Continuous Integration via Travis

.travis.yml

@@ -0,0 +1,50 @@
+language: cpp
+
+services:
+- docker
+
+jobs:
+  include:
+  - os: linux
+    dist: focal
+    sudo: required
+    env: NUMWI=1
+  - os: linux
+    dist: focal
+    sudo: required
+    env: NUMWI=4
+  - os: linux
+    dist: focal
+    sudo: required
+    env: NUMWI=8
+  - os: linux
+    dist: focal
+    sudo: required
+    env: NUMWI=16
+  - os: linux
+    dist: focal
+    sudo: required
+    env: NUMWI=32
+  - os: linux
+    dist: focal
+    sudo: required
+    env: NUMWI=64
+  - os: linux
+    dist: bionic
+    sudo: required
+    env: NUMWI=16
+  - os: linux
+    dist: xenial
+    sudo: required
+    env: NUMWI=16
+
+before_install:
+- export GIT_BRANCH=docker
+- export GIT_SLUG=L30nardoSV/AutoDock-GPU
+#- export GIT_BRANCH=develop
+#- export GIT_SLUG=ccsb-scripps/AutoDock-GPU
+- docker build --build-arg git_branch=${GIT_BRANCH} --build-arg git_slug=${GIT_SLUG} -t adgpu .
+
+script:
+- export numwi=${NUMWI}
+- docker run -e numwi adgpu

.travis/install_intel_opencl.sh

@@ -0,0 +1,22 @@
+#!/bin/bash
+
+set -ev
+
+###########################
+# Get Intel OpenCL Runtime
+###########################
+
+# Code taken from here:
+# https://github.com/KhronosGroup/SyclParallelSTL/blob/master/.travis/install_intel_opencl.sh
+#
+# Intel OpenCL drivers available here:
+# https://software.intel.com/en-us/articles/opencl-drivers#latest_CPU_runtime
+
+PACKAGE_URL=http://registrationcenter-download.intel.com/akdlm/irc_nas/12556/opencl_runtime_16.1.2_x64_rh_6.4.0.37.tgz
+PACKAGE_NAME=opencl_runtime_16.1.2_x64_rh_6.4.0.37
+
+wget -q ${PACKAGE_URL} -O /tmp/opencl_runtime.tgz
+tar -xzf /tmp/opencl_runtime.tgz -C /tmp
+sed 's/decline/accept/g' -i /tmp/${PACKAGE_NAME}/silent.cfg
+apt-get install -yq cpio
+/tmp/${PACKAGE_NAME}/install.sh -s /tmp/${PACKAGE_NAME}/silent.cfg

.travis/run_test.sh

@@ -0,0 +1,90 @@
+#!/bin/bash
+
+set -o xtrace
+
+###########################
+# Run test
+###########################
+
+# This script is invoked from the Dockerfile,
+# but can also be invoked independently (for local tests).
+# E.g.: source .travis/run_test.sh 4
+# The argument "4" passes the NUMWI value.
+
+info="[INFO]"
+asterix_line="========================================================================"
+
+function verify_sourced_script() {
+  echo " "
+  echo "${lines}"
+  echo "${info}: Verifying if script is being sourced"
+  echo "${lines}"
+  echo " "
+  if [[ ${BASH_SOURCE[0]} != $0 ]]; then
+    echo "${info}: OK. Script "${BASH_SOURCE[0]}" is sourced"
+  else
+    echo "${info}: Run \"source ${BASH_SOURCE[0]}\" instead!"
+    echo "Terminating!" && exit 1
+  fi
+}
+
+function run_clinfo() {
+    echo " "
+    echo "${asterix_line}"
+    echo "${info}: Running clinfo"
+    echo "${asterix_line}"
+    echo " "
+    clinfo
+}
+
+#ADGPU_DIR=~/Desktop/AutoDock-GPU
+ADGPU_DIR=/AutoDock-GPU
+BIN_DIR=${ADGPU_DIR}/bin
+DEVICE=CPU
+
+function compile_adgpu() {
+    echo " "
+    echo "${asterix_line}"
+    echo "${info}: Compiling AutoDock-GPU"
+    echo "${asterix_line}"
+    echo " "
+    cd ${ADGPU_DIR}
+    make DEVICE=${DEVICE} NUMWI=${1}
+    ls -asl ${BIN_DIR}
+}
+
+function run_test() {
+    echo " "
+    echo "${asterix_line}"
+    echo "${info}: Running automated test"
+    echo "${asterix_line}"
+    echo " "
+    for pdb in "3ce3" "1stp"; do
+        for lsmet in "sw" "ad"; do
+            for nrun in 1 10; do
+                for ngen in 10 100; do
+                    for psize in 10 50; do
+                        ${BIN_DIR}/autodock_cpu_${1}wi \
+                        -ffile ./input/${pdb}/derived/${pdb}_protein.maps.fld \
+                        -lfile ./input/${pdb}/derived/${pdb}_ligand.pdbqt \
+                        -lsmet ${lsmet} \
+                        -nrun ${nrun} \
+                        -ngen ${ngen} \
+                        -psize ${psize} \
+                        -resnam ${pdb}-${lsmet}-${nrun}-${ngen}-${psize}-"`date +"%Y-%m-%d-%H:%M:%S"`" \
+                        -xmloutput 0
+                        echo " "
+	                    tail -30 ${pdb}-${lsmet}-${nrun}-${ngen}-${psize}-*.dlg
+                    done
+                done
+            done
+        done
+    done        
+    echo " "
+    ls -asl *.dlg
+}
+
+verify_sourced_script
+run_clinfo
+compile_adgpu ${1}
+run_test ${1}

Dockerfile

@@ -0,0 +1,31 @@
+FROM ubuntu:bionic
+
+# Build arguments
+ARG git_branch
+ARG git_slug
+
+# Execution arguments
+ENV numwi 16
+
+# Utilities
+RUN apt-get -yq update
+
+RUN apt-get install -yq --allow-downgrades --allow-remove-essential            \
+    --allow-change-held-packages git wget apt-utils cmake unzip clinfo         \
+    g++ gcc clang libboost-all-dev software-properties-common 
+
+RUN add-apt-repository -y ppa:ubuntu-toolchain-r/test
+
+RUN apt-get -yq update
+
+# OpenCL ICD Loader
+RUN apt-get install -yq --allow-downgrades --allow-remove-essential           \
+    --allow-change-held-packages ocl-icd-opencl-dev ocl-icd-dev opencl-headers
+
+# AutoDock-GPU
+RUN git clone https://github.com/${git_slug}.git -b ${git_branch} /AutoDock-GPU
+
+# Intel OpenCL Runtime
+RUN bash /AutoDock-GPU/.travis/install_intel_opencl.sh
+
+CMD bash -c "source /AutoDock-GPU/.travis/run_test.sh ${numwi}"

Makefile.Cuda

@@ -190,46 +190,28 @@ odock: check-env-all kernels $(SRC)
 	-o$(BIN_DIR)/$(TARGET) \
 	$(DEV) $(NWI) $(PIPELINE) $(OPT) $(DD) $(REP) $(KFLAGS)
 
-# Example
-# 1ac8: for testing gradients of translation and rotation genes
-# 7cpa: for testing gradients of torsion genes (15 torsions) 
-# 3tmn: for testing gradients of torsion genes (1 torsion)
+# ------------------------------------------------------
 
 PDB      := 3ce3
 NRUN     := 100
 NGEN     := 27000
-POPSIZE  := 150
-TESTNAME := test
-TESTLS   := sw
+PSIZE    := 150
+RESNAM   := test
+LSMET    := sw
 
 test: odock
 	$(BIN_DIR)/$(TARGET) \
 	-ffile ./input/$(PDB)/derived/$(PDB)_protein.maps.fld \
 	-lfile ./input/$(PDB)/derived/$(PDB)_ligand.pdbqt \
+	-lsmet $(LSMET) \
 	-nrun $(NRUN) \
 	-ngen $(NGEN) \
-	-psize $(POPSIZE) \
-	-resnam $(TESTNAME) \
+	-psize $(PSIZE) \
+	-resnam $(RESNAM) \
 	-gfpop 0 \
-	-lsmet $(TESTLS)
-
-ASTEX_PDB := 2bsm
-ASTEX_NRUN:= 10
-ASTEX_POPSIZE := 10
-ASTEX_TESTNAME := test_astex
-ASTEX_LS := sw
+	-xmloutput 0
 
-astex: odock
-	$(BIN_DIR)/$(TARGET) \
-	-ffile ./input_tsri/search-set-astex/$(ASTEX_PDB)/protein.maps.fld \
-	-lfile ./input_tsri/search-set-astex/$(ASTEX_PDB)/flex-xray.pdbqt \
-	-nrun $(ASTEX_NRUN) \
-	-psize $(ASTEX_POPSIZE) \
-	-resnam $(ASTEX_TESTNAME) \
-	-gfpop 1 \
-	-lsmet $(ASTEX_LS)
-
-#	$(BIN_DIR)/$(TARGET) -ffile ./input_tsri/search-set-astex/$(ASTEX_PDB)/protein.maps.fld -lfile ./input_tsri/search-set-astex/$(ASTEX_PDB)/flex-xray.pdbqt -nrun $(ASTEX_NRUN) -psize $(ASTEX_POPSIZE) -resnam $(ASTEX_TESTNAME) -gfpop 1 | tee ./input_tsri/search-set-astex/intrapairs/$(ASTEX_PDB)_intrapair.txt
+# ------------------------------------------------------
 
 clean:
 	rm -f $(BIN_DIR)/* initpop.txt $(HOST_INC_DIR)/performdocking.h $(HOST_SRC_DIR)/performdocking.cpp

Makefile.OpenCL

@@ -250,46 +250,28 @@ odock: check-env-all stringify $(SRC)
 	-o$(BIN_DIR)/$(TARGET) \
 	$(DEV) $(NWI) $(PIPELINE) $(OPT) $(DD) $(REP) $(KFLAGS)
 
-# Example
-# 1ac8: for testing gradients of translation and rotation genes
-# 7cpa: for testing gradients of torsion genes (15 torsions) 
-# 3tmn: for testing gradients of torsion genes (1 torsion)
+# ------------------------------------------------------
 
 PDB      := 3ce3
 NRUN     := 100
 NGEN     := 27000
-POPSIZE  := 150
-TESTNAME := test
-TESTLS   := sw
+PSIZE    := 150
+RESNAM   := test
+LSMET    := sw
 
 test: odock
 	$(BIN_DIR)/$(TARGET) \
 	-ffile ./input/$(PDB)/derived/$(PDB)_protein.maps.fld \
 	-lfile ./input/$(PDB)/derived/$(PDB)_ligand.pdbqt \
+	-lsmet $(LSMET) \
 	-nrun $(NRUN) \
 	-ngen $(NGEN) \
-	-psize $(POPSIZE) \
-	-resnam $(TESTNAME) \
+	-psize $(PSIZE) \
+	-resnam $(RESNAM) \
 	-gfpop 0 \
-	-lsmet $(TESTLS)
-
-ASTEX_PDB := 2bsm
-ASTEX_NRUN:= 10
-ASTEX_POPSIZE := 10
-ASTEX_TESTNAME := test_astex
-ASTEX_LS := sw
+	-xmloutput 0
 
-astex: odock
-	$(BIN_DIR)/$(TARGET) \
-	-ffile ./input_tsri/search-set-astex/$(ASTEX_PDB)/protein.maps.fld \
-	-lfile ./input_tsri/search-set-astex/$(ASTEX_PDB)/flex-xray.pdbqt \
-	-nrun $(ASTEX_NRUN) \
-	-psize $(ASTEX_POPSIZE) \
-	-resnam $(ASTEX_TESTNAME) \
-	-gfpop 1 \
-	-lsmet $(ASTEX_LS)
-
-#	$(BIN_DIR)/$(TARGET) -ffile ./input_tsri/search-set-astex/$(ASTEX_PDB)/protein.maps.fld -lfile ./input_tsri/search-set-astex/$(ASTEX_PDB)/flex-xray.pdbqt -nrun $(ASTEX_NRUN) -psize $(ASTEX_POPSIZE) -resnam $(ASTEX_TESTNAME) -gfpop 1 | tee ./input_tsri/search-set-astex/intrapairs/$(ASTEX_PDB)_intrapair.txt
+# ------------------------------------------------------
 
 clean:
 	rm -f $(BIN_DIR)/* initpop.txt $(HOST_INC_DIR)/performdocking.h $(HOST_SRC_DIR)/performdocking.cpp