SpectraFlux

regression/spectraflux/Makefile

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+VPP := $(XILINX_VITIS)/bin/v++
+TAPAC := $(HOME)/.local/bin/tapac
+EMCONFIGUTIL := $(XILINX_VITIS)/bin/emconfigutil
+MODE := hw
+PLATFORM := xilinx_u55c_gen3x16_xdma_3_202210_1
+
+# sources
+KERNEL_SRC := src/kernel/hac.cpp
+KERNEL_HEADER := src/kernel/hac.h
+HOST_SRC := src/host/host.cpp
+HOST_P2P_SRC := src/host_p2p/host.cpp src/host_p2p/xcl2/*.cpp
+TAPA_KERNEL_SRC := src/kernel_tap/hac.cpp
+TAPA_KERNEL_HEADER := src/kernel_tap/hac.h
+
+# targets
+HOST_EXE := host.exe
+HOST_P2P_EXE := host_p2p.exe
+WORK_DIR := run3
+
+XOS_ENCODING := encoding_kernel.$(MODE).xo
+XOS_CLUSTERING := clustering_kernel.$(MODE).xo
+XOS_TAPA := $(WORK_DIR)/wrapper.$(MODE).xo
+XOS_WRAPPER := wrapper.$(MODE).xo
+
+XCLBIN_ENCODING := hac_encoding.$(MODE).xclbin
+XCLBIN := hac.$(MODE).xclbin
+EMCONFIG_FILE := emconfig_new.json
+
+VPP_LINK_OPTS := --profile.data all:all:all --profile.memory all --profile.stall all:all --profile.exec all:all --profile_kernel data:all:all:all --config connectivity.cfg
+VPP_COMMON_OPTS := -s -t $(MODE) --platform $(PLATFORM) --report_level 2 --kernel_frequency 300 --optimize 3
+TAPA_OPTS := --platform $(PLATFORM) --connectivity connectivity.cfg --work-dir ${WORK_DIR} --floorplan-output "${WORK_DIR}/wrapper.tcl" 
+
+
+CFLAGS := -g -O3 -std=c++17 -I$(XILINX_XRT)/include -I$(XILINX_HLS)/include
+LFLAGS := -L$(XILINX_XRT)/lib -lxilinxopencl -lpthread -lrt
+NUMDEVICES := 1
+
+# run time args
+EXE_OPT := hac.$(MODE).xclbin
+
+# primary build targets
+.PHONY: xclbin app all
+
+# xclbin:  $(XCLBIN)
+# xclbin_enc: $(XCLBIN_ENCODING)
+
+app: $(HOST_EXE) $(HOST_P2P_EXE)
+
+# xo: $(XOS_ENCODING) $(XOS_CLUSTERING)
+# xo_enc: $(XOS_ENCODING)
+# xo_clu: $(XOS_CLUSTERING)
+xo_tapa: $(XOS_TAPA)
+# all: xclbin app
+xo_wrp: $(XOS_WRAPPER)
+
+# clean:
+# 	-$(RM) $(HOST_EXE) $(EXE_OPT) $(XOS_ENCODING) $(XOS_CLUSTERING) $(EMCONFIG_FILE)
+
+# kernel rules for encoding
+$(XOS_ENCODING): $(KERNEL_SRC) $(KERNEL_HEADER)
+	$(RM) $@
+	$(VPP) $(VPP_COMMON_OPTS) --hls.clock 200000000:encoding_kernel -c -k encoding_kernel -o $@ $+
+
+# kernel rules for clustering
+$(XOS_CLUSTERING): $(KERNEL_SRC) $(KERNEL_HEADER)
+	$(RM) $@
+	$(VPP) $(VPP_COMMON_OPTS) --hls.clock 150000000:clustering_kernel -c -k clustering_kernel -o $@ $+
+$(XOS_WRAPPER): $(KERNEL_SRC) $(KERNEL_HEADER)
+	$(RM) $@
+	$(VPP) $(VPP_COMMON_OPTS) --hls.clock 300000000:top_wrapper -c -k top_wrapper -o $@ $+
+
+$(XOS_TAPA): $(TAPA_KERNEL_SRC) 
+	mkdir -p $(WORK_DIR)
+	$(TAPAC) $(TAPA_OPTS) --top wrapper -o $@ $+ 
+
+
+$(XCLBIN): $(XOS_WRAPPER)# $(XOS_ENCODING) $(XOS_CLUSTERING)
+	$(VPP) $(VPP_COMMON_OPTS) -l -o $@ $^ $(VPP_LINK_OPTS)
+
+# host rules
+$(HOST_EXE): $(HOST_SRC)
+	g++ $(CFLAGS) -o $@ $+ $(LFLAGS)
+	@echo 'Compiled Host Executable: $(HOST_EXE)'
+
+$(HOST_P2P_EXE): $(HOST_P2P_SRC)
+	g++ $(CFLAGS) -o $@ $+ $(LFLAGS)
+	@echo 'Compiled Host Executable: $(HOST_P2P_EXE)'
+
+$(EMCONFIG_FILE):
+	$(EMCONFIGUTIL) --nd $(NUMDEVICES) --od . --platform $(PLATFORM)
+
+check: $(XCLBIN) $(HOST_EXE) $(EMCONFIG_FILE)
+	XCL_EMULATION_MODE=${MODE} ./$(HOST_EXE) $(EXE_OPT)
+

regression/spectraflux/connectivity.cfg

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+[connectivity]
+nk=wrapper:1:wrapper_1
+
+sp=wrapper_1.ID_Level_buffer:HBM[12]
+sp=wrapper_1.peak_mz_buffer:HBM[13]
+sp=wrapper_1.peak_intensity_buffer:HBM[14]
+sp=wrapper_1.peak_count_buffer:HBM[12]
+sp=wrapper_1.num_spectra_buffer:HBM[15]
+
+sp=wrapper_1.c0_num_valid_clusters:HBM[0:1]
+sp=wrapper_1.c0_num_elements:HBM[0:1]
+sp=wrapper_1.c0_consensus:HBM[0:1]
+sp=wrapper_1.c0_elements:HBM[2:3]
+
+sp=wrapper_1.c1_num_valid_clusters:HBM[16:17]
+sp=wrapper_1.c1_num_elements:HBM[16:17]
+sp=wrapper_1.c1_consensus:HBM[16:17]
+sp=wrapper_1.c1_elements:HBM[18:19]
+
+sp=wrapper_1.c2_num_valid_clusters:HBM[24:25]
+sp=wrapper_1.c2_num_elements:HBM[24:25]
+sp=wrapper_1.c2_consensus:HBM[24:25]
+sp=wrapper_1.c2_elements:HBM[26:27]
+
+sp=wrapper_1.c3_num_valid_clusters:HBM[28:29]
+sp=wrapper_1.c3_num_elements:HBM[28:29]
+sp=wrapper_1.c3_consensus:HBM[28:29]
+sp=wrapper_1.c3_elements:HBM[30:31]

regression/spectraflux/data/README

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+Download data from: https://drive.google.com/drive/folders/1qyiS229CryJoqDkScHsO0wNFaPBwOVT-?usp=sharing