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Merge branch 'feature/traceback' into develop
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Jeff Daily committed Sep 6, 2017
2 parents 51dc016 + 025c112 commit a3acbe6
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Showing 433 changed files with 64,865 additions and 6,857 deletions.
244 changes: 243 additions & 1 deletion CMakeLists.txt
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239 changes: 222 additions & 17 deletions Makefile.am
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Original file line number Diff line number Diff line change
Expand Up @@ -96,6 +96,7 @@ nobase_include_HEADERS += parasail/matrices/pam_map.h

AM_CPPFLAGS += -I$(top_srcdir)/contrib
AM_CPPFLAGS += -I$(top_srcdir)/contrib/sais-lite-lcp
AM_CPPFLAGS += -I$(top_srcdir)/src

noinst_LTLIBRARIES += libparasail_novec.la
noinst_LTLIBRARIES += libparasail_novec_table.la
Expand Down Expand Up @@ -135,11 +136,17 @@ SRC_SSE2 =
SRC_SSE41 =
SRC_AVX2 =
SRC_KNC =
SRC_TRACE_NOVEC =
SRC_TRACE_SSE2 =
SRC_TRACE_SSE41 =
SRC_TRACE_AVX2 =
SRC_TRACE_KNC =

#################
# core sources
#################

SRC_CORE += src/cigar.c
SRC_CORE += src/cpuid.c
SRC_CORE += src/function_lookup.c
SRC_CORE += src/io.c
Expand All @@ -152,6 +159,8 @@ SRC_CORE += src/sg_dispatch.c
SRC_CORE += src/sw_dispatch.c
SRC_CORE += src/dispatch_profile.c
SRC_CORE += src/satcheck.c
SRC_CORE += src/striped_unwind.c
SRC_CORE += src/traceback.c
SRC_CORE += parasail/memory.h
SRC_CORE += parasail/stats.h

Expand Down Expand Up @@ -190,6 +199,14 @@ SRC_NOVEC += src/nw_stats_scan.c
SRC_NOVEC += src/sg_stats_scan.c
SRC_NOVEC += src/sw_stats_scan.c

SRC_TRACE_NOVEC += src/nw_trace.c
SRC_TRACE_NOVEC += src/sg_trace.c
SRC_TRACE_NOVEC += src/sw_trace.c

SRC_TRACE_NOVEC += src/nw_trace_scan.c
SRC_TRACE_NOVEC += src/sg_trace_scan.c
SRC_TRACE_NOVEC += src/sw_trace_scan.c

###################
# parallel methods
###################
Expand Down Expand Up @@ -564,17 +581,183 @@ SRC_KNC += src/nw_stats_striped_knc_512_32.c
SRC_KNC += src/sg_stats_striped_knc_512_32.c
SRC_KNC += src/sw_stats_striped_knc_512_32.c

#########################
# parallel trace methods
#########################

# parallel scan methods

SRC_TRACE_SSE2 += src/nw_trace_scan_sse2_128_64.c
SRC_TRACE_SSE2 += src/sg_trace_scan_sse2_128_64.c
SRC_TRACE_SSE2 += src/sw_trace_scan_sse2_128_64.c

SRC_TRACE_SSE2 += src/nw_trace_scan_sse2_128_32.c
SRC_TRACE_SSE2 += src/sg_trace_scan_sse2_128_32.c
SRC_TRACE_SSE2 += src/sw_trace_scan_sse2_128_32.c

SRC_TRACE_SSE2 += src/nw_trace_scan_sse2_128_16.c
SRC_TRACE_SSE2 += src/sg_trace_scan_sse2_128_16.c
SRC_TRACE_SSE2 += src/sw_trace_scan_sse2_128_16.c

SRC_TRACE_SSE2 += src/nw_trace_scan_sse2_128_8.c
SRC_TRACE_SSE2 += src/sg_trace_scan_sse2_128_8.c
SRC_TRACE_SSE2 += src/sw_trace_scan_sse2_128_8.c

SRC_TRACE_SSE41 += src/nw_trace_scan_sse41_128_64.c
SRC_TRACE_SSE41 += src/sg_trace_scan_sse41_128_64.c
SRC_TRACE_SSE41 += src/sw_trace_scan_sse41_128_64.c

SRC_TRACE_SSE41 += src/nw_trace_scan_sse41_128_32.c
SRC_TRACE_SSE41 += src/sg_trace_scan_sse41_128_32.c
SRC_TRACE_SSE41 += src/sw_trace_scan_sse41_128_32.c

SRC_TRACE_SSE41 += src/nw_trace_scan_sse41_128_16.c
SRC_TRACE_SSE41 += src/sg_trace_scan_sse41_128_16.c
SRC_TRACE_SSE41 += src/sw_trace_scan_sse41_128_16.c

SRC_TRACE_SSE41 += src/nw_trace_scan_sse41_128_8.c
SRC_TRACE_SSE41 += src/sg_trace_scan_sse41_128_8.c
SRC_TRACE_SSE41 += src/sw_trace_scan_sse41_128_8.c

SRC_TRACE_AVX2 += src/nw_trace_scan_avx2_256_64.c
SRC_TRACE_AVX2 += src/sg_trace_scan_avx2_256_64.c
SRC_TRACE_AVX2 += src/sw_trace_scan_avx2_256_64.c

SRC_TRACE_AVX2 += src/nw_trace_scan_avx2_256_32.c
SRC_TRACE_AVX2 += src/sg_trace_scan_avx2_256_32.c
SRC_TRACE_AVX2 += src/sw_trace_scan_avx2_256_32.c

SRC_TRACE_AVX2 += src/nw_trace_scan_avx2_256_16.c
SRC_TRACE_AVX2 += src/sg_trace_scan_avx2_256_16.c
SRC_TRACE_AVX2 += src/sw_trace_scan_avx2_256_16.c

SRC_TRACE_AVX2 += src/nw_trace_scan_avx2_256_8.c
SRC_TRACE_AVX2 += src/sg_trace_scan_avx2_256_8.c
SRC_TRACE_AVX2 += src/sw_trace_scan_avx2_256_8.c

SRC_TRACE_KNC += src/nw_trace_scan_knc_512_32.c
SRC_TRACE_KNC += src/sg_trace_scan_knc_512_32.c
SRC_TRACE_KNC += src/sw_trace_scan_knc_512_32.c

# parallel diag methods

SRC_TRACE_SSE2 += src/nw_trace_diag_sse2_128_64.c
SRC_TRACE_SSE2 += src/sg_trace_diag_sse2_128_64.c
SRC_TRACE_SSE2 += src/sw_trace_diag_sse2_128_64.c

SRC_TRACE_SSE2 += src/nw_trace_diag_sse2_128_32.c
SRC_TRACE_SSE2 += src/sg_trace_diag_sse2_128_32.c
SRC_TRACE_SSE2 += src/sw_trace_diag_sse2_128_32.c

SRC_TRACE_SSE2 += src/nw_trace_diag_sse2_128_16.c
SRC_TRACE_SSE2 += src/sg_trace_diag_sse2_128_16.c
SRC_TRACE_SSE2 += src/sw_trace_diag_sse2_128_16.c

SRC_TRACE_SSE2 += src/nw_trace_diag_sse2_128_8.c
SRC_TRACE_SSE2 += src/sg_trace_diag_sse2_128_8.c
SRC_TRACE_SSE2 += src/sw_trace_diag_sse2_128_8.c

SRC_TRACE_SSE41 += src/nw_trace_diag_sse41_128_64.c
SRC_TRACE_SSE41 += src/sg_trace_diag_sse41_128_64.c
SRC_TRACE_SSE41 += src/sw_trace_diag_sse41_128_64.c

SRC_TRACE_SSE41 += src/nw_trace_diag_sse41_128_32.c
SRC_TRACE_SSE41 += src/sg_trace_diag_sse41_128_32.c
SRC_TRACE_SSE41 += src/sw_trace_diag_sse41_128_32.c

SRC_TRACE_SSE41 += src/nw_trace_diag_sse41_128_16.c
SRC_TRACE_SSE41 += src/sg_trace_diag_sse41_128_16.c
SRC_TRACE_SSE41 += src/sw_trace_diag_sse41_128_16.c

SRC_TRACE_SSE41 += src/nw_trace_diag_sse41_128_8.c
SRC_TRACE_SSE41 += src/sg_trace_diag_sse41_128_8.c
SRC_TRACE_SSE41 += src/sw_trace_diag_sse41_128_8.c

SRC_TRACE_AVX2 += src/nw_trace_diag_avx2_256_64.c
SRC_TRACE_AVX2 += src/sg_trace_diag_avx2_256_64.c
SRC_TRACE_AVX2 += src/sw_trace_diag_avx2_256_64.c

SRC_TRACE_AVX2 += src/nw_trace_diag_avx2_256_32.c
SRC_TRACE_AVX2 += src/sg_trace_diag_avx2_256_32.c
SRC_TRACE_AVX2 += src/sw_trace_diag_avx2_256_32.c

SRC_TRACE_AVX2 += src/nw_trace_diag_avx2_256_16.c
SRC_TRACE_AVX2 += src/sg_trace_diag_avx2_256_16.c
SRC_TRACE_AVX2 += src/sw_trace_diag_avx2_256_16.c

SRC_TRACE_AVX2 += src/nw_trace_diag_avx2_256_8.c
SRC_TRACE_AVX2 += src/sg_trace_diag_avx2_256_8.c
SRC_TRACE_AVX2 += src/sw_trace_diag_avx2_256_8.c

SRC_TRACE_KNC += src/nw_trace_diag_knc_512_32.c
SRC_TRACE_KNC += src/sg_trace_diag_knc_512_32.c
SRC_TRACE_KNC += src/sw_trace_diag_knc_512_32.c

# parallel striped methods

SRC_TRACE_SSE2 += src/nw_trace_striped_sse2_128_64.c
SRC_TRACE_SSE2 += src/sg_trace_striped_sse2_128_64.c
SRC_TRACE_SSE2 += src/sw_trace_striped_sse2_128_64.c

SRC_TRACE_SSE2 += src/nw_trace_striped_sse2_128_32.c
SRC_TRACE_SSE2 += src/sg_trace_striped_sse2_128_32.c
SRC_TRACE_SSE2 += src/sw_trace_striped_sse2_128_32.c

SRC_TRACE_SSE2 += src/nw_trace_striped_sse2_128_16.c
SRC_TRACE_SSE2 += src/sg_trace_striped_sse2_128_16.c
SRC_TRACE_SSE2 += src/sw_trace_striped_sse2_128_16.c

SRC_TRACE_SSE2 += src/nw_trace_striped_sse2_128_8.c
SRC_TRACE_SSE2 += src/sg_trace_striped_sse2_128_8.c
SRC_TRACE_SSE2 += src/sw_trace_striped_sse2_128_8.c

SRC_TRACE_SSE41 += src/nw_trace_striped_sse41_128_64.c
SRC_TRACE_SSE41 += src/sg_trace_striped_sse41_128_64.c
SRC_TRACE_SSE41 += src/sw_trace_striped_sse41_128_64.c

SRC_TRACE_SSE41 += src/nw_trace_striped_sse41_128_32.c
SRC_TRACE_SSE41 += src/sg_trace_striped_sse41_128_32.c
SRC_TRACE_SSE41 += src/sw_trace_striped_sse41_128_32.c

SRC_TRACE_SSE41 += src/nw_trace_striped_sse41_128_16.c
SRC_TRACE_SSE41 += src/sg_trace_striped_sse41_128_16.c
SRC_TRACE_SSE41 += src/sw_trace_striped_sse41_128_16.c

SRC_TRACE_SSE41 += src/nw_trace_striped_sse41_128_8.c
SRC_TRACE_SSE41 += src/sg_trace_striped_sse41_128_8.c
SRC_TRACE_SSE41 += src/sw_trace_striped_sse41_128_8.c

SRC_TRACE_AVX2 += src/nw_trace_striped_avx2_256_64.c
SRC_TRACE_AVX2 += src/sg_trace_striped_avx2_256_64.c
SRC_TRACE_AVX2 += src/sw_trace_striped_avx2_256_64.c

SRC_TRACE_AVX2 += src/nw_trace_striped_avx2_256_32.c
SRC_TRACE_AVX2 += src/sg_trace_striped_avx2_256_32.c
SRC_TRACE_AVX2 += src/sw_trace_striped_avx2_256_32.c

SRC_TRACE_AVX2 += src/nw_trace_striped_avx2_256_16.c
SRC_TRACE_AVX2 += src/sg_trace_striped_avx2_256_16.c
SRC_TRACE_AVX2 += src/sw_trace_striped_avx2_256_16.c

SRC_TRACE_AVX2 += src/nw_trace_striped_avx2_256_8.c
SRC_TRACE_AVX2 += src/sg_trace_striped_avx2_256_8.c
SRC_TRACE_AVX2 += src/sw_trace_striped_avx2_256_8.c

SRC_TRACE_KNC += src/nw_trace_striped_knc_512_32.c
SRC_TRACE_KNC += src/sg_trace_striped_knc_512_32.c
SRC_TRACE_KNC += src/sw_trace_striped_knc_512_32.c

#########################
# library magic
#########################

libparasail_la_SOURCES = $(SRC_CORE)

libparasail_novec_la_SOURCES = $(SRC_NOVEC)
libparasail_sse2_la_SOURCES = $(SRC_SSE2)
libparasail_sse41_la_SOURCES = $(SRC_SSE41)
libparasail_avx2_la_SOURCES = $(SRC_AVX2)
libparasail_knc_la_SOURCES = $(SRC_KNC)
libparasail_novec_la_SOURCES = $(SRC_NOVEC) $(SRC_TRACE_NOVEC)
libparasail_sse2_la_SOURCES = $(SRC_SSE2) $(SRC_TRACE_SSE2)
libparasail_sse41_la_SOURCES = $(SRC_SSE41) $(SRC_TRACE_SSE41)
libparasail_avx2_la_SOURCES = $(SRC_AVX2) $(SRC_TRACE_AVX2)
libparasail_knc_la_SOURCES = $(SRC_KNC) $(SRC_TRACE_KNC)

libparasail_novec_la_CFLAGS = $(AM_CFLAGS)
libparasail_sse2_la_CFLAGS = $(AM_CFLAGS) $(SSE2_CFLAGS)
Expand Down Expand Up @@ -683,6 +866,7 @@ if HAVE_CILK
bin_PROGRAMS += apps/parasail_aligner_cilk
endif

check_PROGRAMS += tests/traceback
check_PROGRAMS += tests/test_align
check_PROGRAMS += tests/test_gcups
check_PROGRAMS += tests/test_isa
Expand All @@ -694,6 +878,7 @@ check_PROGRAMS += tests/test_sw_dispatch
check_PROGRAMS += tests/test_verify
check_PROGRAMS += tests/test_verify_tables
check_PROGRAMS += tests/test_verify_rowcols
check_PROGRAMS += tests/test_verify_traces
if HAVE_SSE2
check_PROGRAMS += tests/test_ssw
endif
Expand All @@ -716,7 +901,12 @@ apps_parasail_aligner_cilk_LDADD += tests/libsais.la

apps_parasail_stats_SOURCES = apps/parasail_stats.c

tests_test_align_SOURCES = tests/test_align.c
tests_traceback_SOURCES = tests/traceback.c

tests_test_align_SOURCES =
tests_test_align_SOURCES += tests/test_align.c
tests_test_align_SOURCES += tests/timer.h
tests_test_align_SOURCES += tests/timer_real.h

tests_test_gcups_SOURCES = tests/test_gcups.c
tests_test_gcups_LDADD =
Expand All @@ -727,7 +917,10 @@ tests_test_isa_SOURCES = tests/test_isa.c

tests_test_matrix_SOURCES = tests/test_matrix.c

tests_test_openmp_SOURCES = tests/test_openmp.c
tests_test_openmp_SOURCES =
tests_test_openmp_SOURCES += tests/test_openmp.c
tests_test_openmp_SOURCES += tests/timer.h
tests_test_openmp_SOURCES += tests/timer_real.h
tests_test_openmp_CFLAGS = $(AM_CFLAGS) $(OPENMP_CFLAGS)
tests_test_openmp_LDFLAGS = $(AM_LDFLAGS) $(OPENMP_CFLAGS)
tests_test_openmp_LDADD =
Expand All @@ -736,11 +929,17 @@ if HAVE_SSE2
tests_test_openmp_LDADD += tests/libssw.la
endif

tests_test_query_SOURCES = tests/test_query.c
tests_test_query_SOURCES =
tests_test_query_SOURCES += tests/test_query.c
tests_test_query_SOURCES += tests/timer.h
tests_test_query_SOURCES += tests/timer_real.h
tests_test_query_CFLAGS = $(AM_CFLAGS) $(OPENMP_CFLAGS)
tests_test_query_LDFLAGS = $(AM_LDFLAGS) $(OPENMP_CFLAGS)

tests_test_scatter_SOURCES = tests/test_scatter.c
tests_test_scatter_SOURCES =
tests_test_scatter_SOURCES += tests/test_scatter.c
tests_test_scatter_SOURCES += tests/timer.h
tests_test_scatter_SOURCES += tests/timer_real.h
tests_test_scatter_CFLAGS = $(AM_CFLAGS) $(OPENMP_CFLAGS)
tests_test_scatter_LDFLAGS = $(AM_LDFLAGS) $(OPENMP_CFLAGS)
tests_test_scatter_LDADD =
Expand All @@ -759,23 +958,28 @@ tests_test_ssw_LDADD += tests/libssw.la

tests_test_sw_dispatch_SOURCES = tests/test_sw_dispatch.c

tests_test_verify_SOURCES = tests/test_verify.c
tests_test_verify_SOURCES = tests/test_verify.c tests/func_verify.h
tests_test_verify_CFLAGS = $(AM_CFLAGS) $(OPENMP_CFLAGS)
tests_test_verify_LDFLAGS = $(AM_LDFLAGS) $(OPENMP_CFLAGS)

tests_test_verify_tables_SOURCES = tests/test_verify_tables.c
tests_test_verify_tables_SOURCES =
tests_test_verify_tables_SOURCES += tests/test_verify_tables.c
tests_test_verify_tables_SOURCES += tests/func_verify_tables.h
tests_test_verify_tables_CFLAGS = $(AM_CFLAGS) $(OPENMP_CFLAGS)
tests_test_verify_tables_LDFLAGS = $(AM_LDFLAGS) $(OPENMP_CFLAGS)

tests_test_verify_rowcols_SOURCES = tests/test_verify_rowcols.c
tests_test_verify_rowcols_SOURCES =
tests_test_verify_rowcols_SOURCES += tests/test_verify_rowcols.c
tests_test_verify_rowcols_SOURCES += tests/func_verify_rowcols.h
tests_test_verify_rowcols_CFLAGS = $(AM_CFLAGS) $(OPENMP_CFLAGS)
tests_test_verify_rowcols_LDFLAGS = $(AM_LDFLAGS) $(OPENMP_CFLAGS)

EXTRA_DIST += .gitignore
EXTRA_DIST += .travis.yml
EXTRA_DIST += CHANGELOG.md
EXTRA_DIST += CMakeLists.txt
EXTRA_DIST += COPYING
tests_test_verify_traces_SOURCES =
tests_test_verify_traces_SOURCES += tests/test_verify_traces.c
tests_test_verify_traces_SOURCES += tests/func_verify_traces.h
tests_test_verify_traces_CFLAGS = $(AM_CFLAGS) $(OPENMP_CFLAGS)
tests_test_verify_traces_LDFLAGS = $(AM_LDFLAGS) $(OPENMP_CFLAGS)

EXTRA_DIST += DISCLAIMER
EXTRA_DIST += README.md
EXTRA_DIST += aclocal.m4
Expand Down Expand Up @@ -819,6 +1023,7 @@ EXTRA_DIST += util/diff_all.sh
EXTRA_DIST += util/dispatcher.py
EXTRA_DIST += util/func_group_rowcols.py
EXTRA_DIST += util/func_group_tables.py
EXTRA_DIST += util/func_group_traces.py
EXTRA_DIST += util/func_groups.py
EXTRA_DIST += util/funcs.py
EXTRA_DIST += util/gap_tester.py
Expand Down
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