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This commit is contained in:
Bill March
2007-10-16 15:56:57 +00:00
parent 24b7019171
commit 84a6162f2d
14 changed files with 840 additions and 0 deletions
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fastlib/u/march/.gdb_history
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run --data=test.txt
backtrace
quit
fastlib/u/march/data/.gdb_history
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break protein_conversion.h:54
run
step
step
step
step
print alpha
restart
help
help running
continue
print num_atoms
print 1/num_atoms
quit
fastlib/u/march/data/Makefile
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/Users/Antoninus/Desktop/fastlib/u/march/data/protein_conversion: /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/u/march/data/protein_conversion /Users/Antoninus/Desktop/fastlib/u/march/data/Makefile
@echo '... Making /Users/Antoninus/Desktop/fastlib/u/march/data/protein_conversion'
@rm -f /Users/Antoninus/Desktop/fastlib/u/march/data/protein_conversion
@ln -s -f /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/u/march/data/protein_conversion /Users/Antoninus/Desktop/fastlib/u/march/data/protein_conversion
@echo '*** Created 1 symlinks in /Users/Antoninus/Desktop/fastlib/u/march/data/.'
/Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/u/march/data/protein_conversion: /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libmath_math.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libdata_data.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libbase_base.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libu_march_data_protein_conversion__auto.a /Users/Antoninus/Desktop/fastlib/bin_keep/i386_Darwin_COMMON_gcc_COMMON/libblaspack.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libla_la.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libfile_file.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libcol_col.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libfx_fx.a
@echo '... Making bin/i386_Darwin_fast_gcc_/u/march/data/protein_conversion'
@mkdir -p /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/u/march/data
@g++ -o /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/u/march/data/protein_conversion -O2 -finline-functions -finline-limit=2000 -fomit-frame-pointer -g -DNDEBUG /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libu_march_data_protein_conversion__auto.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libmath_math.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libdata_data.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libfile_file.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libfx_fx.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libla_la.a /Users/Antoninus/Desktop/fastlib/bin_keep/i386_Darwin_COMMON_gcc_COMMON/libblaspack.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libcol_col.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libbase_base.a -lm -lpthread -lg2c
pseudo_4: /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libmath_math.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libdata_data.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libbase_base.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libu_march_data_protein_conversion__auto.a /Users/Antoninus/Desktop/fastlib/bin_keep/i386_Darwin_COMMON_gcc_COMMON/libblaspack.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libla_la.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libfile_file.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libcol_col.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libfx_fx.a
@echo '*** Done with /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libmath_math.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libdata_data.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libbase_base.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libu_march_data_protein_conversion__auto.a /Users/Antoninus/Desktop/fastlib/bin_keep/i386_Darwin_COMMON_gcc_COMMON/libblaspack.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libla_la.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libfile_file.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libcol_col.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libfx_fx.a'
/Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libu_march_data_protein_conversion__auto.a: /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj/u_march_data_protein_conversion.o
@echo '... Making bin/i386_Darwin_fast_gcc_/libu_march_data_protein_conversion__auto.a'
@mkdir -p /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_
@ar r /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libu_march_data_protein_conversion__auto.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj/u_march_data_protein_conversion.o
/Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj/u_march_data_protein_conversion.o: /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON/libfastlib_fastlib.h /Users/Antoninus/Desktop/fastlib/u/march/data/protein_conversion.h /Users/Antoninus/Desktop/fastlib/u/march/data/protein_conversion.cc
@echo '... Making bin/i386_Darwin_fast_gcc_/obj/u_march_data_protein_conversion.o'
@mkdir -p /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj
@cd /Users/Antoninus/Desktop/fastlib/u/march/data && g++ -Wall -Woverloaded-virtual -fno-exceptions -Wparentheses -fno-exceptions -I/Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON -I/Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_ -I/Users/Antoninus/Desktop/fastlib -O2 -finline-functions -finline-limit=2000 -fomit-frame-pointer -g -DNDEBUG -c protein_conversion.cc -o /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj/u_march_data_protein_conversion.o
/Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON/libfastlib_fastlib.h: /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON/libla_la.h /Users/Antoninus/Desktop/fastlib/fastlib/fastlib.h /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON/libdata_data.h /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON/libbase_base.h /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON/libmath_math.h /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON/libcol_col.h /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON/libfile_file.h /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON/libfx_fx.h
@echo '... Making bin/i386_Darwin_COMMON_gcc_COMMON/libfastlib_fastlib.h'
@mkdir -p /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON
@touch /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON/libfastlib_fastlib.h
/Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON/libmath_math.h: /Users/Antoninus/Desktop/fastlib/math/math.h /Users/Antoninus/Desktop/fastlib/math/kernel.h /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON/libbase_base.h /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON/libcol_col.h /Users/Antoninus/Desktop/fastlib/math/discrete.h /Users/Antoninus/Desktop/fastlib/math/geometry.h
@echo '... Making bin/i386_Darwin_COMMON_gcc_COMMON/libmath_math.h'
@mkdir -p /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON
@touch /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON/libmath_math.h
/Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON/libdata_data.h: /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON/libbase_base.h /Users/Antoninus/Desktop/fastlib/data/dataset.h /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON/libfile_file.h /Users/Antoninus/Desktop/fastlib/data/crossvalidation.h /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON/libla_la.h
@echo '... Making bin/i386_Darwin_COMMON_gcc_COMMON/libdata_data.h'
@mkdir -p /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON
@touch /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON/libdata_data.h
/Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON/libfx_fx.h: /Users/Antoninus/Desktop/fastlib/fx/timer.h /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON/libbase_base.h /Users/Antoninus/Desktop/fastlib/fx/fx.h /Users/Antoninus/Desktop/fastlib/fx/datastore.h
@echo '... Making bin/i386_Darwin_COMMON_gcc_COMMON/libfx_fx.h'
@mkdir -p /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON
@touch /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON/libfx_fx.h
pseudo_14: /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libmath_math.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libdata_data.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libbase_base.a /Users/Antoninus/Desktop/fastlib/bin_keep/i386_Darwin_COMMON_gcc_COMMON/libblaspack.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libla_la.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libfile_file.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libcol_col.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libfx_fx.a
@echo '*** Done with /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libmath_math.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libdata_data.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libbase_base.a /Users/Antoninus/Desktop/fastlib/bin_keep/i386_Darwin_COMMON_gcc_COMMON/libblaspack.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libla_la.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libfile_file.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libcol_col.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libfx_fx.a'
pseudo_16: /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libbase_base.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libmath_math.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libcol_col.a
@echo '*** Done with /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libbase_base.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libmath_math.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libcol_col.a'
/Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libmath_math.a: /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj/math_geometry.o /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj/math_discrete.o
@echo '... Making bin/i386_Darwin_fast_gcc_/libmath_math.a'
@mkdir -p /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_
@ar r /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libmath_math.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj/math_discrete.o /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj/math_geometry.o
/Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj/math_geometry.o: /Users/Antoninus/Desktop/fastlib/math/math.h /Users/Antoninus/Desktop/fastlib/math/kernel.h /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON/libbase_base.h /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON/libcol_col.h /Users/Antoninus/Desktop/fastlib/math/discrete.h /Users/Antoninus/Desktop/fastlib/math/geometry.h /Users/Antoninus/Desktop/fastlib/math/geometry.cc
@echo '... Making bin/i386_Darwin_fast_gcc_/obj/math_geometry.o'
@mkdir -p /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj
@cd /Users/Antoninus/Desktop/fastlib/math && g++ -Wall -Woverloaded-virtual -fno-exceptions -Wparentheses -fno-exceptions -I/Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON -I/Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_ -I/Users/Antoninus/Desktop/fastlib -O2 -finline-functions -finline-limit=2000 -fomit-frame-pointer -g -DNDEBUG -c geometry.cc -o /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj/math_geometry.o
/Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj/math_discrete.o: /Users/Antoninus/Desktop/fastlib/math/math.h /Users/Antoninus/Desktop/fastlib/math/kernel.h /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON/libbase_base.h /Users/Antoninus/Desktop/fastlib/math/discrete.cc /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON/libcol_col.h /Users/Antoninus/Desktop/fastlib/math/discrete.h /Users/Antoninus/Desktop/fastlib/math/geometry.h
@echo '... Making bin/i386_Darwin_fast_gcc_/obj/math_discrete.o'
@mkdir -p /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj
@cd /Users/Antoninus/Desktop/fastlib/math && g++ -Wall -Woverloaded-virtual -fno-exceptions -Wparentheses -fno-exceptions -I/Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON -I/Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_ -I/Users/Antoninus/Desktop/fastlib -O2 -finline-functions -finline-limit=2000 -fomit-frame-pointer -g -DNDEBUG -c discrete.cc -o /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj/math_discrete.o
pseudo_26: /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libdata_data.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libbase_base.a /Users/Antoninus/Desktop/fastlib/bin_keep/i386_Darwin_COMMON_gcc_COMMON/libblaspack.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libla_la.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libfile_file.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libcol_col.a
@echo '*** Done with /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libdata_data.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libbase_base.a /Users/Antoninus/Desktop/fastlib/bin_keep/i386_Darwin_COMMON_gcc_COMMON/libblaspack.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libla_la.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libfile_file.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libcol_col.a'
/Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libdata_data.a: /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj/data_dataset.o
@echo '... Making bin/i386_Darwin_fast_gcc_/libdata_data.a'
@mkdir -p /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_
@ar r /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libdata_data.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj/data_dataset.o
/Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj/data_dataset.o: /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON/libla_la.h /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON/libbase_base.h /Users/Antoninus/Desktop/fastlib/data/crossvalidation.h /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON/libfile_file.h /Users/Antoninus/Desktop/fastlib/data/dataset.cc /Users/Antoninus/Desktop/fastlib/data/dataset.h
@echo '... Making bin/i386_Darwin_fast_gcc_/obj/data_dataset.o'
@mkdir -p /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj
@cd /Users/Antoninus/Desktop/fastlib/data && g++ -Wall -Woverloaded-virtual -fno-exceptions -Wparentheses -fno-exceptions -I/Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON -I/Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_ -I/Users/Antoninus/Desktop/fastlib -O2 -finline-functions -finline-limit=2000 -fomit-frame-pointer -g -DNDEBUG -c dataset.cc -o /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj/data_dataset.o
/Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON/libla_la.h: /Users/Antoninus/Desktop/fastlib/la/blas.h /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON/libbase_base.h /Users/Antoninus/Desktop/fastlib/la/la.h /Users/Antoninus/Desktop/fastlib/la/matrix.h /Users/Antoninus/Desktop/fastlib/la/clapack.h /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON/libcol_col.h /Users/Antoninus/Desktop/fastlib/la/uselapack.h
@echo '... Making bin/i386_Darwin_COMMON_gcc_COMMON/libla_la.h'
@mkdir -p /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON
@touch /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON/libla_la.h
/Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON/libfile_file.h: /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON/libbase_base.h /Users/Antoninus/Desktop/fastlib/file/textfile.h /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON/libcol_col.h
@echo '... Making bin/i386_Darwin_COMMON_gcc_COMMON/libfile_file.h'
@mkdir -p /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON
@touch /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON/libfile_file.h
pseudo_34: /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libbase_base.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libfile_file.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libcol_col.a
@echo '*** Done with /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libbase_base.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libfile_file.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libcol_col.a'
/Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libfile_file.a: /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj/file_textfile.o
@echo '... Making bin/i386_Darwin_fast_gcc_/libfile_file.a'
@mkdir -p /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_
@ar r /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libfile_file.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj/file_textfile.o
/Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj/file_textfile.o: /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON/libbase_base.h /Users/Antoninus/Desktop/fastlib/file/textfile.h /Users/Antoninus/Desktop/fastlib/file/textfile.cc /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON/libcol_col.h
@echo '... Making bin/i386_Darwin_fast_gcc_/obj/file_textfile.o'
@mkdir -p /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj
@cd /Users/Antoninus/Desktop/fastlib/file && g++ -Wall -Woverloaded-virtual -fno-exceptions -Wparentheses -fno-exceptions -I/Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON -I/Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_ -I/Users/Antoninus/Desktop/fastlib -O2 -finline-functions -finline-limit=2000 -fomit-frame-pointer -g -DNDEBUG -c textfile.cc -o /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj/file_textfile.o
pseudo_39: /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libbase_base.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libfx_fx.a
@echo '*** Done with /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libbase_base.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libfx_fx.a'
/Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libfx_fx.a: /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj/fx_fx.o /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj/fx_timer.o /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj/fx_datastore.o
@echo '... Making bin/i386_Darwin_fast_gcc_/libfx_fx.a'
@mkdir -p /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_
@ar r /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libfx_fx.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj/fx_datastore.o /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj/fx_timer.o /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj/fx_fx.o
/Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj/fx_fx.o: /Users/Antoninus/Desktop/fastlib/fx/timer.h /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON/libbase_base.h /Users/Antoninus/Desktop/fastlib/fx/fx.h /Users/Antoninus/Desktop/fastlib/fx/datastore.h /Users/Antoninus/Desktop/fastlib/fx/fx.c
@echo '... Making bin/i386_Darwin_fast_gcc_/obj/fx_fx.o'
@mkdir -p /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj
@cd /Users/Antoninus/Desktop/fastlib/fx && gcc -I/Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON -I/Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_ -I/Users/Antoninus/Desktop/fastlib -O2 -finline-functions -finline-limit=2000 -fomit-frame-pointer -g -DNDEBUG -c fx.c -o /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj/fx_fx.o -Wall
/Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj/fx_timer.o: /Users/Antoninus/Desktop/fastlib/fx/timer.h /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON/libbase_base.h /Users/Antoninus/Desktop/fastlib/fx/fx.h /Users/Antoninus/Desktop/fastlib/fx/timer.c /Users/Antoninus/Desktop/fastlib/fx/datastore.h
@echo '... Making bin/i386_Darwin_fast_gcc_/obj/fx_timer.o'
@mkdir -p /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj
@cd /Users/Antoninus/Desktop/fastlib/fx && gcc -I/Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON -I/Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_ -I/Users/Antoninus/Desktop/fastlib -O2 -finline-functions -finline-limit=2000 -fomit-frame-pointer -g -DNDEBUG -c timer.c -o /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj/fx_timer.o -Wall
/Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj/fx_datastore.o: /Users/Antoninus/Desktop/fastlib/fx/timer.h /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON/libbase_base.h /Users/Antoninus/Desktop/fastlib/fx/fx.h /Users/Antoninus/Desktop/fastlib/fx/datastore.h /Users/Antoninus/Desktop/fastlib/fx/datastore.c
@echo '... Making bin/i386_Darwin_fast_gcc_/obj/fx_datastore.o'
@mkdir -p /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj
@cd /Users/Antoninus/Desktop/fastlib/fx && gcc -I/Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON -I/Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_ -I/Users/Antoninus/Desktop/fastlib -O2 -finline-functions -finline-limit=2000 -fomit-frame-pointer -g -DNDEBUG -c datastore.c -o /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj/fx_datastore.o -Wall
pseudo_50: /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libbase_base.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libla_la.a /Users/Antoninus/Desktop/fastlib/bin_keep/i386_Darwin_COMMON_gcc_COMMON/libblaspack.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libcol_col.a
@echo '*** Done with /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libbase_base.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libla_la.a /Users/Antoninus/Desktop/fastlib/bin_keep/i386_Darwin_COMMON_gcc_COMMON/libblaspack.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libcol_col.a'
/Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libla_la.a: /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj/la_uselapack.o
@echo '... Making bin/i386_Darwin_fast_gcc_/libla_la.a'
@mkdir -p /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_
@ar r /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libla_la.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj/la_uselapack.o
/Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj/la_uselapack.o: /Users/Antoninus/Desktop/fastlib/la/blas.h /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON/libbase_base.h /Users/Antoninus/Desktop/fastlib/la/la.h /Users/Antoninus/Desktop/fastlib/la/matrix.h /Users/Antoninus/Desktop/fastlib/la/clapack.h /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON/libcol_col.h /Users/Antoninus/Desktop/fastlib/la/uselapack.cc /Users/Antoninus/Desktop/fastlib/la/uselapack.h
@echo '... Making bin/i386_Darwin_fast_gcc_/obj/la_uselapack.o'
@mkdir -p /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj
@cd /Users/Antoninus/Desktop/fastlib/la && g++ -Wall -Woverloaded-virtual -fno-exceptions -Wparentheses -fno-exceptions -I/Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON -I/Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_ -I/Users/Antoninus/Desktop/fastlib -O2 -finline-functions -finline-limit=2000 -fomit-frame-pointer -g -DNDEBUG -c uselapack.cc -o /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj/la_uselapack.o
/Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON/libcol_col.h: /Users/Antoninus/Desktop/fastlib/col/arraylist.h /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON/libbase_base.h /Users/Antoninus/Desktop/fastlib/col/string.h /Users/Antoninus/Desktop/fastlib/col/queue.h /Users/Antoninus/Desktop/fastlib/col/fastalloc.h /Users/Antoninus/Desktop/fastlib/col/intmap.h /Users/Antoninus/Desktop/fastlib/col/rangeset.h /Users/Antoninus/Desktop/fastlib/col/heap.h
@echo '... Making bin/i386_Darwin_COMMON_gcc_COMMON/libcol_col.h'
@mkdir -p /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON
@touch /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON/libcol_col.h
/Users/Antoninus/Desktop/fastlib/bin_keep/i386_Darwin_COMMON_gcc_COMMON/libblaspack.a: /Users/Antoninus/Desktop/fastlib/la/blaspack.tgz
@echo '... Making /Users/Antoninus/Desktop/fastlib/bin_keep/i386_Darwin_COMMON_gcc_COMMON/libblaspack.a'
@mkdir -p /Users/Antoninus/Desktop/fastlib/bin_keep/i386_Darwin_COMMON_gcc_COMMON
@echo '... Extracting FORTRAN files...'
@mkdir -p /Users/Antoninus/Desktop/fastlib/bin_keep/i386_Darwin_COMMON_gcc_COMMON/libblaspack_workspace
@cd /Users/Antoninus/Desktop/fastlib/bin_keep/i386_Darwin_COMMON_gcc_COMMON/libblaspack_workspace && tar -xzf /Users/Antoninus/Desktop/fastlib/la/blaspack.tgz
@echo '*** Compiling LAPACK with BLAS reference implementation.'
@echo '!!! LAPACK WARNING: For better performance, install ATLAS or Intel MKL.'
@echo '... Our compilation differs slightly from regular LAPACK/BLAS:'
@echo '... NOTE 2: We omit complex-number routines (halves compile time).'
@echo '... NOTE 3: We require case sensitivity for LAPACK/BLAS string parameters.'
@echo '... This may take several minutes (about 800 FORTRAN files).'
@cd /Users/Antoninus/Desktop/fastlib/bin_keep/i386_Darwin_COMMON_gcc_COMMON/libblaspack_workspace && g77 -O2 -c src/*.f
@echo '... Almost done with LAPACK/BLAS...'
@cd /Users/Antoninus/Desktop/fastlib/bin_keep/i386_Darwin_COMMON_gcc_COMMON/libblaspack_workspace && g77 -O0 -c src/dlamch.f src/slamch.f
@cd /Users/Antoninus/Desktop/fastlib/bin_keep/i386_Darwin_COMMON_gcc_COMMON/libblaspack_workspace && ar r /Users/Antoninus/Desktop/fastlib/bin_keep/i386_Darwin_COMMON_gcc_COMMON/libblaspack.a *.o
@echo '... Created archive, cleaning up.'
@rm -rf /Users/Antoninus/Desktop/fastlib/bin_keep/i386_Darwin_COMMON_gcc_COMMON/libblaspack_workspace
@echo '*** Done with LAPACK and BLAS!'
/Users/Antoninus/Desktop/fastlib/la/blaspack.tgz:
@echo '... Making /Users/Antoninus/Desktop/fastlib/la/blaspack.tgz'
@echo 'Downloading the file using curl...'
@cd /Users/Antoninus/Desktop/fastlib/la && curl -L -o blaspack.tgz "http://www.cc.gatech.edu/~garryb/fastlib/blaspack.tgz"
pseudo_62: /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libbase_base.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libcol_col.a
@echo '*** Done with /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libbase_base.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libcol_col.a'
/Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libcol_col.a: /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj/col_col.o
@echo '... Making bin/i386_Darwin_fast_gcc_/libcol_col.a'
@mkdir -p /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_
@ar r /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libcol_col.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj/col_col.o
/Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj/col_col.o: /Users/Antoninus/Desktop/fastlib/col/arraylist.h /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON/libbase_base.h /Users/Antoninus/Desktop/fastlib/col/string.h /Users/Antoninus/Desktop/fastlib/col/col.cc /Users/Antoninus/Desktop/fastlib/col/queue.h /Users/Antoninus/Desktop/fastlib/col/fastalloc.h /Users/Antoninus/Desktop/fastlib/col/intmap.h /Users/Antoninus/Desktop/fastlib/col/rangeset.h /Users/Antoninus/Desktop/fastlib/col/heap.h
@echo '... Making bin/i386_Darwin_fast_gcc_/obj/col_col.o'
@mkdir -p /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj
@cd /Users/Antoninus/Desktop/fastlib/col && g++ -Wall -Woverloaded-virtual -fno-exceptions -Wparentheses -fno-exceptions -I/Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON -I/Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_ -I/Users/Antoninus/Desktop/fastlib -O2 -finline-functions -finline-limit=2000 -fomit-frame-pointer -g -DNDEBUG -c col.cc -o /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj/col_col.o
/Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON/libbase_base.h: /Users/Antoninus/Desktop/fastlib/base/compiler.h /Users/Antoninus/Desktop/fastlib/base/ccmem.h /Users/Antoninus/Desktop/fastlib/base/common.h /Users/Antoninus/Desktop/fastlib/base/cc.h /Users/Antoninus/Desktop/fastlib/base/fortran.h /Users/Antoninus/Desktop/fastlib/base/debug.h /Users/Antoninus/Desktop/fastlib/base/scale.h /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON/base/basic_types.h /Users/Antoninus/Desktop/fastlib/base/test.h /Users/Antoninus/Desktop/fastlib/base/otrav_impl.h /Users/Antoninus/Desktop/fastlib/base/compiler_impl.h /Users/Antoninus/Desktop/fastlib/base/otrav.h
@echo '... Making bin/i386_Darwin_COMMON_gcc_COMMON/libbase_base.h'
@mkdir -p /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON
@touch /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON/libbase_base.h
pseudo_74: /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libbase_base.a
@echo '*** Done with /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libbase_base.a'
/Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libbase_base.a: /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj/base_ccmem.o /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj/base_otrav.o /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj/base_common.o /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj/base_cc.o
@echo '... Making bin/i386_Darwin_fast_gcc_/libbase_base.a'
@mkdir -p /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_
@ar r /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/libbase_base.a /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj/base_common.o /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj/base_cc.o /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj/base_ccmem.o /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj/base_otrav.o
/Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj/base_otrav.o: /Users/Antoninus/Desktop/fastlib/base/otrav.cc /Users/Antoninus/Desktop/fastlib/base/compiler.h /Users/Antoninus/Desktop/fastlib/base/ccmem.h /Users/Antoninus/Desktop/fastlib/base/common.h /Users/Antoninus/Desktop/fastlib/base/cc.h /Users/Antoninus/Desktop/fastlib/base/fortran.h /Users/Antoninus/Desktop/fastlib/base/debug.h /Users/Antoninus/Desktop/fastlib/base/scale.h /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON/base/basic_types.h /Users/Antoninus/Desktop/fastlib/base/test.h /Users/Antoninus/Desktop/fastlib/base/otrav_impl.h /Users/Antoninus/Desktop/fastlib/base/compiler_impl.h /Users/Antoninus/Desktop/fastlib/base/otrav.h
@echo '... Making bin/i386_Darwin_fast_gcc_/obj/base_otrav.o'
@mkdir -p /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj
@cd /Users/Antoninus/Desktop/fastlib/base && g++ -Wall -Woverloaded-virtual -fno-exceptions -Wparentheses -fno-exceptions -I/Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON -I/Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_ -I/Users/Antoninus/Desktop/fastlib -O2 -finline-functions -finline-limit=2000 -fomit-frame-pointer -g -DNDEBUG -c otrav.cc -o /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj/base_otrav.o
/Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj/base_ccmem.o: /Users/Antoninus/Desktop/fastlib/base/ccmem.cc /Users/Antoninus/Desktop/fastlib/base/compiler.h /Users/Antoninus/Desktop/fastlib/base/ccmem.h /Users/Antoninus/Desktop/fastlib/base/common.h /Users/Antoninus/Desktop/fastlib/base/cc.h /Users/Antoninus/Desktop/fastlib/base/fortran.h /Users/Antoninus/Desktop/fastlib/base/debug.h /Users/Antoninus/Desktop/fastlib/base/scale.h /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON/base/basic_types.h /Users/Antoninus/Desktop/fastlib/base/test.h /Users/Antoninus/Desktop/fastlib/base/otrav_impl.h /Users/Antoninus/Desktop/fastlib/base/compiler_impl.h /Users/Antoninus/Desktop/fastlib/base/otrav.h
@echo '... Making bin/i386_Darwin_fast_gcc_/obj/base_ccmem.o'
@mkdir -p /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj
@cd /Users/Antoninus/Desktop/fastlib/base && g++ -Wall -Woverloaded-virtual -fno-exceptions -Wparentheses -fno-exceptions -I/Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON -I/Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_ -I/Users/Antoninus/Desktop/fastlib -O2 -finline-functions -finline-limit=2000 -fomit-frame-pointer -g -DNDEBUG -c ccmem.cc -o /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj/base_ccmem.o
/Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj/base_cc.o: /Users/Antoninus/Desktop/fastlib/base/cc.cc /Users/Antoninus/Desktop/fastlib/base/compiler.h /Users/Antoninus/Desktop/fastlib/base/ccmem.h /Users/Antoninus/Desktop/fastlib/base/common.h /Users/Antoninus/Desktop/fastlib/base/cc.h /Users/Antoninus/Desktop/fastlib/base/fortran.h /Users/Antoninus/Desktop/fastlib/base/debug.h /Users/Antoninus/Desktop/fastlib/base/scale.h /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON/base/basic_types.h /Users/Antoninus/Desktop/fastlib/base/test.h /Users/Antoninus/Desktop/fastlib/base/otrav_impl.h /Users/Antoninus/Desktop/fastlib/base/compiler_impl.h /Users/Antoninus/Desktop/fastlib/base/otrav.h
@echo '... Making bin/i386_Darwin_fast_gcc_/obj/base_cc.o'
@mkdir -p /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj
@cd /Users/Antoninus/Desktop/fastlib/base && g++ -Wall -Woverloaded-virtual -fno-exceptions -Wparentheses -fno-exceptions -I/Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON -I/Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_ -I/Users/Antoninus/Desktop/fastlib -O2 -finline-functions -finline-limit=2000 -fomit-frame-pointer -g -DNDEBUG -c cc.cc -o /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj/base_cc.o
/Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj/base_common.o: /Users/Antoninus/Desktop/fastlib/base/common.c /Users/Antoninus/Desktop/fastlib/base/compiler.h /Users/Antoninus/Desktop/fastlib/base/ccmem.h /Users/Antoninus/Desktop/fastlib/base/common.h /Users/Antoninus/Desktop/fastlib/base/cc.h /Users/Antoninus/Desktop/fastlib/base/fortran.h /Users/Antoninus/Desktop/fastlib/base/debug.h /Users/Antoninus/Desktop/fastlib/base/scale.h /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON/base/basic_types.h /Users/Antoninus/Desktop/fastlib/base/test.h /Users/Antoninus/Desktop/fastlib/base/otrav_impl.h /Users/Antoninus/Desktop/fastlib/base/compiler_impl.h /Users/Antoninus/Desktop/fastlib/base/otrav.h
@echo '... Making bin/i386_Darwin_fast_gcc_/obj/base_common.o'
@mkdir -p /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj
@cd /Users/Antoninus/Desktop/fastlib/base && gcc -I/Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON -I/Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_ -I/Users/Antoninus/Desktop/fastlib -O2 -finline-functions -finline-limit=2000 -fomit-frame-pointer -g -DNDEBUG -c common.c -o /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_fast_gcc_/obj/base_common.o -Wall
/Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON/base/basic_types.h: /Users/Antoninus/Desktop/fastlib/script/config.py /Users/Antoninus/Desktop/fastlib/base/config/template_types.c
@echo '... Making bin/i386_Darwin_COMMON_gcc_COMMON/base/basic_types.h'
@/Users/Antoninus/Desktop/fastlib/script/config.py --genfiles_dir=/Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON --source_dir=/Users/Antoninus/Desktop/fastlib
@mkdir -p /Users/Antoninus/Desktop/fastlib/bin/i386_Darwin_COMMON_gcc_COMMON/base
clean:
@echo 'Removing the bin/ directory.'
rm -rf /Users/Antoninus/Desktop/fastlib/bin/*
fastlib/u/march/data/build.py
+7
View File
@@ -0,0 +1,7 @@
binrule(
name = "protein_conversion",
sources = ["protein_conversion.cc"],
headers = ["protein_conversion.h"],
linkables = ["fastlib:fastlib"]
)
fastlib/u/march/data/protein_conversion.cc
+40
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@@ -0,0 +1,40 @@
#include "protein_conversion.h"
int main(int argc, char *argv[]) {
fx_init(argc, argv);
const char* data = fx_param_str(NULL, "data", "test.csv");
const char* output_string = fx_param_str(NULL, "output", "default_output.csv");
Dataset dataset;
if (!PASSED(dataset.InitFromFile(data))) {
fprintf(stderr, "You suck\n");
return 1;
}
//printf("features: %d, points: %d\n", dataset.n_features(), dataset.n_points());
index_t nFeats = dataset.n_features();
index_t nPoints = dataset.n_points();
Protein_Converter conv;
conv.Init(nPoints, output_string);
for (index_t i = 0; i < nPoints; i++) {
double *temp = dataset.point(i);
Matrix structure;
structure.Copy(temp, 3, (nFeats/3));
//structure.PrintDebug();
conv.computeFeatures(structure);
}
conv.PrintData();
fx_done();
}
fastlib/u/march/data/protein_conversion.h
+264
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@@ -0,0 +1,264 @@
#ifndef PROTEIN_CONVERSION_H
#define PROTEIN_CONVERSION_H
#include <fastlib/fastlib.h>
/*
Needs to:
Take the structures one at a time
Compute the features for that structure
Write the features as a point in a dataset
Write the dataset to a file
the features:
1-3 moments of center of mass
4-6 moments of atom nearest center
7-9 moments of atom farthest from center
10-12 moments of atom farthest from farthest
*/
class Protein_Converter {
public:
void Init(int num_structures, const char* output_file_name) {
output_file = output_file_name;
data.Init(num_features, num_structures);
current_structure = 0;
}
void computeFeatures(Matrix structure) {
//the matrix has x, y, z as its rows, each atom is a column
index_t num_atoms = structure.n_cols();
Vector center;
center.Init(3);
center.SetAll(0.0);
for (index_t i = 0; i < num_atoms; i++) {
Vector current;
structure.MakeColumnVector(i, &current);
la::AddTo(current, &center);
}
la::Scale((1.0/num_atoms), &center);
/* printf("center:\n");
center.PrintDebug();
*/
double min_dist = DBL_MAX;
index_t min_index = -1;
double max_dist = 0.0;
index_t max_index = -1;
// Compute the atom nearest the center and the one farthest from it
for (index_t i = 0; i < num_atoms; i++) {
Vector current;
structure.MakeColumnVector(i, &current);
double current_dist;
current_dist = la::DistanceSqEuclidean(current, center);
if (current_dist < min_dist) {
min_dist = current_dist;
min_index = i;
}
if (current_dist > max_dist) {
max_dist = current_dist;
max_index = i;
}
}
DEBUG_ASSERT(max_index > -1);
DEBUG_ASSERT(min_index > -1);
Vector center_atom;
Vector far_atom_1;
structure.MakeColumnVector(min_index, &center_atom);
structure.MakeColumnVector(max_index, &far_atom_1);
/*printf("center_atom:\n");
center_atom.PrintDebug();
printf("far_atom_1:\n");
far_atom_1.PrintDebug();
*/
max_dist = 0.0;
max_index = -1;
//compute the atom farthest from the previous outlier
for (index_t i = 0; i < num_atoms; i++) {
Vector current;
structure.MakeColumnVector(i, &current);
double current_dist;
current_dist = la::DistanceSqEuclidean(current, far_atom_1);
if (current_dist > max_dist) {
max_dist = current_dist;
max_index = i;
}
}
DEBUG_ASSERT(max_index > -1);
Vector far_atom_2;
structure.MakeColumnVector(max_index, &far_atom_2);
/*printf("far_atom_2:\n");
far_atom_2.PrintDebug();
*/
/* Now, compute the 4xnum_atoms matrix of distances from all the atoms to these four */
Matrix distances;
distances.Init(4, num_atoms);
for (index_t i = 0; i < num_atoms; i++) {
Vector current;
structure.MakeColumnVector(i, &current);
double center_dist, center_atom_dist, far_atom_dist_1, far_atom_dist_2;
center_dist = sqrt(la::DistanceSqEuclidean(current, center));
center_atom_dist = sqrt(la::DistanceSqEuclidean(current, center_atom));
far_atom_dist_1 = sqrt(la::DistanceSqEuclidean(current, far_atom_1));
far_atom_dist_2 = sqrt(la::DistanceSqEuclidean(current, far_atom_2));
distances.set(0, i, center_dist);
distances.set(1, i, center_atom_dist);
distances.set(2, i, far_atom_dist_1);
distances.set(3, i, far_atom_dist_2);
}
//distances.PrintDebug();
/* Now, compute the new features, the first three sample moments of the distances matrix */
double total1 = 0.0;
double total2 = 0.0;
double total3 = 0.0;
double total4 = 0.0;
for (index_t i = 0; i < num_atoms; i++) {
total1 = total1 + distances.get(0, i);
total2 = total2 + distances.get(1, i);
total3 = total3 + distances.get(2, i);
total4 = total4 + distances.get(3, i);
}
double sample_mean1 = total1/num_atoms;
double sample_mean2 = total2/num_atoms;
double sample_mean3 = total3/num_atoms;
double sample_mean4 = total4/num_atoms;
//printf("sample_mean1 = %f, 2 = %f, 3 = %f, 4 = %f\n", sample_mean1, sample_mean2, sample_mean3, sample_mean4);
total1 = 0.0;
total2 = 0.0;
total3 = 0.0;
total4 = 0.0;
double skew_total1 = 0.0;
double skew_total2 = 0.0;
double skew_total3 = 0.0;
double skew_total4 = 0.0;
for (index_t i = 0; i < num_atoms; i++) {
double temp;
temp = distances.get(0, i) - sample_mean1;
total1 = total1 + temp*temp;
skew_total1 = skew_total1 + temp*temp*temp;
temp = distances.get(1, i) - sample_mean2;
total2 = total2 + temp*temp;
skew_total2 = skew_total2 + temp*temp*temp;
temp = distances.get(2, i) - sample_mean3;
total3 = total3 + temp*temp;
skew_total3 = skew_total3 + temp*temp*temp;
temp = distances.get(3, i) - sample_mean4;
total4 = total4 + temp*temp;
skew_total4 = skew_total4 + temp*temp*temp;
}
DEBUG_ASSERT(num_atoms > 1);
double sample_variance1 = total1/(num_atoms - 1);
double sample_variance2 = total2/(num_atoms - 1);
double sample_variance3 = total3/(num_atoms - 1);
double sample_variance4 = total4/(num_atoms - 1);
double sample_skew1 = sqrt((double)num_atoms) * skew_total1/(pow(sample_variance1, 1.5));
double sample_skew2 = sqrt(num_atoms) * skew_total2/(pow(sample_variance2, 1.5));
double sample_skew3 = sqrt(num_atoms) * skew_total3/(pow(sample_variance3, 1.5));
double sample_skew4 = sqrt(num_atoms) * skew_total4/(pow(sample_variance4, 1.5));
// printf("sample_skew1 = %f\n", sample_skew1);
/* Now, all that is left is to write these into the output matrix, which is num_features x num_structures
* the matrix will have all four means, followed by variances, then skews */
DEBUG_ASSERT(current_structure < data.n_cols());
data.set(0, current_structure, sample_mean1);
data.set(1, current_structure, sample_mean2);
data.set(2, current_structure, sample_mean3);
data.set(3, current_structure, sample_mean4);
data.set(4, current_structure, sample_variance1);
data.set(5, current_structure, sample_variance2);
data.set(6, current_structure, sample_variance3);
data.set(7, current_structure, sample_variance4);
data.set(8, current_structure, sample_skew1);
data.set(9, current_structure, sample_skew2);
data.set(10, current_structure, sample_skew3);
data.set(11, current_structure, sample_skew4);
current_structure++;
/*if (current_structure == data.n_cols()) {
data.PrintDebug();
}*/
}
void PrintData() {
/* make sure to only call this after the data have been filled in */
data::Save(output_file, data);
}
private:
const char* output_file;
Matrix data;
index_t current_structure;
const static int num_features = 12;
};
#endif
fastlib/u/march/emst/build.py
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binrule(
name = "emst",
sources = ["emst.cc"],
headers = ["emst.h", "emsttree.h"],
linkables = ["fastlib:fastlib"]
)
fastlib/u/march/emst/emst.cc
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#include "emst.h"
int main(int argc, char *argv[]) {
fx_init(argc, argv);
const char* data = fx_param_str(NULL, "data", "test.txt");
int leafsize;
leafsize = fx_param_int(NULL, "leafsize", 1);
Dataset dataset;
if (!PASSED(dataset.InitFromFile(data))) {
fprintf(stderr, "Couldn't open file '%s'.\n", data);
return 1;
}
Matrix points;
points.Copy(dataset.matrix());
EmstTree tree;
tree.Init(points, leafsize);
fx_done();
}
fastlib/u/march/emst/emst.h
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#ifndef EMST_H
#define EMST_H
#include<fastlib/fastlib.h>
#include "emsttree.h"
#endif
fastlib/u/march/emst/emsttree.h
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#ifndef EMST_TREE_H
#define EMST_TREE_H
const int metric = 2;
/********************** EmstTreeNode ***********************************/
class EmstTreeNode {
public:
void Init(Matrix& data, int leaf_size);
EmstTreeNode get_left();
EmstTreeNode get_right();
int numPoints();
bool isLeaf();
double minDist(EmstTreeNode& other);
private:
DHrectBound<metric> bounding_box;
EmstTreeNode left;
EmstTreeNode right;
int num_points;
int num_dimensions;
Matrix &data;
};
void EmstTreeNode::Init(Matrix& data, int leaf_size) {
num_points = data.n_cols();
num_dimensions = data.n_rows();
if (num_points < leaf_size) {
left = NULL;
right = NULL;
}
else {
/*
1) split the data
2) build the children
3) expand the bounding box
*/
Matrix& left_data = data;
Matrix& right_data = data;
left.Init(left_data, leaf_size);
right.Init(right_data, leaf_size);
}
bounding_box.Init(num_dimensions);
printf("bounding_box.dim() = %d\n", bounding_box.dim());
}
int EmstTreeNode::numPoints() {
return num_points;
}
bool EmstTreeNode::isLeaf() {
return(this.left==NULL);
}
double EmstTreeNode::minDist(EmstTreeNode& other) {
return 0.0;
}
/******************* EmstTree *********************************************/
class EmstTree {
public:
void Init(Matrix data, int leaf_size);
void findNeighbors();
EmstTreeNode* Root();
int numPoints();
int numDimensions();
private:
int num_points;
int num_dimensions;
EmstTreeNode root;
};
void EmstTree::Init(Matrix data, int leaf_size) {
num_points = data.n_cols();
num_dimensions = data.n_rows();
//DEBUG_ASSERT_MSG(num_points > num_dimensions, "num_points = %d, num_dimensions = %d\n", num_points, num_dimensions);
EmstTreeNode new_root;
new_root.Init(data, leaf_size);
}
void EmstTree::findNeighbors() {
DEBUG_GOT_HERE(0);
}
EmstTreeNode* EmstTree::Root() {
return root;
}
int EmstTree::numPoints() {
return num_points;
}
int EmstTree::numDimensions() {
return num_dimensions;
}
#endif
fastlib/u/march/hf/hf.cc
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#include "u/dongrel/multibody.h"
#include "u/dongrel/multibody_kernel.h"
#include "hf_kernel.h"
int main(int argc, char *argv[]) {
fx_init(argc, argv);
/* for now, assuming global fixed bandwidth */
double bandwidth;
bandwidth = fx_param_double(NULL, "bandwidth", 0.1);
/* not sure what this means yet */
double tau;
tau = fx_param_double(NULL, "tau", 0.1);
/* to add, check for basic HF vs. multitree HF, implement both */
printf("Starting multibody HF\n");
fx_timer_start(NULL, "multibodyHF");
MultitreeMultibody<GaussianThreeBodyKernel, GaussianKernel, GaussianKernelDerivative> mthf;
mthf.Init(bandwidth);
mthf.Compute(tau);
fx_timer_stop(NULL, "multibodyHF");
printf("Multibody HF complete\n");
fx_done();
}
fastlib/u/march/hf/hf.h
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#ifndef HF_H
#define HF_H
class HFMultibody {
public:
void Init() {
/*
Build the tree
*/
}
void Compute() {
/*
Need to properly expand the nodes of the tree
Be able to store the results and errors
Responsible for allocating error?
*/
}
}
#endif
fastlib/u/march/hf/hf_kernel.h
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#ifndef HF_KERNEL_H
#define HF_KERNEL_H
/**
* @file hf_kernel.h
*
* Kernels for the Hartree-Fock molecular orbital calculation
*
*/
/**
* Evaluates the kernel given four centers.
*
* Note: currently assuming a global fixed bandwidth
*/
class HFFourBodyKernel {
private:
HFKernel hf_kernel_;
//I believe this is the 4x4 distances matrix;
Matrix distmat_;
public:
/**
* Initializes to a specific bandwidth
*
* @param bandwidth_in the given bandwidth
*/
void Init(double bandwidth_in) {
hf_kernel_.Init(bandwidth_in);
distmat_.Init(3,3);
}
//Need to figure out what this is, exactly . . .
int order() {
return 4;
}
/**
* Evaluates the potential on a given set of distances
*
* Note: why does this need to be a matrix, it only depends on 3 distances
*
* @param sqdists the 4x4 matrix of distances i, j, k, l
*/
double EvalUnnormOnSq(const Matrix &sqdists) const {
double result = 1;
// compute the two Gaussian kernel distances
// then, compute the weird function on the average distance
return result;
}
}
class HFKernel {
//Does Dong's code create one of these for every bounds computation?
// Seems inefficient to do so, can just reuse the same one with different distances
private:
GaussianKernel gauss_kernel_;
double bandwidth;
public:
void Init(double bandwidth_in) {
bandwidth = bandwidth_in;
gauss_kernel_.Init(bandwidth_in);
}
double EvalUnnormOnSq(double sqdist) const {
//Need to return the full computation here
double total;
return(total);
}
}
#endif
fastlib/u/march/sasa/sasa.cc
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/* Need to make this someday */