Remove the GSL dependency from sss and xlqc

CMakeLists.txt

@@ -24,7 +24,7 @@ set(CMAKE_CXX_EXTENSIONS OFF)
 find_package(Boost)
 find_package(MPI)
 find_package(GDAL CONFIG)
-find_package(GSL)
+find_package(Eigen3)
 find_package(BZip2)
 
 # Build options - which programming models to enable

README.md

@@ -10,11 +10,11 @@ Z. Jin and J. S. Vetter, "A Benchmark Suite for Improving Performance Portabilit
 [NVIDIA HPC SDK](https://developer.nvidia.com/hpc-sdk)
 
 # Dependencies
-Certain benchmarks require [Boost](https://www.boost.org/releases/latest/), [GSL](https://www.gnu.org/software/gsl), [GDAL](https://github.com/OSGeo/gdal), GPU-aware Message Passing Interface(MPI) or vendors' collective communication libraries (e.g. NCCL).<br>
+Certain benchmarks require [Boost](https://www.boost.org/releases/latest/), [Eigen](https://eigen.tuxfamily.org), [GDAL](https://github.com/OSGeo/gdal), GPU-aware Message Passing Interface(MPI) or vendors' collective communication libraries (e.g. NCCL).<br>
 Boost: hbc, ge-spmm, mmcsf, warpsort, gerbil<br>
 MPI:   miniDGS, miniWeather, pingpong, sparkler, allreduce, ccl, halo-finder<br>
 CCL:   ccl<br>
-GSL:   sss, xlqc<br>
+Eigen: xlqc<br>
 GDAL:  stsg<br>
 BZip2: gerbil
 

cmake/modules/BenchmarkMacros.cmake

@@ -11,8 +11,8 @@ set(DEPEND_ON_BOOST "hbc" "ge-spmm" "mmcsf" "warpsort" "gerbil")
 # Global list for benchmarks that require MPI
 set(DEPEND_ON_MPI "miniDGS" "miniWeather" "pingpong" "sparkler" "allreduce" "ccl" "halo-finder")
 
-# Global list for benchmarks that require GSL
-set(DEPEND_ON_GSL "sss" "xlqc")
+# Global list for benchmarks that require Eigen
+set(DEPEND_ON_EIGEN "xlqc")
 
 # Global list for benchmarks that require GDAL
 set(DEPEND_ON_GDAL "stsg")
@@ -116,9 +116,10 @@ function(add_hecbench_benchmark)
         endif()
     endif()
 
-    if(${BENCH_NAME} IN_LIST DEPEND_ON_GSL)
-        if(NOT GSL_FOUND)
-            message(STATUS "Skipping ${BENCH_NAME}-${BENCH_MODEL_LOWER} (GSL not found)")
+    if(${BENCH_NAME} IN_LIST DEPEND_ON_EIGEN)
+        # Eigen is header-only; the imported target carries the include path
+        if(NOT TARGET Eigen3::Eigen)
+            message(STATUS "Skipping ${BENCH_NAME}-${BENCH_MODEL_LOWER} (Eigen not found)")
             return()
         endif()
     endif()

src/sss-cuda/CMakeLists.txt

@@ -4,7 +4,5 @@ add_hecbench_benchmark(
     NAME sss
     MODEL cuda
     SOURCES main.cu
-    INCLUDE_DIRS ${GSL_INCLUDE_DIRS}
     CATEGORIES algorithms
-    LINK_LIBRARIES gsl  
 )

src/sss-cuda/DPmixGGM.cpp

@@ -1,3 +1,4 @@
+#include <cmath>
 #define DPMIXGGM_CPP
 #ifndef GRAPH_CPP
 #include "graph.cpp"

src/sss-cuda/Makefile

@@ -7,7 +7,6 @@ CC        = nvcc
 OPTIMIZE  = yes
 DEBUG     = no
 ARCH      = sm_60
-GSL       = /path/to/GSL
 LAUNCHER  =
 
 #===============================================================================
@@ -25,11 +24,10 @@ obj = $(source:.cu=.o)
 #===============================================================================
 
 # Standard Flags
-CFLAGS := $(EXTRA_CFLAGS) -std=c++17 -Xcompiler -Wall -arch=$(ARCH) \
-          -I$(GSL)/include
+CFLAGS := $(EXTRA_CFLAGS) -std=c++17 -Xcompiler -Wall -arch=$(ARCH)
 
 # Linker Flags
-LDFLAGS = -L$(GSL)/lib -lgsl
+LDFLAGS =
 
 # Debug Flags
 ifeq ($(DEBUG),yes)
@@ -49,11 +47,11 @@ $(program): $(obj) Makefile
 	$(CC) $(CFLAGS) $(obj) -o $@ $(LDFLAGS)
 
 %.o: %.cu DPmixGGM.cpp  DPmixGGM_Lists.cpp  DPmixGGM_SSSmoves.cpp  \
-           kernels.cu graph.cpp  gwish.cpp  utilities.cpp Makefile
+           kernels.cu graph.cpp  gwish.cpp  utilities.cpp gsl_compat.h Makefile
 	$(CC) $(CFLAGS) -c $< -o $@
 
 clean:
 	rm -rf $(program) $(obj) RES/f9_n150_p50_modes_GPU.txt
 
 run: $(program)
-	$(LAUNCHER) GSL_RNG_SEED=123 ./$(program) f9_n150_p50
+	$(LAUNCHER) ./$(program) f9_n150_p50

src/sss-cuda/README.md

@@ -1,22 +1,28 @@
 DPmixGGM
 ========
 
-This folder contains source codes for the "GPU-powered Stochastic Shotgun Search for Dirichlet proces mixtures of Gaussian Graphical Models" 
+This folder contains source codes for the "GPU-powered Stochastic Shotgun Search for Dirichlet proces mixtures of Gaussian Graphical Models" 
 by Chiranjit Mukherjee and Abel Rodriguez. 
-
-The "DPmixGGM_SSS_main.cpp" file contains tuning parameters for the algorithm, as elaborated below:
+
+The "DPmixGGM_SSS_main.cpp" file contains tuning parameters for the algorithm, as elaborated below:
 1. Run the SSS 
-2. Run GPU/CPU versions of the SSS by enabling / disabling the macro CUDA.
-3. Specify maximum number of mixture components that the model should accommodate (for pre-allocation of memory).
-4. Set SSS runtime parameters C, D, R, S, M, g, h, f, t.
-5. Set SSS number of chain parameters. User needs to provide at least one initial point.
-7. Set hyperparameters of for the prior on (mu, K | G) with N0, DELTA0.
-
+2. Run GPU/CPU versions of the SSS by enabling / disabling the macro CUDA.
+3. Specify maximum number of mixture components that the model should accommodate (for pre-allocation of memory).
+4. Set SSS runtime parameters C, D, R, S, M, g, h, f, t.
+5. Set SSS number of chain parameters. User needs to provide at least one initial point.
+7. Set hyperparameters of for the prior on (mu, K | G) with N0, DELTA0.
+
 Complie source codes using the "make" command and run with "./main f9_n150_p50" command.
-
-The program expects an input-data file (e.g. f9_n150_p50) in the DATA/ folder and at least one initialization point (e.g. f9_n150_p50_init1). 
-The input-data file should specify n and p in the first row and then provide n rows of length p. The initial point data-file should specify n, p
-and L of the initial model configuration in the first row and xi-indices of the initial point in the second row. Subsequent L rows specify 
-G_l (l=1:L).
-
+
+The program expects an input-data file (e.g. f9_n150_p50) in the DATA/ folder and at least one initialization point (e.g. f9_n150_p50_init1). 
+The input-data file should specify n and p in the first row and then provide n rows of length p. The initial point data-file should specify n, p
+and L of the initial model configuration in the first row and xi-indices of the initial point in the second row. Subsequent L rows specify 
+G_l (l=1:L).
+
 A list of highest-score models is stored in folder RES/.
+
+Dependencies
+------------
+None beyond a C++17 compiler. The uniform random number generator (MT19937) and
+the adaptive Gauss-Kronrod quadrature the sampler needs are implemented in
+`gsl_compat.h` in this folder.