scottransom · jintaoluo · May 16, 2014 · May 16, 2014 · May 23, 2014 · Sep 5, 2014
diff --git a/Howto_GPU.md b/Howto_GPU.md
@@ -0,0 +1,23 @@
+#GPUed PRESTO
+
+The program of accelsearch in PRESTO was accelerated with CUDA by Jintao Luo. Any questions on how to compile and use the GPU routine may go to [email protected]
+
+##How to compile
+
+###compile for CPU-only
+By default PRESTO will be compiled for CPU-only. This is controlled by line 22 in $PRESTO/src/Makefile. For CPU-only, this line should be as:
+>use_cuda = no# yes/no
+
+###compile with GPU routines
+Open the $PRESTO/src/Makefile
+
+1.	Make sure line 22 is:
+>use_cuda = yes# yes/no
+
+2.	Check the CUDA-related variables and flags, and modify them if necessary.
+
+##How to use
+To run accelsearch on GPU, use the -cuda option. Or the program will run on CPU. For example: 
+>accelsearch -numharm 16 -zmax 256 ur_data.dat -cuda 0
+
+0 means using the 1st GPU in your machine.
diff --git a/include/accel_utils_gpu.h b/include/accel_utils_gpu.h
@@ -0,0 +1,70 @@
+/* ACCEL_USELEN must be less than 65536 since we  */
+/* use unsigned short ints to index our arrays... */
+/* #define ACCEL_USELEN 32160 */
+/* #define ACCEL_USELEN 16000 */
+#define ACCEL_USELEN 7560 
+#define ACCEL_NUMBETWEEN 2
+/* Stepsize in Fourier Freq */
+#define ACCEL_DR  0.5
+/* Reciprocal of ACCEL_DR */
+#define ACCEL_RDR 2
+/* Stepsize in Fourier F-dot */
+#define ACCEL_DZ  2
+/* Reciprocal of ACCEL_DZ */
+#define ACCEL_RDZ 0.5
+/* Closest candidates we will accept as independent */
+#define ACCEL_CLOSEST_R 15.0
+/* Padding for .dat file reading so that we don't SEGFAULT */
+#define ACCEL_PADDING 2000
+
+
+#ifndef DBLCORRECT
+#define DBLCORRECT    1e-14
+#endif
+
+#ifndef _ACCEL_UTILS_GPU_
+#define _ACCEL_UTILS_GPU_
+
+typedef struct accel_cand_gpu{
+	float pow;					/*pow of selected candidate*/
+	int		nof_cand;			/*number of candidates in sub_array/plane */
+	int		z_ind;				/*z_index of the selected candidate*/
+	int		r_ind;				/*r_index of the selected candidate*/
+}	accel_cand_gpu;
+
+#ifndef _FCOMPLEX_DECLARED_
+typedef struct fcomplex {
+    float r, i;
+} fcomplex;
+#define _FCOMPLEX_DECLARED_
+#endif				/* _FCOMPLEX_DECLARED_ */
+
+typedef struct kernel{
+  int z;               /* The fourier f-dot of the kernel */
+  int fftlen;          /* Number of complex points in the kernel */
+  int numgoodbins;     /* The number of good points you can get back */
+  int numbetween;      /* Fourier freq resolution (2=interbin) */
+  int kern_half_width; /* Half width (bins) of the raw kernel. */
+  fcomplex *data;      /* The FFTd kernel itself */
+} kernel;
+
+typedef struct subharminfo{
+  int numharm;       /* The number of sub-harmonics */
+  int harmnum;       /* The sub-harmonic number (fundamental = numharm) */
+  int zmax;          /* The maximum Fourier f-dot for this harmonic */
+  int numkern;       /* Number of kernels in the vector */
+  kernel *kern;      /* The kernels themselves */
+  unsigned short *rinds; /* Table of indices for Fourier Freqs */
+} subharminfo;
+
+
+/*  Constants used in the correlation/convolution routines */
+typedef enum {
+  CONV, CORR, INPLACE_CONV, INPLACE_CORR
+} presto_optype;
+
+typedef enum {
+  FFTDK, FFTD, FFTK, NOFFTS
+} presto_ffts;
+
+#endif
diff --git a/include/accelsearch_cmd.h b/include/accelsearch_cmd.h
@@ -72,6 +72,11 @@ typedef struct s_Cmdline {
   /*@null*/char **argv;
   /***** the whole command line concatenated */
   char *full_cmd_line;
+  /***** cuda device parameters */
+  #ifdef USECUDA
+  char cudaP;
+  char cuda;  
+  #endif
 } Cmdline;
 
 

diff --git a/src/Makefile b/src/Makefile
@@ -1,5 +1,6 @@
 #  Makefile for PRESTO
 #   by Scott M. Ransom
+#		GPU-related sections by Jintao Luo
 
 # OS type
 OS = Linux
@@ -8,13 +9,60 @@ OS = Linux
 # Linux is the first choice
 ifeq ($(OS),Linux)
 	LIBSUFFIX = .so
-	LIBCMD = -shared
+	LIBCMD = -shared	
 # else assume Darwin (i.e. OSX)
 else
 	LIBSUFFIX = .dylib
 	LIBCMD = -dynamiclib
 endif
 
+
+#------------------------------------------------------------------------------------------
+#determine if compile with CUDA
+use_cuda = yes# yes/no
+
+ifeq ($(use_cuda),yes)
+$(info Compile with CUDA)
+#******************************************************************
+#                     for GUP version, CUDA 
+# CUDA compile option
+# CUDA code generation flags
+	GENCODE_SM10    := -gencode arch=compute_10,code=sm_10
+	GENCODE_SM10    := -gencode arch=compute_11,code=sm_11
+	GENCODE_SM20    := -gencode arch=compute_20,code=sm_20
+	GENCODE_SM30    := -gencode arch=compute_30,code=sm_30 -gencode arch=compute_35,code=sm_35
+	GENCODE_FLAGS   := $(GENCODE_SM10) $(GENCODE_SM20) $(GENCODE_SM30)
+# Location of the CUDA Toolkit binaries and libraries
+#modify it if necessary
+#CUDA_PATH       ?= /usr/local/cuda-5.0
+	CUDA_PATH       ?= /usr/local/cuda
+
+#modify it if necessary
+	CUDA_INC_PATH   ?= -I $(CUDA_PATH)/include -I. -I.. -I $(CUDA_PATH)/samples/common/inc/ -I$(PRESTO)/include
+
+	CUDA_BIN_PATH   ?= $(CUDA_PATH)/bin
+	NVCC            ?= $(CUDA_BIN_PATH)/nvcc
+
+#modify it if necessary, for example, if 32-bit machine, -m32
+	NVCCFLAGS 			?= -m64 -ccbin g++
+
+	EXTRA_NVCCFLAGS ?= -Xcompiler -fPIC -O2
+
+#modify it if necessary, -m64 to -m32 for 32-bit machine
+	LINKCOMMAND_CUDA = g++ -m64 -O2 -o	
+
+#modify it if necessary, maybe lib64 should be lib32?
+	CUDA_LINK_EXTRA_FLAGS = -L $(CUDA_PATH)/lib64 -lcufft  -lcudart
+#******************************************************************
+endif
+
+ifeq ($(use_cuda),no)
+$(info Compile without CUDA)
+endif
+#------------------------------------------------------------------------------------------
+
+
+
 # How to link with some needed libraries of PGPLOT
 X11LINK := $(shell pkg-config --libs x11)
 PNGLINK := $(shell pkg-config --libs libpng)
@@ -37,7 +85,14 @@ CFITSIOINC := $(shell pkg-config --cflags cfitsio)
 CFITSIOLINK := $(shell pkg-config --libs cfitsio)
 
 # The standard PRESTO libraries to link into executables
+#PRESTOLINK = $(CFITSIOLINK) -L$(PRESTO)/lib -lpresto $(FFTLINK)
+ifeq ($(use_cuda),no)
 PRESTOLINK = $(CFITSIOLINK) -L$(PRESTO)/lib -lpresto $(FFTLINK)
+endif
+
+ifeq ($(use_cuda),yes)
+PRESTOLINK = $(CFITSIOLINK) -L$(PRESTO)/lib -lpresto $(FFTLINK) $(CUDA_LINK_EXTRA_FLAGS) -L $(SYSDIR)/lib/x86_64-linux-gnu -lstdc++
+endif
 
 CC = gcc
 FC = gfortran
@@ -46,6 +101,11 @@ FC = gfortran
 CFLAGS = -I$(PRESTO)/include $(GLIBINC) $(CFITSIOINC) $(PGPLOTINC) $(FFTINC) \
 	-DUSEFFTW -DUSEMMAP -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 \
 	-g -O3 -ffast-math -Wall -W -fPIC
+
+ifeq ($(use_cuda),yes)
+	CFLAGS += -DUSECUDA
+endif
+
 #	-g -Wall -W -fPIC
 CLINKFLAGS = $(CFLAGS)
 # NOTE:  Be careful of upping the optimization on the
@@ -69,6 +129,7 @@ CLIG = clig
 	mv ../clig/$*_cmd.c .
 	cp ../clig/$*.1 ../docs/
 
+ifeq ($(use_cuda),yes)
 PRESTOOBJS = amoeba.o atwood.o barycenter.o birdzap.o cand_output.o\
 	characteristics.o cldj.o chkio.o corr_prep.o corr_routines.o\
 	correlations.o database.o dcdflib.o dispersion.o\
@@ -79,7 +140,21 @@ PRESTOOBJS = amoeba.o atwood.o barycenter.o birdzap.o cand_output.o\
 	rzinterp.o rzwinterp.o select.o sorter.o swapendian.o\
 	transpose.o twopass.o twopass_real_fwd.o\
 	twopass_real_inv.o vectors.o multifiles.o mask.o\
-	fitsfile.o hget.o hput.o imio.o djcl.o
+	fitsfile.o hget.o hput.o imio.o djcl.o accel_utils_gpu.o
+endif
+ifeq ($(use_cuda),no)
+PRESTOOBJS = amoeba.o atwood.o barycenter.o birdzap.o cand_output.o\
+	characteristics.o cldj.o chkio.o corr_prep.o corr_routines.o\
+	correlations.o database.o dcdflib.o dispersion.o\
+	fastffts.o fftcalls.o fminbr.o fold.o fresnl.o ioinf.o\
+	get_candidates.o iomak.o ipmpar.o maximize_r.o maximize_rz.o\
+	median.o minifft.o misc_utils.o clipping.o\
+	orbint.o output.o read_fft.o responses.o\
+	rzinterp.o rzwinterp.o select.o sorter.o swapendian.o\
+	transpose.o twopass.o twopass_real_fwd.o\
+	twopass_real_inv.o vectors.o multifiles.o mask.o\
+	fitsfile.o hget.o hput.o imio.o djcl.o 
+endif
 
 INSTRUMENTOBJS = backend_common.o zerodm.o sigproc_fb.o psrfits.o
 
@@ -112,6 +187,14 @@ indent:
 prep:
 	touch *_cmd.c
 
+ifeq ($(use_cuda),yes)
+accel_utils_gpu.o:	accel_utils_gpu.cu	  
+	$(NVCC) $(EXTRA_NVCCFLAGS) $(NVCCFLAGS) $(CUDA_INC_PATH)  $(GENCODE_FLAGS) -o $@ -c $<
+endif
+ifeq ($(use_cuda),no)
+$(info accel_utils_gpu.o will not be compiled)
+endif
+
 makewisdom:
 	$(CC) $(CLINKFLAGS) -o $@ makewisdom.c $(FFTLINK)
 	./makewisdom
@@ -124,8 +207,18 @@ timetest:
 
 libpresto: libpresto$(LIBSUFFIX)
 
+ifeq ($(use_cuda),yes)
 libpresto$(LIBSUFFIX): $(PRESTOOBJS)
-	$(LINKCOMMAND1) $(PRESTO)/lib/$@ $(PRESTOOBJS) $(FFTLINK)
+	$(LINKCOMMAND1) $(PRESTO)/lib/$@ $(PRESTOOBJS) $(FFTLINK) $(CUDA_LINK_EXTRA_FLAGS) -L $(SYSDIR)/lib/x86_64-linux-gnu -lstdc++
+endif
+
+ifeq ($(use_cuda),no)
+libpresto$(LIBSUFFIX): $(PRESTOOBJS)
+	$(LINKCOMMAND1) $(PRESTO)/lib/$@ $(PRESTOOBJS) $(FFTLINK) 
+endif
+
+#libpresto$(LIBSUFFIX): $(PRESTOOBJS)	
+	#$(LINKCOMMAND1) $(PRESTO)/lib/$@ $(PRESTOOBJS) $(FFTLINK)
 
 slalib: libsla$(LIBSUFFIX)
 	cd slalib ; $(FC) -o sla_test sla_test.f -fno-second-underscore -L$(PRESTO)/lib -lsla
@@ -138,6 +231,17 @@ libsla$(LIBSUFFIX):
 
 binaries: $(BINARIES)
 
+ifeq ($(use_cuda),yes)
+$(info link accelsearch with CUDA)
+accelsearch: accelsearch_cmd.c accelsearch_cmd.o accel_utils.o accelsearch.o zapping.o accel_utils_gpu.o 
+	$(CC) $(CLINKFLAGS) -o $(PRESTO)/bin/$@ accelsearch_cmd.o accel_utils.o accelsearch.o zapping.o accel_utils_gpu.o $(PRESTOLINK) -lglib-2.0 -lm $(CUDA_LINK_EXTRA_FLAGS)
+endif
+ifeq ($(use_cuda),no)
+$(info link accelsearch without CUDA)
+accelsearch: accelsearch_cmd.c accelsearch_cmd.o accel_utils.o accelsearch.o zapping.o
+	$(CC) $(CLINKFLAGS) -o $(PRESTO)/bin/$@ accelsearch_cmd.o accel_utils.o accelsearch.o zapping.o $(PRESTOLINK) $(GLIBLINK) -lm
+endif
+
 mpi: mpiprepsubband
 
 mpiprepsubband_utils.o: mpiprepsubband_utils.c
@@ -149,8 +253,8 @@ mpiprepsubband.o: mpiprepsubband.c
 mpiprepsubband: mpiprepsubband_cmd.c mpiprepsubband_cmd.o mpiprepsubband_utils.o mpiprepsubband.o $(INSTRUMENTOBJS)
 	mpicc $(CLINKFLAGS) -o $(PRESTO)/bin/$@ mpiprepsubband_cmd.o mpiprepsubband_utils.o mpiprepsubband.o $(INSTRUMENTOBJS) $(PRESTOLINK) -lcfitsio -lm
 
-accelsearch: accelsearch_cmd.c accelsearch_cmd.o accel_utils.o accelsearch.o zapping.o
-	$(CC) $(CLINKFLAGS) -o $(PRESTO)/bin/$@ accelsearch_cmd.o accel_utils.o accelsearch.o zapping.o $(PRESTOLINK) $(GLIBLINK) -lm
+#accelsearch: accelsearch_cmd.c accelsearch_cmd.o accel_utils.o accelsearch.o zapping.o
+#	$(CC) $(CLINKFLAGS) -o $(PRESTO)/bin/$@ accelsearch_cmd.o accel_utils.o accelsearch.o zapping.o $(PRESTOLINK) $(GLIBLINK) -lm
 
 bary: bary.o
 	$(CC) $(CLINKFLAGS) -o $(PRESTO)/bin/$@ bary.o $(PRESTOLINK) -lm
@@ -305,3 +409,4 @@ squeaky:  cleaner
 	cd $(PRESTO)/docs ; rm -f *# *~
 	cd $(PRESTO)/python ; rm -f *# *~ *.o *.pyc *.pyo
 	cd $(PRESTO)/include ; rm -f *# *~
+