|
||||
}
|
||||
} H5E_END_TRY;
|
||||
|
||||
/* process files from command-line */
|
||||
for (argno=3; argno<argc; argno++) {
|
||||
|
||||
/* Open the file */
|
||||
if ((dset_name=strrchr (argv[argno], '/'))) dset_name++;
|
||||
else dset_name = argv[argno];
|
||||
fprintf (stderr, "%s\n", dset_name);
|
||||
if ((fd=open (argv[argno], O_RDONLY))<0) {
|
||||
perror (argv[argno]);
|
||||
goto next;
|
||||
}
|
||||
if (fstat (fd, &sb)<0) {
|
||||
perror (argv[argno]);
|
||||
goto next;
|
||||
}
|
||||
|
||||
/* Data space */
|
||||
size[0] = sb.st_size;
|
||||
if ((space = H5Screate_simple (1, size, size))<0) goto next;
|
||||
|
||||
/* Dataset */
|
||||
if ((dset=H5Dcreate (file, dset_name, H5T_NATIVE_SCHAR,
|
||||
space, H5P_DEFAULT))<0) goto next;
|
||||
|
||||
|
||||
|
||||
next:
|
||||
if (fd>=0) close (fd);
|
||||
fd = -1;
|
||||
H5E_BEGIN_TRY {
|
||||
if (space>=0) {
|
||||
H5Sclose (space);
|
||||
space = -1;
|
||||
}
|
||||
if (dset>=0) {
|
||||
H5Dclose (dset);
|
||||
dset = -1;
|
||||
}
|
||||
} H5E_END_TRY;
|
||||
}
|
||||
|
||||
/* Close the file */
|
||||
H5Fclose (file);
|
||||
return 0;
|
||||
}
|
||||
@ -1,527 +0,0 @@
|
||||
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
|
||||
* 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 files COPYING and Copyright.html. COPYING can be found at the root *
|
||||
* of the source code distribution tree; Copyright.html can be found at the *
|
||||
* root level of an installed copy of the electronic HDF5 document set and *
|
||||
* is linked from the top-level documents page. It can also be found at *
|
||||
* http://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html. If you do not have *
|
||||
* access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. *
|
||||
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
|
||||
|
||||
/*
|
||||
* Programmer: Robb Matzke <matzke@llnl.gov>
|
||||
* Tuesday, October 12, 1999
|
||||
*
|
||||
* Purpose: Creates an HDF5 file from a PDB file. The raw data can be
|
||||
* left in the PDB file, creating an HDF5 file that contains
|
||||
* meta data that points into the PDB file.
|
||||
*/
|
||||
#include <assert.h>
|
||||
#include <stdio.h>
|
||||
#include <string.h>
|
||||
|
||||
#include "hdf5.h"
|
||||
|
||||
/* Strictly speaking, the "ifdef H5_HAVE_PDB_H" is unnecessary, since this
|
||||
* file won't be compiled unless PDB is available (see the Makefile.in for
|
||||
* this directory, as well as the PDB detection in the main configure.in).
|
||||
* However, the Intel C compiler, v7.1, seems to have problems generating
|
||||
* correct dependencies with the -MG flag when include files are not found
|
||||
* and having this ifdef here removes the PDB headers from its consideration.
|
||||
* QAK - 2004/02/07
|
||||
*/
|
||||
#ifdef H5_HAVE_PDB_H
|
||||
|
||||
#include "pdb.h"
|
||||
#include "score.h"
|
||||
|
||||
/*
|
||||
* libsilo renames all the PDB functions. However, this source files uses
|
||||
* their documented names, so we have #define's to translate them to Silo
|
||||
* terminology.
|
||||
*/
|
||||
#ifdef H5_HAVE_LIBSILO
|
||||
# define PD_open lite_PD_open
|
||||
# define PD_close lite_PD_close
|
||||
# define PD_ls lite_PD_ls
|
||||
# define PD_cd lite_PD_cd
|
||||
# define PD_inquire_entry lite_PD_inquire_entry
|
||||
# define PD_read lite_PD_read
|
||||
# define _PD_fixname _lite_PD_fixname
|
||||
# define _PD_rl_defstr _lite_PD_rl_defstr
|
||||
# define SC_free lite_SC_free
|
||||
#endif
|
||||
|
||||
static int verbose_g = 0; /*verbose output? */
|
||||
static int cached_g = 0; /*use core file driver? */
|
||||
|
||||
|
||||
/*-------------------------------------------------------------------------
|
||||
* Function: usage
|
||||
*
|
||||
* Purpose: Print a usage message.
|
||||
*
|
||||
* Return: void
|
||||
*
|
||||
* Programmer: Robb Matzke
|
||||
* Tuesday, October 12, 1999
|
||||
*
|
||||
* Modifications:
|
||||
*
|
||||
*-------------------------------------------------------------------------
|
||||
*/
|
||||
static void
|
||||
usage(const char *arg0)
|
||||
{
|
||||
char *progname;
|
||||
|
||||
if ((progname=strrchr(arg0, '/')) && progname[1]) progname++;
|
||||
else progname = arg0;
|
||||
|
||||
fprintf(stderr, "\
|
||||
usage: %s [OPTIONS] [PDBFILE ...]\n\
|
||||
OPTIONS\n\
|
||||
-h, -?, --help Print a usage message and exit\n\
|
||||
-c, --cached Cache all data in memory before writing the output\n\
|
||||
-v, --verbose Print the name of each object processed\n\
|
||||
-V, --version Show the version number of this program\n\
|
||||
\n\
|
||||
The options and PDB file names may be interspersed and are processed from\n\
|
||||
left to right.\n\
|
||||
\n\
|
||||
The name of the HDF5 file is generated by taking the basename of the PDB\n\
|
||||
file and replacing the last extension (or appending if no extension) with\n\
|
||||
the characters \".h5\". For example, \"/tmp/test/eos.data\" would result\n\
|
||||
in an HDF5 file called \"eos.h5\" in the current directory.\n",
|
||||
progname);
|
||||
|
||||
}
|
||||
|
||||
|
||||
/*-------------------------------------------------------------------------
|
||||
* Function: version
|
||||
*
|
||||
* Purpose: Print the version number.
|
||||
*
|
||||
* Return: void
|
||||
*
|
||||
* Programmer: Robb Matzke
|
||||
* Friday, October 15, 1999
|
||||
*
|
||||
* Modifications:
|
||||
*
|
||||
*-------------------------------------------------------------------------
|
||||
*/
|
||||
static void
|
||||
version(const char *arg0)
|
||||
{
|
||||
const char *progname;
|
||||
|
||||
if ((progname=strrchr(arg0, '/')) && progname[1]) progname++;
|
||||
else progname = arg0;
|
||||
print_version(progname);
|
||||
}
|
||||
|
||||
|
||||
/*-------------------------------------------------------------------------
|
||||
* Function: fix_name
|
||||
*
|
||||
* Purpose: Given a PDB file name create the corresponding HDF5 file
|
||||
* name. This is done by taking the base name of the PDB file
|
||||
* and replacing (or appending) the last extension with ".h5".
|
||||
*
|
||||
* Return: Success: HDF_NAME
|
||||
*
|
||||
* Failure: NULL
|
||||
*
|
||||
* Programmer: Robb Matzke
|
||||
* Tuesday, October 12, 1999
|
||||
*
|
||||
* Modifications:
|
||||
*
|
||||
*-------------------------------------------------------------------------
|
||||
*/
|
||||
static char *
|
||||
fix_name(const char *pdb_name, char *hdf_name, size_t size)
|
||||
{
|
||||
char *s;
|
||||
const char *ext;
|
||||
|
||||
if (!pdb_name || !hdf_name) return NULL;
|
||||
if ((s=strrchr(pdb_name, '/'))) pdb_name = s;
|
||||
if (NULL==(ext=strrchr(pdb_name, '.'))) ext = pdb_name + strlen(pdb_name);
|
||||
if ((size_t)((ext-pdb_name)+4) > size) return NULL; /*overflow*/
|
||||
memcpy(hdf_name, pdb_name, ext-pdb_name);
|
||||
strcpy(hdf_name+(ext-pdb_name), ".h5");
|
||||
return hdf_name;
|
||||
}
|
||||
|
||||
|
||||
/*-------------------------------------------------------------------------
|
||||
* Function: fix_type
|
||||
*
|
||||
* Purpose: Given a PDB datatype return a corresponding hdf5 datatype.
|
||||
* The hdf5 datatype should be closed when the caller is
|
||||
* finished using it.
|
||||
*
|
||||
* Return: Success: HDF5 datatype
|
||||
*
|
||||
* Failure: negative
|
||||
*
|
||||
* Programmer: Robb Matzke
|
||||
* Tuesday, October 12, 1999
|
||||
*
|
||||
* Modifications:
|
||||
*
|
||||
*-------------------------------------------------------------------------
|
||||
*/
|
||||
static hid_t
|
||||
fix_type(PDBfile *pdb, const char *s)
|
||||
{
|
||||
hid_t type = -1;
|
||||
defstr *d = _lite_PD_lookup_type((char*)s, pdb->chart);
|
||||
|
||||
/* PDB checking */
|
||||
assert(d);
|
||||
assert(d->size>0);
|
||||
if (d->onescmp) return -1;
|
||||
|
||||
|
||||
if (!strcmp(s, "char")) {
|
||||
/*
|
||||
* Character datatypes. Use whatever sign the native system uses by
|
||||
* default.
|
||||
*/
|
||||
type = H5Tcopy(H5T_NATIVE_CHAR);
|
||||
|
||||
} else if (!strcmp(s, "integer")) {
|
||||
/*
|
||||
* Integer datatypes. PDB supports various sizes of signed or
|
||||
* unsigned integers.
|
||||
*/
|
||||
type = H5Tcopy(d->unsgned?H5T_NATIVE_UINT:H5T_NATIVE_INT);
|
||||
H5Tset_size(type, d->size);
|
||||
H5Tset_precision(type, 8*d->size);
|
||||
assert(NORMAL_ORDER==d->order_flag || REVERSE_ORDER==d->order_flag);
|
||||
H5Tset_order(type,
|
||||
NORMAL_ORDER==d->order_flag?H5T_ORDER_BE:H5T_ORDER_LE);
|
||||
|
||||
} else if (!strcmp(s, "float") || !strcmp(s, "double")) {
|
||||
/*
|
||||
* Floating-point datatypes
|
||||
*/
|
||||
size_t nbits, spos, epos, esize, mpos, msize;
|
||||
|
||||
type = H5Tcopy(H5T_NATIVE_FLOAT);
|
||||
H5Tset_size(type, d->size);
|
||||
H5Tset_precision(type, 8*d->size);
|
||||
assert(d->order);
|
||||
H5Tset_order(type, 1==d->order[0]?H5T_ORDER_BE:H5T_ORDER_LE);
|
||||
|
||||
/*
|
||||
* format[0] = # of bits per number
|
||||
* format[1] = # of bits in exponent
|
||||
* format[2] = # of bits in mantissa
|
||||
* format[3] = start bit of sign
|
||||
* format[4] = start bit of exponent
|
||||
* format[5] = start bit of mantissa
|
||||
* format[6] = high order mantissa bit (CRAY needs this)
|
||||
* format[7] = bias of exponent
|
||||
*/
|
||||
assert(d->format && d->format[0] == 8*d->size);
|
||||
nbits = d->format[0];
|
||||
spos = nbits - (d->format[3]+1);
|
||||
esize = d->format[1];
|
||||
epos = nbits - (d->format[4]+esize);
|
||||
msize = d->format[2];
|
||||
mpos = nbits - (d->format[5]+msize);
|
||||
H5Tset_fields(type, spos, epos, esize, mpos, msize);
|
||||
H5Tset_ebias(type, d->format[7]);
|
||||
}
|
||||
return type;
|
||||
}
|
||||
|
||||
|
||||
/*-------------------------------------------------------------------------
|
||||
* Function: fix_space
|
||||
*
|
||||
* Purpose: Convert a PDB dimension list into an HDF5 data space.
|
||||
*
|
||||
* Return: Success: HDF5 data space
|
||||
*
|
||||
* Failure: negative
|
||||
*
|
||||
* Programmer: Robb Matzke
|
||||
* Tuesday, October 12, 1999
|
||||
*
|
||||
* Modifications:
|
||||
*
|
||||
*-------------------------------------------------------------------------
|
||||
*/
|
||||
static hid_t
|
||||
fix_space(const dimdes *dim)
|
||||
{
|
||||
hsize_t size[H5S_MAX_RANK];
|
||||
int rank;
|
||||
|
||||
for (rank=0; rank<H5S_MAX_RANK && dim; rank++, dim=dim->next) {
|
||||
size[rank] = dim->number;
|
||||
}
|
||||
if (rank>=H5S_MAX_RANK) return -1;
|
||||
return H5Screate_simple(rank, size, NULL);
|
||||
}
|
||||
|
||||
|
||||
/*-------------------------------------------------------------------------
|
||||
* Function: fix_external
|
||||
*
|
||||
* Purpose: Sets the external file information for a dataset creation
|
||||
* property list based on information from PDB.
|
||||
*
|
||||
* Return: Success: non-negative
|
||||
*
|
||||
* Failure: negative
|
||||
*
|
||||
* Programmer: Robb Matzke
|
||||
* Tuesday, October 12, 1999
|
||||
*
|
||||
* Modifications:
|
||||
*
|
||||
*-------------------------------------------------------------------------
|
||||
*/
|
||||
static int
|
||||
fix_external(hid_t dcpl, const char *pdb_file_name, long nelmts,
|
||||
hsize_t elmt_size, symblock *block)
|
||||
{
|
||||
int i;
|
||||
|
||||
for (i=0; nelmts>0; i++) {
|
||||
hsize_t nbytes = block[i].number * elmt_size;
|
||||
H5Pset_external(dcpl, pdb_file_name, block[i].diskaddr, nbytes);
|
||||
nelmts -= block[i].number;
|
||||
}
|
||||
return 0;
|
||||
}
|
||||
|
||||
|
||||
/*-------------------------------------------------------------------------
|
||||
* Function: traverse
|
||||
*
|
||||
* Purpose: Traverse the current working directory of the PDB file.
|
||||
*
|
||||
* Return: Success: 0
|
||||
*
|
||||
* Failure: -1
|
||||
*
|
||||
* Programmer: Robb Matzke
|
||||
* Tuesday, October 12, 1999
|
||||
*
|
||||
* Modifications:
|
||||
*
|
||||
*-------------------------------------------------------------------------
|
||||
*/
|
||||
static int
|
||||
traverse(PDBfile *pdb, const char *pdb_file_name, hid_t hdf)
|
||||
{
|
||||
int nitems, i, in_subdir=FALSE;
|
||||
char **list=NULL;
|
||||
hid_t group=-1, h_type=-1, h_space=-1, dset=-1, dcpl=-1;
|
||||
hsize_t elmt_size;
|
||||
const syment *ep=NULL;
|
||||
|
||||
if (NULL==(list=PD_ls(pdb, ".", NULL, &nitems))) {
|
||||
fprintf(stderr, "cannot obtain PDB directory contents\n");
|
||||
goto error;
|
||||
}
|
||||
|
||||
for (i=0; i<nitems; i++) {
|
||||
ep = PD_inquire_entry(pdb, list[i], TRUE, NULL);
|
||||
if (verbose_g) {
|
||||
printf("%s %s\n", _PD_fixname(pdb, list[i]), ep->type);
|
||||
fflush(stdout);
|
||||
}
|
||||
|
||||
|
||||
if ('/'==list[i][strlen(list[i])-1]) {
|
||||
/*
|
||||
* This is a PDB directory. Make a corresponding HDF5 group and
|
||||
* traverse into that PDB directory and HDF5 group
|
||||
*/
|
||||
if ((group=H5Gcreate(hdf, list[i], 0))<0) {
|
||||
fprintf(stderr, "cannot create HDF group %s\n", list[i]);
|
||||
goto error;
|
||||
}
|
||||
if (!PD_cd(pdb, list[i])) {
|
||||
fprintf(stderr, "cannot cd into PDB directory %s\n", list[i]);
|
||||
goto error;
|
||||
} else {
|
||||
in_subdir = TRUE;
|
||||
}
|
||||
|
||||
traverse(pdb, pdb_file_name, group);
|
||||
if (!PD_cd(pdb, "..")) {
|
||||
fprintf(stderr, "cannot traverse out of PDB %s\n", list[i]);
|
||||
goto error;
|
||||
}
|
||||
H5Gclose(group);
|
||||
|
||||
} else {
|
||||
/* This is some non-directory PDB object */
|
||||
|
||||
/* Create an HDF5 datatype from the PDB type */
|
||||
if ((h_type=fix_type(pdb, ep->type))<0) {
|
||||
fprintf(stderr, "cannot create datatype for %s (%s)\n",
|
||||
list[i], ep->type);
|
||||
continue;
|
||||
}
|
||||
elmt_size = H5Tget_size(h_type);
|
||||
|
||||
/* Create an HDF5 dataspace from the PDB dimensions */
|
||||
if ((h_space=fix_space(ep->dimensions))<0) {
|
||||
fprintf(stderr, "cannot create datatype for %s\n", list[i]);
|
||||
continue;
|
||||
}
|
||||
|
||||
/* Create pointers to the external PDB data */
|
||||
dcpl = H5Pcreate(H5P_DATASET_CREATE);
|
||||
fix_external(dcpl, pdb_file_name, ep->number, elmt_size,
|
||||
ep->blocks);
|
||||
|
||||
/* Create the dataset */
|
||||
if ((dset=H5Dcreate(hdf, list[i], h_type, h_space, dcpl))<0) {
|
||||
fprintf(stderr, "cannot create dataset for %s\n", list[i]);
|
||||
}
|
||||
|
||||
H5Pclose(dcpl);
|
||||
H5Dclose(dset);
|
||||
H5Sclose(h_space);
|
||||
H5Tclose(h_type);
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
for (i=0; i<nitems; i++) {
|
||||
SC_free(list[i]);
|
||||
}
|
||||
SC_free(list);
|
||||
return 0;
|
||||
|
||||
error:
|
||||
if (group>=0) H5Gclose(group);
|
||||
if (in_subdir) PD_cd(pdb, "..");
|
||||
if (list) {
|
||||
for (i=0; i<nitems; i++) {
|
||||
SC_free(list[i]);
|
||||
}
|
||||
SC_free(list);
|
||||
}
|
||||
return -1;
|
||||
}
|
||||
|
||||
|
||||
/*-------------------------------------------------------------------------
|
||||
* Function: main
|
||||
*
|
||||
* Purpose: Create an HDF5 file from a PDB file.
|
||||
*
|
||||
* Return: Success: 0
|
||||
*
|
||||
* Failure: non-zero
|
||||
*
|
||||
* Programmer: Robb Matzke
|
||||
* Tuesday, October 12, 1999
|
||||
*
|
||||
* Modifications:
|
||||
*
|
||||
*-------------------------------------------------------------------------
|
||||
*/
|
||||
int
|
||||
main(int argc, char *argv[])
|
||||
{
|
||||
int argno;
|
||||
char _hdf_name[512], *hdf_name, *pdb_name, *s;
|
||||
PDBfile *pdb;
|
||||
hid_t hdf, fapl;
|
||||
|
||||
/* Print a help message if called with no arguments */
|
||||
if (1==argc) {
|
||||
usage(argv[0]);
|
||||
exit(1);
|
||||
}
|
||||
|
||||
/* Process arguments in order; switches interspersed with files */
|
||||
for (argno=1; argno<argc; argno++) {
|
||||
if (!strcmp("--help", argv[argno])) {
|
||||
usage(argv[0]);
|
||||
exit(1);
|
||||
} else if (!strcmp("--verbose", argv[argno])) {
|
||||
verbose_g++;
|
||||
} else if (!strcmp("--cached", argv[argno])) {
|
||||
cached_g++;
|
||||
} else if (!strcmp("--version", argv[argno])) {
|
||||
version(argv[0]);
|
||||
} else if ('-'==argv[argno][0] && '-'!=argv[argno][1]) {
|
||||
for (s=argv[argno]+1; *s; s++) {
|
||||
switch (*s) {
|
||||
case '?':
|
||||
case 'h': /*--help*/
|
||||
usage(argv[0]);
|
||||
exit(0);
|
||||
case 'c': /*--cached*/
|
||||
cached_g++;
|
||||
break;
|
||||
case 'v': /*--verbose*/
|
||||
verbose_g++;
|
||||
break;
|
||||
case 'V': /*--version*/
|
||||
version(argv[0]);
|
||||
break;
|
||||
default:
|
||||
usage(argv[0]);
|
||||
exit(1);
|
||||
}
|
||||
}
|
||||
} else if ('-'==argv[argno][0]) {
|
||||
usage(argv[0]);
|
||||
exit(1);
|
||||
} else {
|
||||
/* This must be a file name. Process it. */
|
||||
fapl = H5Pcreate(H5P_FILE_ACCESS);
|
||||
if (cached_g) H5Pset_fapl_core(fapl, 1024*1024, TRUE);
|
||||
|
||||
pdb_name = argv[argno];
|
||||
hdf_name = fix_name(argv[argno], _hdf_name, sizeof _hdf_name);
|
||||
if (NULL==(pdb=PD_open(pdb_name, "r"))) {
|
||||
fprintf(stderr, "%s: unable to open PDB file\n", pdb_name);
|
||||
exit(1);
|
||||
}
|
||||
if ((hdf=H5Fcreate(hdf_name, H5F_ACC_TRUNC, H5P_DEFAULT,
|
||||
fapl))<0) {
|
||||
fprintf(stderr, "%s: unable to open HDF file\n", hdf_name);
|
||||
exit(1);
|
||||
}
|
||||
H5Pclose(fapl);
|
||||
|
||||
/*
|
||||
* Traverse the PDB file to create the HDF5 file.
|
||||
*/
|
||||
traverse(pdb, pdb_name, hdf);
|
||||
|
||||
/* Close the files */
|
||||
if (!PD_close(pdb)) {
|
||||
fprintf(stderr, "%s: problems closing PDB file\n", pdb_name);
|
||||
exit(1);
|
||||
}
|
||||
if (H5Fclose(hdf)<0) {
|
||||
fprintf(stderr, "%s: problems closing HDF file\n", hdf_name);
|
||||
exit(1);
|
||||
}
|
||||
}
|
||||
}
|
||||
return 0;
|
||||
}
|
||||
#endif /* H5_HAVE_PDB_H */
|
||||
Loading…
x
Reference in New Issue
Block a user