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Porting to Arm #16

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Porting to Arm #16

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c5247db
BSW Arm-SVE version
LorienLV Sep 28, 2023
fde80f4
CHAIN does not need minimap2 to work
LorienLV Sep 29, 2023
9d834c5
CHAIN Arm-specific bug fix
LorienLV Sep 29, 2023
262de4c
Vectorized version of CHAIN, FAST-CHAIN, added
LorienLV Sep 29, 2023
228bf7e
KMER-CNT now uses OpenMP to make thread binding easier
LorienLV Sep 29, 2023
d4232f1
KMER-CNT version for high-memory systems
LorienLV Oct 2, 2023
33e2773
WFA with support for Arm-SVE added
LorienLV Oct 2, 2023
323b429
Added command line parameter to KMER-CNT to select between high-memor…
LorienLV Oct 16, 2023
46c4750
Now WFA uses the same inputs as BSW
LorienLV Nov 2, 2023
bf0e194
NN-VARIANT migrated to Clair3
LorienLV Nov 3, 2023
ce5e9b3
New kernels added to execution scripts
LorienLV Nov 3, 2023
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2 changes: 2 additions & 0 deletions Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -24,6 +24,7 @@ all:
cd benchmarks/pileup; $(MAKE) CC=$(CC) arch=$(ARCH) VTUNE_HOME=$(VTUNE_HOME)
cd benchmarks/kmer-cnt; $(MAKE) CXX=$(CXX) arch=$(ARCH) VTUNE_HOME=$(VTUNE_HOME)
cd benchmarks/grm/2.0/build_dynamic; $(MAKE) CC=$(CC) CXX=$(CXX) arch=$(ARCH) VTUNE_HOME=$(VTUNE_HOME) MKLROOT=$(MKLROOT) MKL_IOMP5_DIR=$(MKL_IOMP5_DIR) #needs MKL
cd benchmarks/wfa; $(MAKE) CXX=$(CXX) arch=$(ARCH) VTUNE_HOME=$(VTUNE_HOME)

gpu:
cd benchmarks/abea; $(MAKE) CUDA_LIB=$(CUDA_LIB)
Expand All @@ -41,3 +42,4 @@ clean:
cd benchmarks/pileup; $(MAKE) clean
cd benchmarks/kmer-cnt; $(MAKE) clean
cd benchmarks/grm/2.0/build_dynamic; $(MAKE) clean
cd benchmarks/wfa; $(MAKE) clean
7 changes: 4 additions & 3 deletions benchmarks/bsw/Makefile
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Expand Up @@ -56,7 +56,8 @@ else ifneq ($(arch),)
ARCH_FLAGS=$(arch)
endif

CXXFLAGS= -DSORT_PAIRS -DENABLE_PREFETCH -DBWA_OTHER_ELE=0 -O3 -std=c++11 -fopenmp $(ARCH_FLAGS) #-mtune=native -march=native
# fno-strict-aliasing is required to prevent errors in vector code.
CXXFLAGS= -DSORT_PAIRS -DENABLE_PREFETCH -DBWA_OTHER_ELE=0 -O3 -std=c++11 -fno-strict-aliasing -fopenmp $(ARCH_FLAGS) #-mtune=native -march=native
#VTUNE_HOME= /opt/intel/oneapi/vtune/2021.1.1
INCLUDES=
LIBS= -fopenmp -lz -ldl
Expand All @@ -83,5 +84,5 @@ clean:


# DO NOT DELETE
main_banded.o: bandedSWA.h macro.h utils.h
bandedSWA.o: bandedSWA.h macro.h utils.h
main_banded.o: bandedSWA.h macro.h utils.h sse2sve.h
bandedSWA.o: bandedSWA.h macro.h utils.h sse2sve.h
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