added kernel-stringify support

.gitignore

@@ -2,7 +2,7 @@
 initpop.txt
 *.dlg
 *.xml
-input/2bxd/
+input/albumin_dock/
 ocladock.wiki/
 
 # ===================

Makefile

-# ocladock Makefile
+# OCLADock Makefile
 
 # CPU config
 INTEL_INCLUDE_PATH=$(INTELOCLSDKROOT)/include
@@ -128,7 +128,10 @@ endif
 
 all: odock
 
-odock: $(SRC)
+stringify:
+	./stringify_ocl_krnls.sh
+
+odock: stringify $(SRC)
 	g++ $(SRC) $(CFLAGS) -lOpenCL -o$(BIN_DIR)/$(TARGET) $(DEV) $(NWI) $(OPT) $(DD) $(REP) $(KFLAGS)
 
 clean:

host/src/performdocking.cpp

@@ -64,6 +64,7 @@
 #define OPT_PROG INC KNWI REP KGDB
 
 #include "performdocking.h"
+#include "stringify.h"
 
 int docking_with_gpu(const Gridinfo*   mygrid,
 	             	 /*const*/ float*      cpu_floatgrids,
@@ -98,8 +99,13 @@ filled with clock() */
 	cl_context context;
 	cl_command_queue command_queue;
 
+#ifdef _WIN32
 	const char *filename = KRNL_FILE;
 	printf("\n%-40s %-40s\n", "Kernel source file: ", filename);  fflush(stdout);
+#else
+	printf("\n%-40s %-40s\n", "Kernel source used for development: ", "./device/calcenergy.cl");  fflush(stdout);
+	printf(  "%-40s %-40s\n", "Kernel string used for building: ",    "./host/inc/stringify.h");  fflush(stdout);
+#endif
 
 	const char* options_program = OPT_PROG;
 	printf("%-40s %-40s\n", "Kernel compilation flags: ", options_program); fflush(stdout);
@@ -136,10 +142,17 @@ filled with clock() */
 	if (createCommandQueue(context,device_id[0],&command_queue) != 0) return 1;
 
 	// Create program and kernel from source
+#ifdef _WIN32
 	if (ImportSource(filename, name_k1, device_id, context, options_program, &kernel1) != 0) return 1;
 	if (ImportSource(filename, name_k2, device_id, context, options_program, &kernel2) != 0) return 1;
 	if (ImportSource(filename, name_k3, device_id, context, options_program, &kernel3) != 0) return 1;
 	if (ImportSource(filename, name_k4, device_id, context, options_program, &kernel4) != 0) return 1;
+#else
+	if (ImportSource(calcenergy_ocl, name_k1, device_id, context, options_program, &kernel1) != 0) return 1;
+	if (ImportSource(calcenergy_ocl, name_k2, device_id, context, options_program, &kernel2) != 0) return 1;
+	if (ImportSource(calcenergy_ocl, name_k3, device_id, context, options_program, &kernel3) != 0) return 1;
+	if (ImportSource(calcenergy_ocl, name_k4, device_id, context, options_program, &kernel4) != 0) return 1;
+#endif
 
 // End of OpenCL Host Setup
 // =======================================================================

stringify_ocl_krnls.sh

+#!/bin/bash
+
+# kernel-header files
+HEADER_DIR="./common"
+IN_HEADER1=$HEADER_DIR/"defines.h"
+IN_HEADER2=$HEADER_DIR/"calcenergy_basic.h"
+
+echo " "
+echo "Stringified input header-files: "
+echo $IN_HEADER1
+echo $IN_HEADER2
+
+# kernel files
+KERNEL_DIR="./device"
+IN_KERNELm=$KERNEL_DIR/"calcenergy.cl"
+IN_KERNEL1=$KERNEL_DIR/"kernel1.cl"
+IN_KERNEL2=$KERNEL_DIR/"kernel2.cl"
+IN_KERNELa=$KERNEL_DIR/"auxiliary_genetic.cl"
+IN_KERNEL3=$KERNEL_DIR/"kernel3.cl"
+IN_KERNEL4=$KERNEL_DIR/"kernel4.cl"
+
+echo " "
+echo "Stringified input kernel-files: "
+echo $IN_KERNELm
+echo $IN_KERNEL1
+echo $IN_KERNEL2
+echo $IN_KERNELa
+echo $IN_KERNEL3
+echo $IN_KERNEL4
+
+# output file
+OUT=host/inc/stringify.h
+
+echo " "
+echo "Stringified output file: "
+echo $OUT
+echo " "
+
+# temporal file
+TMP=$KERNEL_DIR/stringify_tmp
+
+echo "// OCLADOCK: AUTOMATICALLY GENERATED FILE, DO NOT EDIT" >$TMP
+echo "#ifndef STRINGIFY_H" >>$TMP
+echo "#define STRINGIFY_H" >>$TMP
+
+echo "const char *calcenergy_ocl =" >>$TMP
+sed 's/\\/\\\\/g;s/"/\\"/g;s/^/"/;s/$/\\n"/' $IN_HEADER1 >> $TMP
+sed 's/\\/\\\\/g;s/"/\\"/g;s/^/"/;s/$/\\n"/' $IN_HEADER2 >> $TMP
+sed 's/\\/\\\\/g;s/"/\\"/g;s/^/"/;s/$/\\n"/' $IN_KERNELm >> $TMP
+sed 's/\\/\\\\/g;s/"/\\"/g;s/^/"/;s/$/\\n"/' $IN_KERNEL1 >> $TMP
+sed 's/\\/\\\\/g;s/"/\\"/g;s/^/"/;s/$/\\n"/' $IN_KERNEL2 >> $TMP
+sed 's/\\/\\\\/g;s/"/\\"/g;s/^/"/;s/$/\\n"/' $IN_KERNELa >> $TMP
+sed 's/\\/\\\\/g;s/"/\\"/g;s/^/"/;s/$/\\n"/' $IN_KERNEL3 >> $TMP
+sed 's/\\/\\\\/g;s/"/\\"/g;s/^/"/;s/$/\\n"/' $IN_KERNEL4 >> $TMP
+echo ";" >>$TMP
+
+echo "#endif // End of STRINGIFY_H" >>$TMP
+
+# remove "#include" lines
+grep -v '#include' $TMP > $OUT

wrapcl/src/ImportSource.cpp

@@ -41,10 +41,15 @@ int ImportSource(const char*    filename,
 {
 	cl_int err;
 
+#ifdef _WIN32
 	// Create the compute program ONLINE
 	string sourceStr;
 	err = convertToString2(filename, sourceStr);
 	const char *source = sourceStr.c_str();
+#else
+	// Added as kernel is stringified already
+	const char *source = filename;
+#endif
 
 	// L30nardoSV
 	size_t sourceSize[] = { strlen(source) };