Version of the code ready for the paper that should just compile and run with minimal effort

Makefile.am

+# This file is part of SWIFT.
+# Coypright (c) 2012 pedro.gonnet@durham.ac.uk.
+# 
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+# 
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+# Automake stuff
+ACLOCAL_AMFLAGS = -I m4
+
+# Show the way...
+SUBDIRS = src examples doc

src/CUDACompile.sh

 #!/bin/bash
 FLAGS2="-Xcompiler=-fsanitize=address -Xcompiler=-fno-omit-frame-pointer"
 DEBUG_FLAGS="-G -DDEBUG_GPU"
-FLAGS="-O3 -g -DCPU_TPS=3.1e9 -lineinfo -src-in-ptx -Xptxas -dlcm=cg --maxrregcount=32 -gencode arch=compute_30,code=sm_30 -ftz=true -fmad=true -DFPTYPE_SINGLE -lgomp -DWITH_CUDA -DTIMERS -ccbin=/usr/bin/gcc-4.8"
+FLAGS="-O3 -g -DCPU_TPS=3.1e9 -lineinfo -src-in-ptx -Xptxas -dlcm=cg --maxrregcount=32 -gencode arch=compute_30,code=sm_30 -ftz=true -fmad=true -DFPTYPE_SINGLE -lgomp -DWITH_CUDA -DTIMERS -ccbin=gcc"
 # -DGPU_locks -Xptxas -dlcm=cg  -Xptxas="-v"" 
 # -DNO_LOADS
 #-DSIM
-#-lprofiler
+#
 
 CFLAGS="-fsanitize=address -fno-omit-frame-pointer"
 
-gcc-4.8 -std=gnu99 -DHAVE_CONFIG_H -I. -I.. -g -O3 -Wall -Werror -ffast-math -fstrict-aliasing -ftree-vectorize -funroll-loops -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -fopenmp -DTIMERS -DWITH_CUDA -g -O2 -march=native -pthread -MT qsched.lo -MD -MP -MF .deps/qsched.Tpo -c qsched.c -o qsched.o -lprofiler #-fsanitize=address -fno-omit-frame-pointer
-gcc-4.8 -std=gnu99 -DHAVE_CONFIG_H -I. -I.. -g -O3 -Wall -Werror -ffast-math -fstrict-aliasing -ftree-vectorize -funroll-loops -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -fopenmp -DTIMERS -DWITH_CUDA -g -O2 -march=native -pthread -MT qsched.lo -MD -MP -MF .deps/qsched.Tpo -c queue.c -o queue.o -lprofiler #-fsanitize=address -fno-omit-frame-pointer
+gcc -std=gnu99 -DHAVE_CONFIG_H -I. -I.. -g -O3 -Wall -Werror -ffast-math -fstrict-aliasing -ftree-vectorize -funroll-loops -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -fopenmp -DTIMERS -DWITH_CUDA -g -O2 -march=native -pthread -MT qsched.lo -MD -MP -MF .deps/qsched.Tpo -c qsched.c -o qsched.o  #-fsanitize=address -fno-omit-frame-pointer
+gcc -std=gnu99 -DHAVE_CONFIG_H -I. -I.. -g -O3 -Wall -Werror -ffast-math -fstrict-aliasing -ftree-vectorize -funroll-loops -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -fopenmp -DTIMERS -DWITH_CUDA -g -O2 -march=native -pthread -MT qsched.lo -MD -MP -MF .deps/qsched.Tpo -c queue.c -o queue.o  #-fsanitize=address -fno-omit-frame-pointer
 
 
-/home/aidan/cuda_7.0/bin/nvcc $FLAGS -dc cuda_queue.cu qsched.o queue.o -lprofiler
+nvcc $FLAGS -dc cuda_queue.cu qsched.o queue.o -lm
 
-/home/aidan/cuda_7.0/bin/nvcc $FLAGS  -lib cuda_queue.o qsched.o queue.o -o .libs/libquicksched_cuda.a -lprofiler
+nvcc $FLAGS  -lib cuda_queue.o qsched.o queue.o -o .libs/libquicksched_cuda.a -lm
 
-/home/aidan/cuda_7.0/bin/nvcc $FLAGS  -DGPU_locks -dc cuda_queue.cu qsched.o queue.o -lprofiler
+nvcc $FLAGS  -DGPU_locks -dc cuda_queue.cu qsched.o queue.o -lm
 
-/home/aidan/cuda_7.0/bin/nvcc $FLAGS  -lib cuda_queue.o qsched.o queue.o -o .libs/libquicksched_cuda_locks.a -lprofiler
+nvcc $FLAGS  -lib cuda_queue.o qsched.o queue.o -o .libs/libquicksched_cuda_locks.a -lm
 
 cd ../examples
 
-/home/aidan/cuda_7.0/bin/nvcc $FLAGS  -dc -m64 -I../src -dc -L/home/aidan/cuda_7.0/lib -L/home/aidan/cuda_7.0/lib64 -lcudart -lcuda  test_gpu_simple.cu -lprofiler
+nvcc $FLAGS  -dc -m64 -I../src -dc -lcudart -lcuda  test_gpu_simple.cu -lm
 
-/home/aidan/cuda_7.0/bin/nvcc $FLAGS  -m64 -I../src -L/home/aidan/cuda_7.0/lib -L/home/aidan/cuda_7.0/lib64 -Xnvlink -v test_gpu_simple.o ../src/.libs/libquicksched_cuda.a -o simple_cuda_test -lprofiler
+nvcc $FLAGS  -m64 -I../src -Xnvlink -v test_gpu_simple.o ../src/.libs/libquicksched_cuda.a -o simple_cuda_test -lm
 
 
-/home/aidan/cuda_7.0/bin/nvcc $FLAGS  -dc -m64 -I../src -dc -lf77blas -lcblas -latlas -lm -I$CULA_INC_PATH -L$CULA_LIB_PATH_64 -L/home/aidan/ATLAS/ATLAS_linux/lib/ -L/home/aidan/cuda_7.0/lib -L/home/aidan/cuda_7.0/lib64 -lcudart -lcula_lapack -lcuda /usr/lib64/atlas/libcblas.a /usr/lib64/atlas/libptcblas.a test_qr.cu -lprofiler
+nvcc $FLAGS  -dc -m64 -I../src -dc -lcudart -lcuda -lm test_qr.cu
 
-/home/aidan/cuda_7.0/bin/nvcc $FLAGS  -m64 -I../src -lf77blas -lcblas -latlas -lm -I$CULA_INC_PATH -L$CULA_LIB_PATH_64 -L/home/aidan/ATLAS/ATLAS_linux/lib/ -L/home/aidan/cuda_7.0/lib -L/home/aidan/cuda_7.0/lib64 -lcula_lapack -Xnvlink -v test_qr.o ../src/.libs/libquicksched_cuda.a /usr/lib64/atlas/libcblas.a /usr/lib64/atlas/libptcblas.a -o qr_cuda_test -lprofiler
+nvcc $FLAGS  -m64 -I../src -lm -Xnvlink -v test_qr.o ../src/.libs/libquicksched_cuda.a -o test_qr_gpu 
 
-/home/aidan/cuda_7.0/bin/nvcc $FLAGS  -dc -m64 -I../src -dc -L/home/aidan/cuda_7.0/lib -L/home/aidan/cuda_7.0/lib64 -lcudart -lcuda  test_hierarchy.cu -lprofiler
+nvcc $FLAGS  -dc -m64 -I../src -dc -lcudart -lcuda  test_hierarchy.cu -lm
 
-/home/aidan/cuda_7.0/bin/nvcc $FLAGS  -m64 -I../src -L/home/aidan/cuda_7.0/lib -L/home/aidan/cuda_7.0/lib64 -Xnvlink -v test_hierarchy.o ../src/.libs/libquicksched_cuda.a -o test_heirarchy -lprofiler
+nvcc $FLAGS  -m64 -I../src -Xnvlink -v test_hierarchy.o ../src/.libs/libquicksched_cuda.a -o test_heirarchy -lm
 
-/home/aidan/cuda_7.0/bin/nvcc $FLAGS  -dc -m64 -I../src -dc -L/home/aidan/cuda_7.0/lib -L/home/aidan/cuda_7.0/lib64 -lcudart -lcuda  test_bh_2.cu -lprofiler
+nvcc $FLAGS  -dc -m64 -I../src -dc -lcudart -lcuda  test_bh.cu -lm
 
-/home/aidan/cuda_7.0/bin/nvcc $FLAGS  -m64 -I../src -L/home/aidan/cuda_7.0/lib -L/home/aidan/cuda_7.0/lib64 -Xnvlink -v test_bh_2.o ../src/.libs/libquicksched_cuda.a -o test_bh_2 -lprofiler
-
-/home/aidan/cuda_7.0/bin/nvcc $FLAGS  -dc -m64 -I../src -dc -L/home/aidan/cuda_7.0/lib -L/home/aidan/cuda_7.0/lib64 -lcudart -lcuda  test_bh_3.cu -lprofiler
-
-/home/aidan/cuda_7.0/bin/nvcc $FLAGS  -m64 -I../src -L/home/aidan/cuda_7.0/lib -L/home/aidan/cuda_7.0/lib64 -Xnvlink -v test_bh_3.o ../src/.libs/libquicksched_cuda.a -o test_bh_3 -lprofiler
-
-/home/aidan/cuda_7.0/bin/nvcc $FLAGS  -dc -m64 -I../src -dc -L/home/aidan/cuda_7.0/lib -L/home/aidan/cuda_7.0/lib64 -lcudart -lcuda  test_bh_4.cu -lprofiler
-
-/home/aidan/cuda_7.0/bin/nvcc $FLAGS  -m64 -I../src -L/home/aidan/cuda_7.0/lib -L/home/aidan/cuda_7.0/lib64 -Xnvlink -v test_bh_4.o ../src/.libs/libquicksched_cuda.a -o test_bh_4 -lprofiler
+nvcc $FLAGS  -m64 -I../src -Xnvlink -v test_bh.o ../src/.libs/libquicksched_cuda.a -o test_bh -lm

src/Makefile.am

+# This file is part of Quicksched.
+# Coypright (c) 2013 Pedro Gonnet (pedro.gonnet@durham.ac.uk),
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+# Add the debug flag to the whole thing
+AM_CFLAGS = -g -O3 -Wall -Werror -ffast-math -fstrict-aliasing -ftree-vectorize \
+    -funroll-loops $(SIMD_FLAGS) $(OPENMP_CFLAGS) -DTIMERS \
+    # -fsanitize=address -fno-omit-frame-pointer
+
+# Assign a "safe" version number
+AM_LDFLAGS = -version-info 0:0:0
+
+# Build the libquicksched library
+lib_LTLIBRARIES = libquicksched.la
+libquicksched_la_SOURCES = qsched.c queue.c
+
+# List required headers
+include_HEADERS = atomic.h lock.h queue.h qsched.h task.h res.h error.h
+
+# Private headers.
+noinst_HEADERS = cycle.h quicksched.h