diff --git a/fastlib/u/march/.gdb_history b/fastlib/u/march/.gdb_history new file mode 100644 index 0000000000..91cd051b84 --- /dev/null +++ b/fastlib/u/march/.gdb_history @@ -0,0 +1,3 @@ +run --data=test.txt +backtrace +quit diff --git a/fastlib/u/march/data/.gdb_history b/fastlib/u/march/data/.gdb_history new file mode 100644 index 0000000000..76078e40d2 --- /dev/null +++ b/fastlib/u/march/data/.gdb_history @@ -0,0 +1,14 @@ +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 diff --git a/fastlib/u/march/data/Makefile b/fastlib/u/march/data/Makefile new file mode 100644 index 0000000000..062920c424 --- /dev/null +++ b/fastlib/u/march/data/Makefile @@ -0,0 +1,177 @@ +/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/* diff --git a/fastlib/u/march/data/build.py b/fastlib/u/march/data/build.py new file mode 100644 index 0000000000..06b91f24aa --- /dev/null +++ b/fastlib/u/march/data/build.py @@ -0,0 +1,7 @@ +binrule( + name = "protein_conversion", + sources = ["protein_conversion.cc"], + headers = ["protein_conversion.h"], + linkables = ["fastlib:fastlib"] + +) \ No newline at end of file diff --git a/fastlib/u/march/data/protein_conversion.cc b/fastlib/u/march/data/protein_conversion.cc new file mode 100644 index 0000000000..b4915079ad --- /dev/null +++ b/fastlib/u/march/data/protein_conversion.cc @@ -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(); + + +} diff --git a/fastlib/u/march/data/protein_conversion.h b/fastlib/u/march/data/protein_conversion.h new file mode 100644 index 0000000000..54804514c2 --- /dev/null +++ b/fastlib/u/march/data/protein_conversion.h @@ -0,0 +1,264 @@ +#ifndef PROTEIN_CONVERSION_H +#define PROTEIN_CONVERSION_H + +#include + +/* + 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, ¤t); + la::AddTo(current, ¢er); + + } + + la::Scale((1.0/num_atoms), ¢er); + + /* 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, ¤t); + + 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, ¢er_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, ¤t); + + 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, ¤t); + + 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 diff --git a/fastlib/u/march/emst/build.py b/fastlib/u/march/emst/build.py new file mode 100644 index 0000000000..9d7d35f84f --- /dev/null +++ b/fastlib/u/march/emst/build.py @@ -0,0 +1,6 @@ +binrule( + name = "emst", + sources = ["emst.cc"], + headers = ["emst.h", "emsttree.h"], + linkables = ["fastlib:fastlib"] +) \ No newline at end of file diff --git a/fastlib/u/march/emst/emst.cc b/fastlib/u/march/emst/emst.cc new file mode 100644 index 0000000000..8fbd4bd726 --- /dev/null +++ b/fastlib/u/march/emst/emst.cc @@ -0,0 +1,28 @@ +#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(); + +} diff --git a/fastlib/u/march/emst/emst.h b/fastlib/u/march/emst/emst.h new file mode 100644 index 0000000000..10c610a86d --- /dev/null +++ b/fastlib/u/march/emst/emst.h @@ -0,0 +1,12 @@ +#ifndef EMST_H +#define EMST_H + +#include +#include "emsttree.h" + + + + + + +#endif diff --git a/fastlib/u/march/emst/emsttree.h b/fastlib/u/march/emst/emsttree.h new file mode 100644 index 0000000000..a94be7bb33 --- /dev/null +++ b/fastlib/u/march/emst/emsttree.h @@ -0,0 +1,125 @@ +#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 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 diff --git a/fastlib/u/march/hf/hf.cc b/fastlib/u/march/hf/hf.cc new file mode 100644 index 0000000000..4de3ad45a2 --- /dev/null +++ b/fastlib/u/march/hf/hf.cc @@ -0,0 +1,31 @@ +#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 mthf; + mthf.Init(bandwidth); + mthf.Compute(tau); + fx_timer_stop(NULL, "multibodyHF"); + printf("Multibody HF complete\n"); + + + fx_done(); + +} \ No newline at end of file diff --git a/fastlib/u/march/hf/hf.h b/fastlib/u/march/hf/hf.h new file mode 100644 index 0000000000..28779cf9b2 --- /dev/null +++ b/fastlib/u/march/hf/hf.h @@ -0,0 +1,29 @@ +#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 \ No newline at end of file diff --git a/fastlib/u/march/hf/hf_kernel.h b/fastlib/u/march/hf/hf_kernel.h new file mode 100644 index 0000000000..2c374cfec6 --- /dev/null +++ b/fastlib/u/march/hf/hf_kernel.h @@ -0,0 +1,103 @@ +#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 \ No newline at end of file diff --git a/fastlib/u/march/sasa/sasa.cc b/fastlib/u/march/sasa/sasa.cc new file mode 100644 index 0000000000..6fc5a0c0e8 --- /dev/null +++ b/fastlib/u/march/sasa/sasa.cc @@ -0,0 +1 @@ +/* Need to make this someday */