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Merge pull request #78 from DougTownsend/thalfixes
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Major Performance Improvements for thal
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@untergasser
untergasser authored Aug 3, 2024
2 parents 7f9f17d + b2efa38 commit af3ca52
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Showing 12 changed files with 4,501 additions and 3,347 deletions.
40 changes: 14 additions & 26 deletions src/Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -56,7 +56,7 @@ AR = ar
CC = gcc
CXX = g++
O_OPTS = -O2
CC_OPTS = -g -Wall
CC_OPTS = -g -Wall -march=native
P_DEFINES =

CFLAGS = $(CC_OPTS) $(O_OPTS)
Expand Down Expand Up @@ -97,21 +97,19 @@ LIBDPAL = libdpal.a
LIBDPAL_DYN = libdpal.a.so.1.0.0
LIBTHAL = libthal.a
LIBTHAL_DYN = libthal.a.so.1.0.0
LIBTHALPARA = libthalpara.a
LIBTHALPARA_DYN = libthalpara.a.so.1.0.0
LIBPRIMER3 = libprimer3.a
LIBPRIMER3_DYN = libprimer3.so.1.0.0

ifeq ($(TESTOPTS),--windows)
$(info windows)
LIBRARIES = $(LIBPRIMER3) $(LIBDPAL) $(LIBTHAL) $(LIBTHALPARA) $(LIBAMPTM) $(LIBOLIGOTM)
DYNLIBS = $(LIBPRIMER3_DYN) $(LIBDPAL_DYN) $(LIBTHAL_DYN) $(LIBTHALPARA_DYN) $(LIBAMPTM_DYN) $(LIBOLIGOTM_DYN)
LIBRARIES = $(LIBPRIMER3) $(LIBDPAL) $(LIBTHAL) $(LIBAMPTM) $(LIBOLIGOTM)
DYNLIBS = $(LIBPRIMER3_DYN) $(LIBDPAL_DYN) $(LIBTHAL_DYN) $(LIBAMPTM_DYN) $(LIBOLIGOTM_DYN)
else
$(info no windows)
LIBMASKER = libmasker.a
LIBMASKER_DYN = libmasker.a.so.1.0.0
LIBRARIES = $(LIBPRIMER3) $(LIBDPAL) $(LIBTHAL) $(LIBTHALPARA) $(LIBOLIGOTM) $(LIBAMPTM) $(LIBMASKER)
DYNLIBS = $(LIBPRIMER3_DYN) $(LIBDPAL_DYN) $(LIBTHAL_DYN) $(LIBTHALPARA_DYN) $(LIBAMPTM_DYN) $(LIBOLIGOTM_DYN) $(LIBMASKER_DYN)
LIBRARIES = $(LIBPRIMER3) $(LIBDPAL) $(LIBTHAL) $(LIBOLIGOTM) $(LIBAMPTM) $(LIBMASKER)
DYNLIBS = $(LIBPRIMER3_DYN) $(LIBDPAL_DYN) $(LIBTHAL_DYN) $(LIBAMPTM_DYN) $(LIBOLIGOTM_DYN) $(LIBMASKER_DYN)
endif

RANLIB = ranlib
Expand Down Expand Up @@ -176,13 +174,6 @@ $(LIBTHAL): thal_primer.o
$(LIBTHAL_DYN): thal_primer.o
$(CC) -shared -W1,-soname,libthal.so.1 -o $(LIBTHAL_DYN_LIB) thal_primer.o

$(LIBTHALPARA): thal_parameters.o
$(AR) rv $@ thal_parameters.o
$(RANLIB) $@

$(LIBTHALPARA_DYN): thal_parameters.o
$(CC) -shared -W1,-soname,libthalpara.so.1 -o $(LIBTHALPARA_DYN_LIB) thal_parameters.o

$(LIBPRIMER3): libprimer3.o p3_seq_lib.o
$(AR) rv $@ libprimer3.o p3_seq_lib.o
$(RANLIB) $@
Expand All @@ -200,14 +191,14 @@ $(LIBMASKER_DYN): masker.o
$(PRIMER_EXE): $(PRIMER_OBJECTS)
$(CXX) $(CXXFLAGS) -lstdc++ $(LDFLAGS) -o $@ $(PRIMER_OBJECTS) $(LIBOPTS) $(LDLIBS)

libprimer3.o: libprimer3.cc libprimer3.h p3_seq_lib.h dpal.h thal.h thal_parameters.h oligotm.h
libprimer3.o: libprimer3.cc libprimer3.h p3_seq_lib.h dpal.h thal.h oligotm.h thal_default_params.h
$(CXX) -c $(CXXFLAGS) $(P_DEFINES) -o $@ libprimer3.cc

$(NTDPAL_EXE): ntdpal_main.o dpal.o
$(CC) $(LDFLAGS) -o $@ ntdpal_main.o dpal.o

$(NTTHAL_EXE): thal_main.o thal.o thal_parameters.o
$(CC) $(LDFLAGS) -o $@ thal_main.o thal.o thal_parameters.o $(LDLIBS)
$(NTTHAL_EXE): thal_main.o thal.o
$(CC) $(LDFLAGS) -o $@ thal_main.o thal.o $(LDLIBS)

$(OLIGOTM_EXE): oligotm_main.c oligotm.h $(LIBOLIGOTM)
$(CC) $(CFLAGS) -o $@ oligotm_main.c $(LIBOLIGOTM) $(LIBOPTS) $(LDLIBS)
Expand All @@ -221,7 +212,7 @@ $(LONG_SEQ_EXE): long_seq_tm_test_main.c oligotm.o
$(MASKER_EXE): masker_main.c $(LIBRARIES)
$(CXX) $(CXXFLAGS) -lstdc++ -o $@ masker_main.c $(LIBRARIES) $(LIBOPTS) $(LDLIBS)

read_boulder.o: read_boulder.c read_boulder.h libprimer3.h dpal.h thal.h thal_parameters.h p3_seq_lib.h
read_boulder.o: read_boulder.c read_boulder.h libprimer3.h dpal.h thal.h p3_seq_lib.h thal_default_params.h
$(CC) -c $(CFLAGS) $(P_DEFINES) -o $@ read_boulder.c

print_boulder.o: print_boulder.c print_boulder.h libprimer3.h p3_seq_lib.h
Expand All @@ -232,28 +223,25 @@ dpal.o: dpal.c dpal.h

# We use '-ffloat-store' on windows to prevent undesirable
# precision which may lead to differences in floating point results.
thal.o: thal.c thal.h thal_parameters.h
thal.o: thal.c thal.h thal_default_params.h
$(CC) -c $(CFLAGS) -ffloat-store -o $@ thal.c

thal_parameters.o: thal_parameters.c thal_parameters.h thal.h
$(CC) -c $(CFLAGS) -ffloat-store $(P_DEFINES) -o $@ thal_parameters.c

p3_seq_lib.o: p3_seq_lib.c p3_seq_lib.h libprimer3.h
$(CC) -c $(CFLAGS) -o $@ p3_seq_lib.c

dpal_primer.o: dpal.c dpal.h
$(CC) -c $(CFLAGS) $(P_DEFINES) -o $@ dpal.c

thal_primer.o: thal.c thal.h thal_parameters.h
thal_primer.o: thal.c thal.h thal_default_params.h
$(CC) -c $(CFLAGS) -ffloat-store $(P_DEFINES) -o $@ thal.c

format_output.o: format_output.c format_output.h libprimer3.h dpal.h thal.h p3_seq_lib.h
format_output.o: format_output.c format_output.h libprimer3.h dpal.h thal.h p3_seq_lib.h thal_default_params.h
$(CC) -c $(CFLAGS) $(P_DEFINES) -o $@ format_output.c

ntdpal_main.o: ntdpal_main.c dpal.h
$(CC) -c $(CC_OPTS) -o $@ ntdpal_main.c

thal_main.o: thal_main.c thal.h thal_parameters.h
thal_main.o: thal_main.c thal.h thal_default_params.h
$(CC) -c $(CFLAGS) -o $@ thal_main.c
# We use CC_OPTS above rather than CFLAGS because
# gcc 2.7.2 crashes while compiling ntdpal_main.c with -O2
Expand All @@ -262,7 +250,7 @@ amplicontm.o: amplicontm.c amplicontm.h

oligotm.o: oligotm.c oligotm.h

primer3_boulder_main.o: primer3_boulder_main.c libprimer3.h dpal.h thal.h thal_parameters.h oligotm.h format_output.h print_boulder.h read_boulder.h
primer3_boulder_main.o: primer3_boulder_main.c libprimer3.h dpal.h thal.h oligotm.h format_output.h print_boulder.h read_boulder.h thal_default_params.h
$(CC) -c $(CFLAGS) $(P_DEFINES) primer3_boulder_main.c

masker.o: masker.c masker.h libprimer3.h
Expand Down
1 change: 0 additions & 1 deletion src/libprimer3.cc
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Original file line number Diff line number Diff line change
Expand Up @@ -707,7 +707,6 @@ pr_set_default_global_args_1(p3_global_settings *a)
a->thermodynamic_oligo_alignment = 0;
a->thermodynamic_template_alignment = 0;
thal_set_null_parameters(&a->thermodynamic_parameters);
set_default_thal_parameters(&a->thermodynamic_parameters);
a->show_secondary_structure_alignment = 0;
a->liberal_base = 0;
a->primer_task = generic;
Expand Down
1 change: 0 additions & 1 deletion src/libprimer3.h
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Original file line number Diff line number Diff line change
Expand Up @@ -117,7 +117,6 @@ typedef struct pr_append_str {
#include "oligotm.h"
#include "masker.h"
#include "thal.h"
#include "thal_parameters.h"
#include "dpal.h"

/*
Expand Down
6 changes: 0 additions & 6 deletions src/primer3_boulder_main.c
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Original file line number Diff line number Diff line change
Expand Up @@ -238,12 +238,6 @@ main(int argc, char *argv[])
print_usage();
exit(-1);
}
/* Load default thal parameters */
thal_results o;
if (get_thermodynamic_values(&global_pa->thermodynamic_parameters, &o)) {
fprintf(stderr, "%s\n", o.msg);
exit(-1);
}

if (!global_pa) {
exit(-2); /* Out of memory. */
Expand Down
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