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added necessary makefiles
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‎docking/AUTODOCK_GPU_DIR/MAKEFILE

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# AutoDock-GPU Cuda Makefile
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# ------------------------------------------------------
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# Note that environment variables must be defined
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# before compiling
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# DEVICE?
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# if DEVICE=CPU: CPU_INCLUDE_PATH?, CPU_LIBRARY_PATH?
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# if DEVICE=GPU: GPU_INCLUDE_PATH?, GPU_LIBRARY_PATH?
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# ------------------------------------------------------
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# Choose OpenCL device
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# Valid values: CPU, GPU
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NVCC = nvcc
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CPP = g++
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UNAME := $(shell uname)
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TARGETS = 52 60 61 70 80
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ifeq ($(TENSOR), ON)
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NVTENSOR=-DUSE_NVTENSOR
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NVTENSOR+=-I./wmma_extension/include
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TARGETS = 80
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endif
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# Replace the gencode line with SASS+PTX for each target:
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CUDA_TARGETS=$(foreach t,$(TARGETS),-gencode arch=compute_$(t),code=[sm_$(t),compute_$(t)])
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ifeq ($(DEVICE), CPU)
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DEV =-DCPU_DEVICE
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else ifeq ($(DEVICE), GPU)
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DEV =-DGPU_DEVICE
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endif
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# ------------------------------------------------------
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# Project directories
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# opencl_lvs: wrapper for OpenCL APIs
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COMMON_DIR=./common
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HOST_INC_DIR=./host/inc
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HOST_SRC_DIR=./host/src
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KRNL_DIR=./cuda
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KCMN_DIR=$(COMMON_DIR)
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BIN_DIR=./bin
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LIB_CUDA = kernels.o -lcurand -lcudart -DUSE_CUDA
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TARGET := autodock
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TOOL_TARGET := adgpu_analysis
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IFLAGS=-I$(COMMON_DIR) -I$(HOST_INC_DIR) -I$(GPU_INCLUDE_PATH) -I$(KRNL_DIR)
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LFLAGS=-L$(GPU_LIBRARY_PATH) -Wl,-rpath=$(GPU_LIBRARY_PATH):$(CPU_LIBRARY_PATH)
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CFLAGS=-std=c++17 $(IFLAGS) $(LFLAGS)
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TOOL_CFLAGS=-std=c++17 -I$(COMMON_DIR) -I$(HOST_INC_DIR)
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ifeq ($(DEVICE), CPU)
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TARGET:=$(TARGET)_cpu
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else ifeq ($(DEVICE), GPU)
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NWI=-DN64WI
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TARGET:=$(TARGET)_gpu
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endif
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ifeq ($(OVERLAP), ON)
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PIPELINE=-DUSE_PIPELINE -fopenmp
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endif
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BIN := $(wildcard $(TARGET)*)
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# ------------------------------------------------------
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# Number of work-items (wi)
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# Valid values: 32, 64, 128, 256
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NUMWI=
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ifeq ($(NUMWI), 32)
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ifeq ($(TENSOR), ON)
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$(error NUMWI needs to be at least 64 with TENSOR=ON)
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endif
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NWI=-DN32WI
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TARGET:=$(TARGET)_32wi
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else ifeq ($(NUMWI), 64)
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NWI=-DN64WI
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TARGET:=$(TARGET)_64wi
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else ifeq ($(NUMWI), 128)
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NWI=-DN128WI
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TARGET:=$(TARGET)_128wi
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else ifeq ($(NUMWI), 256)
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NWI=-DN256WI
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TARGET:=$(TARGET)_256wi
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else
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ifeq ($(DEVICE), CPU)
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NWI=-DN16WI
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TARGET:=$(TARGET)_16wi
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else ifeq ($(DEVICE), GPU)
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NWI=-DN128WI
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TARGET:=$(TARGET)_128wi
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endif
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endif
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# ------------------------------------------------------
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# Configuration
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# FDEBUG (full) : enables debugging on both host + device
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# LDEBUG (light): enables debugging on host
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# RELEASE
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CONFIG=RELEASE
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#CONFIG=FDEBUG
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ifeq ($(CONFIG),FDEBUG)
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OPT =-O0 -g3 -Wall -DDOCK_DEBUG
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CUDA_FLAGS = -G -use_fast_math --ptxas-options="-v" $(CUDA_TARGETS) -std=c++11
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else ifeq ($(CONFIG),LDEBUG)
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OPT =-O0 -g3 -Wall
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CUDA_FLAGS = -use_fast_math --ptxas-options="-v" $(CUDA_TARGETS) -std=c++11
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else ifeq ($(CONFIG),RELEASE)
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OPT =-O3
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CUDA_FLAGS = -use_fast_math --ptxas-options="-v" $(CUDA_TARGETS) -std=c++11
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else
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OPT =
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CUDA_FLAGS = -use_fast_math --ptxas-options="-v" $(CUDA_TARGETS) -std=c++11
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endif
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# ------------------------------------------------------
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# Reproduce results (remove randomness)
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REPRO=NO
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ifeq ($(REPRO),YES)
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REP =-DREPRO
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else
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REP =
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endif
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# ------------------------------------------------------
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all: otool odock
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check-env-dev:
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@if test -z "$$DEVICE"; then \
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echo "Please set DEVICE to either CPU, GPU, CUDA, or OCLGPU to build docking software."; \
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exit 1; \
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else \
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if [ "$$DEVICE" = "CPU" ]; then \
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echo "DEVICE is set to $$DEVICE which is not a valid Cuda device."; \
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exit 1; \
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else \
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if [ "$$DEVICE" = "GPU" ]; then \
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echo "DEVICE is set to $$DEVICE"; \
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else \
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echo "DEVICE value is invalid. Please set DEVICE to either CPU, GPU, CUDA, or OCLGPU"; \
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exit 1; \
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fi; \
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fi; \
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fi; \
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echo " "
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check-env-cpu:
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@if test -z "$$CPU_INCLUDE_PATH"; then \
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echo "CPU_INCLUDE_PATH is undefined"; \
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else \
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echo "CPU_INCLUDE_PATH is set to $$CPU_INCLUDE_PATH"; \
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fi; \
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if test -z "$$CPU_LIBRARY_PATH"; then \
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echo "CPU_LIBRARY_PATH is undefined"; \
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else \
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echo "CPU_LIBRARY_PATH is set to $$CPU_LIBRARY_PATH"; \
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fi; \
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echo " "
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check-env-gpu:
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@if test -z "$$GPU_INCLUDE_PATH"; then \
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echo "GPU_INCLUDE_PATH is undefined"; \
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else \
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echo "GPU_INCLUDE_PATH is set to $$GPU_INCLUDE_PATH"; \
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fi; \
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if test -z "$$GPU_LIBRARY_PATH"; then \
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echo "GPU_LIBRARY_PATH is undefined"; \
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else \
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echo "GPU_LIBRARY_PATH is set to $$GPU_LIBRARY_PATH"; \
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fi; \
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echo " "
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check-env-all: check-env-dev check-env-cpu check-env-gpu
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# ------------------------------------------------------
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# Priting out its git version hash
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GIT_VERSION := $(shell ./version_string.sh)
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CFLAGS+=-DVERSION=\"$(GIT_VERSION)\"
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TOOL_CFLAGS+=-DVERSION=\"$(GIT_VERSION)\"
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# ------------------------------------------------------
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kernels: $(KERNEL_SRC)
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$(NVCC) $(NWI) $(REP) $(CUDA_FLAGS) $(IFLAGS) $(CUDA_INCLUDES) $(NVTENSOR) -c $(KRNL_DIR)/kernels.cu
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otool:
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@echo "Building" $(TOOL_TARGET) "..."
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$(CPP) \
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$(shell ls $(HOST_SRC_DIR)/*.cpp) \
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$(TOOL_CFLAGS) \
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-o$(BIN_DIR)/$(TOOL_TARGET) \
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$(PIPELINE) $(NVTENSOR) $(OPT) -DTOOLMODE $(REP)
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odock: check-env-all kernels
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@echo "Building" $(TARGET) "..."
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$(CPP) \
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$(shell ls $(HOST_SRC_DIR)/*.cpp) \
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$(CFLAGS) \
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$(LIB_CUDA) \
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-o$(BIN_DIR)/$(TARGET) \
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$(DEV) $(NWI) $(PIPELINE) $(NVTENSOR) $(OPT) $(DD) $(REP) $(KFLAGS)
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# Example
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# 1ac8: for testing gradients of translation and rotation genes
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# 7cpa: for testing gradients of torsion genes (15 torsions)
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# 3tmn: for testing gradients of torsion genes (1 torsion)
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PDB := 3ce3
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NRUN := 100
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NGEN := 27000
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POPSIZE := 150
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TESTNAME := test
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TESTLS := ad
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test: odock
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$(BIN_DIR)/$(TARGET) \
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-ffile ./input/$(PDB)/derived/$(PDB)_protein.maps.fld \
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-lfile ./input/$(PDB)/derived/$(PDB)_ligand.pdbqt \
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-nrun $(NRUN) \
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-ngen $(NGEN) \
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-psize $(POPSIZE) \
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-resnam $(TESTNAME) \
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-gfpop 0 \
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-lsmet $(TESTLS)
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.PHONY: clean

‎docking/AUTODOCK_GPU_DIR/Makefile

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@@ -63,4 +63,4 @@ $(info Please make sure to set environment variables)
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$(info GPU_INCLUDE_PATH and GPU_LIBRARY_PATH)
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$(info )
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include Makefile.OpenCL
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endif
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endif

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