diff options
| author | Robb Matzke <matzke@llnl.gov> | 1999-10-15 14:53:57 (GMT) |
|---|---|---|
| committer | Robb Matzke <matzke@llnl.gov> | 1999-10-15 14:53:57 (GMT) |
| commit | 34e44e399edd8903f8104f8a6b74e96151150b16 (patch) | |
| tree | f2cc428e6292eb4d60646b4e8f47e71f5cec29d8 | |
| parent | 5246411f704970a2f6568dc7aaf9e7b5b7269505 (diff) | |
| download | hdf5-34e44e399edd8903f8104f8a6b74e96151150b16.zip hdf5-34e44e399edd8903f8104f8a6b74e96151150b16.tar.gz hdf5-34e44e399edd8903f8104f8a6b74e96151150b16.tar.bz2 | |
[svn-r1753] Changes since 19991007
----------------------
./configure.in
./src/H5config.h.in [REGENERATED]
The /usr/ncsa/{include,lib} directories are only added if they
actually exist. This fixes a warning on some systems.
Checks for the <pdb.h> header file and also for either the PDB or Silo
library, and if found prepares to compile the pdb2hdf program.
./config/distdep
Relative path names for include files are changed to base names since
the makefile contains the logic for searching and since it's likely
that building the .distdep files happed from a location other than
where they would be used in the file system.
./config/conclude.in
Fixed shell errors when `for' loops iterate over nothing for the
`uninstall' target.
./src/H5D.c
./src/H5Oefl.c
File names for the external files are added to the heap when the
dataset is created instead of when the object header is written. This
fixes a rare infinite recursion bug.
./src/H5FD.c
./src/H5FDpublic.h
Optimization to the free list causes H5FD_alloc() usage to go from >10
seconds to <0.4 second for one example (converting a 30MB equation of
state file from PDB to HDF5 format). The optimization is to simply
keep track of the largest item in the free list and not search the
free list when the largest item is not big enough to satisfy the
request.
./src/H5FDcore.c
./src/H5FDcore.h
./test/h5test.c
If the `backing_store' property is true then a flush causes the entire
contents of memory to be written to the specified file. This is in
preparation for the ASCI/red optimizations and is currently tested by
the pdb2hdf `--cached' switch.
./src/H5Odtypes.c
Wrapped three long lines.
./tools/Makefile.in
./tools/pdb2hdf.c [NEW]
A PDB-to-HDF5 translator. It only translates meta data -- the
resulting HDF5 points into the PDB file for the raw data.
| -rw-r--r-- | README | 2 | ||||
| -rw-r--r-- | bin/distdep | 7 | ||||
| -rw-r--r-- | config/conclude.in | 18 | ||||
| -rwxr-xr-x | configure | 578 | ||||
| -rw-r--r-- | configure.in | 14 | ||||
| -rw-r--r-- | src/H5D.c | 15 | ||||
| -rw-r--r-- | src/H5FD.c | 12 | ||||
| -rw-r--r-- | src/H5FDcore.c | 86 | ||||
| -rw-r--r-- | src/H5FDcore.h | 6 | ||||
| -rw-r--r-- | src/H5FDpublic.h | 1 | ||||
| -rw-r--r-- | src/H5Odtype.c | 9 | ||||
| -rw-r--r-- | src/H5Oefl.c | 23 | ||||
| -rw-r--r-- | src/H5config.h.in | 9 | ||||
| -rw-r--r-- | test/h5test.c | 2 | ||||
| -rw-r--r-- | tools/Makefile.in | 7 | ||||
| -rw-r--r-- | tools/pdb2hdf.c | 500 |
16 files changed, 1025 insertions, 264 deletions
@@ -1,4 +1,4 @@ -This is hdf5-1.3.2 currently under development +This is hdf5-1.3.2 released on Mon Oct 11 10:41:12 EDT 1999 Please refer to the INSTALL file for installation instructions. ------------------------------------------------------------------------------ diff --git a/bin/distdep b/bin/distdep index 287ce84..1a7b0ad 100644 --- a/bin/distdep +++ b/bin/distdep @@ -1,6 +1,11 @@ #!/usr/bin/perl -p # Usage: $0 [<].depend + # Takes dependency info and generates on stdout dependencies suitable for -# distribution by removing all the system include files from the list. +# distribution by removing all the system include files from the list and +# removing all but the base name of other include files (since the Makefiles +# contain the logic for searching). + ($h,$_)=/\s*\\/?$h.$`:("","$h\n"); s|( +/\S*)*( *)|$2?" \\\n ":""|eg; +s|(([-\w\.]+)/)+([-\w\.]+)|\3|g; diff --git a/config/conclude.in b/config/conclude.in index bdd0b90..0405219 100644 --- a/config/conclude.in +++ b/config/conclude.in @@ -83,19 +83,17 @@ install: $(PUB_LIB) $(PUB_HDR) $(PROGS) $(libdir) $(includedir) $(bindir) ## Removes those things that `make install' (would have) installed. uninstall: - @if test "X$(LIB)" != X; then \ - for f in $(LIB); do \ - $(LT_UNINSTALL) $(libdir)/$$f; \ - done; \ - fi + @for f in libhdf5.settings $(LIB); do \ + $(LT_UNINSTALL) $(libdir)/$$f; \ + done @if test "X$(PUB_HDR)" != X; then \ set -x; cd $(includedir) && $(RM) $(PUB_HDR); \ fi - @if test "X$(PROGS)" != X; then \ - for f in $(PROGS); do \ - $(LT_UNINSTALL) $(bindir)/$$f; \ - done; \ - fi + @for f in X $(PROGS); do \ + if test $$f != X; then \ + $(LT_UNINSTALL) $(bindir)/$$f; \ + fi; \ + done ## Removes temporary files without removing the final target files. That is, ## remove things like object files but not libraries or executables. @@ -3436,12 +3436,15 @@ H5TOH4=h5toh4 TESTH5TOH4='$(srcdir)/testh5toh4' +test -d /usr/ncsa/include && CPPFLAGS="$CPPFLAGS -I/usr/ncsa/include" +test -d /usr/ncsa/lib && LDFLAGS="$LDFLAGS -L/usr/ncsa/lib" + # Check whether --with-hdf4 or --without-hdf4 was given. if test "${with_hdf4+set}" = set; then withval="$with_hdf4" : else - withval=/usr/ncsa/include,/usr/ncsa/lib + withval=yes fi case $withval in @@ -3450,17 +3453,17 @@ case $withval in do ac_safe=`echo "$ac_hdr" | sed 'y%./+-%__p_%'` echo $ac_n "checking for $ac_hdr""... $ac_c" 1>&6 -echo "configure:3454: checking for $ac_hdr" >&5 +echo "configure:3457: checking for $ac_hdr" >&5 if eval "test \"`echo '$''{'ac_cv_header_$ac_safe'+set}'`\" = set"; then echo $ac_n "(cached) $ac_c" 1>&6 else cat > conftest.$ac_ext <<EOF -#line 3459 "configure" +#line 3462 "configure" #include "confdefs.h" #include <$ac_hdr> EOF ac_try="$ac_cpp conftest.$ac_ext >/dev/null 2>conftest.out" -{ (eval echo configure:3464: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; } +{ (eval echo configure:3467: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; } ac_err=`grep -v '^ *+' conftest.out` if test -z "$ac_err"; then rm -rf conftest* @@ -3488,7 +3491,7 @@ fi done echo $ac_n "checking for deflate in -lz""... $ac_c" 1>&6 -echo "configure:3492: checking for deflate in -lz" >&5 +echo "configure:3495: checking for deflate in -lz" >&5 ac_lib_var=`echo z'_'deflate | sed 'y%./+-%__p_%'` if eval "test \"`echo '$''{'ac_cv_lib_$ac_lib_var'+set}'`\" = set"; then echo $ac_n "(cached) $ac_c" 1>&6 @@ -3496,7 +3499,7 @@ else ac_save_LIBS="$LIBS" LIBS="-lz $LIBS" cat > conftest.$ac_ext <<EOF -#line 3500 "configure" +#line 3503 "configure" #include "confdefs.h" /* Override any gcc2 internal prototype to avoid an error. */ /* We use char because int might match the return type of a gcc2 @@ -3507,7 +3510,7 @@ int main() { deflate() ; return 0; } EOF -if { (eval echo configure:3511: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then +if { (eval echo configure:3514: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then rm -rf conftest* eval "ac_cv_lib_$ac_lib_var=yes" else @@ -3536,7 +3539,7 @@ unset H5TOH4 TESTH5TOH4 fi echo $ac_n "checking for jpeg_start_compress in -ljpeg""... $ac_c" 1>&6 -echo "configure:3540: checking for jpeg_start_compress in -ljpeg" >&5 +echo "configure:3543: checking for jpeg_start_compress in -ljpeg" >&5 ac_lib_var=`echo jpeg'_'jpeg_start_compress | sed 'y%./+-%__p_%'` if eval "test \"`echo '$''{'ac_cv_lib_$ac_lib_var'+set}'`\" = set"; then echo $ac_n "(cached) $ac_c" 1>&6 @@ -3544,7 +3547,7 @@ else ac_save_LIBS="$LIBS" LIBS="-ljpeg $LIBS" cat > conftest.$ac_ext <<EOF -#line 3548 "configure" +#line 3551 "configure" #include "confdefs.h" /* Override any gcc2 internal prototype to avoid an error. */ /* We use char because int might match the return type of a gcc2 @@ -3555,7 +3558,7 @@ int main() { jpeg_start_compress() ; return 0; } EOF -if { (eval echo configure:3559: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then +if { (eval echo configure:3562: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then rm -rf conftest* eval "ac_cv_lib_$ac_lib_var=yes" else @@ -3584,7 +3587,7 @@ unset H5TOH4 TESTH5TOH4 fi echo $ac_n "checking for Hstartaccess in -ldf""... $ac_c" 1>&6 -echo "configure:3588: checking for Hstartaccess in -ldf" >&5 +echo "configure:3591: checking for Hstartaccess in -ldf" >&5 ac_lib_var=`echo df'_'Hstartaccess | sed 'y%./+-%__p_%'` if eval "test \"`echo '$''{'ac_cv_lib_$ac_lib_var'+set}'`\" = set"; then echo $ac_n "(cached) $ac_c" 1>&6 @@ -3592,7 +3595,7 @@ else ac_save_LIBS="$LIBS" LIBS="-ldf $LIBS" cat > conftest.$ac_ext <<EOF -#line 3596 "configure" +#line 3599 "configure" #include "confdefs.h" /* Override any gcc2 internal prototype to avoid an error. */ /* We use char because int might match the return type of a gcc2 @@ -3603,7 +3606,7 @@ int main() { Hstartaccess() ; return 0; } EOF -if { (eval echo configure:3607: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then +if { (eval echo configure:3610: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then rm -rf conftest* eval "ac_cv_lib_$ac_lib_var=yes" else @@ -3632,7 +3635,7 @@ unset H5TOH4 TESTH5TOH4 fi echo $ac_n "checking for SDstart in -lmfhdf""... $ac_c" 1>&6 -echo "configure:3636: checking for SDstart in -lmfhdf" >&5 +echo "configure:3639: checking for SDstart in -lmfhdf" >&5 ac_lib_var=`echo mfhdf'_'SDstart | sed 'y%./+-%__p_%'` if eval "test \"`echo '$''{'ac_cv_lib_$ac_lib_var'+set}'`\" = set"; then echo $ac_n "(cached) $ac_c" 1>&6 @@ -3640,7 +3643,7 @@ else ac_save_LIBS="$LIBS" LIBS="-lmfhdf $LIBS" cat > conftest.$ac_ext <<EOF -#line 3644 "configure" +#line 3647 "configure" #include "confdefs.h" /* Override any gcc2 internal prototype to avoid an error. */ /* We use char because int might match the return type of a gcc2 @@ -3651,7 +3654,7 @@ int main() { SDstart() ; return 0; } EOF -if { (eval echo configure:3655: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then +if { (eval echo configure:3658: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then rm -rf conftest* eval "ac_cv_lib_$ac_lib_var=yes" else @@ -3682,7 +3685,7 @@ fi ;; no) echo $ac_n "checking for HDF4""... $ac_c" 1>&6 -echo "configure:3686: checking for HDF4" >&5 +echo "configure:3689: checking for HDF4" >&5 echo "$ac_t""suppressed" 1>&6 unset H5TOH4 TESTH5TOH4 ;; @@ -3695,17 +3698,17 @@ echo "configure:3686: checking for HDF4" >&5 do ac_safe=`echo "$ac_hdr" | sed 'y%./+-%__p_%'` echo $ac_n "checking for $ac_hdr""... $ac_c" 1>&6 -echo "configure:3699: checking for $ac_hdr" >&5 +echo "configure:3702: checking for $ac_hdr" >&5 if eval "test \"`echo '$''{'ac_cv_header_$ac_safe'+set}'`\" = set"; then echo $ac_n "(cached) $ac_c" 1>&6 else cat > conftest.$ac_ext <<EOF -#line 3704 "configure" +#line 3707 "configure" #include "confdefs.h" #include <$ac_hdr> EOF ac_try="$ac_cpp conftest.$ac_ext >/dev/null 2>conftest.out" -{ (eval echo configure:3709: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; } +{ (eval echo configure:3712: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; } ac_err=`grep -v '^ *+' conftest.out` if test -z "$ac_err"; then rm -rf conftest* @@ -3739,17 +3742,17 @@ done do ac_safe=`echo "$ac_hdr" | sed 'y%./+-%__p_%'` echo $ac_n "checking for $ac_hdr""... $ac_c" 1>&6 -echo "configure:3743: checking for $ac_hdr" >&5 +echo "configure:3746: checking for $ac_hdr" >&5 if eval "test \"`echo '$''{'ac_cv_header_$ac_safe'+set}'`\" = set"; then echo $ac_n "(cached) $ac_c" 1>&6 else cat > conftest.$ac_ext <<EOF -#line 3748 "configure" +#line 3751 "configure" #include "confdefs.h" #include <$ac_hdr> EOF ac_try="$ac_cpp conftest.$ac_ext >/dev/null 2>conftest.out" -{ (eval echo configure:3753: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; } +{ (eval echo configure:3756: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; } ac_err=`grep -v '^ *+' conftest.out` if test -z "$ac_err"; then rm -rf conftest* @@ -3782,7 +3785,7 @@ done saved_LDFLAGS="$LDFLAGS" LDFLAGS="$LDFLAGS -L$hdf4_lib" echo $ac_n "checking for deflate in -lz""... $ac_c" 1>&6 -echo "configure:3786: checking for deflate in -lz" >&5 +echo "configure:3789: checking for deflate in -lz" >&5 ac_lib_var=`echo z'_'deflate | sed 'y%./+-%__p_%'` if eval "test \"`echo '$''{'ac_cv_lib_$ac_lib_var'+set}'`\" = set"; then echo $ac_n "(cached) $ac_c" 1>&6 @@ -3790,7 +3793,7 @@ else ac_save_LIBS="$LIBS" LIBS="-lz $LIBS" cat > conftest.$ac_ext <<EOF -#line 3794 "configure" +#line 3797 "configure" #include "confdefs.h" /* Override any gcc2 internal prototype to avoid an error. */ /* We use char because int might match the return type of a gcc2 @@ -3801,7 +3804,7 @@ int main() { deflate() ; return 0; } EOF -if { (eval echo configure:3805: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then +if { (eval echo configure:3808: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then rm -rf conftest* eval "ac_cv_lib_$ac_lib_var=yes" else @@ -3830,7 +3833,7 @@ unset H5TOH4 TESTH5TOH4 fi echo $ac_n "checking for jpeg_start_compress in -ljpeg""... $ac_c" 1>&6 -echo "configure:3834: checking for jpeg_start_compress in -ljpeg" >&5 +echo "configure:3837: checking for jpeg_start_compress in -ljpeg" >&5 ac_lib_var=`echo jpeg'_'jpeg_start_compress | sed 'y%./+-%__p_%'` if eval "test \"`echo '$''{'ac_cv_lib_$ac_lib_var'+set}'`\" = set"; then echo $ac_n "(cached) $ac_c" 1>&6 @@ -3838,7 +3841,7 @@ else ac_save_LIBS="$LIBS" LIBS="-ljpeg $LIBS" cat > conftest.$ac_ext <<EOF -#line 3842 "configure" +#line 3845 "configure" #include "confdefs.h" /* Override any gcc2 internal prototype to avoid an error. */ /* We use char because int might match the return type of a gcc2 @@ -3849,7 +3852,7 @@ int main() { jpeg_start_compress() ; return 0; } EOF -if { (eval echo configure:3853: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then +if { (eval echo configure:3856: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then rm -rf conftest* eval "ac_cv_lib_$ac_lib_var=yes" else @@ -3878,7 +3881,7 @@ unset H5TOH4 TESTH5TOH4 fi echo $ac_n "checking for Hstartaccess in -ldf""... $ac_c" 1>&6 -echo "configure:3882: checking for Hstartaccess in -ldf" >&5 +echo "configure:3885: checking for Hstartaccess in -ldf" >&5 ac_lib_var=`echo df'_'Hstartaccess | sed 'y%./+-%__p_%'` if eval "test \"`echo '$''{'ac_cv_lib_$ac_lib_var'+set}'`\" = set"; then echo $ac_n "(cached) $ac_c" 1>&6 @@ -3886,7 +3889,7 @@ else ac_save_LIBS="$LIBS" LIBS="-ldf $LIBS" cat > conftest.$ac_ext <<EOF -#line 3890 "configure" +#line 3893 "configure" #include "confdefs.h" /* Override any gcc2 internal prototype to avoid an error. */ /* We use char because int might match the return type of a gcc2 @@ -3897,7 +3900,7 @@ int main() { Hstartaccess() ; return 0; } EOF -if { (eval echo configure:3901: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then +if { (eval echo configure:3904: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then rm -rf conftest* eval "ac_cv_lib_$ac_lib_var=yes" else @@ -3926,7 +3929,7 @@ unset H5TOH4 TESTH5TOH4 fi echo $ac_n "checking for SDstart in -lmfhdf""... $ac_c" 1>&6 -echo "configure:3930: checking for SDstart in -lmfhdf" >&5 +echo "configure:3933: checking for SDstart in -lmfhdf" >&5 ac_lib_var=`echo mfhdf'_'SDstart | sed 'y%./+-%__p_%'` if eval "test \"`echo '$''{'ac_cv_lib_$ac_lib_var'+set}'`\" = set"; then echo $ac_n "(cached) $ac_c" 1>&6 @@ -3934,7 +3937,7 @@ else ac_save_LIBS="$LIBS" LIBS="-lmfhdf $LIBS" cat > conftest.$ac_ext <<EOF -#line 3938 "configure" +#line 3941 "configure" #include "confdefs.h" /* Override any gcc2 internal prototype to avoid an error. */ /* We use char because int might match the return type of a gcc2 @@ -3945,7 +3948,7 @@ int main() { SDstart() ; return 0; } EOF -if { (eval echo configure:3949: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then +if { (eval echo configure:3952: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then rm -rf conftest* eval "ac_cv_lib_$ac_lib_var=yes" else @@ -3975,7 +3978,7 @@ fi else echo $ac_n "checking for deflate in -lz""... $ac_c" 1>&6 -echo "configure:3979: checking for deflate in -lz" >&5 +echo "configure:3982: checking for deflate in -lz" >&5 ac_lib_var=`echo z'_'deflate | sed 'y%./+-%__p_%'` if eval "test \"`echo '$''{'ac_cv_lib_$ac_lib_var'+set}'`\" = set"; then echo $ac_n "(cached) $ac_c" 1>&6 @@ -3983,7 +3986,7 @@ else ac_save_LIBS="$LIBS" LIBS="-lz $LIBS" cat > conftest.$ac_ext <<EOF -#line 3987 "configure" +#line 3990 "configure" #include "confdefs.h" /* Override any gcc2 internal prototype to avoid an error. */ /* We use char because int might match the return type of a gcc2 @@ -3994,7 +3997,7 @@ int main() { deflate() ; return 0; } EOF -if { (eval echo configure:3998: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then +if { (eval echo configure:4001: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then rm -rf conftest* eval "ac_cv_lib_$ac_lib_var=yes" else @@ -4023,7 +4026,7 @@ unset H5TOH4 TESTH5TOH4 fi echo $ac_n "checking for jpeg_start_compress in -ljpeg""... $ac_c" 1>&6 -echo "configure:4027: checking for jpeg_start_compress in -ljpeg" >&5 +echo "configure:4030: checking for jpeg_start_compress in -ljpeg" >&5 ac_lib_var=`echo jpeg'_'jpeg_start_compress | sed 'y%./+-%__p_%'` if eval "test \"`echo '$''{'ac_cv_lib_$ac_lib_var'+set}'`\" = set"; then echo $ac_n "(cached) $ac_c" 1>&6 @@ -4031,7 +4034,7 @@ else ac_save_LIBS="$LIBS" LIBS="-ljpeg $LIBS" cat > conftest.$ac_ext <<EOF -#line 4035 "configure" +#line 4038 "configure" #include "confdefs.h" /* Override any gcc2 internal prototype to avoid an error. */ /* We use char because int might match the return type of a gcc2 @@ -4042,7 +4045,7 @@ int main() { jpeg_start_compress() ; return 0; } EOF -if { (eval echo configure:4046: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then +if { (eval echo configure:4049: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then rm -rf conftest* eval "ac_cv_lib_$ac_lib_var=yes" else @@ -4071,7 +4074,7 @@ unset H5TOH4 TESTH5TOH4 fi echo $ac_n "checking for Hstartaccess in -ldf""... $ac_c" 1>&6 -echo "configure:4075: checking for Hstartaccess in -ldf" >&5 +echo "configure:4078: checking for Hstartaccess in -ldf" >&5 ac_lib_var=`echo df'_'Hstartaccess | sed 'y%./+-%__p_%'` if eval "test \"`echo '$''{'ac_cv_lib_$ac_lib_var'+set}'`\" = set"; then echo $ac_n "(cached) $ac_c" 1>&6 @@ -4079,7 +4082,7 @@ else ac_save_LIBS="$LIBS" LIBS="-ldf $LIBS" cat > conftest.$ac_ext <<EOF -#line 4083 "configure" +#line 4086 "configure" #include "confdefs.h" /* Override any gcc2 internal prototype to avoid an error. */ /* We use char because int might match the return type of a gcc2 @@ -4090,7 +4093,7 @@ int main() { Hstartaccess() ; return 0; } EOF -if { (eval echo configure:4094: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then +if { (eval echo configure:4097: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then rm -rf conftest* eval "ac_cv_lib_$ac_lib_var=yes" else @@ -4118,7 +4121,7 @@ else fi echo $ac_n "checking for SDstart in -lmfhdf""... $ac_c" 1>&6 -echo "configure:4122: checking for SDstart in -lmfhdf" >&5 +echo "configure:4125: checking for SDstart in -lmfhdf" >&5 ac_lib_var=`echo mfhdf'_'SDstart | sed 'y%./+-%__p_%'` if eval "test \"`echo '$''{'ac_cv_lib_$ac_lib_var'+set}'`\" = set"; then echo $ac_n "(cached) $ac_c" 1>&6 @@ -4126,7 +4129,7 @@ else ac_save_LIBS="$LIBS" LIBS="-lmfhdf $LIBS" cat > conftest.$ac_ext <<EOF -#line 4130 "configure" +#line 4133 "configure" #include "confdefs.h" /* Override any gcc2 internal prototype to avoid an error. */ /* We use char because int might match the return type of a gcc2 @@ -4137,7 +4140,7 @@ int main() { SDstart() ; return 0; } EOF -if { (eval echo configure:4141: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then +if { (eval echo configure:4144: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then rm -rf conftest* eval "ac_cv_lib_$ac_lib_var=yes" else @@ -4183,17 +4186,17 @@ case $withval in do ac_safe=`echo "$ac_hdr" | sed 'y%./+-%__p_%'` echo $ac_n "checking for $ac_hdr""... $ac_c" 1>&6 -echo "configure:4187: checking for $ac_hdr" >&5 +echo "configure:4190: checking for $ac_hdr" >&5 if eval "test \"`echo '$''{'ac_cv_header_$ac_safe'+set}'`\" = set"; then echo $ac_n "(cached) $ac_c" 1>&6 else cat > conftest.$ac_ext <<EOF -#line 4192 "configure" +#line 4195 "configure" #include "confdefs.h" #include <$ac_hdr> EOF ac_try="$ac_cpp conftest.$ac_ext >/dev/null 2>conftest.out" -{ (eval echo configure:4197: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; } +{ (eval echo configure:4200: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; } ac_err=`grep -v '^ *+' conftest.out` if test -z "$ac_err"; then rm -rf conftest* @@ -4220,7 +4223,7 @@ fi done echo $ac_n "checking for compress in -lz""... $ac_c" 1>&6 -echo "configure:4224: checking for compress in -lz" >&5 +echo "configure:4227: checking for compress in -lz" >&5 ac_lib_var=`echo z'_'compress | sed 'y%./+-%__p_%'` if eval "test \"`echo '$''{'ac_cv_lib_$ac_lib_var'+set}'`\" = set"; then echo $ac_n "(cached) $ac_c" 1>&6 @@ -4228,7 +4231,7 @@ else ac_save_LIBS="$LIBS" LIBS="-lz $LIBS" cat > conftest.$ac_ext <<EOF -#line 4232 "configure" +#line 4235 "configure" #include "confdefs.h" /* Override any gcc2 internal prototype to avoid an error. */ /* We use char because int might match the return type of a gcc2 @@ -4239,7 +4242,7 @@ int main() { compress() ; return 0; } EOF -if { (eval echo configure:4243: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then +if { (eval echo configure:4246: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then rm -rf conftest* eval "ac_cv_lib_$ac_lib_var=yes" else @@ -4269,7 +4272,7 @@ fi ;; no) echo $ac_n "checking for GNU zlib""... $ac_c" 1>&6 -echo "configure:4273: checking for GNU zlib" >&5 +echo "configure:4276: checking for GNU zlib" >&5 echo "$ac_t""suppressed" 1>&6 ;; *) @@ -4281,17 +4284,17 @@ echo "configure:4273: checking for GNU zlib" >&5 do ac_safe=`echo "$ac_hdr" | sed 'y%./+-%__p_%'` echo $ac_n "checking for $ac_hdr""... $ac_c" 1>&6 -echo "configure:4285: checking for $ac_hdr" >&5 +echo "configure:4288: checking for $ac_hdr" >&5 if eval "test \"`echo '$''{'ac_cv_header_$ac_safe'+set}'`\" = set"; then echo $ac_n "(cached) $ac_c" 1>&6 else cat > conftest.$ac_ext <<EOF -#line 4290 "configure" +#line 4293 "configure" #include "confdefs.h" #include <$ac_hdr> EOF ac_try="$ac_cpp conftest.$ac_ext >/dev/null 2>conftest.out" -{ (eval echo configure:4295: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; } +{ (eval echo configure:4298: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; } ac_err=`grep -v '^ *+' conftest.out` if test -z "$ac_err"; then rm -rf conftest* @@ -4323,17 +4326,17 @@ done do ac_safe=`echo "$ac_hdr" | sed 'y%./+-%__p_%'` echo $ac_n "checking for $ac_hdr""... $ac_c" 1>&6 -echo "configure:4327: checking for $ac_hdr" >&5 +echo "configure:4330: checking for $ac_hdr" >&5 if eval "test \"`echo '$''{'ac_cv_header_$ac_safe'+set}'`\" = set"; then echo $ac_n "(cached) $ac_c" 1>&6 else cat > conftest.$ac_ext <<EOF -#line 4332 "configure" +#line 4335 "configure" #include "confdefs.h" #include <$ac_hdr> EOF ac_try="$ac_cpp conftest.$ac_ext >/dev/null 2>conftest.out" -{ (eval echo configure:4337: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; } +{ (eval echo configure:4340: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; } ac_err=`grep -v '^ *+' conftest.out` if test -z "$ac_err"; then rm -rf conftest* @@ -4366,7 +4369,7 @@ done saved_LDFLAGS="$LDFLAGS" LDFLAGS="$LDFLAGS -L$zlib_lib" echo $ac_n "checking for compress in -lz""... $ac_c" 1>&6 -echo "configure:4370: checking for compress in -lz" >&5 +echo "configure:4373: checking for compress in -lz" >&5 ac_lib_var=`echo z'_'compress | sed 'y%./+-%__p_%'` if eval "test \"`echo '$''{'ac_cv_lib_$ac_lib_var'+set}'`\" = set"; then echo $ac_n "(cached) $ac_c" 1>&6 @@ -4374,7 +4377,7 @@ else ac_save_LIBS="$LIBS" LIBS="-lz $LIBS" cat > conftest.$ac_ext <<EOF -#line 4378 "configure" +#line 4381 "configure" #include "confdefs.h" /* Override any gcc2 internal prototype to avoid an error. */ /* We use char because int might match the return type of a gcc2 @@ -4385,7 +4388,7 @@ int main() { compress() ; return 0; } EOF -if { (eval echo configure:4389: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then +if { (eval echo configure:4392: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then rm -rf conftest* eval "ac_cv_lib_$ac_lib_var=yes" else @@ -4415,7 +4418,7 @@ fi else echo $ac_n "checking for compress in -lz""... $ac_c" 1>&6 -echo "configure:4419: checking for compress in -lz" >&5 +echo "configure:4422: checking for compress in -lz" >&5 ac_lib_var=`echo z'_'compress | sed 'y%./+-%__p_%'` if eval "test \"`echo '$''{'ac_cv_lib_$ac_lib_var'+set}'`\" = set"; then echo $ac_n "(cached) $ac_c" 1>&6 @@ -4423,7 +4426,7 @@ else ac_save_LIBS="$LIBS" LIBS="-lz $LIBS" cat > conftest.$ac_ext <<EOF -#line 4427 "configure" +#line 4430 "configure" #include "confdefs.h" /* Override any gcc2 internal prototype to avoid an error. */ /* We use char because int might match the return type of a gcc2 @@ -4434,7 +4437,7 @@ int main() { compress() ; return 0; } EOF -if { (eval echo configure:4438: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then +if { (eval echo configure:4441: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then rm -rf conftest* eval "ac_cv_lib_$ac_lib_var=yes" else @@ -4484,17 +4487,17 @@ case $withval in do ac_safe=`echo "$ac_hdr" | sed 'y%./+-%__p_%'` echo $ac_n "checking for $ac_hdr""... $ac_c" 1>&6 -echo "configure:4488: checking for $ac_hdr" >&5 +echo "configure:4491: checking for $ac_hdr" >&5 if eval "test \"`echo '$''{'ac_cv_header_$ac_safe'+set}'`\" = set"; then echo $ac_n "(cached) $ac_c" 1>&6 else cat > conftest.$ac_ext <<EOF -#line 4493 "configure" +#line 4496 "configure" #include "confdefs.h" #include <$ac_hdr> EOF ac_try="$ac_cpp conftest.$ac_ext >/dev/null 2>conftest.out" -{ (eval echo configure:4498: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; } +{ (eval echo configure:4501: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; } ac_err=`grep -v '^ *+' conftest.out` if test -z "$ac_err"; then rm -rf conftest* @@ -4522,7 +4525,7 @@ fi done echo $ac_n "checking for main in -lxnet""... $ac_c" 1>&6 -echo "configure:4526: checking for main in -lxnet" >&5 +echo "configure:4529: checking for main in -lxnet" >&5 ac_lib_var=`echo xnet'_'main | sed 'y%./+-%__p_%'` if eval "test \"`echo '$''{'ac_cv_lib_$ac_lib_var'+set}'`\" = set"; then echo $ac_n "(cached) $ac_c" 1>&6 @@ -4530,14 +4533,14 @@ else ac_save_LIBS="$LIBS" LIBS="-lxnet $LIBS" cat > conftest.$ac_ext <<EOF -#line 4534 "configure" +#line 4537 "configure" #include "confdefs.h" int main() { main() ; return 0; } EOF -if { (eval echo configure:4541: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then +if { (eval echo configure:4544: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then rm -rf conftest* eval "ac_cv_lib_$ac_lib_var=yes" else @@ -4566,7 +4569,7 @@ unset GASS TESTGASS fi echo $ac_n "checking for globus_module_activate in -lglobus_common""... $ac_c" 1>&6 -echo "configure:4570: checking for globus_module_activate in -lglobus_common" >&5 +echo "configure:4573: checking for globus_module_activate in -lglobus_common" >&5 ac_lib_var=`echo globus_common'_'globus_module_activate | sed 'y%./+-%__p_%'` if eval "test \"`echo '$''{'ac_cv_lib_$ac_lib_var'+set}'`\" = set"; then echo $ac_n "(cached) $ac_c" 1>&6 @@ -4574,7 +4577,7 @@ else ac_save_LIBS="$LIBS" LIBS="-lglobus_common $LIBS" cat > conftest.$ac_ext <<EOF -#line 4578 "configure" +#line 4581 "configure" #include "confdefs.h" /* Override any gcc2 internal prototype to avoid an error. */ /* We use char because int might match the return type of a gcc2 @@ -4585,7 +4588,7 @@ int main() { globus_module_activate() ; return 0; } EOF -if { (eval echo configure:4589: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then +if { (eval echo configure:4592: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then rm -rf conftest* eval "ac_cv_lib_$ac_lib_var=yes" else @@ -4614,7 +4617,7 @@ unset GASS TESTGASS fi echo $ac_n "checking for main in -lglobus_dc""... $ac_c" 1>&6 -echo "configure:4618: checking for main in -lglobus_dc" >&5 +echo "configure:4621: checking for main in -lglobus_dc" >&5 ac_lib_var=`echo globus_dc'_'main | sed 'y%./+-%__p_%'` if eval "test \"`echo '$''{'ac_cv_lib_$ac_lib_var'+set}'`\" = set"; then echo $ac_n "(cached) $ac_c" 1>&6 @@ -4622,14 +4625,14 @@ else ac_save_LIBS="$LIBS" LIBS="-lglobus_dc $LIBS" cat > conftest.$ac_ext <<EOF -#line 4626 "configure" +#line 4629 "configure" #include "confdefs.h" int main() { main() ; return 0; } EOF -if { (eval echo configure:4633: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then +if { (eval echo configure:4636: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then rm -rf conftest* eval "ac_cv_lib_$ac_lib_var=yes" else @@ -4658,7 +4661,7 @@ unset GASS TESTGASS fi echo $ac_n "checking for main in -lglobus_nexus""... $ac_c" 1>&6 -echo "configure:4662: checking for main in -lglobus_nexus" >&5 +echo "configure:4665: checking for main in -lglobus_nexus" >&5 ac_lib_var=`echo globus_nexus'_'main | sed 'y%./+-%__p_%'` if eval "test \"`echo '$''{'ac_cv_lib_$ac_lib_var'+set}'`\" = set"; then echo $ac_n "(cached) $ac_c" 1>&6 @@ -4666,14 +4669,14 @@ else ac_save_LIBS="$LIBS" LIBS="-lglobus_nexus $LIBS" cat > conftest.$ac_ext <<EOF -#line 4670 "configure" +#line 4673 "configure" #include "confdefs.h" int main() { main() ; return 0; } EOF -if { (eval echo configure:4677: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then +if { (eval echo configure:4680: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then rm -rf conftest* eval "ac_cv_lib_$ac_lib_var=yes" else @@ -4702,7 +4705,7 @@ unset GASS TESTGASS fi echo $ac_n "checking for main in -lglobus_gass_client""... $ac_c" 1>&6 -echo "configure:4706: checking for main in -lglobus_gass_client" >&5 +echo "configure:4709: checking for main in -lglobus_gass_client" >&5 ac_lib_var=`echo globus_gass_client'_'main | sed 'y%./+-%__p_%'` if eval "test \"`echo '$''{'ac_cv_lib_$ac_lib_var'+set}'`\" = set"; then echo $ac_n "(cached) $ac_c" 1>&6 @@ -4710,14 +4713,14 @@ else ac_save_LIBS="$LIBS" LIBS="-lglobus_gass_client $LIBS" cat > conftest.$ac_ext <<EOF -#line 4714 "configure" +#line 4717 "configure" #include "confdefs.h" int main() { main() ; return 0; } EOF -if { (eval echo configure:4721: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then +if { (eval echo configure:4724: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then rm -rf conftest* eval "ac_cv_lib_$ac_lib_var=yes" else @@ -4746,7 +4749,7 @@ unset GASS TESTGASS fi echo $ac_n "checking for main in -lglobus_gass_cache""... $ac_c" 1>&6 -echo "configure:4750: checking for main in -lglobus_gass_cache" >&5 +echo "configure:4753: checking for main in -lglobus_gass_cache" >&5 ac_lib_var=`echo globus_gass_cache'_'main | sed 'y%./+-%__p_%'` if eval "test \"`echo '$''{'ac_cv_lib_$ac_lib_var'+set}'`\" = set"; then echo $ac_n "(cached) $ac_c" 1>&6 @@ -4754,14 +4757,14 @@ else ac_save_LIBS="$LIBS" LIBS="-lglobus_gass_cache $LIBS" cat > conftest.$ac_ext <<EOF -#line 4758 "configure" +#line 4761 "configure" #include "confdefs.h" int main() { main() ; return 0; } EOF -if { (eval echo configure:4765: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then +if { (eval echo configure:4768: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then rm -rf conftest* eval "ac_cv_lib_$ac_lib_var=yes" else @@ -4790,7 +4793,7 @@ unset GASS TESTGASS fi echo $ac_n "checking for globus_gass_open in -lglobus_gass_file""... $ac_c" 1>&6 -echo "configure:4794: checking for globus_gass_open in -lglobus_gass_file" >&5 +echo "configure:4797: checking for globus_gass_open in -lglobus_gass_file" >&5 ac_lib_var=`echo globus_gass_file'_'globus_gass_open | sed 'y%./+-%__p_%'` if eval "test \"`echo '$''{'ac_cv_lib_$ac_lib_var'+set}'`\" = set"; then echo $ac_n "(cached) $ac_c" 1>&6 @@ -4798,7 +4801,7 @@ else ac_save_LIBS="$LIBS" LIBS="-lglobus_gass_file $LIBS" cat > conftest.$ac_ext <<EOF -#line 4802 "configure" +#line 4805 "configure" #include "confdefs.h" /* Override any gcc2 internal prototype to avoid an error. */ /* We use char because int might match the return type of a gcc2 @@ -4809,7 +4812,7 @@ int main() { globus_gass_open() ; return 0; } EOF -if { (eval echo configure:4813: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then +if { (eval echo configure:4816: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then rm -rf conftest* eval "ac_cv_lib_$ac_lib_var=yes" else @@ -4840,7 +4843,7 @@ fi ;; no) echo $ac_n "checking for GASS""... $ac_c" 1>&6 -echo "configure:4844: checking for GASS" >&5 +echo "configure:4847: checking for GASS" >&5 echo "$ac_t""suppressed" 1>&6 unset GASS TESTGASS ;; @@ -4853,17 +4856,17 @@ echo "configure:4844: checking for GASS" >&5 do ac_safe=`echo "$ac_hdr" | sed 'y%./+-%__p_%'` echo $ac_n "checking for $ac_hdr""... $ac_c" 1>&6 -echo "configure:4857: checking for $ac_hdr" >&5 +echo "configure:4860: checking for $ac_hdr" >&5 if eval "test \"`echo '$''{'ac_cv_header_$ac_safe'+set}'`\" = set"; then echo $ac_n "(cached) $ac_c" 1>&6 else cat > conftest.$ac_ext <<EOF -#line 4862 "configure" +#line 4865 "configure" #include "confdefs.h" #include <$ac_hdr> EOF ac_try="$ac_cpp conftest.$ac_ext >/dev/null 2>conftest.out" -{ (eval echo configure:4867: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; } +{ (eval echo configure:4870: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; } ac_err=`grep -v '^ *+' conftest.out` if test -z "$ac_err"; then rm -rf conftest* @@ -4897,17 +4900,17 @@ done do ac_safe=`echo "$ac_hdr" | sed 'y%./+-%__p_%'` echo $ac_n "checking for $ac_hdr""... $ac_c" 1>&6 -echo "configure:4901: checking for $ac_hdr" >&5 +echo "configure:4904: checking for $ac_hdr" >&5 if eval "test \"`echo '$''{'ac_cv_header_$ac_safe'+set}'`\" = set"; then echo $ac_n "(cached) $ac_c" 1>&6 else cat > conftest.$ac_ext <<EOF -#line 4906 "configure" +#line 4909 "configure" #include "confdefs.h" #include <$ac_hdr> EOF ac_try="$ac_cpp conftest.$ac_ext >/dev/null 2>conftest.out" -{ (eval echo configure:4911: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; } +{ (eval echo configure:4914: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; } ac_err=`grep -v '^ *+' conftest.out` if test -z "$ac_err"; then rm -rf conftest* @@ -4940,7 +4943,7 @@ done saved_LDFLAGS="$LDFLAGS" LDFLAGS="$LDFLAGS -L$gass_lib" echo $ac_n "checking for main in -lxnet""... $ac_c" 1>&6 -echo "configure:4944: checking for main in -lxnet" >&5 +echo "configure:4947: checking for main in -lxnet" >&5 ac_lib_var=`echo xnet'_'main | sed 'y%./+-%__p_%'` if eval "test \"`echo '$''{'ac_cv_lib_$ac_lib_var'+set}'`\" = set"; then echo $ac_n "(cached) $ac_c" 1>&6 @@ -4948,14 +4951,14 @@ else ac_save_LIBS="$LIBS" LIBS="-lxnet $LIBS" cat > conftest.$ac_ext <<EOF -#line 4952 "configure" +#line 4955 "configure" #include "confdefs.h" int main() { main() ; return 0; } EOF -if { (eval echo configure:4959: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then +if { (eval echo configure:4962: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then rm -rf conftest* eval "ac_cv_lib_$ac_lib_var=yes" else @@ -4984,7 +4987,7 @@ unset GASS TESTGASS fi echo $ac_n "checking for globus_module_activate in -lglobus_common""... $ac_c" 1>&6 -echo "configure:4988: checking for globus_module_activate in -lglobus_common" >&5 +echo "configure:4991: checking for globus_module_activate in -lglobus_common" >&5 ac_lib_var=`echo globus_common'_'globus_module_activate | sed 'y%./+-%__p_%'` if eval "test \"`echo '$''{'ac_cv_lib_$ac_lib_var'+set}'`\" = set"; then echo $ac_n "(cached) $ac_c" 1>&6 @@ -4992,7 +4995,7 @@ else ac_save_LIBS="$LIBS" LIBS="-lglobus_common $LIBS" cat > conftest.$ac_ext <<EOF -#line 4996 "configure" +#line 4999 "configure" #include "confdefs.h" /* Override any gcc2 internal prototype to avoid an error. */ /* We use char because int might match the return type of a gcc2 @@ -5003,7 +5006,7 @@ int main() { globus_module_activate() ; return 0; } EOF -if { (eval echo configure:5007: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then +if { (eval echo configure:5010: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then rm -rf conftest* eval "ac_cv_lib_$ac_lib_var=yes" else @@ -5032,7 +5035,7 @@ unset GASS TESTGASS fi echo $ac_n "checking for main in -lglobus_dc""... $ac_c" 1>&6 -echo "configure:5036: checking for main in -lglobus_dc" >&5 +echo "configure:5039: checking for main in -lglobus_dc" >&5 ac_lib_var=`echo globus_dc'_'main | sed 'y%./+-%__p_%'` if eval "test \"`echo '$''{'ac_cv_lib_$ac_lib_var'+set}'`\" = set"; then echo $ac_n "(cached) $ac_c" 1>&6 @@ -5040,14 +5043,14 @@ else ac_save_LIBS="$LIBS" LIBS="-lglobus_dc $LIBS" cat > conftest.$ac_ext <<EOF -#line 5044 "configure" +#line 5047 "configure" #include "confdefs.h" int main() { main() ; return 0; } EOF -if { (eval echo configure:5051: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then +if { (eval echo configure:5054: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then rm -rf conftest* eval "ac_cv_lib_$ac_lib_var=yes" else @@ -5076,7 +5079,7 @@ unset GASS TESTGASS fi echo $ac_n "checking for main in -lglobus_nexus""... $ac_c" 1>&6 -echo "configure:5080: checking for main in -lglobus_nexus" >&5 +echo "configure:5083: checking for main in -lglobus_nexus" >&5 ac_lib_var=`echo globus_nexus'_'main | sed 'y%./+-%__p_%'` if eval "test \"`echo '$''{'ac_cv_lib_$ac_lib_var'+set}'`\" = set"; then echo $ac_n "(cached) $ac_c" 1>&6 @@ -5084,14 +5087,14 @@ else ac_save_LIBS="$LIBS" LIBS="-lglobus_nexus $LIBS" cat > conftest.$ac_ext <<EOF -#line 5088 "configure" +#line 5091 "configure" #include "confdefs.h" int main() { main() ; return 0; } EOF -if { (eval echo configure:5095: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then +if { (eval echo configure:5098: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then rm -rf conftest* eval "ac_cv_lib_$ac_lib_var=yes" else @@ -5120,7 +5123,7 @@ unset GASS TESTGASS fi echo $ac_n "checking for main in -lglobus_gass_client""... $ac_c" 1>&6 -echo "configure:5124: checking for main in -lglobus_gass_client" >&5 +echo "configure:5127: checking for main in -lglobus_gass_client" >&5 ac_lib_var=`echo globus_gass_client'_'main | sed 'y%./+-%__p_%'` if eval "test \"`echo '$''{'ac_cv_lib_$ac_lib_var'+set}'`\" = set"; then echo $ac_n "(cached) $ac_c" 1>&6 @@ -5128,14 +5131,14 @@ else ac_save_LIBS="$LIBS" LIBS="-lglobus_gass_client $LIBS" cat > conftest.$ac_ext <<EOF -#line 5132 "configure" +#line 5135 "configure" #include "confdefs.h" int main() { main() ; return 0; } EOF -if { (eval echo configure:5139: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then +if { (eval echo configure:5142: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then rm -rf conftest* eval "ac_cv_lib_$ac_lib_var=yes" else @@ -5164,7 +5167,7 @@ unset GASS TESTGASS fi echo $ac_n "checking for main in -lglobus_gass_cache""... $ac_c" 1>&6 -echo "configure:5168: checking for main in -lglobus_gass_cache" >&5 +echo "configure:5171: checking for main in -lglobus_gass_cache" >&5 ac_lib_var=`echo globus_gass_cache'_'main | sed 'y%./+-%__p_%'` if eval "test \"`echo '$''{'ac_cv_lib_$ac_lib_var'+set}'`\" = set"; then echo $ac_n "(cached) $ac_c" 1>&6 @@ -5172,14 +5175,14 @@ else ac_save_LIBS="$LIBS" LIBS="-lglobus_gass_cache $LIBS" cat > conftest.$ac_ext <<EOF -#line 5176 "configure" +#line 5179 "configure" #include "confdefs.h" int main() { main() ; return 0; } EOF -if { (eval echo configure:5183: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then +if { (eval echo configure:5186: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then rm -rf conftest* eval "ac_cv_lib_$ac_lib_var=yes" else @@ -5208,7 +5211,7 @@ unset GASS TESTGASS fi echo $ac_n "checking for globus_gass_open in -lglobus_gass_file""... $ac_c" 1>&6 -echo "configure:5212: checking for globus_gass_open in -lglobus_gass_file" >&5 +echo "configure:5215: checking for globus_gass_open in -lglobus_gass_file" >&5 ac_lib_var=`echo globus_gass_file'_'globus_gass_open | sed 'y%./+-%__p_%'` if eval "test \"`echo '$''{'ac_cv_lib_$ac_lib_var'+set}'`\" = set"; then echo $ac_n "(cached) $ac_c" 1>&6 @@ -5216,7 +5219,7 @@ else ac_save_LIBS="$LIBS" LIBS="-lglobus_gass_file $LIBS" cat > conftest.$ac_ext <<EOF -#line 5220 "configure" +#line 5223 "configure" #include "confdefs.h" /* Override any gcc2 internal prototype to avoid an error. */ /* We use char because int might match the return type of a gcc2 @@ -5227,7 +5230,7 @@ int main() { globus_gass_open() ; return 0; } EOF -if { (eval echo configure:5231: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then +if { (eval echo configure:5234: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then rm -rf conftest* eval "ac_cv_lib_$ac_lib_var=yes" else @@ -5257,7 +5260,7 @@ fi else echo $ac_n "checking for main in -lxnet""... $ac_c" 1>&6 -echo "configure:5261: checking for main in -lxnet" >&5 +echo "configure:5264: checking for main in -lxnet" >&5 ac_lib_var=`echo xnet'_'main | sed 'y%./+-%__p_%'` if eval "test \"`echo '$''{'ac_cv_lib_$ac_lib_var'+set}'`\" = set"; then echo $ac_n "(cached) $ac_c" 1>&6 @@ -5265,14 +5268,14 @@ else ac_save_LIBS="$LIBS" LIBS="-lxnet $LIBS" cat > conftest.$ac_ext <<EOF -#line 5269 "configure" +#line 5272 "configure" #include "confdefs.h" int main() { main() ; return 0; } EOF -if { (eval echo configure:5276: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then +if { (eval echo configure:5279: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then rm -rf conftest* eval "ac_cv_lib_$ac_lib_var=yes" else @@ -5301,7 +5304,7 @@ unset GASS TESTGASS fi echo $ac_n "checking for globus_module_activate in -lglobus_common""... $ac_c" 1>&6 -echo "configure:5305: checking for globus_module_activate in -lglobus_common" >&5 +echo "configure:5308: checking for globus_module_activate in -lglobus_common" >&5 ac_lib_var=`echo globus_common'_'globus_module_activate | sed 'y%./+-%__p_%'` if eval "test \"`echo '$''{'ac_cv_lib_$ac_lib_var'+set}'`\" = set"; then echo $ac_n "(cached) $ac_c" 1>&6 @@ -5309,7 +5312,7 @@ else ac_save_LIBS="$LIBS" LIBS="-lglobus_common $LIBS" cat > conftest.$ac_ext <<EOF -#line 5313 "configure" +#line 5316 "configure" #include "confdefs.h" /* Override any gcc2 internal prototype to avoid an error. */ /* We use char because int might match the return type of a gcc2 @@ -5320,7 +5323,7 @@ int main() { globus_module_activate() ; return 0; } EOF -if { (eval echo configure:5324: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then +if { (eval echo configure:5327: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then rm -rf conftest* eval "ac_cv_lib_$ac_lib_var=yes" else @@ -5349,7 +5352,7 @@ unset GASS TESTGASS fi echo $ac_n "checking for main in -lglobus_dc""... $ac_c" 1>&6 -echo "configure:5353: checking for main in -lglobus_dc" >&5 +echo "configure:5356: checking for main in -lglobus_dc" >&5 ac_lib_var=`echo globus_dc'_'main | sed 'y%./+-%__p_%'` if eval "test \"`echo '$''{'ac_cv_lib_$ac_lib_var'+set}'`\" = set"; then echo $ac_n "(cached) $ac_c" 1>&6 @@ -5357,14 +5360,14 @@ else ac_save_LIBS="$LIBS" LIBS="-lglobus_dc $LIBS" cat > conftest.$ac_ext <<EOF -#line 5361 "configure" +#line 5364 "configure" #include "confdefs.h" int main() { main() ; return 0; } EOF -if { (eval echo configure:5368: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then +if { (eval echo configure:5371: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then rm -rf conftest* eval "ac_cv_lib_$ac_lib_var=yes" else @@ -5393,7 +5396,7 @@ unset GASS TESTGASS fi echo $ac_n "checking for main in -lglobus_nexus""... $ac_c" 1>&6 -echo "configure:5397: checking for main in -lglobus_nexus" >&5 +echo "configure:5400: checking for main in -lglobus_nexus" >&5 ac_lib_var=`echo globus_nexus'_'main | sed 'y%./+-%__p_%'` if eval "test \"`echo '$''{'ac_cv_lib_$ac_lib_var'+set}'`\" = set"; then echo $ac_n "(cached) $ac_c" 1>&6 @@ -5401,14 +5404,14 @@ else ac_save_LIBS="$LIBS" LIBS="-lglobus_nexus $LIBS" cat > conftest.$ac_ext <<EOF -#line 5405 "configure" +#line 5408 "configure" #include "confdefs.h" int main() { main() ; return 0; } EOF -if { (eval echo configure:5412: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then +if { (eval echo configure:5415: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then rm -rf conftest* eval "ac_cv_lib_$ac_lib_var=yes" else @@ -5437,7 +5440,7 @@ unset GASS TESTGASS fi echo $ac_n "checking for main in -lglobus_gass_client""... $ac_c" 1>&6 -echo "configure:5441: checking for main in -lglobus_gass_client" >&5 +echo "configure:5444: checking for main in -lglobus_gass_client" >&5 ac_lib_var=`echo globus_gass_client'_'main | sed 'y%./+-%__p_%'` if eval "test \"`echo '$''{'ac_cv_lib_$ac_lib_var'+set}'`\" = set"; then echo $ac_n "(cached) $ac_c" 1>&6 @@ -5445,14 +5448,14 @@ else ac_save_LIBS="$LIBS" LIBS="-lglobus_gass_client $LIBS" cat > conftest.$ac_ext <<EOF -#line 5449 "configure" +#line 5452 "configure" #include "confdefs.h" int main() { main() ; return 0; } EOF -if { (eval echo configure:5456: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then +if { (eval echo configure:5459: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then rm -rf conftest* eval "ac_cv_lib_$ac_lib_var=yes" else @@ -5481,7 +5484,7 @@ unset GASS TESTGASS fi echo $ac_n "checking for main in -lglobus_gass_cache""... $ac_c" 1>&6 -echo "configure:5485: checking for main in -lglobus_gass_cache" >&5 +echo "configure:5488: checking for main in -lglobus_gass_cache" >&5 ac_lib_var=`echo globus_gass_cache'_'main | sed 'y%./+-%__p_%'` if eval "test \"`echo '$''{'ac_cv_lib_$ac_lib_var'+set}'`\" = set"; then echo $ac_n "(cached) $ac_c" 1>&6 @@ -5489,14 +5492,14 @@ else ac_save_LIBS="$LIBS" LIBS="-lglobus_gass_cache $LIBS" cat > conftest.$ac_ext <<EOF -#line 5493 "configure" +#line 5496 "configure" #include "confdefs.h" int main() { main() ; return 0; } EOF -if { (eval echo configure:5500: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then +if { (eval echo configure:5503: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then rm -rf conftest* eval "ac_cv_lib_$ac_lib_var=yes" else @@ -5525,7 +5528,7 @@ unset GASS TESTGASS fi echo $ac_n "checking for globus_gass_open in -lglobus_gass_file""... $ac_c" 1>&6 -echo "configure:5529: checking for globus_gass_open in -lglobus_gass_file" >&5 +echo "configure:5532: checking for globus_gass_open in -lglobus_gass_file" >&5 ac_lib_var=`echo globus_gass_file'_'globus_gass_open | sed 'y%./+-%__p_%'` if eval "test \"`echo '$''{'ac_cv_lib_$ac_lib_var'+set}'`\" = set"; then echo $ac_n "(cached) $ac_c" 1>&6 @@ -5533,7 +5536,7 @@ else ac_save_LIBS="$LIBS" LIBS="-lglobus_gass_file $LIBS" cat > conftest.$ac_ext <<EOF -#line 5537 "configure" +#line 5540 "configure" #include "confdefs.h" /* Override any gcc2 internal prototype to avoid an error. */ /* We use char because int might match the return type of a gcc2 @@ -5544,7 +5547,7 @@ int main() { globus_gass_open() ; return 0; } EOF -if { (eval echo configure:5548: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then +if { (eval echo configure:5551: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then rm -rf conftest* eval "ac_cv_lib_$ac_lib_var=yes" else @@ -5583,10 +5586,146 @@ EOF fi +echo $ac_n "checking for PD_open in -lpdb""... $ac_c" 1>&6 +echo "configure:5591: checking for PD_open in -lpdb" >&5 +ac_lib_var=`echo pdb'_'PD_open | sed 'y%./+-%__p_%'` +if eval "test \"`echo '$''{'ac_cv_lib_$ac_lib_var'+set}'`\" = set"; then + echo $ac_n "(cached) $ac_c" 1>&6 +else + ac_save_LIBS="$LIBS" +LIBS="-lpdb $LIBS" +cat > conftest.$ac_ext <<EOF +#line 5599 "configure" +#include "confdefs.h" +/* Override any gcc2 internal prototype to avoid an error. */ +/* We use char because int might match the return type of a gcc2 + builtin and then its argument prototype would still apply. */ +char PD_open(); + +int main() { +PD_open() +; return 0; } +EOF +if { (eval echo configure:5610: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then + rm -rf conftest* + eval "ac_cv_lib_$ac_lib_var=yes" +else + echo "configure: failed program was:" >&5 + cat conftest.$ac_ext >&5 + rm -rf conftest* + eval "ac_cv_lib_$ac_lib_var=no" +fi +rm -f conftest* +LIBS="$ac_save_LIBS" + +fi +if eval "test \"`echo '$ac_cv_lib_'$ac_lib_var`\" = yes"; then + echo "$ac_t""yes" 1>&6 + ac_tr_lib=HAVE_LIB`echo pdb | sed -e 's/[^a-zA-Z0-9_]/_/g' \ + -e 'y/abcdefghijklmnopqrstuvwxyz/ABCDEFGHIJKLMNOPQRSTUVWXYZ/'` + cat >> confdefs.h <<EOF +#define $ac_tr_lib 1 +EOF + + LIBS="-lpdb $LIBS" + +else + echo "$ac_t""no" 1>&6 +fi + +echo $ac_n "checking for lite_PD_open in -lsilo""... $ac_c" 1>&6 +echo "configure:5638: checking for lite_PD_open in -lsilo" >&5 +ac_lib_var=`echo silo'_'lite_PD_open | sed 'y%./+-%__p_%'` +if eval "test \"`echo '$''{'ac_cv_lib_$ac_lib_var'+set}'`\" = set"; then + echo $ac_n "(cached) $ac_c" 1>&6 +else + ac_save_LIBS="$LIBS" +LIBS="-lsilo $LIBS" +cat > conftest.$ac_ext <<EOF +#line 5646 "configure" +#include "confdefs.h" +/* Override any gcc2 internal prototype to avoid an error. */ +/* We use char because int might match the return type of a gcc2 + builtin and then its argument prototype would still apply. */ +char lite_PD_open(); + +int main() { +lite_PD_open() +; return 0; } +EOF +if { (eval echo configure:5657: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then + rm -rf conftest* + eval "ac_cv_lib_$ac_lib_var=yes" +else + echo "configure: failed program was:" >&5 + cat conftest.$ac_ext >&5 + rm -rf conftest* + eval "ac_cv_lib_$ac_lib_var=no" +fi +rm -f conftest* +LIBS="$ac_save_LIBS" + +fi +if eval "test \"`echo '$ac_cv_lib_'$ac_lib_var`\" = yes"; then + echo "$ac_t""yes" 1>&6 + ac_tr_lib=HAVE_LIB`echo silo | sed -e 's/[^a-zA-Z0-9_]/_/g' \ + -e 'y/abcdefghijklmnopqrstuvwxyz/ABCDEFGHIJKLMNOPQRSTUVWXYZ/'` + cat >> confdefs.h <<EOF +#define $ac_tr_lib 1 +EOF + + LIBS="-lsilo $LIBS" + +else + echo "$ac_t""no" 1>&6 +fi + +for ac_hdr in pdb.h +do +ac_safe=`echo "$ac_hdr" | sed 'y%./+-%__p_%'` +echo $ac_n "checking for $ac_hdr""... $ac_c" 1>&6 +echo "configure:5688: checking for $ac_hdr" >&5 +if eval "test \"`echo '$''{'ac_cv_header_$ac_safe'+set}'`\" = set"; then + echo $ac_n "(cached) $ac_c" 1>&6 +else + cat > conftest.$ac_ext <<EOF +#line 5693 "configure" +#include "confdefs.h" +#include <$ac_hdr> +EOF +ac_try="$ac_cpp conftest.$ac_ext >/dev/null 2>conftest.out" +{ (eval echo configure:5698: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; } +ac_err=`grep -v '^ *+' conftest.out` +if test -z "$ac_err"; then + rm -rf conftest* + eval "ac_cv_header_$ac_safe=yes" +else + echo "$ac_err" >&5 + echo "configure: failed program was:" >&5 + cat conftest.$ac_ext >&5 + rm -rf conftest* + eval "ac_cv_header_$ac_safe=no" +fi +rm -f conftest* +fi +if eval "test \"`echo '$ac_cv_header_'$ac_safe`\" = yes"; then + echo "$ac_t""yes" 1>&6 + ac_tr_hdr=HAVE_`echo $ac_hdr | sed 'y%abcdefghijklmnopqrstuvwxyz./-%ABCDEFGHIJKLMNOPQRSTUVWXYZ___%'` + cat >> confdefs.h <<EOF +#define $ac_tr_hdr 1 +EOF + PDB2HDF=pdb2hdf +else + echo "$ac_t""no" 1>&6 +fi +done + + + echo $ac_n "checking for tm_gmtoff in struct tm""... $ac_c" 1>&6 -echo "configure:5588: checking for tm_gmtoff in struct tm" >&5 +echo "configure:5727: checking for tm_gmtoff in struct tm" >&5 cat > conftest.$ac_ext <<EOF -#line 5590 "configure" +#line 5729 "configure" #include "confdefs.h" #include <sys/time.h> @@ -5595,7 +5734,7 @@ int main() { struct tm tm; tm.tm_gmtoff=0; ; return 0; } EOF -if { (eval echo configure:5599: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then +if { (eval echo configure:5738: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then rm -rf conftest* cat >> confdefs.h <<\EOF #define HAVE_TM_GMTOFF 1 @@ -5611,9 +5750,9 @@ fi rm -f conftest* echo $ac_n "checking for __tm_gmtoff in struct tm""... $ac_c" 1>&6 -echo "configure:5615: checking for __tm_gmtoff in struct tm" >&5 +echo "configure:5754: checking for __tm_gmtoff in struct tm" >&5 cat > conftest.$ac_ext <<EOF -#line 5617 "configure" +#line 5756 "configure" #include "confdefs.h" #include <sys/time.h> @@ -5622,7 +5761,7 @@ int main() { struct tm tm; tm.__tm_gmtoff=0; ; return 0; } EOF -if { (eval echo configure:5626: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then +if { (eval echo configure:5765: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then rm -rf conftest* cat >> confdefs.h <<\EOF #define HAVE___TM_GMTOFF 1 @@ -5638,9 +5777,9 @@ fi rm -f conftest* echo $ac_n "checking for global timezone variable""... $ac_c" 1>&6 -echo "configure:5642: checking for global timezone variable" >&5 +echo "configure:5781: checking for global timezone variable" >&5 cat > conftest.$ac_ext <<EOF -#line 5644 "configure" +#line 5783 "configure" #include "confdefs.h" #include <sys/time.h> @@ -5649,7 +5788,7 @@ int main() { timezone=0; ; return 0; } EOF -if { (eval echo configure:5653: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then +if { (eval echo configure:5792: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then rm -rf conftest* cat >> confdefs.h <<\EOF #define HAVE_TIMEZONE 1 @@ -5665,12 +5804,12 @@ fi rm -f conftest* echo $ac_n "checking whether struct tm is in sys/time.h or time.h""... $ac_c" 1>&6 -echo "configure:5669: checking whether struct tm is in sys/time.h or time.h" >&5 +echo "configure:5808: checking whether struct tm is in sys/time.h or time.h" >&5 if eval "test \"`echo '$''{'ac_cv_struct_tm'+set}'`\" = set"; then echo $ac_n "(cached) $ac_c" 1>&6 else cat > conftest.$ac_ext <<EOF -#line 5674 "configure" +#line 5813 "configure" #include "confdefs.h" #include <sys/types.h> #include <time.h> @@ -5678,7 +5817,7 @@ int main() { struct tm *tp; tp->tm_sec; ; return 0; } EOF -if { (eval echo configure:5682: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then +if { (eval echo configure:5821: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then rm -rf conftest* ac_cv_struct_tm=time.h else @@ -5699,12 +5838,12 @@ EOF fi echo $ac_n "checking for tm_zone in struct tm""... $ac_c" 1>&6 -echo "configure:5703: checking for tm_zone in struct tm" >&5 +echo "configure:5842: checking for tm_zone in struct tm" >&5 if eval "test \"`echo '$''{'ac_cv_struct_tm_zone'+set}'`\" = set"; then echo $ac_n "(cached) $ac_c" 1>&6 else cat > conftest.$ac_ext <<EOF -#line 5708 "configure" +#line 5847 "configure" #include "confdefs.h" #include <sys/types.h> #include <$ac_cv_struct_tm> @@ -5712,7 +5851,7 @@ int main() { struct tm tm; tm.tm_zone; ; return 0; } EOF -if { (eval echo configure:5716: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then +if { (eval echo configure:5855: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then rm -rf conftest* ac_cv_struct_tm_zone=yes else @@ -5732,12 +5871,12 @@ EOF else echo $ac_n "checking for tzname""... $ac_c" 1>&6 -echo "configure:5736: checking for tzname" >&5 +echo "configure:5875: checking for tzname" >&5 if eval "test \"`echo '$''{'ac_cv_var_tzname'+set}'`\" = set"; then echo $ac_n "(cached) $ac_c" 1>&6 else cat > conftest.$ac_ext <<EOF -#line 5741 "configure" +#line 5880 "configure" #include "confdefs.h" #include <time.h> #ifndef tzname /* For SGI. */ @@ -5747,7 +5886,7 @@ int main() { atoi(*tzname); ; return 0; } EOF -if { (eval echo configure:5751: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then +if { (eval echo configure:5890: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then rm -rf conftest* ac_cv_var_tzname=yes else @@ -5769,9 +5908,9 @@ EOF fi echo $ac_n "checking for struct timezone""... $ac_c" 1>&6 -echo "configure:5773: checking for struct timezone" >&5 +echo "configure:5912: checking for struct timezone" >&5 cat > conftest.$ac_ext <<EOF -#line 5775 "configure" +#line 5914 "configure" #include "confdefs.h" #include <sys/types.h> @@ -5781,7 +5920,7 @@ int main() { struct timezone tz; tz.tz_minuteswest=0; ; return 0; } EOF -if { (eval echo configure:5785: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then +if { (eval echo configure:5924: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then rm -rf conftest* cat >> confdefs.h <<\EOF #define HAVE_STRUCT_TIMEZONE 1 @@ -5797,9 +5936,9 @@ fi rm -f conftest* echo $ac_n "checking for st_blocks in struct stat""... $ac_c" 1>&6 -echo "configure:5801: checking for st_blocks in struct stat" >&5 +echo "configure:5940: checking for st_blocks in struct stat" >&5 cat > conftest.$ac_ext <<EOF -#line 5803 "configure" +#line 5942 "configure" #include "confdefs.h" #include <sys/stat.h> @@ -5807,7 +5946,7 @@ int main() { struct stat sb; sb.st_blocks=0; ; return 0; } EOF -if { (eval echo configure:5811: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then +if { (eval echo configure:5950: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then rm -rf conftest* cat >> confdefs.h <<\EOF #define HAVE_STAT_ST_BLOCKS 1 @@ -5825,12 +5964,12 @@ rm -f conftest* for ac_func in _getvideoconfig gettextinfo GetConsoleScreenBufferInfo do echo $ac_n "checking for $ac_func""... $ac_c" 1>&6 -echo "configure:5829: checking for $ac_func" >&5 +echo "configure:5968: checking for $ac_func" >&5 if eval "test \"`echo '$''{'ac_cv_func_$ac_func'+set}'`\" = set"; then echo $ac_n "(cached) $ac_c" 1>&6 else cat > conftest.$ac_ext <<EOF -#line 5834 "configure" +#line 5973 "configure" #include "confdefs.h" /* System header to define __stub macros and hopefully few prototypes, which can conflict with char $ac_func(); below. */ @@ -5853,7 +5992,7 @@ $ac_func(); ; return 0; } EOF -if { (eval echo configure:5857: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then +if { (eval echo configure:5996: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then rm -rf conftest* eval "ac_cv_func_$ac_func=yes" else @@ -5880,12 +6019,12 @@ done for ac_func in _scrsize ioctl do echo $ac_n "checking for $ac_func""... $ac_c" 1>&6 -echo "configure:5884: checking for $ac_func" >&5 +echo "configure:6023: checking for $ac_func" >&5 if eval "test \"`echo '$''{'ac_cv_func_$ac_func'+set}'`\" = set"; then echo $ac_n "(cached) $ac_c" 1>&6 else cat > conftest.$ac_ext <<EOF -#line 5889 "configure" +#line 6028 "configure" #include "confdefs.h" /* System header to define __stub macros and hopefully few prototypes, which can conflict with char $ac_func(); below. */ @@ -5908,7 +6047,7 @@ $ac_func(); ; return 0; } EOF -if { (eval echo configure:5912: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then +if { (eval echo configure:6051: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then rm -rf conftest* eval "ac_cv_func_$ac_func=yes" else @@ -5934,16 +6073,16 @@ done echo $ac_n "checking for struct videoconfig""... $ac_c" 1>&6 -echo "configure:5938: checking for struct videoconfig" >&5 +echo "configure:6077: checking for struct videoconfig" >&5 cat > conftest.$ac_ext <<EOF -#line 5940 "configure" +#line 6079 "configure" #include "confdefs.h" int main() { struct videoconfig w; w.numtextcols=0; ; return 0; } EOF -if { (eval echo configure:5947: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then +if { (eval echo configure:6086: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then rm -rf conftest* cat >> confdefs.h <<\EOF #define HAVE_STRUCT_VIDEOCONFIG 1 @@ -5959,16 +6098,16 @@ fi rm -f conftest* echo $ac_n "checking for struct text_info""... $ac_c" 1>&6 -echo "configure:5963: checking for struct text_info" >&5 +echo "configure:6102: checking for struct text_info" >&5 cat > conftest.$ac_ext <<EOF -#line 5965 "configure" +#line 6104 "configure" #include "confdefs.h" int main() { struct text_info w; w.screenwidth=0; ; return 0; } EOF -if { (eval echo configure:5972: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then +if { (eval echo configure:6111: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then rm -rf conftest* cat >> confdefs.h <<\EOF #define HAVE_STRUCT_TEXT_INFO 1 @@ -5984,16 +6123,16 @@ fi rm -f conftest* echo $ac_n "checking for TIOCGWINSZ""... $ac_c" 1>&6 -echo "configure:5988: checking for TIOCGWINSZ" >&5 +echo "configure:6127: checking for TIOCGWINSZ" >&5 cat > conftest.$ac_ext <<EOF -#line 5990 "configure" +#line 6129 "configure" #include "confdefs.h" #include <sys/ioctl.h> int main() { int w=TIOCGWINSZ; ; return 0; } EOF -if { (eval echo configure:5997: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then +if { (eval echo configure:6136: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then rm -rf conftest* cat >> confdefs.h <<\EOF #define HAVE_TIOCGWINSZ 1 @@ -6009,16 +6148,16 @@ fi rm -f conftest* echo $ac_n "checking for TIOCGGETD""... $ac_c" 1>&6 -echo "configure:6013: checking for TIOCGGETD" >&5 +echo "configure:6152: checking for TIOCGGETD" >&5 cat > conftest.$ac_ext <<EOF -#line 6015 "configure" +#line 6154 "configure" #include "confdefs.h" #include <sys/ioctl.h> int main() { int w=TIOCGETD; ; return 0; } EOF -if { (eval echo configure:6022: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then +if { (eval echo configure:6161: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then rm -rf conftest* cat >> confdefs.h <<\EOF #define HAVE_TIOCGETD 1 @@ -6037,12 +6176,12 @@ rm -f conftest* for ac_func in getpwuid gethostname system getrusage fork waitpid do echo $ac_n "checking for $ac_func""... $ac_c" 1>&6 -echo "configure:6041: checking for $ac_func" >&5 +echo "configure:6180: checking for $ac_func" >&5 if eval "test \"`echo '$''{'ac_cv_func_$ac_func'+set}'`\" = set"; then echo $ac_n "(cached) $ac_c" 1>&6 else cat > conftest.$ac_ext <<EOF -#line 6046 "configure" +#line 6185 "configure" #include "confdefs.h" /* System header to define __stub macros and hopefully few prototypes, which can conflict with char $ac_func(); below. */ @@ -6065,7 +6204,7 @@ $ac_func(); ; return 0; } EOF -if { (eval echo configure:6069: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then +if { (eval echo configure:6208: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then rm -rf conftest* eval "ac_cv_func_$ac_func=yes" else @@ -6092,12 +6231,12 @@ done for ac_func in gettimeofday BSDgettimeofday difftime snprintf vsnprintf do echo $ac_n "checking for $ac_func""... $ac_c" 1>&6 -echo "configure:6096: checking for $ac_func" >&5 +echo "configure:6235: checking for $ac_func" >&5 if eval "test \"`echo '$''{'ac_cv_func_$ac_func'+set}'`\" = set"; then echo $ac_n "(cached) $ac_c" 1>&6 else cat > conftest.$ac_ext <<EOF -#line 6101 "configure" +#line 6240 "configure" #include "confdefs.h" /* System header to define __stub macros and hopefully few prototypes, which can conflict with char $ac_func(); below. */ @@ -6120,7 +6259,7 @@ $ac_func(); ; return 0; } EOF -if { (eval echo configure:6124: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then +if { (eval echo configure:6263: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then rm -rf conftest* eval "ac_cv_func_$ac_func=yes" else @@ -6147,12 +6286,12 @@ done for ac_func in compress2 setsysinfo longjmp signal sigaction do echo $ac_n "checking for $ac_func""... $ac_c" 1>&6 -echo "configure:6151: checking for $ac_func" >&5 +echo "configure:6290: checking for $ac_func" >&5 if eval "test \"`echo '$''{'ac_cv_func_$ac_func'+set}'`\" = set"; then echo $ac_n "(cached) $ac_c" 1>&6 else cat > conftest.$ac_ext <<EOF -#line 6156 "configure" +#line 6295 "configure" #include "confdefs.h" /* System header to define __stub macros and hopefully few prototypes, which can conflict with char $ac_func(); below. */ @@ -6175,7 +6314,7 @@ $ac_func(); ; return 0; } EOF -if { (eval echo configure:6179: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then +if { (eval echo configure:6318: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then rm -rf conftest* eval "ac_cv_func_$ac_func=yes" else @@ -6200,24 +6339,24 @@ fi done cat > conftest.$ac_ext <<EOF -#line 6204 "configure" +#line 6343 "configure" #include "confdefs.h" #include<sys/types.h> int main() { off64_t n = 0; ; return 0; } EOF -if { (eval echo configure:6211: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then +if { (eval echo configure:6350: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then rm -rf conftest* for ac_func in lseek64 fseek64 do echo $ac_n "checking for $ac_func""... $ac_c" 1>&6 -echo "configure:6216: checking for $ac_func" >&5 +echo "configure:6355: checking for $ac_func" >&5 if eval "test \"`echo '$''{'ac_cv_func_$ac_func'+set}'`\" = set"; then echo $ac_n "(cached) $ac_c" 1>&6 else cat > conftest.$ac_ext <<EOF -#line 6221 "configure" +#line 6360 "configure" #include "confdefs.h" /* System header to define __stub macros and hopefully few prototypes, which can conflict with char $ac_func(); below. */ @@ -6240,7 +6379,7 @@ $ac_func(); ; return 0; } EOF -if { (eval echo configure:6244: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then +if { (eval echo configure:6383: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then rm -rf conftest* eval "ac_cv_func_$ac_func=yes" else @@ -6275,12 +6414,12 @@ rm -f conftest* echo $ac_n "checking for working const""... $ac_c" 1>&6 -echo "configure:6279: checking for working const" >&5 +echo "configure:6418: checking for working const" >&5 if eval "test \"`echo '$''{'ac_cv_c_const'+set}'`\" = set"; then echo $ac_n "(cached) $ac_c" 1>&6 else cat > conftest.$ac_ext <<EOF -#line 6284 "configure" +#line 6423 "configure" #include "confdefs.h" int main() { @@ -6329,7 +6468,7 @@ ccp = (char const *const *) p; ; return 0; } EOF -if { (eval echo configure:6333: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then +if { (eval echo configure:6472: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then rm -rf conftest* ac_cv_c_const=yes else @@ -6350,21 +6489,21 @@ EOF fi echo $ac_n "checking for inline""... $ac_c" 1>&6 -echo "configure:6354: checking for inline" >&5 +echo "configure:6493: checking for inline" >&5 if eval "test \"`echo '$''{'ac_cv_c_inline'+set}'`\" = set"; then echo $ac_n "(cached) $ac_c" 1>&6 else ac_cv_c_inline=no for ac_kw in inline __inline__ __inline; do cat > conftest.$ac_ext <<EOF -#line 6361 "configure" +#line 6500 "configure" #include "confdefs.h" int main() { } $ac_kw foo() { ; return 0; } EOF -if { (eval echo configure:6368: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then +if { (eval echo configure:6507: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then rm -rf conftest* ac_cv_c_inline=$ac_kw; break else @@ -6391,16 +6530,16 @@ esac echo $ac_n "checking for __attribute__ extension""... $ac_c" 1>&6 -echo "configure:6395: checking for __attribute__ extension" >&5 +echo "configure:6534: checking for __attribute__ extension" >&5 cat > conftest.$ac_ext <<EOF -#line 6397 "configure" +#line 6536 "configure" #include "confdefs.h" int main() { int __attribute__((unused)) x ; return 0; } EOF -if { (eval echo configure:6404: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then +if { (eval echo configure:6543: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then rm -rf conftest* cat >> confdefs.h <<\EOF #define HAVE_ATTRIBUTE 1 @@ -6416,16 +6555,16 @@ fi rm -f conftest* echo $ac_n "checking for __FUNCTION__ extension""... $ac_c" 1>&6 -echo "configure:6420: checking for __FUNCTION__ extension" >&5 +echo "configure:6559: checking for __FUNCTION__ extension" >&5 cat > conftest.$ac_ext <<EOF -#line 6422 "configure" +#line 6561 "configure" #include "confdefs.h" int main() { (void)__FUNCTION__ ; return 0; } EOF -if { (eval echo configure:6429: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then +if { (eval echo configure:6568: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then rm -rf conftest* cat >> confdefs.h <<\EOF #define HAVE_FUNCTION 1 @@ -6441,7 +6580,7 @@ fi rm -f conftest* echo $ac_n "checking how to print long long""... $ac_c" 1>&6 -echo "configure:6445: checking how to print long long" >&5 +echo "configure:6584: checking how to print long long" >&5 if eval "test \"`echo '$''{'hdf5_cv_printf_ll'+set}'`\" = set"; then echo $ac_n "(cached) $ac_c" 1>&6 else @@ -6450,7 +6589,7 @@ else { echo "configure: error: can not run test program while cross compiling" 1>&2; exit 1; } else cat > conftest.$ac_ext <<EOF -#line 6454 "configure" +#line 6593 "configure" #include "confdefs.h" #include <stdio.h> @@ -6461,7 +6600,7 @@ else sprintf(s,"%${hdf5_cv_printf_ll}d",x); exit (strcmp(s,"1099511627776"));} EOF -if { (eval echo configure:6465: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest && (./conftest; exit) 2>/dev/null +if { (eval echo configure:6604: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest && (./conftest; exit) 2>/dev/null then break else @@ -6481,7 +6620,7 @@ EOF echo $ac_n "checking for debug flags""... $ac_c" 1>&6 -echo "configure:6485: checking for debug flags" >&5 +echo "configure:6624: checking for debug flags" >&5 # Check whether --enable-debug or --disable-debug was given. if test "${enable_debug+set}" = set; then enableval="$enable_debug" @@ -6514,7 +6653,7 @@ if test "X" != "X$DEBUG_PKG"; then fi echo $ac_n "checking for API tracing""... $ac_c" 1>&6 -echo "configure:6518: checking for API tracing" >&5; +echo "configure:6657: checking for API tracing" >&5; # Check whether --enable-trace or --disable-trace was given. if test "${enable_trace+set}" = set; then enableval="$enable_trace" @@ -6544,7 +6683,7 @@ case "$CC_BASENAME" in # exists. PARALLEL=mpicc echo $ac_n "checking for mpirun""... $ac_c" 1>&6 -echo "configure:6548: checking for mpirun" >&5 +echo "configure:6687: checking for mpirun" >&5 # Find the path where mpicc is located. cmd=`echo $CC |cut -f1 -d' '` @@ -6589,7 +6728,7 @@ fi echo $ac_n "checking for parallel support files""... $ac_c" 1>&6 -echo "configure:6593: checking for parallel support files" >&5 +echo "configure:6732: checking for parallel support files" >&5 case "X-$enable_parallel" in X-|X-no|X-none) # Either we are not compiling for parallel or the header and library @@ -6620,7 +6759,7 @@ case "X-$enable_parallel" in # is missing. PARALLEL=mpich echo $ac_n "checking for MPI_Init in -lmpich""... $ac_c" 1>&6 -echo "configure:6624: checking for MPI_Init in -lmpich" >&5 +echo "configure:6763: checking for MPI_Init in -lmpich" >&5 ac_lib_var=`echo mpich'_'MPI_Init | sed 'y%./+-%__p_%'` if eval "test \"`echo '$''{'ac_cv_lib_$ac_lib_var'+set}'`\" = set"; then echo $ac_n "(cached) $ac_c" 1>&6 @@ -6628,7 +6767,7 @@ else ac_save_LIBS="$LIBS" LIBS="-lmpich $LIBS" cat > conftest.$ac_ext <<EOF -#line 6632 "configure" +#line 6771 "configure" #include "confdefs.h" /* Override any gcc2 internal prototype to avoid an error. */ /* We use char because int might match the return type of a gcc2 @@ -6639,7 +6778,7 @@ int main() { MPI_Init() ; return 0; } EOF -if { (eval echo configure:6643: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then +if { (eval echo configure:6782: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then rm -rf conftest* eval "ac_cv_lib_$ac_lib_var=yes" else @@ -6688,10 +6827,10 @@ EOF # Display what we found about running programs echo $ac_n "checking prefix for running on one processor""... $ac_c" 1>&6 -echo "configure:6692: checking prefix for running on one processor" >&5 +echo "configure:6831: checking prefix for running on one processor" >&5 echo "$ac_t""$RUNSERIAL" 1>&6 echo $ac_n "checking prefix for running in parallel""... $ac_c" 1>&6 -echo "configure:6695: checking prefix for running in parallel" >&5 +echo "configure:6834: checking prefix for running in parallel" >&5 echo "$ac_t""$RUNPARALLEL" 1>&6 # Check that we can link a simple MPI and MPI-IO application @@ -6954,6 +7093,7 @@ s%@H5TOH4@%$H5TOH4%g s%@TESTH5TOH4@%$TESTH5TOH4%g s%@GASS@%$GASS%g s%@TESTGASS@%$TESTGASS%g +s%@PDB2HDF@%$PDB2HDF%g s%@DEBUG_PKG@%$DEBUG_PKG%g s%@TRACE_API@%$TRACE_API%g s%@PARALLEL@%$PARALLEL%g diff --git a/configure.in b/configure.in index 2ba8b3c..f1bab1c 100644 --- a/configure.in +++ b/configure.in @@ -283,7 +283,11 @@ H5TOH4=h5toh4 AC_SUBST(TESTH5TOH4) TESTH5TOH4='$(srcdir)/testh5toh4' -AC_ARG_WITH(hdf4,[ --with-hdf4=INC,LIB Use the HDF4 library],,withval=[/usr/ncsa/include,/usr/ncsa/lib]) +dnl NCSA keeps hdf4 in a funny place, but for most sites we don't want these. +test -d /usr/ncsa/include && CPPFLAGS="$CPPFLAGS -I/usr/ncsa/include" +test -d /usr/ncsa/lib && LDFLAGS="$LDFLAGS -L/usr/ncsa/lib" + +AC_ARG_WITH(hdf4,[ --with-hdf4=INC,LIB Use the HDF4 library],,withval=yes) case $withval in yes) AC_CHECK_HEADERS(mfhdf.h,,unset H5TOH4 TESTH5TOH4) @@ -434,6 +438,14 @@ if test "X-" != "X-$GASS"; then fi dnl ---------------------------------------------------------------------- +dnl Is LLNL's PDB present? If so then we'll compile the PDB-to-HDF5 +dnl translator. +AC_SUBST(PDB2HDF) +AC_CHECK_LIB(pdb,PD_open) +AC_CHECK_LIB(silo,lite_PD_open) +AC_CHECK_HEADERS(pdb.h,PDB2HDF=pdb2hdf) + +dnl ---------------------------------------------------------------------- dnl How does one figure out the local time zone? Anyone know of a dnl Posix way to do this? dnl @@ -865,6 +865,10 @@ done: * Robb Matzke, 27 Jul 1998 * Added the MTIME message to the dataset object header. * + * Robb Matzke, 1999-10-14 + * The names for the external file list are entered into the heap hear + * instead of when the efl message is encoded, preventing a possible + * infinite recursion situation. *------------------------------------------------------------------------- */ H5D_t * @@ -1066,6 +1070,17 @@ H5D_create(H5G_entry_t *loc, const char *name, const H5T_t *type, HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL, "unable to create external file list name heap"); } + for (i=0; i<efl->nused; i++) { + size_t offset = H5HL_insert(f, efl->heap_addr, + HDstrlen(efl->slot[i].name)+1, + efl->slot[i].name); + assert(0==efl->slot[i].name_offset); + if ((size_t)(-1)==offset) { + HGOTO_ERROR(H5E_EFL, H5E_CANTINIT, NULL, + "unable to insert URL into name heap"); + } + efl->slot[i].name_offset = offset; + } if (H5O_modify (&(new_dset->ent), H5O_EFL, 0, H5O_FLAG_CONSTANT, efl)<0) { HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL, @@ -1083,17 +1083,21 @@ H5FD_alloc(H5FD_t *file, H5FD_mem_t type, hsize_t size) /* * Try to satisfy the request from the free list. First try to find an - * exact match, otherwise use the best match. + * exact match, otherwise use the best match. Only perform the search if + * the free list has the potential of satisfying the request. */ - if (mapped_type>=0) { + if (mapped_type>=0 && + (0==file->maxsize || size<=file->maxsize)) { H5FD_free_t *prev=NULL, *best=NULL; H5FD_free_t *cur = file->fl[mapped_type]; while (cur) { + file->maxsize = MAX(file->maxsize, cur->size); if (cur->size==size) { ret_value = cur->addr; if (prev) prev->next = cur->next; else file->fl[mapped_type] = cur->next; H5MM_xfree(cur); + if (size==file->maxsize) file->maxsize=0; /*unknown*/ HRETURN(ret_value); } else if (cur->size>size && (!best || cur->size<best->size)) { @@ -1103,6 +1107,7 @@ H5FD_alloc(H5FD_t *file, H5FD_mem_t type, hsize_t size) cur = cur->next; } if (best) { + if (best->size==file->maxsize) file->maxsize=0; /*unknown*/ ret_value = best->addr; best->addr += size; best->size -= size; @@ -1232,6 +1237,9 @@ H5FD_free(H5FD_t *file, H5FD_mem_t type, haddr_t addr, hsize_t size) cur->size = size; cur->next = file->fl[mapped_type]; file->fl[mapped_type] = cur; + if (file->maxsize && size>file->maxsize) { + file->maxsize = size; + } } else if (file->cls->free) { if ((file->cls->free)(file, type, addr, size)<0) { HRETURN_ERROR(H5E_VFL, H5E_CANTINIT, FAIL, diff --git a/src/H5FDcore.c b/src/H5FDcore.c index 64f93c0..51f57c4 100644 --- a/src/H5FDcore.c +++ b/src/H5FDcore.c @@ -35,11 +35,14 @@ typedef struct H5FD_core_t { haddr_t eoa; /*end of allocated region */ haddr_t eof; /*current allocated size */ size_t increment; /*multiples for mem allocation */ + int fd; /*backing store file descriptor */ + hbool_t dirty; /*changes not saved? */ } H5FD_core_t; /* Driver-specific file access properties */ typedef struct H5FD_core_fapl_t { size_t increment; /*how much to grow memory */ + hbool_t backing_store; /*write to file name on flush */ } H5FD_core_fapl_t; /* Allocate memory in multiples of this size by default */ @@ -71,6 +74,7 @@ typedef struct H5FD_core_fapl_t { static void *H5FD_core_fapl_get(H5FD_t *_file); static H5FD_t *H5FD_core_open(const char *name, unsigned flags, hid_t fapl_id, haddr_t maxaddr); +static herr_t H5FD_core_flush(H5FD_t *_file); static herr_t H5FD_core_close(H5FD_t *_file); static int H5FD_core_cmp(const H5FD_t *_f1, const H5FD_t *_f2); static haddr_t H5FD_core_get_eoa(H5FD_t *_file); @@ -104,7 +108,7 @@ static const H5FD_class_t H5FD_core_g = { H5FD_core_get_eof, /*get_eof */ H5FD_core_read, /*read */ H5FD_core_write, /*write */ - NULL, /*flush */ + H5FD_core_flush, /*flush */ H5FD_FLMAP_SINGLE, /*fl_map */ }; @@ -149,17 +153,21 @@ H5FD_core_init(void) * Thursday, February 19, 1998 * * Modifications: - * + * Robb Matzke, 1999-10-19 + * Added the BACKING_STORE argument. If set then the entire file + * contents are flushed to a file with the same name as this + * core file. *------------------------------------------------------------------------- */ herr_t -H5Pset_fapl_core(hid_t fapl_id, size_t increment) +H5Pset_fapl_core(hid_t fapl_id, size_t increment, hbool_t backing_store) { H5FD_core_fapl_t fa; /* NO TRACE */ if (H5P_FILE_ACCESS!=H5Pget_class(fapl_id)) return -1; fa.increment = increment; + fa.backing_store = backing_store; return H5Pset_driver(fapl_id, H5FD_CORE, &fa); } @@ -177,11 +185,13 @@ H5Pset_fapl_core(hid_t fapl_id, size_t increment) * Tuesday, August 10, 1999 * * Modifications: - * + * Robb Matzke, 1999-10-19 + * Added the BACKING_STORE argument. *------------------------------------------------------------------------- */ herr_t -H5Pget_fapl_core(hid_t fapl_id, size_t *increment/*out*/) +H5Pget_fapl_core(hid_t fapl_id, size_t *increment/*out*/, + hbool_t *backing_store/*out*/) { H5FD_core_fapl_t *fa; @@ -189,7 +199,10 @@ H5Pget_fapl_core(hid_t fapl_id, size_t *increment/*out*/) if (H5P_FILE_ACCESS!=H5Pget_class(fapl_id)) return -1; if (H5FD_CORE!=H5Pget_driver(fapl_id)) return -1; if (NULL==(fa=H5Pget_driver_info(fapl_id))) return -1; + if (increment) *increment = fa->increment; + if (backing_store) *backing_store = fa->backing_store; + return 0; } @@ -217,6 +230,7 @@ H5FD_core_fapl_get(H5FD_t *_file) H5FD_core_fapl_t *fa = calloc(1, sizeof(H5FD_core_fapl_t)); fa->increment = file->increment; + fa->backing_store = (file->fd>=0); return fa; } @@ -236,7 +250,8 @@ H5FD_core_fapl_get(H5FD_t *_file) * Thursday, July 29, 1999 * * Modifications: - * + * Robb Matzke, 1999-10-19 + * The backing store file is created and opened if specified. *------------------------------------------------------------------------- */ static H5FD_t * @@ -245,14 +260,22 @@ H5FD_core_open(const char *name, unsigned UNUSED flags, hid_t fapl_id, { H5FD_core_t *file=NULL; H5FD_core_fapl_t *fa=NULL; + int fd=-1; /* Check arguments */ if (0==maxaddr || HADDR_UNDEF==maxaddr) return NULL; if (ADDR_OVERFLOW(maxaddr)) return NULL; if (H5P_DEFAULT!=fapl_id) fa = H5Pget_driver_info(fapl_id); + /* Open backing store */ + if (fa && fa->backing_store && name && + (fd=open(name, O_CREAT|O_TRUNC|O_RDWR, 0666))<0) { + return NULL; + } + /* Create the new file struct */ file = calloc(1, sizeof(H5FD_core_t)); + file->fd = fd; if (name && *name) { file->name = malloc(strlen(name)+1); strcpy(file->name, name); @@ -271,6 +294,47 @@ H5FD_core_open(const char *name, unsigned UNUSED flags, hid_t fapl_id, /*------------------------------------------------------------------------- + * Function: H5FD_core_flush + * + * Purpose: Flushes the file to backing store if there is any and if the + * dirty flag is set. + * + * Return: Success: 0 + * + * Failure: -1 + * + * Programmer: Robb Matzke + * Friday, October 15, 1999 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +static herr_t +H5FD_core_flush(H5FD_t *_file) +{ + H5FD_core_t *file = (H5FD_core_t*)_file; + + /* Write to backing store */ + if (file->dirty && file->fd>=0) { + haddr_t size = file->eof; + unsigned char *ptr = file->mem; + if (0!=lseek(file->fd, 0, SEEK_SET)) return -1; + + while (size) { + ssize_t n = write(file->fd, ptr, size); + if (n<0 && EINTR==errno) continue; + if (n<0) return -1; + ptr += (size_t)n; + size -= (size_t)n; + } + file->dirty = FALSE; + } + return 0; +} + + +/*------------------------------------------------------------------------- * Function: H5FD_core_close * * Purpose: Closes the file. @@ -283,7 +347,9 @@ H5FD_core_open(const char *name, unsigned UNUSED flags, hid_t fapl_id, * Thursday, July 29, 1999 * * Modifications: - * + * Robb Matzke, 1999-10-19 + * The contents of memory are written to the backing store if + * one is open. *------------------------------------------------------------------------- */ static herr_t @@ -291,6 +357,11 @@ H5FD_core_close(H5FD_t *_file) { H5FD_core_t *file = (H5FD_core_t*)_file; + /* Flush */ + if (H5FD_core_flush(_file)<0) return -1; + + /* Release resources */ + if (file->fd>=0) close(file->fd); if (file->name) free(file->name); if (file->mem) free(file->mem); memset(file, 0, sizeof(H5FD_core_t)); @@ -520,5 +591,6 @@ H5FD_core_write(H5FD_t *_file, hid_t UNUSED dxpl_id, haddr_t addr, /* Write from BUF to memory */ memcpy(file->mem+addr, buf, size); + file->dirty = TRUE; return 0; } diff --git a/src/H5FDcore.h b/src/H5FDcore.h index 223bb0a..f0d338a 100644 --- a/src/H5FDcore.h +++ b/src/H5FDcore.h @@ -15,7 +15,9 @@ #define H5FD_CORE (H5FD_core_init()) __DLL__ hid_t H5FD_core_init(void); -__DLL__ herr_t H5Pset_fapl_core(hid_t fapl_id, size_t increment); -__DLL__ herr_t H5Pget_fapl_core(hid_t fapl_id, size_t *increment/*out*/); +__DLL__ herr_t H5Pset_fapl_core(hid_t fapl_id, size_t increment, + hbool_t backing_store); +__DLL__ herr_t H5Pget_fapl_core(hid_t fapl_id, size_t *increment/*out*/, + hbool_t *backing_store/*out*/); #endif diff --git a/src/H5FDpublic.h b/src/H5FDpublic.h index fdd07f5..40e4afc 100644 --- a/src/H5FDpublic.h +++ b/src/H5FDpublic.h @@ -125,6 +125,7 @@ struct H5FD_t { const H5FD_class_t *cls; /*constant class info */ haddr_t maxaddr; /*for this file, overrides class*/ H5FD_free_t *fl[H5FD_MEM_NTYPES];/*freelist per allocation type*/ + hsize_t maxsize; /*largest object on FL, or zero */ }; #ifdef __cplusplus diff --git a/src/H5Odtype.c b/src/H5Odtype.c index 039d6c2..4d4322b 100644 --- a/src/H5Odtype.c +++ b/src/H5Odtype.c @@ -301,15 +301,18 @@ H5O_dtype_decode_helper(H5F_t *f, const uint8_t **pp, H5T_t *dt) /* Decode base type of VL information */ if (NULL==(dt->parent = H5MM_calloc(sizeof(H5T_t)))) - HRETURN_ERROR (H5E_DATATYPE, H5E_NOSPACE, FAIL, "memory allocation failed"); + HRETURN_ERROR (H5E_DATATYPE, H5E_NOSPACE, FAIL, + "memory allocation failed"); dt->parent->ent.header = HADDR_UNDEF; if (H5O_dtype_decode_helper(f, pp, dt->parent)<0) - HRETURN_ERROR(H5E_DATATYPE, H5E_CANTDECODE, FAIL, "unable to decode VL parent type"); + HRETURN_ERROR(H5E_DATATYPE, H5E_CANTDECODE, FAIL, + "unable to decode VL parent type"); dt->force_conv=TRUE; /* Mark this type as on disk */ if (H5T_vlen_mark(dt, f, H5T_VLEN_DISK)<0) - HRETURN_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "invalid VL location"); + HRETURN_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, + "invalid VL location"); break; default: diff --git a/src/H5Oefl.c b/src/H5Oefl.c index c14203b..8030005 100644 --- a/src/H5Oefl.c +++ b/src/H5Oefl.c @@ -144,6 +144,11 @@ H5O_efl_decode(H5F_t *f, const uint8_t *p, H5O_shared_t UNUSED *sh) * Modifications: * Robb Matzke, 1998-07-20 * Rearranged the message to add a version number near the beginning. + * + * Robb Matzke, 1999-10-14 + * Entering the name into the local heap happens when the dataset is + * created. Otherwise we could end up in infinite recursion if the heap + * happens to hash to the same cache slot as the object header. * *------------------------------------------------------------------------- */ @@ -152,8 +157,6 @@ H5O_efl_encode(H5F_t *f, uint8_t *p, const void *_mesg) { const H5O_efl_t *mesg = (const H5O_efl_t *)_mesg; int i; - size_t offset; - FUNC_ENTER(H5O_efl_encode, FAIL); @@ -183,20 +186,10 @@ H5O_efl_encode(H5F_t *f, uint8_t *p, const void *_mesg) /* Encode file list */ for (i=0; i<mesg->nused; i++) { /* - * If the name has not been added to the heap yet then do so now. + * The name should have been added to the heap when the dataset was + * created. */ - if (0==mesg->slot[i].name_offset) { - offset = H5HL_insert (f, mesg->heap_addr, - HDstrlen (mesg->slot[i].name)+1, - mesg->slot[i].name); - if ((size_t)(-1)==offset) { - HRETURN_ERROR (H5E_EFL, H5E_CANTINIT, FAIL, - "unable to insert URL into name heap"); - } - mesg->slot[i].name_offset = offset; - } - - /* Encode the file info */ + assert(mesg->slot[i].name_offset); H5F_encode_length (f, p, mesg->slot[i].name_offset); H5F_encode_length (f, p, mesg->slot[i].offset); H5F_encode_length (f, p, mesg->slot[i].size); diff --git a/src/H5config.h.in b/src/H5config.h.in index 0ae9639..d94856a 100644 --- a/src/H5config.h.in +++ b/src/H5config.h.in @@ -260,6 +260,9 @@ /* Define if you have the <mfhdf.h> header file. */ #undef HAVE_MFHDF_H +/* Define if you have the <pdb.h> header file. */ +#undef HAVE_PDB_H + /* Define if you have the <setjmp.h> header file. */ #undef HAVE_SETJMP_H @@ -335,6 +338,12 @@ /* Define if you have the nsl library (-lnsl). */ #undef HAVE_LIBNSL +/* Define if you have the pdb library (-lpdb). */ +#undef HAVE_LIBPDB + +/* Define if you have the silo library (-lsilo). */ +#undef HAVE_LIBSILO + /* Define if you have the xnet library (-lxnet). */ #undef HAVE_LIBXNET diff --git a/test/h5test.c b/test/h5test.c index dfece89..9af7ca7 100644 --- a/test/h5test.c +++ b/test/h5test.c @@ -286,7 +286,7 @@ h5_fileaccess(void) if (H5Pset_fapl_sec2(fapl)<0) return -1; } else if (!strcmp(name, "core")) { /* In-core temporary file with 1MB increment */ - if (H5Pset_fapl_core(fapl, 1024*1024)<0) return -1; + if (H5Pset_fapl_core(fapl, 1024*1024, FALSE)<0) return -1; } else if (!strcmp(name, "split")) { /* Split meta data and raw data each using default driver */ if (H5Pset_fapl_split(fapl, diff --git a/tools/Makefile.in b/tools/Makefile.in index dfc6c9f..0740ece 100644 --- a/tools/Makefile.in +++ b/tools/Makefile.in @@ -25,7 +25,7 @@ TEST_SCRIPTS=$(srcdir)/testh5dump.sh @TESTH5TOH4@ LT_LINK_LIB=$(LT) --mode=link $(CC) -static -rpath $(libdir) LIB=libh5tools.la LIBHDF5=../src/libhdf5.la -PROGS=h5debug h5import h5ls h5repart h5dump h5dumptst @H5TOH4@ +PROGS=h5debug h5import h5ls h5repart h5dump h5dumptst @H5TOH4@ @PDB2HDF@ ## Source and object files for the library; do not install LIB_SRC=h5tools.c h5findshd.c @@ -34,7 +34,7 @@ PUB_LIB= ## Source and object files for programs... PROG_SRC=h5debug.c h5import.c h5ls.c h5repart.c h5dump.c h5dumputil.c \ - h5toh4.c h5dumptst.c + h5toh4.c h5dumptst.c pdb2hdf.c PROG_OBJ=$(PROG_SRC:.c=.lo) PRIVATE_HDR=h5tools.h @@ -70,4 +70,7 @@ h5toh4: h5toh4.lo h5dumptst: h5dumptst.lo @$(LT_LINK_EXE) $(CFLAGS) -o $@ h5dumptst.lo $(LIB) $(LIBHDF5) $(LDFLAGS) $(LIBS) +pdb2hdf: pdb2hdf.lo + @$(LT_LINK_EXE) $(CFLAGS) -o $@ pdb2hdf.lo $(LIB) $(LIBHDF5) $(LDFLAGS) $(LIBS) + @CONCLUDE@ diff --git a/tools/pdb2hdf.c b/tools/pdb2hdf.c new file mode 100644 index 0000000..10a4a86 --- /dev/null +++ b/tools/pdb2hdf.c @@ -0,0 +1,500 @@ +/* + * Copyright © 1999 Spizella Software + * All rights reserved. + * + * Programmer: Robb Matzke <robb@arborea.spizella.com> + * 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 <hdf5.h> +#include <pdb.h> +#include <score.h> +#include <stdio.h> +#include <string.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 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) +{ + char *progname; + + if ((progname=strrchr(arg0, '/')) && progname[1]) progname++; + else progname = arg0; + + printf("This is %s version %u.%u release %u\n", + progname, H5_VERS_MAJOR, H5_VERS_MINOR, H5_VERS_RELEASE); +} + + +/*------------------------------------------------------------------------- + * 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; + } + + } 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); + } + + } + 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; +} |