add fpga build in Makefile + init_aoc_esa.sh

.gitignore

@@ -2,7 +2,15 @@
 PDBs/*
 ofdock_taskpar_alt/Krnl_GA/*
 ofdock_taskpar_alt/device/docking_fpga_leo/*
+
+# Ignore FPGA binaries
+ofdock_taskpar_alt/docking/*
+ofdock_taskpar_alt/docking.aoco
+ofdock_taskpar_alt/docking.aocx
+
+# Ignore docking debug/tmp output
 *~
+final_population_run*
 
 # ===================
 # C gitignore

README.md

 Version compiled with Intel Altera Tools 16.1
 
+Source first: init_aoc_esa.sh
+
 ofdock_datapar_xl: data parallel version for altera taken from feanor
 		   Machine: feanor
 		   Path: /home/wimi/lvs/altera/ofdock_altera/ofdock
 
 ofdock_taskpar_xl: task parallel version for altera
+

ofdock_taskpar_alt/Makefile

@@ -199,7 +199,6 @@ else
 	REP=
 endif
 
-
 # =============================
 
 
@@ -220,38 +219,89 @@ $(TARGET_DIR)/$(TARGET) : Makefile $(SRCS) $(INCS) $(TARGET_DIR)
 			$(foreach D,$(LIB_DIRS),-L$D) \
 			$(foreach L,$(LIBS),-l$L) \
 			-o $(TARGET_DIR)/$(TARGET) $(DOCK_DEBUG_FLAG) $(DEV) $(DOCK_PROG) $(ENABLE_KERNELS) $(REP)
+	@echo " "
+	@echo "================================"
+	@echo "INFO: host binary is under: bin/"
+	@echo "================================"
+	@echo " "
 
 
 
 
 
+# Docking parameters
+PDB  := 1stp
+NRUN := 10
+NEV  := 200000
 
-PDB  := 3ptb
-NRUN := 20
-NEV  := 300000
-
-# Make it all: compilation (host & device) + run
-# Notice, it switches automatically to /bin folder
-
-emu: $(TARGET_DIR)/$(TARGET) keremu runemu
-
+# Device folder
+# Device main kernel name
+# Device main kernel source
 DEV_DIRS := device
 DEV_SRC  := $(DEV_DIRS)/Krnl_GA.cl
 
+## Make it all: compilation (host & device) + run emulation
+## Notice, it switches automatically to /bin folder
+#emu: $(TARGET_DIR)/$(TARGET) keremu runemu
+
+# Build kernel binary only for emulation
+# Creates under bin: 
+	# "docking" folder
+	# docking.aoco
+	# docking.aocx
 keremu: $(DEV_SRC)
 	aoc -march=emulator -v --board a10gx $(DEV_SRC) -o $(TARGET_DIR)/docking.aocx $(REP)
-
-runemu:	$(TARGET)
+	@echo " "
+	@echo "=========================================================="
+	@echo "INFO: emulation files are under: bin/docking(.aoco)(.aocx)"
+	@echo "=========================================================="
+	@echo " "
+
+# Run emulation
+# Compilation (host & device) if not done previously
+# The working directory is changed
+# So .dlg file is written there
+emu: $(TARGET_DIR)/$(TARGET) keremu
 	cd $(TARGET_DIR) && \
 	CL_CONTEXT_EMULATOR_DEVICE_ALTERA=1 ./$(TARGET) -ffile ../input/$(PDB)/derived/$(PDB)_protein.maps.fld -lfile ../input/$(PDB)/derived/$(PDB)_ligand.pdbqt -nev $(NEV) -nrun $(NRUN) -gfpop 1
+	@echo " "
+	@echo "========================================"
+	@echo "INFO: log file is under: bin/docking.dlg"
+	@echo "========================================"
+	@echo " "
+
+
+# Reports are generated
+# Could be used in multistep compilation
+# Creates under bin:
+	# "docking" folder -> /reports/report.html, to see details
+	# docking.aoco
+	# No actual hardware is built (NO .aocx)
+kerrpt: $(DEV_SRC)
+	aoc --board a10gx $(DEV_SRC) -o $(TARGET_DIR)/docking.aoco $(REP) -c --report
+	@echo " "
+	@echo "============================================================="
+	@echo "INFO: report files are under: bin/docking/reports/report.html"
+	@echo "============================================================="
+	@echo " "
+
+# Build hw (FPGA bitstream)
+# NOT integrated yet in a multistep compilation
+# Creates under root folder:
+	# "docking" folder
+	# docking.aoco
+	# docking.aocx
+hw: 	
+	aoc --board a10gx $(DEV_SRC) -o docking.aocx
+	@echo " "
+	@echo "================================="
+	@echo "INFO: FPGA bitstream is under: ./"
+	@echo "================================="
+	@echo " "
 
 
 
 
-#	CL_CONTEXT_EMULATOR_DEVICE_ALTERA=1 ./$(TARGET) -ffile ../input/3ptb/derived/3ptb_protein.maps.fld -lfile ../input/3ptb/derived/3ptb_ligand.pdbqt -nev 250000 -nrun 40
-
-
-
 
 $(TARGET_DIR) :
 	$(ECHO)mkdir $(TARGET_DIR)

ofdock_taskpar_alt/bin/docking.xml

-<?xml version="1.0" ?>
-<result>
-	<clustering_histogram>
-		<cluster cluster_rank="1" lowest_binding_energy="-5.53" run="14" mean_binding_energy="1973785.53" num_in_clus="17" />
-		<cluster cluster_rank="2" lowest_binding_energy="-5.52" run="39" mean_binding_energy="2097147.46" num_in_clus="8" />
-		<cluster cluster_rank="3" lowest_binding_energy="-2.35" run="27" mean_binding_energy="-1.42" num_in_clus="6" />
-		<cluster cluster_rank="4" lowest_binding_energy="-1.90" run="13" mean_binding_energy="-0.55" num_in_clus="9" />
-	</clustering_histogram>
-	<rmsd_table>
-		<run rank="1" sub_rank="1" run="14" binding_energy="-5.53" cluster_rmsd="0.00" reference_rmsd="2.08" />
-		<run rank="1" sub_rank="2" run="4" binding_energy="-5.47" cluster_rmsd="0.73" reference_rmsd="2.03" />
-		<run rank="1" sub_rank="3" run="10" binding_energy="-5.45" cluster_rmsd="0.71" reference_rmsd="2.04" />
-		<run rank="1" sub_rank="4" run="2" binding_energy="-5.43" cluster_rmsd="0.70" reference_rmsd="2.04" />
-		<run rank="1" sub_rank="5" run="17" binding_energy="-5.42" cluster_rmsd="1.50" reference_rmsd="2.42" />
-		<run rank="1" sub_rank="6" run="15" binding_energy="-5.35" cluster_rmsd="0.76" reference_rmsd="2.08" />
-		<run rank="1" sub_rank="7" run="11" binding_energy="-5.35" cluster_rmsd="0.50" reference_rmsd="2.08" />
-		<run rank="1" sub_rank="8" run="7" binding_energy="-5.15" cluster_rmsd="1.36" reference_rmsd="2.48" />
-		<run rank="1" sub_rank="9" run="24" binding_energy="-5.01" cluster_rmsd="0.59" reference_rmsd="2.14" />
-		<run rank="1" sub_rank="10" run="30" binding_energy="-4.58" cluster_rmsd="1.56" reference_rmsd="2.53" />
-		<run rank="1" sub_rank="11" run="23" binding_energy="-4.50" cluster_rmsd="1.11" reference_rmsd="2.17" />
-		<run rank="1" sub_rank="12" run="38" binding_energy="-4.49" cluster_rmsd="1.50" reference_rmsd="2.47" />
-		<run rank="1" sub_rank="13" run="35" binding_energy="-4.48" cluster_rmsd="0.98" reference_rmsd="2.13" />
-		<run rank="1" sub_rank="14" run="16" binding_energy="-4.43" cluster_rmsd="1.06" reference_rmsd="2.15" />
-		<run rank="1" sub_rank="15" run="5" binding_energy="-4.31" cluster_rmsd="1.66" reference_rmsd="2.49" />
-		<run rank="1" sub_rank="16" run="34" binding_energy="-3.66" cluster_rmsd="1.90" reference_rmsd="2.64" />
-		<run rank="1" sub_rank="17" run="40" binding_energy="33554432.60" cluster_rmsd="1.19" reference_rmsd="2.18" />
-		<run rank="2" sub_rank="1" run="39" binding_energy="-5.52" cluster_rmsd="0.00" reference_rmsd="0.36" />
-		<run rank="2" sub_rank="2" run="33" binding_energy="-5.45" cluster_rmsd="1.50" reference_rmsd="1.52" />
-		<run rank="2" sub_rank="3" run="19" binding_energy="-5.43" cluster_rmsd="0.72" reference_rmsd="0.76" />
-		<run rank="2" sub_rank="4" run="12" binding_energy="-5.33" cluster_rmsd="1.49" reference_rmsd="1.50" />
-		<run rank="2" sub_rank="5" run="31" binding_energy="-4.49" cluster_rmsd="1.42" reference_rmsd="1.50" />
-		<run rank="2" sub_rank="6" run="18" binding_energy="-3.73" cluster_rmsd="1.57" reference_rmsd="1.61" />
-		<run rank="2" sub_rank="7" run="9" binding_energy="-2.95" cluster_rmsd="1.36" reference_rmsd="1.45" />
-		<run rank="2" sub_rank="8" run="29" binding_energy="16777212.60" cluster_rmsd="1.32" reference_rmsd="1.26" />
-		<run rank="3" sub_rank="1" run="27" binding_energy="-2.35" cluster_rmsd="0.00" reference_rmsd="4.31" />
-		<run rank="3" sub_rank="2" run="32" binding_energy="-1.85" cluster_rmsd="0.72" reference_rmsd="4.29" />
-		<run rank="3" sub_rank="3" run="28" binding_energy="-1.46" cluster_rmsd="1.61" reference_rmsd="4.39" />
-		<run rank="3" sub_rank="4" run="25" binding_energy="-1.37" cluster_rmsd="0.86" reference_rmsd="4.23" />
-		<run rank="3" sub_rank="5" run="36" binding_energy="-0.94" cluster_rmsd="1.51" reference_rmsd="4.49" />
-		<run rank="3" sub_rank="6" run="6" binding_energy="-0.56" cluster_rmsd="1.80" reference_rmsd="4.31" />
-		<run rank="4" sub_rank="1" run="13" binding_energy="-1.90" cluster_rmsd="0.00" reference_rmsd="3.83" />
-		<run rank="4" sub_rank="2" run="21" binding_energy="-1.89" cluster_rmsd="0.20" reference_rmsd="3.81" />
-		<run rank="4" sub_rank="3" run="37" binding_energy="-1.74" cluster_rmsd="1.35" reference_rmsd="4.01" />
-		<run rank="4" sub_rank="4" run="20" binding_energy="-1.74" cluster_rmsd="1.50" reference_rmsd="3.99" />
-		<run rank="4" sub_rank="5" run="8" binding_energy="-1.37" cluster_rmsd="1.49" reference_rmsd="3.99" />
-		<run rank="4" sub_rank="6" run="3" binding_energy="-1.07" cluster_rmsd="0.73" reference_rmsd="3.84" />
-		<run rank="4" sub_rank="7" run="26" binding_energy="-0.63" cluster_rmsd="0.81" reference_rmsd="3.85" />
-		<run rank="4" sub_rank="8" run="1" binding_energy="1.29" cluster_rmsd="0.77" reference_rmsd="3.85" />
-		<run rank="4" sub_rank="9" run="22" binding_energy="4.10" cluster_rmsd="1.52" reference_rmsd="3.83" />
-	</rmsd_table>
-</result>

ofdock_taskpar_alt/bin/docking/Krnl_GA.log

-Compiler Command: aoc -march=emulator --fp-relaxed --fpc -v --board a10gx device/Krnl_GA.cl -o bin/docking.aocx

ofdock_taskpar_alt/init_aoc_esa.sh

+# This is created to automate the boring 
+# process of setting AOC in celebdil
+# DO NOT FORGET to run it using:
+# >source init_aoc_esa.sh
+
+echo "======================================="
+echo "Setting up Altera OpenCL SDK & Compiler"
+echo "======================================="
+echo ""
+export ALTERAOCLSDKROOT=/opt/cad/altera/altera-16.1/hld
+echo "ALTERAOCLSDKROOT: "
+echo $ALTERAOCLSDKROOT
+echo " "
+source /opt/cad/altera/altera-16.1/hld/init_opencl.sh
+echo " "
+export LM_LICENSE_FILE=/opt/cad/keys/altera
+echo "LM_LICENSE_FILE: "
+echo $LM_LICENSE_FILE
+echo " "
+export PATH=/opt/cad/altera/altera-16.1/quartus/bin/:$PATH
+echo "PATH: "
+echo $PATH
+echo " "
+
+echo "Altera OpenCL SDK version: "
+aocl version
+echo " "
+
+echo "Altera OpenCL Compiler version: "
+aoc --version
+echo " "
+
+#echo $AOCL_BOARD_PACKAGE_ROOT
+echo "List of available boards "
+aoc --list-boards 
+echo " "
+
+echo "Maybe we need to switch to another board?"
+echo " "
+export AOCL_BOARD_PACKAGE_ROOT=/opt/cad/altera/altera-16.1/hld/board/a10_ref
+
+#echo $AOCL_BOARD_PACKAGE_ROOT
+source /opt/cad/altera/altera-16.1/hld/init_opencl.sh
+echo " "
+echo "List of available boards "
+aoc --list-boards
+echo " "