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Commit 1a283eba authored by Leonardo Solis's avatar Leonardo Solis
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add datapar Makefile to build bin_hw

parent e0c024cb
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README.md
View file @ 1a283eba
Version compiled with Intel Altera Tools 16.1
Version compiled with Intel Altera Tools 16.0 (Quartus upgraded and patched)
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_datapar_xl**: data-parallel version
**ofdock_taskpar_xl**: task-parallel version
ofdock_datapar_alt/Makefile
View file @ 1a283eba
......@@ -25,6 +25,8 @@
# See http://www.altera.com/literature/hb/opencl-sdk/aocl_getting_started.pdf
# for more information on installing and configuring the Intel(R) FPGA SDK for OpenCL(TM).
VERBOSE = 1
ifeq ($(VERBOSE),1)
ECHO :=
else
......@@ -43,22 +45,11 @@ endif
AOCL_COMPILE_CONFIG := $(shell aocl compile-config )
AOCL_LINK_CONFIG := $(shell aocl link-config )
#= defines a recursively-expanded variable
#:= defines a simply-expanded variable
DEBUG=1
# Compilation flags
ifeq ($(DEBUG),1)
CXXFLAGS += -g
......@@ -69,10 +60,18 @@ endif
# Compiler
CXX := g++
# Target
# Target name
TARGET := host
# Target folder for host & emulation binaries
TARGET_DIR := bin
# Target folder for FPGA binary
TARGET_DIR_HW := bin_hw
# Target folder for FPGA binary instrumented with performance counters
TARGET_DIR_HW_PROF := bin_hw_profile
# Directories
#INC_DIRS := ../common/inc
INC_DIRS := ../common/inc opencl_lvs/inc host/inc ./
......@@ -168,10 +167,9 @@ else
K4 =
endif
ENABLE_KERNELS = $(K1) $(K2) $(K3) $(K4)
# =============================
# Make it all!
all : $(TARGET_DIR)/$(TARGET)
......@@ -189,9 +187,98 @@ $(TARGET_DIR)/$(TARGET) : Makefile $(SRCS) $(INCS) $(TARGET_DIR)
$(AOCL_COMPILE_CONFIG) $(SRCS) $(AOCL_LINK_CONFIG) \
$(foreach D,$(LIB_DIRS),-L$D) \
$(foreach L,$(LIBS),-l$L) \
-o $(TARGET_DIR)/$(TARGET) $(DOCK_DEBUG_FLAG) $(DEV) $(DOCK_PROG) $(K1) $(K2) $(K3) $(K4)
-o $(TARGET_DIR)/$(TARGET) $(DOCK_DEBUG_FLAG) $(DEV) $(DOCK_PROG) $(ENABLE_KERNELS)
@echo " "
@echo "================================"
@echo "INFO: host binary is under: bin/"
@echo "================================"
@echo " "
# Docking parameters
PDB := 1stp
NRUN := 10
NEV := 200000
# Device folder
# Device main kernel name
# Device main kernel source
DEV_DIRS := device
DEV_SRC := $(DEV_DIRS)/calc_initpop.cl
BOARD_HARP2 := bdw_fpga_v1.0
#keremu
#emu
#kerrpt
# Build hw (FPGA bitstream)
# NOT integrated yet in a multistep compilation
# Creates under bin_hw:
# "docking" folder
# docking.aoco
# docking.aocx
hw:
aoc --board $(BOARD_HARP2) $(DEV_SRC) -o $(TARGET_DIR_HW)/docking.aocx
@echo " "
@echo "==========================================================="
@echo "INFO: FPGA bitstream is under: bin_hw/docking(.aoco)(.aocx)"
@echo "==========================================================="
@echo " "
# Build hw (FPGA bitstream) instrumented with performance counters
# NOT integrated yet in a multistep compilation
# Creates under bin_hw_profile
# "docking" folder
# docking.aoco
# docking.aocx
hw_profile:
aoc --profile --board $(BOARD_HARP2) $(DEV_SRC) -o $(TARGET_DIR_HW_PROF)/docking.aocx
@echo " "
@echo "================================================================================"
@echo "INFO: instrumented FPGA bitstream is under: bin_hw_profile/docking(.aoco)(.aocx)"
@echo "================================================================================"
@echo " "
HARP2_DIR := copyharp2_datapar
HARP2_DIR_DOCK := ofdock_datapar_alt
# Delete an existing folder if previously created
# Create a folder $(HARP2_DIR) in the parent directory
# Copy binaries into $(HARP2_DIR) folder, avoiding the (innecesary) compilation intermediate files
# Copy source files into $(HARP2_DIR) as host is built in the HARP2 front-end
# Create a zip file out of the $(HARP2_DIR) folder
copyharp2: clean_copyharp2
mkdir ../$(HARP2_DIR)
mkdir ../$(HARP2_DIR)/$(HARP2_DIR_DOCK)
mkdir ../$(HARP2_DIR)/$(HARP2_DIR_DOCK)/$(TARGET_DIR_HW)
mkdir ../$(HARP2_DIR)/$(HARP2_DIR_DOCK)/$(TARGET_DIR_HW_PROF)
cp $(TARGET_DIR_HW)/docking.* ../$(HARP2_DIR)/$(HARP2_DIR_DOCK)/$(TARGET_DIR_HW)/
cp $(TARGET_DIR_HW_PROF)/docking.* ../$(HARP2_DIR)/$(HARP2_DIR_DOCK)/$(TARGET_DIR_HW_PROF)/
cp Makefile ../$(HARP2_DIR)/$(HARP2_DIR_DOCK)/
cp defines.h ../$(HARP2_DIR)/$(HARP2_DIR_DOCK)/
cp -r device/ ../$(HARP2_DIR)/$(HARP2_DIR_DOCK)/
cp -r host/ ../$(HARP2_DIR)/$(HARP2_DIR_DOCK)/
cp -r input/ ../$(HARP2_DIR)/$(HARP2_DIR_DOCK)/
cp -r wrapcl/ ../$(HARP2_DIR)/$(HARP2_DIR_DOCK)/
cp -r ../common ../$(HARP2_DIR)/
cd ../; zip -r $(HARP2_DIR).zip $(HARP2_DIR)
@echo "================================================================================"
@echo "The next step is to transfer the .zip file to the HARP2 fron-end: "
@echo "> cd .."
@echo "> scp copyharp2.zip h2solis@fe-1.harp.pc2.uni-paderborn.de:~/ocladock/"
@echo "================================================================================"
@echo " "
clean_copyharp2:
rm -r ../$(HARP2_DIR)
$(TARGET_DIR) :
......
ofdock_datapar_alt/bin/bin_emu_backup/docking.dlg deleted 100644 → 0
View file @ e0c024cb
**********************************************************
** GDOCK AUTODOCKTOOLS-COMPATIBLE DLG FILE **
**********************************************************
DOCKING PARAMETERS
________________________
Ligand file: ../input_data/1hvrl.pdbqt
Grid fld file: ../input_data/1hvr_vegl.maps.fld
Number of runs: 1
Number of energy evaluations: 2500000
Number of generations: 27000
Size of population: 150
Rate of crossover: 80.000000%
Tournament selection probability limit: 60.000000%
Rate of mutation: 2.000000%
Maximal allowed delta movement: +/- 6.000000A
Maximal allowed delta angle: +/- 90.000000
Rate of local search: 6.000000%
Maximal number of local search iterations: 300
Rho lower bound: 0.010000
Spread of local search delta movement: 2.000000A
Spread of local search delta angle: 74.999999
Limit of consecutive successes/failures: 4
Handle symmetry during clustering: NO
RMSD tolerance: 2.000000A
Program call in command line was: ./host -ffile ../input_data/1hvr_vegl.maps.fld -lfile ../input_data/1hvrl.pdbqt
GRID PARAMETERS
________________________
Receptor name: 1hvr_vegl
Number of grid points (x, y, z): 65, 65, 65
Grid size (x, y, z): 24.000000, 24.000000, 24.000000A
Grid spacing: 0.375000A
LIGAND PARAMETERS
________________________
Ligand name: ../input_data/1hvrl
Number of atoms: 48
Number of rotatable bonds: 10
Number of atom types: 5
DUMMY DATA (only for ADT-compatibility)
________________________
DPF> outlev 1
DPF> ga_run 1
DPF> fld 1hvr_vegl.maps.fld
DPF> move ../input_data/1hvrl.pdbqt
INPUT LIGAND PDBQT FILE:
________________________
INPUT-LIGAND-PDBQT: REMARK
INPUT-LIGAND-PDBQT: REMARK 10 active torsions:
INPUT-LIGAND-PDBQT: REMARK status: ('A' for Active; 'I' for Inactive)
INPUT-LIGAND-PDBQT: REMARK 1 A between atoms: C2_4 and N1_3
INPUT-LIGAND-PDBQT: REMARK 2 A between atoms: C8_13 and C2_4
INPUT-LIGAND-PDBQT: REMARK 3 A between atoms: C3_5 and C18_23
INPUT-LIGAND-PDBQT: REMARK 4 A between atoms: O2_7 and C4_6
INPUT-LIGAND-PDBQT: REMARK 5 A between atoms: C5_8 and O3_9
INPUT-LIGAND-PDBQT: REMARK 6 A between atoms: C25_30 and C6_10
INPUT-LIGAND-PDBQT: REMARK 7 A between atoms: N2_11 and C7_12
INPUT-LIGAND-PDBQT: REMARK 8 A between atoms: C7_12 and C32_37
INPUT-LIGAND-PDBQT: REMARK 9 A between atoms: C19_24 and C18_23
INPUT-LIGAND-PDBQT: REMARK 10 A between atoms: C25_30 and C26_31
INPUT-LIGAND-PDBQT: ROOT
INPUT-LIGAND-PDBQT: ATOM 1 C1 <1> d -8.611 15.060 27.954 0.00 0.00 0.681 C
INPUT-LIGAND-PDBQT: ATOM 2 O1 <1> d -7.939 14.039 27.941 0.00 0.00 -0.613 OA
INPUT-LIGAND-PDBQT: ATOM 3 N1 <1> d -8.461 15.923 26.905 0.00 0.00 -0.450 N
INPUT-LIGAND-PDBQT: ATOM 4 C3 <1> d -8.627 17.388 27.011 0.00 0.00 0.205 C
INPUT-LIGAND-PDBQT: ATOM 5 C4 <1> d -10.029 17.910 27.298 0.00 0.00 0.261 C
INPUT-LIGAND-PDBQT: ATOM 6 C5 <1> d -10.461 17.645 28.733 0.00 0.00 0.148 C
INPUT-LIGAND-PDBQT: ATOM 7 C6 <1> d -10.657 16.152 28.964 0.00 0.00 0.189 C
INPUT-LIGAND-PDBQT: ATOM 8 N2 <1> d -9.461 15.294 29.004 0.00 0.00 -0.450 N
INPUT-LIGAND-PDBQT: ENDROOT
INPUT-LIGAND-PDBQT: BRANCH 3 9
INPUT-LIGAND-PDBQT: ATOM 9 C2 <1> d -7.854 15.351 25.696 0.00 0.00 0.253 C
INPUT-LIGAND-PDBQT: BRANCH 9 10
INPUT-LIGAND-PDBQT: ATOM 10 C8 <1> d -8.381 15.730 24.336 0.00 0.00 -0.005 A
INPUT-LIGAND-PDBQT: ATOM 11 C17 <1> d -7.408 15.983 23.346 0.00 0.00 -0.038 A
INPUT-LIGAND-PDBQT: ATOM 12 C16 <1> d -7.828 16.192 22.022 0.00 0.00 0.036 A
INPUT-LIGAND-PDBQT: ATOM 13 C15 <1> d -6.860 16.403 21.006 0.00 0.00 -0.016 A
INPUT-LIGAND-PDBQT: ATOM 14 C11 <1> d -9.219 16.152 21.693 0.00 0.00 0.004 A
INPUT-LIGAND-PDBQT: ATOM 15 C14 <1> d -7.263 16.562 19.662 0.00 0.00 0.010 A
INPUT-LIGAND-PDBQT: ATOM 16 C13 <1> d -8.626 16.508 19.349 0.00 0.00 -0.000 A
INPUT-LIGAND-PDBQT: ATOM 17 C12 <1> d -9.608 16.304 20.349 0.00 0.00 -0.007 A
INPUT-LIGAND-PDBQT: ATOM 18 C10 <1> d -10.195 15.919 22.694 0.00 0.00 0.008 A
INPUT-LIGAND-PDBQT: ATOM 19 C9 <1> d -9.769 15.712 24.022 0.00 0.00 -0.015 A
INPUT-LIGAND-PDBQT: ENDBRANCH 9 10
INPUT-LIGAND-PDBQT: ENDBRANCH 3 9
INPUT-LIGAND-PDBQT: BRANCH 4 20
INPUT-LIGAND-PDBQT: ATOM 20 C18 <1> d -7.476 17.972 27.894 0.00 0.00 -0.009 C
INPUT-LIGAND-PDBQT: BRANCH 20 21
INPUT-LIGAND-PDBQT: ATOM 21 C19 <1> d -6.124 17.890 27.193 0.00 0.00 0.056 A
INPUT-LIGAND-PDBQT: ATOM 22 C24 <1> d -5.803 18.811 26.163 0.00 0.00 -0.044 A
INPUT-LIGAND-PDBQT: ATOM 23 C23 <1> d -4.607 18.660 25.432 0.00 0.00 0.026 A
INPUT-LIGAND-PDBQT: ATOM 24 C22 <1> d -3.730 17.585 25.723 0.00 0.00 -0.029 A
INPUT-LIGAND-PDBQT: ATOM 25 C21 <1> d -4.029 16.667 26.750 0.00 0.00 0.028 A
INPUT-LIGAND-PDBQT: ATOM 26 C20 <1> d -5.226 16.826 27.494 0.00 0.00 -0.030 A
INPUT-LIGAND-PDBQT: ENDBRANCH 20 21
INPUT-LIGAND-PDBQT: ENDBRANCH 4 20
INPUT-LIGAND-PDBQT: BRANCH 5 27
INPUT-LIGAND-PDBQT: ATOM 27 O2 <1> d -9.929 19.274 26.998 0.00 0.00 -0.528 OA
INPUT-LIGAND-PDBQT: ATOM 28 H5 <1> d -9.892 19.779 27.814 0.00 0.00 0.316 HD
INPUT-LIGAND-PDBQT: ENDBRANCH 5 27
INPUT-LIGAND-PDBQT: BRANCH 8 29
INPUT-LIGAND-PDBQT: ATOM 29 C7 <1> d -9.271 14.491 30.215 0.00 0.00 0.248 C
INPUT-LIGAND-PDBQT: BRANCH 29 30
INPUT-LIGAND-PDBQT: ATOM 30 C32 <1> d -9.374 15.148 31.571 0.00 0.00 -0.012 A
INPUT-LIGAND-PDBQT: ATOM 31 C41 <1> d -8.574 16.252 31.962 0.00 0.00 -0.020 A
INPUT-LIGAND-PDBQT: ATOM 32 C40 <1> d -8.605 16.691 33.288 0.00 0.00 0.004 A
INPUT-LIGAND-PDBQT: ATOM 33 C39 <1> d -9.455 16.028 34.212 0.00 0.00 0.007 A
INPUT-LIGAND-PDBQT: ATOM 34 C34 <1> d -10.272 14.926 33.800 0.00 0.00 0.030 A
INPUT-LIGAND-PDBQT: ATOM 35 C38 <1> d -9.540 16.475 35.553 0.00 0.00 -0.010 A
INPUT-LIGAND-PDBQT: ATOM 36 C33 <1> d -10.228 14.492 32.477 0.00 0.00 -0.035 A
INPUT-LIGAND-PDBQT: ATOM 37 C35 <1> d -11.156 14.282 34.709 0.00 0.00 -0.013 A
INPUT-LIGAND-PDBQT: ATOM 38 C36 <1> d -11.245 14.748 36.044 0.00 0.00 0.015 A
INPUT-LIGAND-PDBQT: ATOM 39 C37 <1> d -10.435 15.837 36.451 0.00 0.00 0.006 A
INPUT-LIGAND-PDBQT: ENDBRANCH 29 30
INPUT-LIGAND-PDBQT: ENDBRANCH 8 29
INPUT-LIGAND-PDBQT: BRANCH 6 40
INPUT-LIGAND-PDBQT: ATOM 40 O3 <1> d -11.692 18.254 29.020 0.00 0.00 -0.535 OA
INPUT-LIGAND-PDBQT: ATOM 41 H7 <1> d -11.807 18.311 29.971 0.00 0.00 0.318 HD
INPUT-LIGAND-PDBQT: ENDBRANCH 6 40
INPUT-LIGAND-PDBQT: BRANCH 7 42
INPUT-LIGAND-PDBQT: ATOM 42 C25 <1> d -11.712 15.451 28.079 0.00 0.00 0.012 C
INPUT-LIGAND-PDBQT: BRANCH 42 43
INPUT-LIGAND-PDBQT: ATOM 43 C26 <1> d -12.310 14.248 28.779 0.00 0.00 0.064 A
INPUT-LIGAND-PDBQT: ATOM 44 C31 <1> d -11.992 12.954 28.304 0.00 0.00 -0.036 A
INPUT-LIGAND-PDBQT: ATOM 45 C30 <1> d -12.529 11.814 28.944 0.00 0.00 0.035 A
INPUT-LIGAND-PDBQT: ATOM 46 C29 <1> d -13.374 11.982 30.058 0.00 0.00 -0.032 A
INPUT-LIGAND-PDBQT: ATOM 47 C28 <1> d -13.700 13.281 30.542 0.00 0.00 0.027 A
INPUT-LIGAND-PDBQT: ATOM 48 C27 <1> d -13.167 14.422 29.898 0.00 0.00 -0.058 A
INPUT-LIGAND-PDBQT: ENDBRANCH 42 43
INPUT-LIGAND-PDBQT: ENDBRANCH 7 42
INPUT-LIGAND-PDBQT: TORSDOF 10
FINAL DOCKED STATE:
________________________
Run: 1 / 1
Time taken for this run: 7039.690s
DOCKED: MODEL 1
DOCKED: USER Run = 1
DOCKED: USER
DOCKED: USER Estimated Free Energy of Binding = -8.14 kcal/mol [=(1)+(2)+(3)-(4)]
DOCKED: USER
DOCKED: USER (1) Final Intermolecular Energy = -11.12 kcal/mol
DOCKED: USER vdW + Hbond + desolv Energy = -10.07 kcal/mol
DOCKED: USER Electrostatic Energy = -1.05 kcal/mol
DOCKED: USER (2) Final Total Internal Energy = -2.22 kcal/mol
DOCKED: USER (3) Torsional Free Energy = +2.98 kcal/mol
DOCKED: USER (4) Unbound System's Energy = -2.22 kcal/mol
DOCKED: USER
DOCKED: USER
DOCKED: REMARK
DOCKED: REMARK 10 active torsions:
DOCKED: REMARK status: ('A' for Active; 'I' for Inactive)
DOCKED: REMARK 1 A between atoms: C2_4 and N1_3
DOCKED: REMARK 2 A between atoms: C8_13 and C2_4
DOCKED: REMARK 3 A between atoms: C3_5 and C18_23
DOCKED: REMARK 4 A between atoms: O2_7 and C4_6
DOCKED: REMARK 5 A between atoms: C5_8 and O3_9
DOCKED: REMARK 6 A between atoms: C25_30 and C6_10
DOCKED: REMARK 7 A between atoms: N2_11 and C7_12
DOCKED: REMARK 8 A between atoms: C7_12 and C32_37
DOCKED: REMARK 9 A between atoms: C19_24 and C18_23
DOCKED: REMARK 10 A between atoms: C25_30 and C26_31
DOCKED: USER x y z vdW Elec q Type
DOCKED: USER _______ _______ _______ _____ _____ ______ ____
DOCKED: ROOT
DOCKED: ATOM 1 C1 <1> d -9.005 14.765 27.936 -0.31 +0.11 +0.681 C
DOCKED: ATOM 2 O1 <1> d -8.388 13.709 27.934 -0.94 -0.51 -0.613 OA
DOCKED: ATOM 3 N1 <1> d -8.983 15.506 26.788 -0.21 +0.03 -0.450 N
DOCKED: ATOM 4 C3 <1> d -9.067 16.981 26.756 -0.21 -0.09 +0.205 C
DOCKED: ATOM 5 C4 <1> d -10.383 17.612 27.191 -0.27 -0.31 +0.261 C
DOCKED: ATOM 6 C5 <1> d -10.598 17.521 28.695 -0.32 -0.16 +0.148 C
DOCKED: ATOM 7 C6 <1> d -10.819 16.074 29.115 -0.21 -0.09 +0.189 C
DOCKED: ATOM 8 N2 <1> d -9.670 15.154 29.069 -0.20 +0.04 -0.450 N
DOCKED: ENDROOT
DOCKED: BRANCH 3 9
DOCKED: ATOM 9 C2 <1> d -8.597 14.779 25.571 -0.32 +0.02 +0.253 C
DOCKED: BRANCH 9 10
DOCKED: ATOM 10 C8 <1> d -8.903 15.361 24.215 -0.25 +0.00 -0.005 A
DOCKED: ATOM 11 C17 <1> d -7.821 15.421 23.312 -0.25 +0.00 -0.038 A
DOCKED: ATOM 12 C16 <1> d -8.068 15.810 21.985 -0.26 -0.00 +0.036 A
DOCKED: ATOM 13 C15 <1> d -7.000 15.833 21.052 -0.26 -0.00 -0.016 A
DOCKED: ATOM 14 C11 <1> d -9.395 16.141 21.567 -0.33 -0.00 +0.004 A
DOCKED: ATOM 15 C14 <1> d -7.241 16.171 19.702 -0.26 -0.00 +0.010 A
DOCKED: ATOM 16 C13 <1> d -8.546 16.480 19.301 -0.37 +0.00 -0.000 A
DOCKED: ATOM 17 C12 <1> d -9.625 16.469 20.218 -0.40 +0.00 -0.007 A
DOCKED: ATOM 18 C10 <1> d -10.476 16.100 22.483 -0.29 -0.00 +0.008 A
DOCKED: ATOM 19 C9 <1> d -10.222 15.712 23.815 -0.28 +0.00 -0.015 A
DOCKED: ENDBRANCH 9 10
DOCKED: ENDBRANCH 3 9
DOCKED: BRANCH 4 20
DOCKED: ATOM 20 C18 <1> d -7.768 17.583 27.386 -0.22 +0.00 -0.009 C
DOCKED: BRANCH 20 21
DOCKED: ATOM 21 C19 <1> d -7.036 18.500 26.413 -0.18 -0.02 +0.056 A
DOCKED: ATOM 22 C24 <1> d -7.259 18.375 25.018 -0.14 +0.02 -0.044 A
DOCKED: ATOM 23 C23 <1> d -6.492 19.137 24.112 -0.15 -0.01 +0.026 A
DOCKED: ATOM 24 C22 <1> d -5.496 20.021 24.596 -0.06 +0.00 -0.029 A
DOCKED: ATOM 25 C21 <1> d -5.269 20.165 25.980 -0.23 -0.00 +0.028 A
DOCKED: ATOM 26 C20 <1> d -6.048 19.408 26.892 -0.23 +0.01 -0.030 A
DOCKED: ENDBRANCH 20 21
DOCKED: ENDBRANCH 4 20
DOCKED: BRANCH 5 27
DOCKED: ATOM 27 O2 <1> d -10.272 18.930 26.732 -0.51 +0.80 -0.528 OA
DOCKED: ATOM 28 H5 <1> d -10.996 19.454 27.085 -0.55 -0.89 +0.316 HD
DOCKED: ENDBRANCH 5 27
DOCKED: BRANCH 8 29
DOCKED: ATOM 29 C7 <1> d -9.329 14.469 30.319 -0.29 +0.01 +0.248 C
DOCKED: BRANCH 29 30
DOCKED: ATOM 30 C32 <1> d -9.187 15.266 31.594 -0.24 +0.00 -0.012 A
DOCKED: ATOM 31 C41 <1> d -8.412 16.450 31.687 -0.27 +0.00 -0.020 A
DOCKED: ATOM 32 C40 <1> d -8.189 17.032 32.938 -0.33 -0.00 +0.004 A
DOCKED: ATOM 33 C39 <1> d -8.763 16.429 34.088 -0.34 -0.00 +0.007 A
DOCKED: ATOM 34 C34 <1> d -9.560 15.244 33.978 -0.25 +0.00 +0.030 A
DOCKED: ATOM 35 C38 <1> d -8.590 17.017 35.365 -0.40 +0.00 -0.010 A
DOCKED: ATOM 36 C33 <1> d -9.769 14.668 32.727 -0.23 +0.00 -0.035 A
DOCKED: ATOM 37 C35 <1> d -10.171 14.656 35.120 -0.24 -0.00 -0.013 A
DOCKED: ATOM 38 C36 <1> d -10.005 15.263 36.389 -0.34 -0.00 +0.015 A
DOCKED: ATOM 39 C37 <1> d -9.216 16.434 36.498 -0.39 -0.00 +0.006 A
DOCKED: ENDBRANCH 29 30
DOCKED: ENDBRANCH 8 29
DOCKED: BRANCH 6 40
DOCKED: ATOM 40 O3 <1> d -11.741 18.228 29.095 -0.53 +0.82 -0.535 OA
DOCKED: ATOM 41 H7 <1> d -11.764 19.079 28.651 -0.60 -0.85 +0.318 HD
DOCKED: ENDBRANCH 6 40
DOCKED: BRANCH 7 42
DOCKED: ATOM 42 C25 <1> d -12.029 15.350 28.481 -0.24 -0.01 +0.012 C
DOCKED: BRANCH 42 43
DOCKED: ATOM 43 C26 <1> d -12.369 14.079 29.232 -0.16 -0.01 +0.064 A
DOCKED: ATOM 44 C31 <1> d -12.088 12.832 28.627 -0.28 +0.00 -0.036 A
DOCKED: ATOM 45 C30 <1> d -12.387 11.631 29.309 -0.30 -0.00 +0.035 A
DOCKED: ATOM 46 C29 <1> d -12.959 11.692 30.594 -0.20 +0.00 -0.032 A
DOCKED: ATOM 47 C28 <1> d -13.246 12.943 31.211 -0.14 +0.00 +0.027 A
DOCKED: ATOM 48 C27 <1> d -12.952 14.145 30.526 -0.14 +0.01 -0.058 A
DOCKED: ENDBRANCH 42 43
DOCKED: ENDBRANCH 7 42
DOCKED: TORSDOF 10
DOCKED: TER
DOCKED: ENDMDL
________________________________________________________________________________
CLUSTERING HISTOGRAM
____________________
________________________________________________________________________________
| | | | |
Clus | Lowest | Run | Mean | Num | Histogram
-ter | Binding | | Binding | in |
Rank | Energy | | Energy | Clus| 5 10 15 20 25 30 35
_____|___________|_____|___________|_____|____:____|____:____|____:____|____:___
1 | -8.14 | 1 | -8.14 | 1 |#
_____|___________|_____|___________|_____|______________________________________
RMSD TABLE
__________
_____________________________________________________________________
| | | | | |
Rank | Sub- | Run | Binding | Cluster | Reference | Grep
| Rank | | Energy | RMSD | RMSD | Pattern
_____|______|______|___________|_________|_________________|___________
1 1 1 -8.14 0.00 1.16 RANKING
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<?xml version="1.0" ?>
<result>
<clustering_histogram>
<cluster cluster_rank="1" lowest_binding_energy="-8.14" run="1" mean_binding_energy="-8.14" num_in_clus="1" />
</clustering_histogram>
<rmsd_table>
<run rank="1" sub_rank="1" run="1" binding_energy="-8.14" cluster_rmsd="0.00" reference_rmsd="1.16" />
</rmsd_table>
</result>
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[lvs@celebdil bin]$ CL_CONTEXT_EMULATOR_DEVICE_ALTERA=1 ./host -ffile ../input_data/1hvr_vegl.maps.fld -lfile ../input_data/1hvrl.pdbqt
Querying platform for info:
==========================
CL_PLATFORM_NAME = Intel(R) FPGA SDK for OpenCL(TM)
CL_PLATFORM_VENDOR = Altera Corporation
CL_PLATFORM_VERSION = OpenCL 1.0 Intel(R) FPGA SDK for OpenCL(TM), Version 16.1
Querying device for info:
========================
CL_DEVICE_NAME = EmulatorDevice : Emulated Device
CL_DEVICE_VENDOR = Altera Corporation
CL_DEVICE_VENDOR_ID = 4466
CL_DEVICE_VERSION = OpenCL 1.0 Intel(R) FPGA SDK for OpenCL(TM), Version 16.1
CL_DRIVER_VERSION = 16.1
CL_DEVICE_ADDRESS_BITS = 64
CL_DEVICE_AVAILABLE = true
CL_DEVICE_ENDIAN_LITTLE = true
CL_DEVICE_GLOBAL_MEM_CACHE_SIZE = 32768
CL_DEVICE_GLOBAL_MEM_CACHELINE_SIZE = 0
CL_DEVICE_GLOBAL_MEM_SIZE = 8589934592
CL_DEVICE_IMAGE_SUPPORT = true
CL_DEVICE_LOCAL_MEM_SIZE = 16384
CL_DEVICE_MAX_CLOCK_FREQUENCY = 1000
CL_DEVICE_MAX_COMPUTE_UNITS = 1
CL_DEVICE_MAX_CONSTANT_ARGS = 8
CL_DEVICE_MAX_CONSTANT_BUFFER_SIZE = 2147483648
CL_DEVICE_MAX_WORK_ITEM_DIMENSIONS = 3
CL_DEVICE_MEM_BASE_ADDR_ALIGN = 8192
CL_DEVICE_MIN_DATA_TYPE_ALIGN_SIZE = 1024
CL_DEVICE_PREFERRED_VECTOR_WIDTH_CHAR = 4
CL_DEVICE_PREFERRED_VECTOR_WIDTH_SHORT = 2
CL_DEVICE_PREFERRED_VECTOR_WIDTH_INT = 1
CL_DEVICE_PREFERRED_VECTOR_WIDTH_LONG = 1
CL_DEVICE_PREFERRED_VECTOR_WIDTH_FLOAT = 1
CL_DEVICE_PREFERRED_VECTOR_WIDTH_DOUBLE = 0
Command queue out of order? = false
Command queue profiling enabled? = true
Using AOCX: docking.aocx
Init complete!
Executing docking runs:
20% 40% 60% 80% 100%
---------+---------+---------+---------+---------+
**************************************************
Program run time 7048.609 sec (CORRECTED, used for EVALUATION)
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package require -exact qsys 12.1
set_validation_property AUTOMATIC_VALIDATION false
add_instance kernel_system kernel_system
add_connection board.kernel_clk kernel_system.clock_reset
add_connection board.kernel_clk2x kernel_system.clock_reset2x
add_connection board.kernel_reset kernel_system.clock_reset_reset
add_connection kernel_system.kernel_mem0 board.kernel_mem0
add_connection board.kernel_irq kernel_system.kernel_irq
add_connection board.kernel_cra kernel_system.kernel_cra
add_connection board.acl_internal_snoop kernel_system.cc_snoop
add_connection board.kernel_clk kernel_system.cc_snoop_clk
save_system
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<?xml version="1.0"?>
<board name="a10gx" vfabric="0" big_endian="0">
<global_mem_config name="DDR" mode="burst-interleaved"/>
<kernel name="calc_initpop" csr_addr="0" csr_size="256" work_group_invariant="0" vector_lanes="1" >
<work_group size_x="32" size_y="1" size_z="1" max_size="32"/>
<argument index="0" type="0" category="0" size="1" >
</argument>
<argument index="1" type="0" category="0" size="1" >
</argument>
<argument index="2" type="0" category="0" size="4" >
</argument>
<argument index="3" type="0" category="0" size="1" >
</argument>
<argument index="4" type="0" category="0" size="1" >
</argument>
<argument index="5" type="0" category="0" size="1" >
</argument>
<argument index="6" type="0" category="0" size="4" >
</argument>
<argument index="7" type="2" category="1" size="8" >
</argument>
<argument index="8" type="0" category="0" size="4" >
</argument>
<argument index="9" type="0" category="0" size="4" >
</argument>
<argument index="10" type="0" category="0" size="4" >
</argument>
<argument index="11" type="2" category="1" size="8" >
</argument>
<argument index="12" type="2" category="1" size="8" >
</argument>
<argument index="13" type="2" category="1" size="8" >
</argument>
<argument index="14" type="0" category="0" size="4" >
</argument>
<argument index="15" type="0" category="0" size="4" >
</argument>
<argument index="16" type="2" category="1" size="8" >
</argument>
<local_memory id="5" local_demand="256"/>
<local_memory id="6" local_demand="4"/>
<local_memory id="7" local_demand="128"/>
<local_memory id="8" local_demand="360"/>
<local_memory id="9" local_demand="360"/>
<local_memory id="10" local_demand="360"/>
</kernel>
<kernel name="gen_and_eval_newpops" csr_addr="256" csr_size="256" work_group_invariant="0" vector_lanes="1" >
<work_group size_x="32" size_y="1" size_z="1" max_size="32"/>
<argument index="0" type="0" category="0" size="1" >
</argument>
<argument index="1" type="0" category="0" size="1" >
</argument>
<argument index="2" type="0" category="0" size="4" >
</argument>
<argument index="3" type="0" category="0" size="1" >
</argument>
<argument index="4" type="0" category="0" size="1" >
</argument>
<argument index="5" type="0" category="0" size="1" >