From 8c0df04543f65a964af22c3789cf002892617176 Mon Sep 17 00:00:00 2001 From: "Herbert J. Bernstein" Date: Tue, 4 Dec 2018 14:06:53 -0500 Subject: [PATCH] Update README, add cbflib.ini both for tests and after install -- HJB --- Makefile | 20 ++++++-- Makefile_AIX | 18 ++++++-- Makefile_IRIX_gcc | 20 ++++++-- Makefile_LINUX | 18 ++++++-- Makefile_LINUX_64 | 18 ++++++-- Makefile_LINUX_DMALLOC | 18 ++++++-- Makefile_LINUX_gcc42 | 18 ++++++-- Makefile_LINUX_gcc42_DMALLOC | 18 ++++++-- Makefile_MINGW | 20 ++++++-- Makefile_MSYS2 | 18 ++++++-- Makefile_OSX | 22 +++++++-- Makefile_OSX_gcc42 | 18 ++++++-- Makefile_OSX_gcc42_DMALLOC | 18 ++++++-- README | 88 +++++++++++++++++++++++------------- README.html | 64 +++++++++++++++----------- cbflib.ini | 3 ++ m4/Makefile.m4 | 38 ++++++++++++++-- 17 files changed, 319 insertions(+), 118 deletions(-) create mode 100644 cbflib.ini diff --git a/Makefile b/Makefile index 823665a0..c867a9a9 100644 --- a/Makefile +++ b/Makefile @@ -580,6 +580,7 @@ SOCFLAGS = -fPIC SOLDFLAGS = -shared -Wl,-rpath,$(CBF_PREFIX)/lib JAVAINCLUDES = -I$(JDKDIR)/include -I$(JDKDIR)/include/linux LDPREFIX = LD_LIBRARY_PATH=$(SOLIB):$$LD_LIBRARY_PATH;export LD_LIBRARY_PATH; +RUNLDPREFIX = LD_LIBRARY_PATH=$(CBF_PREFIX)/LIB:$$LD_LIBRARY_PATH;export LD_LIBRARY_PATH; EXTRALIBS = -lm M4FLAGS = -Dfcb_bytes_in_rec=131072 TIME = time @@ -1028,6 +1029,11 @@ Makefile: $(M4)/Makefile.m4 m4 -P $(PYCIFRWDEF) -Dcbf_system=default $(M4)/Makefile.m4 > Makefile.tmp mv Makefile.tmp Makefile +cbflib.ini: $(M4)/Makefile.m4 + echo "$(LDPREFIX)" > cbflib.ini + echo "HDF5_PLUGIN_PATH=$(SOLIB):$$HDF5_PLUGIN_PATH" >> cbflib.ini + echo "export HDF5_PLUGIN_PATH" >> cbflib.ini + symlinksdone: chmod a+x .symlinks chmod a+x .undosymlinks @@ -1073,6 +1079,10 @@ baseinstall: all $(CBF_PREFIX) $(CBF_PREFIX)/lib $(CBF_PREFIX)/bin \ -cp $(CBF_PREFIX)/lib/libfcb.so $(CBF_PREFIX)/lib/libfcb_old.so cp $(SOLIB)/libfcb.so $(CBF_PREFIX)/lib/libfcb.so $(LN) $(CBF_PREFIX)/lib/libfcb.so $(CBF_PREFIX)/lib/lib_fcb.so + -cp $(CBF_PREFIX)/bin/cbflib.ini $(CBF_PREFIX)/bin/cbflib.ini_old + echo "$(RUNLDPREFIX)" > $(CBF_PREFIX)/bin/cbflib.ini + echo "HDF5_PLUGIN_PATH=$(CBF_PREFIX)/lib:$$HDF5_PLUGIN_PATH" >> $(CBF_PREFIX)/bin/cbflib.ini + echo "export HDF5_PLUGIN_PATH" >> $(CBF_PREFIX)/bin/cbflib.ini -cp $(CBF_PREFIX)/bin/adscimg2cbf $(CBF_PREFIX)/bin/adscimg2cbf_old cp $(BIN)/adscimg2cbf $(CBF_PREFIX)/bin/adscimg2cbf -cp $(CBF_PREFIX)/bin/cbf2adscimg $(CBF_PREFIX)/bin/cbf2adscimg_old @@ -1236,7 +1246,7 @@ $(TIFF): build_tiff config.guess config.sub $(TIFF)_INSTALL: $(TIFF) -rm -rf $(TIFF)_install rsync -avz $(TIFF)/ $(TIFF)_install - (cd $(TIFF_install); make distclean; ./configure --prefix=$(CBF_PREFIX); make install) + (cd $(TIFF)_install; make distclean; ./configure --prefix=$(CBF_PREFIX); make install) ifneq ($(CBFLIB_DONT_USE_LOCAL_HDF5),yes) @@ -2071,7 +2081,7 @@ restore_output: $(NEWTESTOUTPUT) $(DATADIRO) $(MINICBF_TEST)/minicbf.h5 cp test_fcb_read_testflatpackedout.out $(DATADIRO)/test_fcb_read_testflatpackedout_orig.out cp XRD1621.cbf $(DATADIRO)/XRD1621_orig.cbf cp XRD1621_I4encbC100.cbf $(DATADIRO)/XRD1621_I4encbC100_orig.cbf - cp minicbf_orig.h5 $(DATADIRO)/minicbf_orig.h5 + cp $(MINICBF_TEST)/minicbf.h5 $(DATADIRO)/minicbf_orig.h5 restore_sigs_only: $(NEWTESTOUTPUT) $(DATADIRS) $(SIGNATURE) < adscconverted_flat.cbf > $(DATADIRS)/adscconverted_flat_orig.cbf$(SEXT) @@ -2089,7 +2099,7 @@ restore_sigs_only: $(NEWTESTOUTPUT) $(DATADIRS) $(SIGNATURE) < test_fcb_read_testflatpackedout.out > $(DATADIRS)/test_fcb_read_testflatpackedout_orig.out$(SEXT) $(SIGNATURE) < XRD1621.cbf > $(DATADIRS)/XRD1621_orig.cbf$(SEXT) $(SIGNATURE) < XRD1621_I4encbC100.cbf > $(DATADIRS)/XRD1621_I4encbC100_orig.cbf$(SEXT) - $(SIGNATURE) < minicbf_orig.h5 > $(DATADIRS)/minicbf_orig.h5$(SEXT) + $(SIGNATURE) < $(MINICBF_TEST)/minicbf.h5 > $(DATADIRS)/minicbf_orig.h5$(SEXT) restore_signatures: restore_output restore_sigs_only # @@ -2241,7 +2251,7 @@ endif $(TIME) $(BIN)/cif2cbf -5 rn $(HDF5REGISTER) -en -cp -i insulin_pilatus6mconverted_enc2.cbf.h5 -o insulin_pilatus6mconverted_enc2.cbf.h5.cbf; \ $(BIN)/cif2cbf -eq -cI -i insulin_pilatus6mconverted_enc2.cbf.h5.cbf -o insulin_pilatus6mconverted_enc2.cbf.h5.eqcI.cbf) -cmp insulin_pilatus6mconverted_enc2.cbf.h5.eqcI.cbf insulin_pilatus6mconverted_orig.cbf.h5.eqcI.cbf - #-rm -f insulin_pilatus6mconverted*.cbf.h5.eqcI.cbf + -rm -f insulin_pilatus6mconverted*.cbf.h5.eqcI.cbf $(LDPREFIX) $(TINE) $(BIN)/test_cbf_airy_disk $(LDPREFIX) $(TIME) $(BIN)/cbf_testxfelread $(LDPREFIX) $(TIME) $(BIN)/testalloc @@ -2256,7 +2266,7 @@ endif -cd $(MINICBF_TEST); $(DIFF) minicbf_original.dump minicbf.dump $(LDPREFIX) cd $(MINICBF_TEST); rm -f minicbf_original.dump $(LDPREFIX) cd $(MINICBF_TEST); rm -f minicbf.dump - cd $(MINICBF_TEST); rm -f minicbf.h5 + #cd $(MINICBF_TEST); rm -f minicbf.h5 $(LDPREFIX) cd $(MINICBF_TEST); $(TIME) $(BIN)/cbf2nexus -c zlib \ --list -o i19-1.h5 ../1191_00005.cbf $(LDPREFIX) cd $(MINICBF_TEST); $(TIME) $(BIN)/nexus2cbf \ diff --git a/Makefile_AIX b/Makefile_AIX index fb648aec..939457f4 100644 --- a/Makefile_AIX +++ b/Makefile_AIX @@ -577,6 +577,7 @@ F90FLAGS = -g -qsuffix=f=f90 F90LDFLAGS = M4FLAGS = -Dfcb_bytes_in_rec=131072 LDPREFIX = LIBPATH=$(SOLIB):$$LIBPATH;export LIBPATH; +RUNLDPREFIX = LIBPATH=$(CBF_PREFIX)/lib:$$LIBPATH;export LIBPATH; EXTRALIBS = -lm TIME = time @@ -1024,6 +1025,11 @@ Makefile: $(M4)/Makefile.m4 m4 -P $(PYCIFRWDEF) -Dcbf_system=default $(M4)/Makefile.m4 > Makefile.tmp mv Makefile.tmp Makefile +cbflib.ini: $(M4)/Makefile.m4 + echo "$(LDPREFIX)" > cbflib.ini + echo "HDF5_PLUGIN_PATH=$(SOLIB):$$HDF5_PLUGIN_PATH" >> cbflib.ini + echo "export HDF5_PLUGIN_PATH" >> cbflib.ini + symlinksdone: chmod a+x .symlinks chmod a+x .undosymlinks @@ -1069,6 +1075,10 @@ baseinstall: all $(CBF_PREFIX) $(CBF_PREFIX)/lib $(CBF_PREFIX)/bin \ -cp $(CBF_PREFIX)/lib/libfcb.so $(CBF_PREFIX)/lib/libfcb_old.so cp $(SOLIB)/libfcb.so $(CBF_PREFIX)/lib/libfcb.so $(LN) $(CBF_PREFIX)/lib/libfcb.so $(CBF_PREFIX)/lib/lib_fcb.so + -cp $(CBF_PREFIX)/bin/cbflib.ini $(CBF_PREFIX)/bin/cbflib.ini_old + echo "$(RUNLDPREFIX)" > $(CBF_PREFIX)/bin/cbflib.ini + echo "HDF5_PLUGIN_PATH=$(CBF_PREFIX)/lib:$$HDF5_PLUGIN_PATH" >> $(CBF_PREFIX)/bin/cbflib.ini + echo "export HDF5_PLUGIN_PATH" >> $(CBF_PREFIX)/bin/cbflib.ini -cp $(CBF_PREFIX)/bin/adscimg2cbf $(CBF_PREFIX)/bin/adscimg2cbf_old cp $(BIN)/adscimg2cbf $(CBF_PREFIX)/bin/adscimg2cbf -cp $(CBF_PREFIX)/bin/cbf2adscimg $(CBF_PREFIX)/bin/cbf2adscimg_old @@ -1232,7 +1242,7 @@ $(TIFF): build_tiff config.guess config.sub $(TIFF)_INSTALL: $(TIFF) -rm -rf $(TIFF)_install rsync -avz $(TIFF)/ $(TIFF)_install - (cd $(TIFF_install); make distclean; ./configure --prefix=$(CBF_PREFIX); make install) + (cd $(TIFF)_install; make distclean; ./configure --prefix=$(CBF_PREFIX); make install) ifneq ($(CBFLIB_DONT_USE_LOCAL_HDF5),yes) @@ -2067,7 +2077,7 @@ restore_output: $(NEWTESTOUTPUT) $(DATADIRO) $(MINICBF_TEST)/minicbf.h5 cp test_fcb_read_testflatpackedout.out $(DATADIRO)/test_fcb_read_testflatpackedout_orig.out cp XRD1621.cbf $(DATADIRO)/XRD1621_orig.cbf cp XRD1621_I4encbC100.cbf $(DATADIRO)/XRD1621_I4encbC100_orig.cbf - cp minicbf_orig.h5 $(DATADIRO)/minicbf_orig.h5 + cp $(MINICBF_TEST)/minicbf.h5 $(DATADIRO)/minicbf_orig.h5 restore_sigs_only: $(NEWTESTOUTPUT) $(DATADIRS) $(SIGNATURE) < adscconverted_flat.cbf > $(DATADIRS)/adscconverted_flat_orig.cbf$(SEXT) @@ -2085,7 +2095,7 @@ restore_sigs_only: $(NEWTESTOUTPUT) $(DATADIRS) $(SIGNATURE) < test_fcb_read_testflatpackedout.out > $(DATADIRS)/test_fcb_read_testflatpackedout_orig.out$(SEXT) $(SIGNATURE) < XRD1621.cbf > $(DATADIRS)/XRD1621_orig.cbf$(SEXT) $(SIGNATURE) < XRD1621_I4encbC100.cbf > $(DATADIRS)/XRD1621_I4encbC100_orig.cbf$(SEXT) - $(SIGNATURE) < minicbf_orig.h5 > $(DATADIRS)/minicbf_orig.h5$(SEXT) + $(SIGNATURE) < $(MINICBF_TEST)/minicbf.h5 > $(DATADIRS)/minicbf_orig.h5$(SEXT) restore_signatures: restore_output restore_sigs_only # @@ -2252,7 +2262,7 @@ endif -cd $(MINICBF_TEST); $(DIFF) minicbf_original.dump minicbf.dump $(LDPREFIX) cd $(MINICBF_TEST); rm -f minicbf_original.dump $(LDPREFIX) cd $(MINICBF_TEST); rm -f minicbf.dump - cd $(MINICBF_TEST); rm -f minicbf.h5 + #cd $(MINICBF_TEST); rm -f minicbf.h5 $(LDPREFIX) cd $(MINICBF_TEST); $(TIME) $(BIN)/cbf2nexus -c zlib \ --list -o i19-1.h5 ../1191_00005.cbf $(LDPREFIX) cd $(MINICBF_TEST); $(TIME) $(BIN)/nexus2cbf \ diff --git a/Makefile_IRIX_gcc b/Makefile_IRIX_gcc index 56a4a2c2..5ad7f138 100644 --- a/Makefile_IRIX_gcc +++ b/Makefile_IRIX_gcc @@ -578,6 +578,9 @@ LDFLAGS = F90C = F90FLAGS = M4FLAGS = -Dfcb_bytes_in_rec=4096 +JAVAINCLUDES = -I$(JDKDIR)/include -I$(JDKDIR)/include/linux +LDPREFIX = LD_LIBRARY_PATH=$(SOLIB):$$LD_LIBRARY_PATH;export LD_LIBRARY_PATH; +RUNLDPREFIX = LD_LIBRARY_PATH=$(CBF_PREFIX)/LIB:$$LD_LIBRARY_PATH;export LD_LIBRARY_PATH; EXTRALIBS = -lm TIME = SHAR = shar @@ -1028,6 +1031,11 @@ Makefile: $(M4)/Makefile.m4 m4 -P $(PYCIFRWDEF) -Dcbf_system=default $(M4)/Makefile.m4 > Makefile.tmp mv Makefile.tmp Makefile +cbflib.ini: $(M4)/Makefile.m4 + echo "$(LDPREFIX)" > cbflib.ini + echo "HDF5_PLUGIN_PATH=$(SOLIB):$$HDF5_PLUGIN_PATH" >> cbflib.ini + echo "export HDF5_PLUGIN_PATH" >> cbflib.ini + symlinksdone: chmod a+x .symlinks chmod a+x .undosymlinks @@ -1073,6 +1081,10 @@ baseinstall: all $(CBF_PREFIX) $(CBF_PREFIX)/lib $(CBF_PREFIX)/bin \ -cp $(CBF_PREFIX)/lib/libfcb.so $(CBF_PREFIX)/lib/libfcb_old.so cp $(SOLIB)/libfcb.so $(CBF_PREFIX)/lib/libfcb.so $(LN) $(CBF_PREFIX)/lib/libfcb.so $(CBF_PREFIX)/lib/lib_fcb.so + -cp $(CBF_PREFIX)/bin/cbflib.ini $(CBF_PREFIX)/bin/cbflib.ini_old + echo "$(RUNLDPREFIX)" > $(CBF_PREFIX)/bin/cbflib.ini + echo "HDF5_PLUGIN_PATH=$(CBF_PREFIX)/lib:$$HDF5_PLUGIN_PATH" >> $(CBF_PREFIX)/bin/cbflib.ini + echo "export HDF5_PLUGIN_PATH" >> $(CBF_PREFIX)/bin/cbflib.ini -cp $(CBF_PREFIX)/bin/adscimg2cbf $(CBF_PREFIX)/bin/adscimg2cbf_old cp $(BIN)/adscimg2cbf $(CBF_PREFIX)/bin/adscimg2cbf -cp $(CBF_PREFIX)/bin/cbf2adscimg $(CBF_PREFIX)/bin/cbf2adscimg_old @@ -1236,7 +1248,7 @@ $(TIFF): build_tiff config.guess config.sub $(TIFF)_INSTALL: $(TIFF) -rm -rf $(TIFF)_install rsync -avz $(TIFF)/ $(TIFF)_install - (cd $(TIFF_install); make distclean; ./configure --prefix=$(CBF_PREFIX); make install) + (cd $(TIFF)_install; make distclean; ./configure --prefix=$(CBF_PREFIX); make install) ifneq ($(CBFLIB_DONT_USE_LOCAL_HDF5),yes) @@ -2071,7 +2083,7 @@ restore_output: $(NEWTESTOUTPUT) $(DATADIRO) $(MINICBF_TEST)/minicbf.h5 cp test_fcb_read_testflatpackedout.out $(DATADIRO)/test_fcb_read_testflatpackedout_orig.out cp XRD1621.cbf $(DATADIRO)/XRD1621_orig.cbf cp XRD1621_I4encbC100.cbf $(DATADIRO)/XRD1621_I4encbC100_orig.cbf - cp minicbf_orig.h5 $(DATADIRO)/minicbf_orig.h5 + cp $(MINICBF_TEST)/minicbf.h5 $(DATADIRO)/minicbf_orig.h5 restore_sigs_only: $(NEWTESTOUTPUT) $(DATADIRS) $(SIGNATURE) < adscconverted_flat.cbf > $(DATADIRS)/adscconverted_flat_orig.cbf$(SEXT) @@ -2089,7 +2101,7 @@ restore_sigs_only: $(NEWTESTOUTPUT) $(DATADIRS) $(SIGNATURE) < test_fcb_read_testflatpackedout.out > $(DATADIRS)/test_fcb_read_testflatpackedout_orig.out$(SEXT) $(SIGNATURE) < XRD1621.cbf > $(DATADIRS)/XRD1621_orig.cbf$(SEXT) $(SIGNATURE) < XRD1621_I4encbC100.cbf > $(DATADIRS)/XRD1621_I4encbC100_orig.cbf$(SEXT) - $(SIGNATURE) < minicbf_orig.h5 > $(DATADIRS)/minicbf_orig.h5$(SEXT) + $(SIGNATURE) < $(MINICBF_TEST)/minicbf.h5 > $(DATADIRS)/minicbf_orig.h5$(SEXT) restore_signatures: restore_output restore_sigs_only # @@ -2256,7 +2268,7 @@ endif -cd $(MINICBF_TEST); $(DIFF) minicbf_original.dump minicbf.dump $(LDPREFIX) cd $(MINICBF_TEST); rm -f minicbf_original.dump $(LDPREFIX) cd $(MINICBF_TEST); rm -f minicbf.dump - cd $(MINICBF_TEST); rm -f minicbf.h5 + #cd $(MINICBF_TEST); rm -f minicbf.h5 $(LDPREFIX) cd $(MINICBF_TEST); $(TIME) $(BIN)/cbf2nexus -c zlib \ --list -o i19-1.h5 ../1191_00005.cbf $(LDPREFIX) cd $(MINICBF_TEST); $(TIME) $(BIN)/nexus2cbf \ diff --git a/Makefile_LINUX b/Makefile_LINUX index fce7061e..36222068 100644 --- a/Makefile_LINUX +++ b/Makefile_LINUX @@ -579,6 +579,7 @@ SOCFLAGS = -fPIC SOLDFLAGS = -shared -Wl,-rpath,$(CBF_PREFIX)/lib JAVAINCLUDES = -I$(JDKDIR)/include -I$(JDKDIR)/include/linux LDPREFIX = LD_LIBRARY_PATH=$(SOLIB):$$LD_LIBRARY_PATH;export LD_LIBRARY_PATH; +RUNLDPREFIX = LD_LIBRARY_PATH=$(CBF_PREFIX)/lib:$$LD_LIBRARY_PATH;export LD_LIBRARY_PATH; EXTRALIBS = -lm M4FLAGS = -Dfcb_bytes_in_rec=131072 TIME = time @@ -1027,6 +1028,11 @@ Makefile: $(M4)/Makefile.m4 m4 -P $(PYCIFRWDEF) -Dcbf_system=default $(M4)/Makefile.m4 > Makefile.tmp mv Makefile.tmp Makefile +cbflib.ini: $(M4)/Makefile.m4 + echo "$(LDPREFIX)" > cbflib.ini + echo "HDF5_PLUGIN_PATH=$(SOLIB):$$HDF5_PLUGIN_PATH" >> cbflib.ini + echo "export HDF5_PLUGIN_PATH" >> cbflib.ini + symlinksdone: chmod a+x .symlinks chmod a+x .undosymlinks @@ -1072,6 +1078,10 @@ baseinstall: all $(CBF_PREFIX) $(CBF_PREFIX)/lib $(CBF_PREFIX)/bin \ -cp $(CBF_PREFIX)/lib/libfcb.so $(CBF_PREFIX)/lib/libfcb_old.so cp $(SOLIB)/libfcb.so $(CBF_PREFIX)/lib/libfcb.so $(LN) $(CBF_PREFIX)/lib/libfcb.so $(CBF_PREFIX)/lib/lib_fcb.so + -cp $(CBF_PREFIX)/bin/cbflib.ini $(CBF_PREFIX)/bin/cbflib.ini_old + echo "$(RUNLDPREFIX)" > $(CBF_PREFIX)/bin/cbflib.ini + echo "HDF5_PLUGIN_PATH=$(CBF_PREFIX)/lib:$$HDF5_PLUGIN_PATH" >> $(CBF_PREFIX)/bin/cbflib.ini + echo "export HDF5_PLUGIN_PATH" >> $(CBF_PREFIX)/bin/cbflib.ini -cp $(CBF_PREFIX)/bin/adscimg2cbf $(CBF_PREFIX)/bin/adscimg2cbf_old cp $(BIN)/adscimg2cbf $(CBF_PREFIX)/bin/adscimg2cbf -cp $(CBF_PREFIX)/bin/cbf2adscimg $(CBF_PREFIX)/bin/cbf2adscimg_old @@ -1235,7 +1245,7 @@ $(TIFF): build_tiff config.guess config.sub $(TIFF)_INSTALL: $(TIFF) -rm -rf $(TIFF)_install rsync -avz $(TIFF)/ $(TIFF)_install - (cd $(TIFF_install); make distclean; ./configure --prefix=$(CBF_PREFIX); make install) + (cd $(TIFF)_install; make distclean; ./configure --prefix=$(CBF_PREFIX); make install) ifneq ($(CBFLIB_DONT_USE_LOCAL_HDF5),yes) @@ -2070,7 +2080,7 @@ restore_output: $(NEWTESTOUTPUT) $(DATADIRO) $(MINICBF_TEST)/minicbf.h5 cp test_fcb_read_testflatpackedout.out $(DATADIRO)/test_fcb_read_testflatpackedout_orig.out cp XRD1621.cbf $(DATADIRO)/XRD1621_orig.cbf cp XRD1621_I4encbC100.cbf $(DATADIRO)/XRD1621_I4encbC100_orig.cbf - cp minicbf_orig.h5 $(DATADIRO)/minicbf_orig.h5 + cp $(MINICBF_TEST)/minicbf.h5 $(DATADIRO)/minicbf_orig.h5 restore_sigs_only: $(NEWTESTOUTPUT) $(DATADIRS) $(SIGNATURE) < adscconverted_flat.cbf > $(DATADIRS)/adscconverted_flat_orig.cbf$(SEXT) @@ -2088,7 +2098,7 @@ restore_sigs_only: $(NEWTESTOUTPUT) $(DATADIRS) $(SIGNATURE) < test_fcb_read_testflatpackedout.out > $(DATADIRS)/test_fcb_read_testflatpackedout_orig.out$(SEXT) $(SIGNATURE) < XRD1621.cbf > $(DATADIRS)/XRD1621_orig.cbf$(SEXT) $(SIGNATURE) < XRD1621_I4encbC100.cbf > $(DATADIRS)/XRD1621_I4encbC100_orig.cbf$(SEXT) - $(SIGNATURE) < minicbf_orig.h5 > $(DATADIRS)/minicbf_orig.h5$(SEXT) + $(SIGNATURE) < $(MINICBF_TEST)/minicbf.h5 > $(DATADIRS)/minicbf_orig.h5$(SEXT) restore_signatures: restore_output restore_sigs_only # @@ -2255,7 +2265,7 @@ endif -cd $(MINICBF_TEST); $(DIFF) minicbf_original.dump minicbf.dump $(LDPREFIX) cd $(MINICBF_TEST); rm -f minicbf_original.dump $(LDPREFIX) cd $(MINICBF_TEST); rm -f minicbf.dump - cd $(MINICBF_TEST); rm -f minicbf.h5 + #cd $(MINICBF_TEST); rm -f minicbf.h5 $(LDPREFIX) cd $(MINICBF_TEST); $(TIME) $(BIN)/cbf2nexus -c zlib \ --list -o i19-1.h5 ../1191_00005.cbf $(LDPREFIX) cd $(MINICBF_TEST); $(TIME) $(BIN)/nexus2cbf \ diff --git a/Makefile_LINUX_64 b/Makefile_LINUX_64 index 60f2bd1e..3b38b55c 100644 --- a/Makefile_LINUX_64 +++ b/Makefile_LINUX_64 @@ -580,6 +580,7 @@ SOCFLAGS = -fPIC SOLDFLAGS = -shared -Wl,-rpath,$(CBF_PREFIX)/lib JAVAINCLUDES = -I$(JDKDIR)/include -I$(JDKDIR)/include/linux LDPREFIX = LD_LIBRARY_PATH=$(SOLIB):$$LD_LIBRARY_PATH;export LD_LIBRARY_PATH; +RUNLDPREFIX = LD_LIBRARY_PATH=$(CBF_PREFIX)/lib:$$LD_LIBRARY_PATH;export LD_LIBRARY_PATH; EXTRALIBS = -lm M4FLAGS = -Dfcb_bytes_in_rec=131072 TIME = time @@ -1028,6 +1029,11 @@ Makefile: $(M4)/Makefile.m4 m4 -P $(PYCIFRWDEF) -Dcbf_system=default $(M4)/Makefile.m4 > Makefile.tmp mv Makefile.tmp Makefile +cbflib.ini: $(M4)/Makefile.m4 + echo "$(LDPREFIX)" > cbflib.ini + echo "HDF5_PLUGIN_PATH=$(SOLIB):$$HDF5_PLUGIN_PATH" >> cbflib.ini + echo "export HDF5_PLUGIN_PATH" >> cbflib.ini + symlinksdone: chmod a+x .symlinks chmod a+x .undosymlinks @@ -1073,6 +1079,10 @@ baseinstall: all $(CBF_PREFIX) $(CBF_PREFIX)/lib $(CBF_PREFIX)/bin \ -cp $(CBF_PREFIX)/lib/libfcb.so $(CBF_PREFIX)/lib/libfcb_old.so cp $(SOLIB)/libfcb.so $(CBF_PREFIX)/lib/libfcb.so $(LN) $(CBF_PREFIX)/lib/libfcb.so $(CBF_PREFIX)/lib/lib_fcb.so + -cp $(CBF_PREFIX)/bin/cbflib.ini $(CBF_PREFIX)/bin/cbflib.ini_old + echo "$(RUNLDPREFIX)" > $(CBF_PREFIX)/bin/cbflib.ini + echo "HDF5_PLUGIN_PATH=$(CBF_PREFIX)/lib:$$HDF5_PLUGIN_PATH" >> $(CBF_PREFIX)/bin/cbflib.ini + echo "export HDF5_PLUGIN_PATH" >> $(CBF_PREFIX)/bin/cbflib.ini -cp $(CBF_PREFIX)/bin/adscimg2cbf $(CBF_PREFIX)/bin/adscimg2cbf_old cp $(BIN)/adscimg2cbf $(CBF_PREFIX)/bin/adscimg2cbf -cp $(CBF_PREFIX)/bin/cbf2adscimg $(CBF_PREFIX)/bin/cbf2adscimg_old @@ -1236,7 +1246,7 @@ $(TIFF): build_tiff config.guess config.sub $(TIFF)_INSTALL: $(TIFF) -rm -rf $(TIFF)_install rsync -avz $(TIFF)/ $(TIFF)_install - (cd $(TIFF_install); make distclean; ./configure --prefix=$(CBF_PREFIX); make install) + (cd $(TIFF)_install; make distclean; ./configure --prefix=$(CBF_PREFIX); make install) ifneq ($(CBFLIB_DONT_USE_LOCAL_HDF5),yes) @@ -2071,7 +2081,7 @@ restore_output: $(NEWTESTOUTPUT) $(DATADIRO) $(MINICBF_TEST)/minicbf.h5 cp test_fcb_read_testflatpackedout.out $(DATADIRO)/test_fcb_read_testflatpackedout_orig.out cp XRD1621.cbf $(DATADIRO)/XRD1621_orig.cbf cp XRD1621_I4encbC100.cbf $(DATADIRO)/XRD1621_I4encbC100_orig.cbf - cp minicbf_orig.h5 $(DATADIRO)/minicbf_orig.h5 + cp $(MINICBF_TEST)/minicbf.h5 $(DATADIRO)/minicbf_orig.h5 restore_sigs_only: $(NEWTESTOUTPUT) $(DATADIRS) $(SIGNATURE) < adscconverted_flat.cbf > $(DATADIRS)/adscconverted_flat_orig.cbf$(SEXT) @@ -2089,7 +2099,7 @@ restore_sigs_only: $(NEWTESTOUTPUT) $(DATADIRS) $(SIGNATURE) < test_fcb_read_testflatpackedout.out > $(DATADIRS)/test_fcb_read_testflatpackedout_orig.out$(SEXT) $(SIGNATURE) < XRD1621.cbf > $(DATADIRS)/XRD1621_orig.cbf$(SEXT) $(SIGNATURE) < XRD1621_I4encbC100.cbf > $(DATADIRS)/XRD1621_I4encbC100_orig.cbf$(SEXT) - $(SIGNATURE) < minicbf_orig.h5 > $(DATADIRS)/minicbf_orig.h5$(SEXT) + $(SIGNATURE) < $(MINICBF_TEST)/minicbf.h5 > $(DATADIRS)/minicbf_orig.h5$(SEXT) restore_signatures: restore_output restore_sigs_only # @@ -2256,7 +2266,7 @@ endif -cd $(MINICBF_TEST); $(DIFF) minicbf_original.dump minicbf.dump $(LDPREFIX) cd $(MINICBF_TEST); rm -f minicbf_original.dump $(LDPREFIX) cd $(MINICBF_TEST); rm -f minicbf.dump - cd $(MINICBF_TEST); rm -f minicbf.h5 + #cd $(MINICBF_TEST); rm -f minicbf.h5 $(LDPREFIX) cd $(MINICBF_TEST); $(TIME) $(BIN)/cbf2nexus -c zlib \ --list -o i19-1.h5 ../1191_00005.cbf $(LDPREFIX) cd $(MINICBF_TEST); $(TIME) $(BIN)/nexus2cbf \ diff --git a/Makefile_LINUX_DMALLOC b/Makefile_LINUX_DMALLOC index cfca6839..e1569b6a 100644 --- a/Makefile_LINUX_DMALLOC +++ b/Makefile_LINUX_DMALLOC @@ -579,6 +579,7 @@ SOCFLAGS = -fPIC SOLDFLAGS = -shared -Wl,-rpath,$(CBF_PREFIX)/lib JAVAINCLUDES = -I$(JDKDIR)/include -I$(JDKDIR)/include/linux LDPREFIX = LD_LIBRARY_PATH=$(SOLIB):$$LD_LIBRARY_PATH;export LD_LIBRARY_PATH; +RUNLDPREFIX = LD_LIBRARY_PATH=$(CBF_PREFIX)/lib:$$LD_LIBRARY_PATH;export LD_LIBRARY_PATH; EXTRALIBS = -lm -L$(HOME)/lib -ldmalloc M4FLAGS = -Dfcb_bytes_in_rec=131072 TIME = time @@ -1027,6 +1028,11 @@ Makefile: $(M4)/Makefile.m4 m4 -P $(PYCIFRWDEF) -Dcbf_system=default $(M4)/Makefile.m4 > Makefile.tmp mv Makefile.tmp Makefile +cbflib.ini: $(M4)/Makefile.m4 + echo "$(LDPREFIX)" > cbflib.ini + echo "HDF5_PLUGIN_PATH=$(SOLIB):$$HDF5_PLUGIN_PATH" >> cbflib.ini + echo "export HDF5_PLUGIN_PATH" >> cbflib.ini + symlinksdone: chmod a+x .symlinks chmod a+x .undosymlinks @@ -1072,6 +1078,10 @@ baseinstall: all $(CBF_PREFIX) $(CBF_PREFIX)/lib $(CBF_PREFIX)/bin \ -cp $(CBF_PREFIX)/lib/libfcb.so $(CBF_PREFIX)/lib/libfcb_old.so cp $(SOLIB)/libfcb.so $(CBF_PREFIX)/lib/libfcb.so $(LN) $(CBF_PREFIX)/lib/libfcb.so $(CBF_PREFIX)/lib/lib_fcb.so + -cp $(CBF_PREFIX)/bin/cbflib.ini $(CBF_PREFIX)/bin/cbflib.ini_old + echo "$(RUNLDPREFIX)" > $(CBF_PREFIX)/bin/cbflib.ini + echo "HDF5_PLUGIN_PATH=$(CBF_PREFIX)/lib:$$HDF5_PLUGIN_PATH" >> $(CBF_PREFIX)/bin/cbflib.ini + echo "export HDF5_PLUGIN_PATH" >> $(CBF_PREFIX)/bin/cbflib.ini -cp $(CBF_PREFIX)/bin/adscimg2cbf $(CBF_PREFIX)/bin/adscimg2cbf_old cp $(BIN)/adscimg2cbf $(CBF_PREFIX)/bin/adscimg2cbf -cp $(CBF_PREFIX)/bin/cbf2adscimg $(CBF_PREFIX)/bin/cbf2adscimg_old @@ -1235,7 +1245,7 @@ $(TIFF): build_tiff config.guess config.sub $(TIFF)_INSTALL: $(TIFF) -rm -rf $(TIFF)_install rsync -avz $(TIFF)/ $(TIFF)_install - (cd $(TIFF_install); make distclean; ./configure --prefix=$(CBF_PREFIX); make install) + (cd $(TIFF)_install; make distclean; ./configure --prefix=$(CBF_PREFIX); make install) ifneq ($(CBFLIB_DONT_USE_LOCAL_HDF5),yes) @@ -2070,7 +2080,7 @@ restore_output: $(NEWTESTOUTPUT) $(DATADIRO) $(MINICBF_TEST)/minicbf.h5 cp test_fcb_read_testflatpackedout.out $(DATADIRO)/test_fcb_read_testflatpackedout_orig.out cp XRD1621.cbf $(DATADIRO)/XRD1621_orig.cbf cp XRD1621_I4encbC100.cbf $(DATADIRO)/XRD1621_I4encbC100_orig.cbf - cp minicbf_orig.h5 $(DATADIRO)/minicbf_orig.h5 + cp $(MINICBF_TEST)/minicbf.h5 $(DATADIRO)/minicbf_orig.h5 restore_sigs_only: $(NEWTESTOUTPUT) $(DATADIRS) $(SIGNATURE) < adscconverted_flat.cbf > $(DATADIRS)/adscconverted_flat_orig.cbf$(SEXT) @@ -2088,7 +2098,7 @@ restore_sigs_only: $(NEWTESTOUTPUT) $(DATADIRS) $(SIGNATURE) < test_fcb_read_testflatpackedout.out > $(DATADIRS)/test_fcb_read_testflatpackedout_orig.out$(SEXT) $(SIGNATURE) < XRD1621.cbf > $(DATADIRS)/XRD1621_orig.cbf$(SEXT) $(SIGNATURE) < XRD1621_I4encbC100.cbf > $(DATADIRS)/XRD1621_I4encbC100_orig.cbf$(SEXT) - $(SIGNATURE) < minicbf_orig.h5 > $(DATADIRS)/minicbf_orig.h5$(SEXT) + $(SIGNATURE) < $(MINICBF_TEST)/minicbf.h5 > $(DATADIRS)/minicbf_orig.h5$(SEXT) restore_signatures: restore_output restore_sigs_only # @@ -2255,7 +2265,7 @@ endif -cd $(MINICBF_TEST); $(DIFF) minicbf_original.dump minicbf.dump $(LDPREFIX) cd $(MINICBF_TEST); rm -f minicbf_original.dump $(LDPREFIX) cd $(MINICBF_TEST); rm -f minicbf.dump - cd $(MINICBF_TEST); rm -f minicbf.h5 + #cd $(MINICBF_TEST); rm -f minicbf.h5 $(LDPREFIX) cd $(MINICBF_TEST); $(TIME) $(BIN)/cbf2nexus -c zlib \ --list -o i19-1.h5 ../1191_00005.cbf $(LDPREFIX) cd $(MINICBF_TEST); $(TIME) $(BIN)/nexus2cbf \ diff --git a/Makefile_LINUX_gcc42 b/Makefile_LINUX_gcc42 index 3e4a6ac1..8ecfa85f 100644 --- a/Makefile_LINUX_gcc42 +++ b/Makefile_LINUX_gcc42 @@ -580,6 +580,7 @@ SOCFLAGS = -fPIC SOLDFLAGS = -shared -Wl,-rpath,$(CBF_PREFIX)/lib JAVAINCLUDES = -I$(JDKDIR)/include -I$(JDKDIR)/include/linux LDPREFIX = LD_LIBRARY_PATH=$(SOLIB):$$LD_LIBRARY_PATH;export LD_LIBRARY_PATH; +RUNLDPREFIX = LD_LIBRARY_PATH=$(CBF_PREFIX)/lib:$$LD_LIBRARY_PATH;export LD_LIBRARY_PATH; EXTRALIBS = -lm M4FLAGS = -Dfcb_bytes_in_rec=131072 TIME = time @@ -1028,6 +1029,11 @@ Makefile: $(M4)/Makefile.m4 m4 -P $(PYCIFRWDEF) -Dcbf_system=default $(M4)/Makefile.m4 > Makefile.tmp mv Makefile.tmp Makefile +cbflib.ini: $(M4)/Makefile.m4 + echo "$(LDPREFIX)" > cbflib.ini + echo "HDF5_PLUGIN_PATH=$(SOLIB):$$HDF5_PLUGIN_PATH" >> cbflib.ini + echo "export HDF5_PLUGIN_PATH" >> cbflib.ini + symlinksdone: chmod a+x .symlinks chmod a+x .undosymlinks @@ -1073,6 +1079,10 @@ baseinstall: all $(CBF_PREFIX) $(CBF_PREFIX)/lib $(CBF_PREFIX)/bin \ -cp $(CBF_PREFIX)/lib/libfcb.so $(CBF_PREFIX)/lib/libfcb_old.so cp $(SOLIB)/libfcb.so $(CBF_PREFIX)/lib/libfcb.so $(LN) $(CBF_PREFIX)/lib/libfcb.so $(CBF_PREFIX)/lib/lib_fcb.so + -cp $(CBF_PREFIX)/bin/cbflib.ini $(CBF_PREFIX)/bin/cbflib.ini_old + echo "$(RUNLDPREFIX)" > $(CBF_PREFIX)/bin/cbflib.ini + echo "HDF5_PLUGIN_PATH=$(CBF_PREFIX)/lib:$$HDF5_PLUGIN_PATH" >> $(CBF_PREFIX)/bin/cbflib.ini + echo "export HDF5_PLUGIN_PATH" >> $(CBF_PREFIX)/bin/cbflib.ini -cp $(CBF_PREFIX)/bin/adscimg2cbf $(CBF_PREFIX)/bin/adscimg2cbf_old cp $(BIN)/adscimg2cbf $(CBF_PREFIX)/bin/adscimg2cbf -cp $(CBF_PREFIX)/bin/cbf2adscimg $(CBF_PREFIX)/bin/cbf2adscimg_old @@ -1236,7 +1246,7 @@ $(TIFF): build_tiff config.guess config.sub $(TIFF)_INSTALL: $(TIFF) -rm -rf $(TIFF)_install rsync -avz $(TIFF)/ $(TIFF)_install - (cd $(TIFF_install); make distclean; ./configure --prefix=$(CBF_PREFIX); make install) + (cd $(TIFF)_install; make distclean; ./configure --prefix=$(CBF_PREFIX); make install) ifneq ($(CBFLIB_DONT_USE_LOCAL_HDF5),yes) @@ -2071,7 +2081,7 @@ restore_output: $(NEWTESTOUTPUT) $(DATADIRO) $(MINICBF_TEST)/minicbf.h5 cp test_fcb_read_testflatpackedout.out $(DATADIRO)/test_fcb_read_testflatpackedout_orig.out cp XRD1621.cbf $(DATADIRO)/XRD1621_orig.cbf cp XRD1621_I4encbC100.cbf $(DATADIRO)/XRD1621_I4encbC100_orig.cbf - cp minicbf_orig.h5 $(DATADIRO)/minicbf_orig.h5 + cp $(MINICBF_TEST)/minicbf.h5 $(DATADIRO)/minicbf_orig.h5 restore_sigs_only: $(NEWTESTOUTPUT) $(DATADIRS) $(SIGNATURE) < adscconverted_flat.cbf > $(DATADIRS)/adscconverted_flat_orig.cbf$(SEXT) @@ -2089,7 +2099,7 @@ restore_sigs_only: $(NEWTESTOUTPUT) $(DATADIRS) $(SIGNATURE) < test_fcb_read_testflatpackedout.out > $(DATADIRS)/test_fcb_read_testflatpackedout_orig.out$(SEXT) $(SIGNATURE) < XRD1621.cbf > $(DATADIRS)/XRD1621_orig.cbf$(SEXT) $(SIGNATURE) < XRD1621_I4encbC100.cbf > $(DATADIRS)/XRD1621_I4encbC100_orig.cbf$(SEXT) - $(SIGNATURE) < minicbf_orig.h5 > $(DATADIRS)/minicbf_orig.h5$(SEXT) + $(SIGNATURE) < $(MINICBF_TEST)/minicbf.h5 > $(DATADIRS)/minicbf_orig.h5$(SEXT) restore_signatures: restore_output restore_sigs_only # @@ -2256,7 +2266,7 @@ endif -cd $(MINICBF_TEST); $(DIFF) minicbf_original.dump minicbf.dump $(LDPREFIX) cd $(MINICBF_TEST); rm -f minicbf_original.dump $(LDPREFIX) cd $(MINICBF_TEST); rm -f minicbf.dump - cd $(MINICBF_TEST); rm -f minicbf.h5 + #cd $(MINICBF_TEST); rm -f minicbf.h5 $(LDPREFIX) cd $(MINICBF_TEST); $(TIME) $(BIN)/cbf2nexus -c zlib \ --list -o i19-1.h5 ../1191_00005.cbf $(LDPREFIX) cd $(MINICBF_TEST); $(TIME) $(BIN)/nexus2cbf \ diff --git a/Makefile_LINUX_gcc42_DMALLOC b/Makefile_LINUX_gcc42_DMALLOC index 99fa3d5f..02078c35 100644 --- a/Makefile_LINUX_gcc42_DMALLOC +++ b/Makefile_LINUX_gcc42_DMALLOC @@ -580,6 +580,7 @@ SOCFLAGS = -fPIC SOLDFLAGS = -shared -Wl,-rpath,$(CBF_PREFIX)/lib JAVAINCLUDES = -I$(JDKDIR)/include -I$(JDKDIR)/include/linux LDPREFIX = LD_LIBRARY_PATH=$(SOLIB):$$LD_LIBRARY_PATH;export LD_LIBRARY_PATH; +RUNLDPREFIX = LD_LIBRARY_PATH=$(CBF_PREFIX)/lib:$$LD_LIBRARY_PATH;export LD_LIBRARY_PATH; EXTRALIBS = -lm -L$(HOME)/lib -ldmalloc M4FLAGS = -Dfcb_bytes_in_rec=131072 TIME = time @@ -1028,6 +1029,11 @@ Makefile: $(M4)/Makefile.m4 m4 -P $(PYCIFRWDEF) -Dcbf_system=default $(M4)/Makefile.m4 > Makefile.tmp mv Makefile.tmp Makefile +cbflib.ini: $(M4)/Makefile.m4 + echo "$(LDPREFIX)" > cbflib.ini + echo "HDF5_PLUGIN_PATH=$(SOLIB):$$HDF5_PLUGIN_PATH" >> cbflib.ini + echo "export HDF5_PLUGIN_PATH" >> cbflib.ini + symlinksdone: chmod a+x .symlinks chmod a+x .undosymlinks @@ -1073,6 +1079,10 @@ baseinstall: all $(CBF_PREFIX) $(CBF_PREFIX)/lib $(CBF_PREFIX)/bin \ -cp $(CBF_PREFIX)/lib/libfcb.so $(CBF_PREFIX)/lib/libfcb_old.so cp $(SOLIB)/libfcb.so $(CBF_PREFIX)/lib/libfcb.so $(LN) $(CBF_PREFIX)/lib/libfcb.so $(CBF_PREFIX)/lib/lib_fcb.so + -cp $(CBF_PREFIX)/bin/cbflib.ini $(CBF_PREFIX)/bin/cbflib.ini_old + echo "$(RUNLDPREFIX)" > $(CBF_PREFIX)/bin/cbflib.ini + echo "HDF5_PLUGIN_PATH=$(CBF_PREFIX)/lib:$$HDF5_PLUGIN_PATH" >> $(CBF_PREFIX)/bin/cbflib.ini + echo "export HDF5_PLUGIN_PATH" >> $(CBF_PREFIX)/bin/cbflib.ini -cp $(CBF_PREFIX)/bin/adscimg2cbf $(CBF_PREFIX)/bin/adscimg2cbf_old cp $(BIN)/adscimg2cbf $(CBF_PREFIX)/bin/adscimg2cbf -cp $(CBF_PREFIX)/bin/cbf2adscimg $(CBF_PREFIX)/bin/cbf2adscimg_old @@ -1236,7 +1246,7 @@ $(TIFF): build_tiff config.guess config.sub $(TIFF)_INSTALL: $(TIFF) -rm -rf $(TIFF)_install rsync -avz $(TIFF)/ $(TIFF)_install - (cd $(TIFF_install); make distclean; ./configure --prefix=$(CBF_PREFIX); make install) + (cd $(TIFF)_install; make distclean; ./configure --prefix=$(CBF_PREFIX); make install) ifneq ($(CBFLIB_DONT_USE_LOCAL_HDF5),yes) @@ -2071,7 +2081,7 @@ restore_output: $(NEWTESTOUTPUT) $(DATADIRO) $(MINICBF_TEST)/minicbf.h5 cp test_fcb_read_testflatpackedout.out $(DATADIRO)/test_fcb_read_testflatpackedout_orig.out cp XRD1621.cbf $(DATADIRO)/XRD1621_orig.cbf cp XRD1621_I4encbC100.cbf $(DATADIRO)/XRD1621_I4encbC100_orig.cbf - cp minicbf_orig.h5 $(DATADIRO)/minicbf_orig.h5 + cp $(MINICBF_TEST)/minicbf.h5 $(DATADIRO)/minicbf_orig.h5 restore_sigs_only: $(NEWTESTOUTPUT) $(DATADIRS) $(SIGNATURE) < adscconverted_flat.cbf > $(DATADIRS)/adscconverted_flat_orig.cbf$(SEXT) @@ -2089,7 +2099,7 @@ restore_sigs_only: $(NEWTESTOUTPUT) $(DATADIRS) $(SIGNATURE) < test_fcb_read_testflatpackedout.out > $(DATADIRS)/test_fcb_read_testflatpackedout_orig.out$(SEXT) $(SIGNATURE) < XRD1621.cbf > $(DATADIRS)/XRD1621_orig.cbf$(SEXT) $(SIGNATURE) < XRD1621_I4encbC100.cbf > $(DATADIRS)/XRD1621_I4encbC100_orig.cbf$(SEXT) - $(SIGNATURE) < minicbf_orig.h5 > $(DATADIRS)/minicbf_orig.h5$(SEXT) + $(SIGNATURE) < $(MINICBF_TEST)/minicbf.h5 > $(DATADIRS)/minicbf_orig.h5$(SEXT) restore_signatures: restore_output restore_sigs_only # @@ -2256,7 +2266,7 @@ endif -cd $(MINICBF_TEST); $(DIFF) minicbf_original.dump minicbf.dump $(LDPREFIX) cd $(MINICBF_TEST); rm -f minicbf_original.dump $(LDPREFIX) cd $(MINICBF_TEST); rm -f minicbf.dump - cd $(MINICBF_TEST); rm -f minicbf.h5 + #cd $(MINICBF_TEST); rm -f minicbf.h5 $(LDPREFIX) cd $(MINICBF_TEST); $(TIME) $(BIN)/cbf2nexus -c zlib \ --list -o i19-1.h5 ../1191_00005.cbf $(LDPREFIX) cd $(MINICBF_TEST); $(TIME) $(BIN)/nexus2cbf \ diff --git a/Makefile_MINGW b/Makefile_MINGW index a9158e0b..c44da345 100644 --- a/Makefile_MINGW +++ b/Makefile_MINGW @@ -578,7 +578,8 @@ F90C = g95 F90FLAGS = -g F90LDFLAGS = M4FLAGS = -Dfcb_bytes_in_rec=4096 -LDPREFIX = PATH=$(SOLIB);$$PATH;export PATH; +LDPREFIX = PATH=$(SOLIB):$$PATH;export PATH; +RUNLDPREFIX = PATH=$(CBF_PREFIX)/lib:$$PATH;export PATH; SOCFLAGS = -D_JNI_IMPLEMENTATION_ SOLDFLAGS = -shared -Wl,--kill-at JAVAINCLUDES = -I$(JDKDIR)/include -I$(JDKDIR)/include/win32 @@ -1041,6 +1042,11 @@ Makefile: $(M4)/Makefile.m4 m4 -P $(PYCIFRWDEF) -Dcbf_system=default $(M4)/Makefile.m4 > Makefile.tmp mv Makefile.tmp Makefile +cbflib.ini: $(M4)/Makefile.m4 + echo "$(LDPREFIX)" > cbflib.ini + echo "HDF5_PLUGIN_PATH=$(SOLIB):$$HDF5_PLUGIN_PATH" >> cbflib.ini + echo "export HDF5_PLUGIN_PATH" >> cbflib.ini + symlinksdone: chmod a+x .symlinks chmod a+x .undosymlinks @@ -1086,6 +1092,10 @@ baseinstall: all $(CBF_PREFIX) $(CBF_PREFIX)/lib $(CBF_PREFIX)/bin \ -cp $(CBF_PREFIX)/lib/libfcb.so $(CBF_PREFIX)/lib/libfcb_old.so cp $(SOLIB)/libfcb.so $(CBF_PREFIX)/lib/libfcb.so $(LN) $(CBF_PREFIX)/lib/libfcb.so $(CBF_PREFIX)/lib/lib_fcb.so + -cp $(CBF_PREFIX)/bin/cbflib.ini $(CBF_PREFIX)/bin/cbflib.ini_old + echo "$(RUNLDPREFIX)" > $(CBF_PREFIX)/bin/cbflib.ini + echo "HDF5_PLUGIN_PATH=$(CBF_PREFIX)/lib:$$HDF5_PLUGIN_PATH" >> $(CBF_PREFIX)/bin/cbflib.ini + echo "export HDF5_PLUGIN_PATH" >> $(CBF_PREFIX)/bin/cbflib.ini -cp $(CBF_PREFIX)/bin/adscimg2cbf $(CBF_PREFIX)/bin/adscimg2cbf_old cp $(BIN)/adscimg2cbf $(CBF_PREFIX)/bin/adscimg2cbf -cp $(CBF_PREFIX)/bin/cbf2adscimg $(CBF_PREFIX)/bin/cbf2adscimg_old @@ -1249,7 +1259,7 @@ $(TIFF): build_tiff config.guess config.sub $(TIFF)_INSTALL: $(TIFF) -rm -rf $(TIFF)_install rsync -avz $(TIFF)/ $(TIFF)_install - (cd $(TIFF_install); make distclean; ./configure --prefix=$(CBF_PREFIX); make install) + (cd $(TIFF)_install; make distclean; ./configure --prefix=$(CBF_PREFIX); make install) ifneq ($(CBFLIB_DONT_USE_LOCAL_HDF5),yes) @@ -2084,7 +2094,7 @@ restore_output: $(NEWTESTOUTPUT) $(DATADIRO) $(MINICBF_TEST)/minicbf.h5 cp test_fcb_read_testflatpackedout.out $(DATADIRO)/test_fcb_read_testflatpackedout_orig.out cp XRD1621.cbf $(DATADIRO)/XRD1621_orig.cbf cp XRD1621_I4encbC100.cbf $(DATADIRO)/XRD1621_I4encbC100_orig.cbf - cp minicbf_orig.h5 $(DATADIRO)/minicbf_orig.h5 + cp $(MINICBF_TEST)/minicbf.h5 $(DATADIRO)/minicbf_orig.h5 restore_sigs_only: $(NEWTESTOUTPUT) $(DATADIRS) $(SIGNATURE) < adscconverted_flat.cbf > $(DATADIRS)/adscconverted_flat_orig.cbf$(SEXT) @@ -2102,7 +2112,7 @@ restore_sigs_only: $(NEWTESTOUTPUT) $(DATADIRS) $(SIGNATURE) < test_fcb_read_testflatpackedout.out > $(DATADIRS)/test_fcb_read_testflatpackedout_orig.out$(SEXT) $(SIGNATURE) < XRD1621.cbf > $(DATADIRS)/XRD1621_orig.cbf$(SEXT) $(SIGNATURE) < XRD1621_I4encbC100.cbf > $(DATADIRS)/XRD1621_I4encbC100_orig.cbf$(SEXT) - $(SIGNATURE) < minicbf_orig.h5 > $(DATADIRS)/minicbf_orig.h5$(SEXT) + $(SIGNATURE) < $(MINICBF_TEST)/minicbf.h5 > $(DATADIRS)/minicbf_orig.h5$(SEXT) restore_signatures: restore_output restore_sigs_only # @@ -2269,7 +2279,7 @@ endif -cd $(MINICBF_TEST); $(DIFF) minicbf_original.dump minicbf.dump $(LDPREFIX) cd $(MINICBF_TEST); rm -f minicbf_original.dump $(LDPREFIX) cd $(MINICBF_TEST); rm -f minicbf.dump - cd $(MINICBF_TEST); rm -f minicbf.h5 + #cd $(MINICBF_TEST); rm -f minicbf.h5 $(LDPREFIX) cd $(MINICBF_TEST); $(TIME) $(BIN)/cbf2nexus -c zlib \ --list -o i19-1.h5 ../1191_00005.cbf $(LDPREFIX) cd $(MINICBF_TEST); $(TIME) $(BIN)/nexus2cbf \ diff --git a/Makefile_MSYS2 b/Makefile_MSYS2 index a90e23bb..a67afcc0 100644 --- a/Makefile_MSYS2 +++ b/Makefile_MSYS2 @@ -579,6 +579,7 @@ SOCFLAGS = -fPIC SOLDFLAGS = -shared -Wl,-rpath,$(CBF_PREFIX)/lib JAVAINCLUDES = -I$(JDKDIR)/include -I$(JDKDIR)/include/linux LDPREFIX = PATH=$(SOLIB);$$PATH;export PATH; +RUNLDPREFIX = PATH=$(CBF_PREFIX)/lib:$$PATH;export PATH; EXTRALIBS = -L/mingw64/bin -lm M4FLAGS = -Dfcb_bytes_in_rec=131072 PYTHON = python2 @@ -1029,6 +1030,11 @@ Makefile: $(M4)/Makefile.m4 m4 -P $(PYCIFRWDEF) -Dcbf_system=default $(M4)/Makefile.m4 > Makefile.tmp mv Makefile.tmp Makefile +cbflib.ini: $(M4)/Makefile.m4 + echo "$(LDPREFIX)" > cbflib.ini + echo "HDF5_PLUGIN_PATH=$(SOLIB):$$HDF5_PLUGIN_PATH" >> cbflib.ini + echo "export HDF5_PLUGIN_PATH" >> cbflib.ini + symlinksdone: chmod a+x .symlinks chmod a+x .undosymlinks @@ -1074,6 +1080,10 @@ baseinstall: all $(CBF_PREFIX) $(CBF_PREFIX)/lib $(CBF_PREFIX)/bin \ -cp $(CBF_PREFIX)/lib/libfcb.so $(CBF_PREFIX)/lib/libfcb_old.so cp $(SOLIB)/libfcb.so $(CBF_PREFIX)/lib/libfcb.so $(LN) $(CBF_PREFIX)/lib/libfcb.so $(CBF_PREFIX)/lib/lib_fcb.so + -cp $(CBF_PREFIX)/bin/cbflib.ini $(CBF_PREFIX)/bin/cbflib.ini_old + echo "$(RUNLDPREFIX)" > $(CBF_PREFIX)/bin/cbflib.ini + echo "HDF5_PLUGIN_PATH=$(CBF_PREFIX)/lib:$$HDF5_PLUGIN_PATH" >> $(CBF_PREFIX)/bin/cbflib.ini + echo "export HDF5_PLUGIN_PATH" >> $(CBF_PREFIX)/bin/cbflib.ini -cp $(CBF_PREFIX)/bin/adscimg2cbf $(CBF_PREFIX)/bin/adscimg2cbf_old cp $(BIN)/adscimg2cbf $(CBF_PREFIX)/bin/adscimg2cbf -cp $(CBF_PREFIX)/bin/cbf2adscimg $(CBF_PREFIX)/bin/cbf2adscimg_old @@ -1237,7 +1247,7 @@ $(TIFF): build_tiff config.guess config.sub $(TIFF)_INSTALL: $(TIFF) -rm -rf $(TIFF)_install rsync -avz $(TIFF)/ $(TIFF)_install - (cd $(TIFF_install); make distclean; ./configure --prefix=$(CBF_PREFIX); make install) + (cd $(TIFF)_install; make distclean; ./configure --prefix=$(CBF_PREFIX); make install) ifneq ($(CBFLIB_DONT_USE_LOCAL_HDF5),yes) @@ -2072,7 +2082,7 @@ restore_output: $(NEWTESTOUTPUT) $(DATADIRO) $(MINICBF_TEST)/minicbf.h5 cp test_fcb_read_testflatpackedout.out $(DATADIRO)/test_fcb_read_testflatpackedout_orig.out cp XRD1621.cbf $(DATADIRO)/XRD1621_orig.cbf cp XRD1621_I4encbC100.cbf $(DATADIRO)/XRD1621_I4encbC100_orig.cbf - cp minicbf_orig.h5 $(DATADIRO)/minicbf_orig.h5 + cp $(MINICBF_TEST)/minicbf.h5 $(DATADIRO)/minicbf_orig.h5 restore_sigs_only: $(NEWTESTOUTPUT) $(DATADIRS) $(SIGNATURE) < adscconverted_flat.cbf > $(DATADIRS)/adscconverted_flat_orig.cbf$(SEXT) @@ -2090,7 +2100,7 @@ restore_sigs_only: $(NEWTESTOUTPUT) $(DATADIRS) $(SIGNATURE) < test_fcb_read_testflatpackedout.out > $(DATADIRS)/test_fcb_read_testflatpackedout_orig.out$(SEXT) $(SIGNATURE) < XRD1621.cbf > $(DATADIRS)/XRD1621_orig.cbf$(SEXT) $(SIGNATURE) < XRD1621_I4encbC100.cbf > $(DATADIRS)/XRD1621_I4encbC100_orig.cbf$(SEXT) - $(SIGNATURE) < minicbf_orig.h5 > $(DATADIRS)/minicbf_orig.h5$(SEXT) + $(SIGNATURE) < $(MINICBF_TEST)/minicbf.h5 > $(DATADIRS)/minicbf_orig.h5$(SEXT) restore_signatures: restore_output restore_sigs_only # @@ -2257,7 +2267,7 @@ endif -cd $(MINICBF_TEST); $(DIFF) minicbf_original.dump minicbf.dump $(LDPREFIX) cd $(MINICBF_TEST); rm -f minicbf_original.dump $(LDPREFIX) cd $(MINICBF_TEST); rm -f minicbf.dump - cd $(MINICBF_TEST); rm -f minicbf.h5 + #cd $(MINICBF_TEST); rm -f minicbf.h5 $(LDPREFIX) cd $(MINICBF_TEST); $(TIME) $(BIN)/cbf2nexus -c zlib \ --list -o i19-1.h5 ../1191_00005.cbf $(LDPREFIX) cd $(MINICBF_TEST); $(TIME) $(BIN)/nexus2cbf \ diff --git a/Makefile_OSX b/Makefile_OSX index d0717372..1cde14b7 100644 --- a/Makefile_OSX +++ b/Makefile_OSX @@ -576,6 +576,11 @@ LDFLAGS = F90C = gfortran F90FLAGS = -g -fno-range-check F90LDFLAGS = -bind_at_load +SOCFLAGS = -fPIC +SOLDFLAGS = -dynamiclib -Wl,-rpath,$(CBF_PREFIX)/lib +JAVAINCLUDES = -I$(JDKDIR)/include -I$(JDKDIR)/include/linux +LDPREFIX = DYLD_LIBRARY_PATH=$(SOLIB):$$DYLD_LIBRARY_PATH;export DYLD_LIBRARY_PATH; +RUNLDPREFIX = DYLD_LIBRARY_PATH=$(CBF_PREFIX)/lib:$$DYLD_LIBRARY_PATH;export DYLD_LIBRARY_PATH; EXTRALIBS = -lm M4FLAGS = -Dfcb_bytes_in_rec=131072 TIME = time @@ -1025,6 +1030,11 @@ Makefile: $(M4)/Makefile.m4 m4 -P $(PYCIFRWDEF) -Dcbf_system=default $(M4)/Makefile.m4 > Makefile.tmp mv Makefile.tmp Makefile +cbflib.ini: $(M4)/Makefile.m4 + echo "$(LDPREFIX)" > cbflib.ini + echo "HDF5_PLUGIN_PATH=$(SOLIB):$$HDF5_PLUGIN_PATH" >> cbflib.ini + echo "export HDF5_PLUGIN_PATH" >> cbflib.ini + symlinksdone: chmod a+x .symlinks chmod a+x .undosymlinks @@ -1070,6 +1080,10 @@ baseinstall: all $(CBF_PREFIX) $(CBF_PREFIX)/lib $(CBF_PREFIX)/bin \ -cp $(CBF_PREFIX)/lib/libfcb.so $(CBF_PREFIX)/lib/libfcb_old.so cp $(SOLIB)/libfcb.so $(CBF_PREFIX)/lib/libfcb.so $(LN) $(CBF_PREFIX)/lib/libfcb.so $(CBF_PREFIX)/lib/lib_fcb.so + -cp $(CBF_PREFIX)/bin/cbflib.ini $(CBF_PREFIX)/bin/cbflib.ini_old + echo "$(RUNLDPREFIX)" > $(CBF_PREFIX)/bin/cbflib.ini + echo "HDF5_PLUGIN_PATH=$(CBF_PREFIX)/lib:$$HDF5_PLUGIN_PATH" >> $(CBF_PREFIX)/bin/cbflib.ini + echo "export HDF5_PLUGIN_PATH" >> $(CBF_PREFIX)/bin/cbflib.ini -cp $(CBF_PREFIX)/bin/adscimg2cbf $(CBF_PREFIX)/bin/adscimg2cbf_old cp $(BIN)/adscimg2cbf $(CBF_PREFIX)/bin/adscimg2cbf -cp $(CBF_PREFIX)/bin/cbf2adscimg $(CBF_PREFIX)/bin/cbf2adscimg_old @@ -1233,7 +1247,7 @@ $(TIFF): build_tiff config.guess config.sub $(TIFF)_INSTALL: $(TIFF) -rm -rf $(TIFF)_install rsync -avz $(TIFF)/ $(TIFF)_install - (cd $(TIFF_install); make distclean; ./configure --prefix=$(CBF_PREFIX); make install) + (cd $(TIFF)_install; make distclean; ./configure --prefix=$(CBF_PREFIX); make install) ifneq ($(CBFLIB_DONT_USE_LOCAL_HDF5),yes) @@ -2068,7 +2082,7 @@ restore_output: $(NEWTESTOUTPUT) $(DATADIRO) $(MINICBF_TEST)/minicbf.h5 cp test_fcb_read_testflatpackedout.out $(DATADIRO)/test_fcb_read_testflatpackedout_orig.out cp XRD1621.cbf $(DATADIRO)/XRD1621_orig.cbf cp XRD1621_I4encbC100.cbf $(DATADIRO)/XRD1621_I4encbC100_orig.cbf - cp minicbf_orig.h5 $(DATADIRO)/minicbf_orig.h5 + cp $(MINICBF_TEST)/minicbf.h5 $(DATADIRO)/minicbf_orig.h5 restore_sigs_only: $(NEWTESTOUTPUT) $(DATADIRS) $(SIGNATURE) < adscconverted_flat.cbf > $(DATADIRS)/adscconverted_flat_orig.cbf$(SEXT) @@ -2086,7 +2100,7 @@ restore_sigs_only: $(NEWTESTOUTPUT) $(DATADIRS) $(SIGNATURE) < test_fcb_read_testflatpackedout.out > $(DATADIRS)/test_fcb_read_testflatpackedout_orig.out$(SEXT) $(SIGNATURE) < XRD1621.cbf > $(DATADIRS)/XRD1621_orig.cbf$(SEXT) $(SIGNATURE) < XRD1621_I4encbC100.cbf > $(DATADIRS)/XRD1621_I4encbC100_orig.cbf$(SEXT) - $(SIGNATURE) < minicbf_orig.h5 > $(DATADIRS)/minicbf_orig.h5$(SEXT) + $(SIGNATURE) < $(MINICBF_TEST)/minicbf.h5 > $(DATADIRS)/minicbf_orig.h5$(SEXT) restore_signatures: restore_output restore_sigs_only # @@ -2253,7 +2267,7 @@ endif -cd $(MINICBF_TEST); $(DIFF) minicbf_original.dump minicbf.dump $(LDPREFIX) cd $(MINICBF_TEST); rm -f minicbf_original.dump $(LDPREFIX) cd $(MINICBF_TEST); rm -f minicbf.dump - cd $(MINICBF_TEST); rm -f minicbf.h5 + #cd $(MINICBF_TEST); rm -f minicbf.h5 $(LDPREFIX) cd $(MINICBF_TEST); $(TIME) $(BIN)/cbf2nexus -c zlib \ --list -o i19-1.h5 ../1191_00005.cbf $(LDPREFIX) cd $(MINICBF_TEST); $(TIME) $(BIN)/nexus2cbf \ diff --git a/Makefile_OSX_gcc42 b/Makefile_OSX_gcc42 index c41831d6..a04853fe 100644 --- a/Makefile_OSX_gcc42 +++ b/Makefile_OSX_gcc42 @@ -581,6 +581,7 @@ SOCFLAGS = -fPIC SOLDFLAGS = -dynamiclib -Wl,-rpath,$(CBF_PREFIX)/lib JAVAINCLUDES = -I$(JDKDIR)/include -I$(JDKDIR)/include/linux LDPREFIX = DYLD_LIBRARY_PATH=$(SOLIB):$$DYLD_LIBRARY_PATH;export DYLD_LIBRARY_PATH; +RUNLDPREFIX = DYLD_LIBRARY_PATH=$(CBF_PREFIX)/lib:$$DYLD_LIBRARY_PATH;export DYLD_LIBRARY_PATH; EXTRALIBS = -lm M4FLAGS = -Dfcb_bytes_in_rec=131072 TIME = time @@ -1030,6 +1031,11 @@ Makefile: $(M4)/Makefile.m4 m4 -P $(PYCIFRWDEF) -Dcbf_system=default $(M4)/Makefile.m4 > Makefile.tmp mv Makefile.tmp Makefile +cbflib.ini: $(M4)/Makefile.m4 + echo "$(LDPREFIX)" > cbflib.ini + echo "HDF5_PLUGIN_PATH=$(SOLIB):$$HDF5_PLUGIN_PATH" >> cbflib.ini + echo "export HDF5_PLUGIN_PATH" >> cbflib.ini + symlinksdone: chmod a+x .symlinks chmod a+x .undosymlinks @@ -1075,6 +1081,10 @@ baseinstall: all $(CBF_PREFIX) $(CBF_PREFIX)/lib $(CBF_PREFIX)/bin \ -cp $(CBF_PREFIX)/lib/libfcb.so $(CBF_PREFIX)/lib/libfcb_old.so cp $(SOLIB)/libfcb.so $(CBF_PREFIX)/lib/libfcb.so $(LN) $(CBF_PREFIX)/lib/libfcb.so $(CBF_PREFIX)/lib/lib_fcb.so + -cp $(CBF_PREFIX)/bin/cbflib.ini $(CBF_PREFIX)/bin/cbflib.ini_old + echo "$(RUNLDPREFIX)" > $(CBF_PREFIX)/bin/cbflib.ini + echo "HDF5_PLUGIN_PATH=$(CBF_PREFIX)/lib:$$HDF5_PLUGIN_PATH" >> $(CBF_PREFIX)/bin/cbflib.ini + echo "export HDF5_PLUGIN_PATH" >> $(CBF_PREFIX)/bin/cbflib.ini -cp $(CBF_PREFIX)/bin/adscimg2cbf $(CBF_PREFIX)/bin/adscimg2cbf_old cp $(BIN)/adscimg2cbf $(CBF_PREFIX)/bin/adscimg2cbf -cp $(CBF_PREFIX)/bin/cbf2adscimg $(CBF_PREFIX)/bin/cbf2adscimg_old @@ -1238,7 +1248,7 @@ $(TIFF): build_tiff config.guess config.sub $(TIFF)_INSTALL: $(TIFF) -rm -rf $(TIFF)_install rsync -avz $(TIFF)/ $(TIFF)_install - (cd $(TIFF_install); make distclean; ./configure --prefix=$(CBF_PREFIX); make install) + (cd $(TIFF)_install; make distclean; ./configure --prefix=$(CBF_PREFIX); make install) ifneq ($(CBFLIB_DONT_USE_LOCAL_HDF5),yes) @@ -2073,7 +2083,7 @@ restore_output: $(NEWTESTOUTPUT) $(DATADIRO) $(MINICBF_TEST)/minicbf.h5 cp test_fcb_read_testflatpackedout.out $(DATADIRO)/test_fcb_read_testflatpackedout_orig.out cp XRD1621.cbf $(DATADIRO)/XRD1621_orig.cbf cp XRD1621_I4encbC100.cbf $(DATADIRO)/XRD1621_I4encbC100_orig.cbf - cp minicbf_orig.h5 $(DATADIRO)/minicbf_orig.h5 + cp $(MINICBF_TEST)/minicbf.h5 $(DATADIRO)/minicbf_orig.h5 restore_sigs_only: $(NEWTESTOUTPUT) $(DATADIRS) $(SIGNATURE) < adscconverted_flat.cbf > $(DATADIRS)/adscconverted_flat_orig.cbf$(SEXT) @@ -2091,7 +2101,7 @@ restore_sigs_only: $(NEWTESTOUTPUT) $(DATADIRS) $(SIGNATURE) < test_fcb_read_testflatpackedout.out > $(DATADIRS)/test_fcb_read_testflatpackedout_orig.out$(SEXT) $(SIGNATURE) < XRD1621.cbf > $(DATADIRS)/XRD1621_orig.cbf$(SEXT) $(SIGNATURE) < XRD1621_I4encbC100.cbf > $(DATADIRS)/XRD1621_I4encbC100_orig.cbf$(SEXT) - $(SIGNATURE) < minicbf_orig.h5 > $(DATADIRS)/minicbf_orig.h5$(SEXT) + $(SIGNATURE) < $(MINICBF_TEST)/minicbf.h5 > $(DATADIRS)/minicbf_orig.h5$(SEXT) restore_signatures: restore_output restore_sigs_only # @@ -2258,7 +2268,7 @@ endif -cd $(MINICBF_TEST); $(DIFF) minicbf_original.dump minicbf.dump $(LDPREFIX) cd $(MINICBF_TEST); rm -f minicbf_original.dump $(LDPREFIX) cd $(MINICBF_TEST); rm -f minicbf.dump - cd $(MINICBF_TEST); rm -f minicbf.h5 + #cd $(MINICBF_TEST); rm -f minicbf.h5 $(LDPREFIX) cd $(MINICBF_TEST); $(TIME) $(BIN)/cbf2nexus -c zlib \ --list -o i19-1.h5 ../1191_00005.cbf $(LDPREFIX) cd $(MINICBF_TEST); $(TIME) $(BIN)/nexus2cbf \ diff --git a/Makefile_OSX_gcc42_DMALLOC b/Makefile_OSX_gcc42_DMALLOC index 5ab75ed6..a79db484 100644 --- a/Makefile_OSX_gcc42_DMALLOC +++ b/Makefile_OSX_gcc42_DMALLOC @@ -581,6 +581,7 @@ SOCFLAGS = -fPIC SOLDFLAGS = -shared -Wl,-rpath,$(CBF_PREFIX)/lib JAVAINCLUDES = -I$(JDKDIR)/include -I$(JDKDIR)/include/linux LDPREFIX = DYLD_LIBRARY_PATH=$(SOLIB):$$DYLD_LIBRARY_PATH;export DYLD_LIBRARY_PATH; +RUNLDPREFIX = DYLD_LIBRARY_PATH=$(CBF_PREFIX)/lib:$$DYLD_LIBRARY_PATH;export DYLD_LIBRARY_PATH; EXTRALIBS = -lm -L$(HOME)/lib -ldmalloc M4FLAGS = -Dfcb_bytes_in_rec=131072 TIME = time @@ -1032,6 +1033,11 @@ Makefile: $(M4)/Makefile.m4 m4 -P $(PYCIFRWDEF) -Dcbf_system=default $(M4)/Makefile.m4 > Makefile.tmp mv Makefile.tmp Makefile +cbflib.ini: $(M4)/Makefile.m4 + echo "$(LDPREFIX)" > cbflib.ini + echo "HDF5_PLUGIN_PATH=$(SOLIB):$$HDF5_PLUGIN_PATH" >> cbflib.ini + echo "export HDF5_PLUGIN_PATH" >> cbflib.ini + symlinksdone: chmod a+x .symlinks chmod a+x .undosymlinks @@ -1077,6 +1083,10 @@ baseinstall: all $(CBF_PREFIX) $(CBF_PREFIX)/lib $(CBF_PREFIX)/bin \ -cp $(CBF_PREFIX)/lib/libfcb.so $(CBF_PREFIX)/lib/libfcb_old.so cp $(SOLIB)/libfcb.so $(CBF_PREFIX)/lib/libfcb.so $(LN) $(CBF_PREFIX)/lib/libfcb.so $(CBF_PREFIX)/lib/lib_fcb.so + -cp $(CBF_PREFIX)/bin/cbflib.ini $(CBF_PREFIX)/bin/cbflib.ini_old + echo "$(RUNLDPREFIX)" > $(CBF_PREFIX)/bin/cbflib.ini + echo "HDF5_PLUGIN_PATH=$(CBF_PREFIX)/lib:$$HDF5_PLUGIN_PATH" >> $(CBF_PREFIX)/bin/cbflib.ini + echo "export HDF5_PLUGIN_PATH" >> $(CBF_PREFIX)/bin/cbflib.ini -cp $(CBF_PREFIX)/bin/adscimg2cbf $(CBF_PREFIX)/bin/adscimg2cbf_old cp $(BIN)/adscimg2cbf $(CBF_PREFIX)/bin/adscimg2cbf -cp $(CBF_PREFIX)/bin/cbf2adscimg $(CBF_PREFIX)/bin/cbf2adscimg_old @@ -1240,7 +1250,7 @@ $(TIFF): build_tiff config.guess config.sub $(TIFF)_INSTALL: $(TIFF) -rm -rf $(TIFF)_install rsync -avz $(TIFF)/ $(TIFF)_install - (cd $(TIFF_install); make distclean; ./configure --prefix=$(CBF_PREFIX); make install) + (cd $(TIFF)_install; make distclean; ./configure --prefix=$(CBF_PREFIX); make install) ifneq ($(CBFLIB_DONT_USE_LOCAL_HDF5),yes) @@ -2075,7 +2085,7 @@ restore_output: $(NEWTESTOUTPUT) $(DATADIRO) $(MINICBF_TEST)/minicbf.h5 cp test_fcb_read_testflatpackedout.out $(DATADIRO)/test_fcb_read_testflatpackedout_orig.out cp XRD1621.cbf $(DATADIRO)/XRD1621_orig.cbf cp XRD1621_I4encbC100.cbf $(DATADIRO)/XRD1621_I4encbC100_orig.cbf - cp minicbf_orig.h5 $(DATADIRO)/minicbf_orig.h5 + cp $(MINICBF_TEST)/minicbf.h5 $(DATADIRO)/minicbf_orig.h5 restore_sigs_only: $(NEWTESTOUTPUT) $(DATADIRS) $(SIGNATURE) < adscconverted_flat.cbf > $(DATADIRS)/adscconverted_flat_orig.cbf$(SEXT) @@ -2093,7 +2103,7 @@ restore_sigs_only: $(NEWTESTOUTPUT) $(DATADIRS) $(SIGNATURE) < test_fcb_read_testflatpackedout.out > $(DATADIRS)/test_fcb_read_testflatpackedout_orig.out$(SEXT) $(SIGNATURE) < XRD1621.cbf > $(DATADIRS)/XRD1621_orig.cbf$(SEXT) $(SIGNATURE) < XRD1621_I4encbC100.cbf > $(DATADIRS)/XRD1621_I4encbC100_orig.cbf$(SEXT) - $(SIGNATURE) < minicbf_orig.h5 > $(DATADIRS)/minicbf_orig.h5$(SEXT) + $(SIGNATURE) < $(MINICBF_TEST)/minicbf.h5 > $(DATADIRS)/minicbf_orig.h5$(SEXT) restore_signatures: restore_output restore_sigs_only # @@ -2260,7 +2270,7 @@ endif -cd $(MINICBF_TEST); $(DIFF) minicbf_original.dump minicbf.dump $(LDPREFIX) cd $(MINICBF_TEST); rm -f minicbf_original.dump $(LDPREFIX) cd $(MINICBF_TEST); rm -f minicbf.dump - cd $(MINICBF_TEST); rm -f minicbf.h5 + #cd $(MINICBF_TEST); rm -f minicbf.h5 $(LDPREFIX) cd $(MINICBF_TEST); $(TIME) $(BIN)/cbf2nexus -c zlib \ --list -o i19-1.h5 ../1191_00005.cbf $(LDPREFIX) cd $(MINICBF_TEST); $(TIME) $(BIN)/nexus2cbf \ diff --git a/README b/README index 4eda923c..20968c00 100644 --- a/README +++ b/README @@ -1,8 +1,21 @@ + +------------------------------------------------------------------------+ + | [IUCr | [CIF | | | Get CBFlib at | + | Home | Home | [CBF/imgCIF] | [CBFlib] | SourceForge.net. Fast, | + | Page] | Page] | | | secure and Free Open | + | | | | | Source software downloads | + +------------------------------------------------------------------------+ + + ---------------------------------------------------------------------- + + | IUCr Home Page | CIF Home Page | CBF/imgCIF | CBFlib | + | NOTICE | doc/GPL | doc/LGPL | imgCIF dictionary | SourceForge CBFlib site | + | Click Here to Make a Donation | + CBFlib README - Information for CBFlib 0.9.5 release of 27 April 2014 + Information for CBFlib 0.9.6 release of 4 December 2018 by Paul J. Ellis @@ -13,7 +26,7 @@ Bernstein + Sons yaya at bernstein-plus-sons dot com - (c) Copyright 2006 -- 2014 Herbert J. Bernstein + © Copyright 2006 -- 2018 Herbert J. Bernstein ---------------------------------------------------------------------- @@ -22,9 +35,9 @@ ALTERNATIVELY YOU MAY REDISTRIBUTE THE CBFLIB API UNDER THE TERMS OF THE LGPL. - All functions in the src, include and examples directories are included - in the term "API" unless explicitly placed under a diferent license in - the header comments of that particular source code. + All functions in the src, include and examples directories are included in + the term "API" unless explicitly placed under a diferent license in the + header comments of that particular source code. ---------------------------------------------------------------------- @@ -39,13 +52,25 @@ for important disclaimers and the IUCr Policy on the Use of the Crystallographic under grants DBI-0610407, DBI-0315281 and EF-0312612, the U. S. National Institutes of Health (NIH) under grants 1R15GM078077 from NIGMS and 1R13RR023192 from NCRR and funding from the International Union for - Crystallography (IUCr). The content is solely the responsibility of the - authors and does not necessarily represent the official views of DOE, NSF, - NIH, NIGMS, NCRR or IUCr. Recent work on integration among CBF, HDF5 and - NeXus supported in part by Pandata ODI (EU 7th Framework Programme) + Crystallography (IUCr) and Dectris, Ltd. The content is solely the + responsibility of the authors and does not necessarily represent the + official views of DOE, NSF, NIH, NIGMS, NCRR, IUCr or Dectris. Recent work + on integration among CBF, HDF5 and NeXus supported in part by Pandata ODI + (EU 7th Framework Programme) ---------------------------------------------------------------------- + CBFlib 0.9.6 is the full release supporting the integration of CBF and + NeXus, including support for the NeXus NXpdb embedding of CIF files in + NeXus files. *** IMPORTANT: Because of the requirements of dynamic loading + to support the compressions used by the Dectris NeXus/HDF5 format, all + applications require setting of library and plugin paths. See the + initialization file cbflib.ini, which should be sourced before running any + applications ***. The primary development source is at + https://github.com/yayahjb/cbflib. The branch pdb_in_nexus, which was used + for much of this development has been merged, is now deprecated, and will + be removed in the near future. + CBFlib 0.9.5 is the full release resulting from the interim effort on 0.9.4, reflecting significant and unfortunately somewhat disruptive changes resulting from changes to the agreed CBF-NeXus mapping. Axis data @@ -178,30 +203,32 @@ for important disclaimers and the IUCr Policy on the Use of the Crystallographic space, for a full installation with complete tests. Read the instructions below carefully, if space is a problem. - A gizpped tarball of this release is available on sourceforge at + You may download clone the git repository with + git clone https://github.com/yayahjb/cbflib.git + or a gizpped tarball of this release is available on sourceforge at - http://downloads.sf.net/cbflib/CBFlib-0.9.5.tar.gz + http://downloads.sf.net/cbflib/CBFlib-0.9.6.tar.gz In addition, - http://downloads.sf.net/cbflib/CBFlib_0.9.5_Data_Files_Input.tar.gz (13 + http://downloads.sf.net/cbflib/CBFlib_0.9.6_Data_Files_Input.tar.gz (13 MB) is a "gzipped" tar of the input data files needed to test the API, - http://downloads.sf.net/cbflib/CBFlib_0.9.5_Data_Files_Output.tar.gz (34 + http://downloads.sf.net/cbflib/CBFlib_0.9.6_Data_Files_Output.tar.gz (34 MB) is a "gzipped" tar of the output data files needed to test the API, and, if space is at a premium, - http://downloads.sf.net/cbflib/CBFlib_0.9.5_Data_Files_Output_Sigs_Only.tar.gz + http://downloads.sf.net/cbflib/CBFlib_0.9.6_Data_Files_Output_Sigs_Only.tar.gz (1KB) is a "gzipped" tar of only the MD5 signatures of the output data - files needed to test the API. Place the CBFlib_0.9.5.tar.gz file in the + files needed to test the API. Place the CBFlib_0.9.6.tar.gz file in the directory that is intended to contain up to 4 new directories, named - CBFlib_0.9.5 (the "top-level" directory), CBFlib_0.9.5_Data_Files_Input - and either CBFlib_0.9.5_Data_Files_Output or - CBFlib_0.9.5_Data_Files_Output_Sigs_Only. If you have wget on your + CBFlib_0.9.6 (the "top-level" directory), CBFlib_0.9.6_Data_Files_Input + and either CBFlib_0.9.6_Data_Files_Output or + CBFlib_0.9.6_Data_Files_Output_Sigs_Only. If you have wget on your machine, you only need to download the source tarball. If you do not have wget, you will need to download all the tarballs into the same directory - Uncompress CBFlib_0.9.5.tar.gz with gunzip and unpack it with tar: + Uncompress CBFlib_0.9.6.tar.gz with gunzip and unpack it with tar: - gunzip CBFlib_0.9.5.tar.gz - tar xvf CBFLIB_0.9.5.tar + gunzip CBFlib_0.9.6.tar.gz + tar xvf CBFLIB_0.9.6.tar To run the test programs, you will also need Paul Ellis's sample MAR345 image, example.mar2300, Chris Nielsen's sample ADSC Quantum 315 image, @@ -210,7 +237,7 @@ for important disclaimers and the IUCr Policy on the Use of the Crystallographic file, 9ins.cif, and 3 special test files testflatin.cbf, testflatpackedin.cbf and testrealin.cbf, and several files related to NeXus and FEL testing. All these files will be dowloaded and extracted by - the Makefile from CBFlib_0.9.5_Data_Files_Input. Do not download copies + the Makefile from CBFlib_0.9.6_Data_Files_Input. Do not download copies into the top level directory. After unpacking the archives, the top-level directory should contain a @@ -278,18 +305,15 @@ for important disclaimers and the IUCr Policy on the Use of the Crystallographic * To use the newer and more popular POSIX pcre regex. If neither CBF_NO_REGEX nor CBF_REGEXLIB_REGEX is defined, pcreposix.h is used. - The default in the supplied Makefiles is to use regex.h. The default in - the CMakeLists.txt is to use pcreposix.h. - Cmake A partial preliminary CMakeLists.txt has been included in this kit. It is not yet complete, but on machines for which the Makefiles are not appropriate, it is worth a try. To use in, create a directory named - CBFlib-0.9.5-build on the same level as CBFlib-0.9.5, and in the new, + CBFlib-0.9.6-build on the same level as CBFlib-0.9.6, and in the new, empty build directory, try - cmake ../CBFlib-0.9.5 + cmake ../CBFlib-0.9.6 make all make test @@ -302,10 +326,10 @@ for important disclaimers and the IUCr Policy on the Use of the Crystallographic shared library or other shared libraries when tests are run prior to those libraries having been installed in locations known to your system's loader. This is handled automatically in the Makefiles, but we do not yet - have a reliable way to do so for cmake ctest tests. Until this is - resolved, you may need to set various system-dependent environment - variables such as DYLD_LIBRARY_PATH, LD_LIBRARY_PATH or PATH. We hope to - resolve this for an upcoming release. + have a reliable way to do so for cmake ctest tests. You may need to set + various system-dependent environment variables such as DYLD_LIBRARY_PATH, + LD_LIBRARY_PATH or PATH. The bash script in the kit cbflib.ini should be + sourced before testing. Please refer to the manual doc/CBFlib.html for more detailed information. @@ -313,4 +337,4 @@ for important disclaimers and the IUCr Policy on the Use of the Crystallographic ---------------------------------------------------------------------- - Updated 27 April 2014. yayahjb at gmail dot com + Updated 4 December 2018. yayahjb at gmail dot com diff --git a/README.html b/README.html index 2e65be00..3ace9f0b 100755 --- a/README.html +++ b/README.html @@ -42,7 +42,7 @@

README

-Information for CBFlib 0.9.5 release of 27 April 2014
+Information for CBFlib 0.9.6 release of 4 December 2018
@@ -65,7 +65,7 @@

yaya at bernstein-plus-sons dot com

-© Copyright 2006 -- 2014 Herbert J. Bernstein +© Copyright 2006 -- 2018 Herbert J. Bernstein

YOU MAY REDISTRIBUTE THE CBFLIB PACKAGE UNDER THE TERMS OF THE GPL. @@ -92,14 +92,24 @@

U. S. National Science Foundation (NSF) under grants DBI-0610407, DBI-0315281 and EF-0312612, the U. S. National Institutes of Health (NIH) under grants 1R15GM078077 from NIGMS and 1R13RR023192 from NCRR and funding from the International -Union for Crystallography (IUCr). The content is solely the responsibility of +Union for Crystallography (IUCr) and Dectris, Ltd. The content is solely the responsibility of the authors and does not necessarily represent the official views of -DOE, NSF, NIH, NIGMS, NCRR or IUCr. +DOE, NSF, NIH, NIGMS, NCRR, IUCr or Dectris. Recent work on integration among CBF, HDF5 and NeXus supported in part by Pandata ODI (EU 7th Framework Programme)

+CBFlib 0.9.6 is the full release supporting the integration of CBF and +NeXus, including support for the NeXus NXpdb embedding of CIF files +in NeXus files. *** IMPORTANT: Because of the requirements of dynamic +loading to support the compressions used by the Dectris NeXus/HDF5 format, all applications +require setting of library and plugin paths. See the initialization +file cbflib.ini, which should be sourced before running any applications ***. +The primary development source is at https://github.com/yayahjb/cbflib. +The branch pdb_in_nexus, which was used for much of this development has been +merged, is now deprecated, and will be removed in the near future. +

CBFlib 0.9.5 is the full release resulting from the interim effort on 0.9.4, reflecting significant and unfortunately somewhat disruptive changes resulting from changes to the agreed CBF-NeXus mapping. @@ -248,37 +258,39 @@

Installation

space, for a full installation with complete tests. Read the instructions below carefully, if space is a problem.

-A gizpped tarball of this release is available on sourceforge at +You may download clone the git repository with
+git clone https://github.com/yayahjb/cbflib.git
+or a gizpped tarball of this release is available on sourceforge at

http://downloads.sf.net/cbflib/CBFlib-0.9.5.tar.gz +href="http://downloads.sf.net/cbflib/CBFlib-0.9.6.tar.gz">http://downloads.sf.net/cbflib/CBFlib-0.9.6.tar.gz

In addition, http://downloads.sf.net/cbflib/CBFlib_0.9.5_Data_Files_Input.tar.gz +href="http://downloads.sf.net/cbflib/CBFlib_0.9.6_Data_Files_Input.tar.gz">http://downloads.sf.net/cbflib/CBFlib_0.9.6_Data_Files_Input.tar.gz (13 MB) is a "gzipped" tar of the input data files needed to test the API, http://downloads.sf.net/cbflib/CBFlib_0.9.5_Data_Files_Output.tar.gz +href="http://downloads.sf.net/cbflib/CBFlib_0.9.6_Data_Files_Output.tar.gz">http://downloads.sf.net/cbflib/CBFlib_0.9.6_Data_Files_Output.tar.gz (34 MB) is a "gzipped" tar of the output data files needed to test the API, and, if space is at a premium, http://downloads.sf.net/cbflib/CBFlib_0.9.5_Data_Files_Output_Sigs_Only.tar.gz +href="http://downloads.sf.net/cbflib/CBFlib_0.9.6_Data_Files_Output_Sigs_Only.tar.gz">http://downloads.sf.net/cbflib/CBFlib_0.9.6_Data_Files_Output_Sigs_Only.tar.gz (1KB) is a "gzipped" tar of only the MD5 signatures of the output data files needed to test the API. -Place the CBFlib_0.9.5.tar.gz file in the directory +Place the CBFlib_0.9.6.tar.gz file in the directory that is intended to contain up to 4 new directories, named -CBFlib_0.9.5 (the "top-level" directory), -CBFlib_0.9.5_Data_Files_Input and either CBFlib_0.9.5_Data_Files_Output or -CBFlib_0.9.5_Data_Files_Output_Sigs_Only. +CBFlib_0.9.6 (the "top-level" directory), +CBFlib_0.9.6_Data_Files_Input and either CBFlib_0.9.6_Data_Files_Output or +CBFlib_0.9.6_Data_Files_Output_Sigs_Only. If you have wget on your machine, you only need to download the source tarball. If you do not have wget, you will need to download all the tarballs into the same directory

-Uncompress CBFlib_0.9.5.tar.gz with gunzip and unpack it with tar: +Uncompress CBFlib_0.9.6.tar.gz with gunzip and unpack it with tar: 

-     gunzip CBFlib_0.9.5.tar.gz
-     tar xvf CBFLIB_0.9.5.tar
+     gunzip CBFlib_0.9.6.tar.gz
+     tar xvf CBFLIB_0.9.6.tar

To run the test programs, you will also need @@ -291,7 +303,7 @@

Installation

testflatin.cbf, testflatpackedin.cbf and testrealin.cbf, and several files related to NeXus and FEL testing. All these files will be -dowloaded and extracted by the Makefile from CBFlib_0.9.5_Data_Files_Input. Do +dowloaded and extracted by the Makefile from CBFlib_0.9.6_Data_Files_Input. Do not download copies into the top level directory.

After unpacking the archives, the top-level directory should contain @@ -372,21 +384,18 @@

regex

is used.

-The default in the supplied Makefiles is to use regex.h. The default in the -CMakeLists.txt is to use pcreposix.h. -

Cmake

A partial preliminary CMakeLists.txt has been included in this kit. It is not yet complete, but on machines for which the Makefiles are not appropriate, it is worth a try. To use in, -create a directory named CBFlib-0.9.5-build on the same level as CBFlib-0.9.5, and in +create a directory named CBFlib-0.9.6-build on the same level as CBFlib-0.9.6, and in the new, empty build directory, try 

-    cmake ../CBFlib-0.9.5
+    cmake ../CBFlib-0.9.6
     make all
     make test
@@ -399,17 +408,18 @@

Cmake

cause is a failure to link example programs to the HDF5 shared library or other shared libraries when tests are run prior to those libraries having been installed in locations known to your system's loader. This is handled automatically in the Makefiles, -but we do not yet have a reliable way to do so for cmake ctest tests. Until this is -resolved, you may need to set various system-dependent environment variables such as -DYLD_LIBRARY_PATH, LD_LIBRARY_PATH or PATH. We hope to resolve this for an upcoming -release. +but we do not yet have a reliable way to do so for cmake ctest tests. +You may need to set various system-dependent environment variables such as +DYLD_LIBRARY_PATH, LD_LIBRARY_PATH or PATH. The bash script in the kit cbflib.ini should be sourced +before testing. +

Please refer to the manual doc/CBFlib.html for more detailed information.

-Updated 27 April 2014. +Updated 4 December 2018.