Autotools: refactor build system output. Begin fixing PuReMD-GPU.

e84cf0a8 · Kurt A. O'Hearn · ca8bbe17 · e84cf0a8 · e84cf0a8 · e84cf0a8
Commit e84cf0a8 authored 8 years ago by Kurt A. O'Hearn
--- a/puremd_rc_1003/PG-PuReMD/Makefile.am
+++ b/puremd_rc_1003/PG-PuReMD/Makefile.am
 if USE_CUDA
 SUFFIXES = .cu
-include cuda.am
+include ../cuda.am
 endif

 AM_CFLAGS = -Wall -O3 -funroll-loops -fstrict-aliasing $(MPI_CFLAGS)
@@ -15,23 +15,23 @@ if USE_CUDA
 #   Note: cc 35 for Kepler K20
 NVCCFLAGS += -use_fast_math 
 NVCCFLAGS += -gencode arch=compute_35,code=sm_35
-NVCCFLAGS += --compiler-options "$(DEFS) -O3 -funroll-loops -fstrict-aliasing $(MPI_CFLAGS)"
+NVCCFLAGS += --compiler-options "$(DEFS) -D__SM_35__ -O3 -funroll-loops -fstrict-aliasing $(MPI_CFLAGS)"
 #NVCCFLAGS += --ptxas-options -v
 endif


-bin_PROGRAMS = src/pg-puremd
-src_pg_puremd_SOURCES = src/allocate.c src/basic_comm.c src/ffield.c src/grid.c src/list.c \
+bin_PROGRAMS = bin/pg-puremd
+bin_pg_puremd_SOURCES = src/allocate.c src/basic_comm.c src/ffield.c src/grid.c src/list.c \
 	src/lookup.c src/io_tools.c src/reset_tools.c src/restart.c src/random.c \
 	src/tool_box.c src/traj.c src/analyze.c src/box.c src/system_props.c \
 	src/control.c src/comm_tools.c src/geo_tools.c src/linear_solvers.c src/neighbors.c \
 	src/qEq.c src/bond_orders.c src/multi_body.c src/bonds.c src/valence_angles.c \
 	src/hydrogen_bonds.c src/torsion_angles.c src/nonbonded.c src/forces.c \
 	src/integrate.c src/init_md.c src/parallelreax.c
-src_pg_puremd_LDADD = src/vector.o
+bin_pg_puremd_LDADD = src/vector.o

 if USE_CUDA
-src_pg_puremd_SOURCES += src/cuda_utils.cu src/dev_alloc.cu src/cuda_environment.cu \
+bin_pg_puremd_SOURCES += src/cuda_utils.cu src/dev_alloc.cu src/cuda_environment.cu \
      src/dev_system_props.cu src/reduction.cu src/center_mass.cu \
      src/cuda_copy.cu src/cuda_reset_tools.cu src/dev_list.cu \
      src/cuda_neighbors.cu src/cuda_bond_orders.cu src/cuda_bonds.cu \
@@ -42,7 +42,7 @@ src_pg_puremd_SOURCES += src/cuda_utils.cu src/dev_alloc.cu src/cuda_environment
      src/cuda_init_md.cu src/validation.cu src/cuda_lookup.cu

 # dummy source to cause C linking
-nodist_EXTRA_src_pg_puremd_SOURCES = src/dummy.c
+nodist_EXTRA_bin_pg_puremd_SOURCES = src/dummy.c

 src_vector.o:
 	$(AM_V_NVCC)$(NVCC) $(NVCCFLAGS) -maxrregcount=$(MAX_REG_COUNT) -o src/vector.o -c src/vector.c
@@ -53,11 +53,11 @@ src_vector.o:
 endif


-src_pg_puremd_CFLAGS = $(AM_CFLAGS) $(CFLAGS)
-src_pg_puremd_CPPFLAGS = $(AM_CPPFLAGS) $(CPPFLAGS)
-src_pg_puremd_LDFLAGS = $(AM_LDFLAGS) $(LDFLAGS)
+bin_pg_puremd_CFLAGS = $(AM_CFLAGS) $(CFLAGS)
+bin_pg_puremd_CPPFLAGS = $(AM_CPPFLAGS) $(CPPFLAGS)
+bin_pg_puremd_LDFLAGS = $(AM_LDFLAGS) $(LDFLAGS)

 if USE_CUDA
-src_pg_puremd_CFLAGS += $(CUDA_CFLAGS)
-src_pg_puremd_LDFLAGS += $(CUDA_LIBS)
+bin_pg_puremd_CFLAGS += $(CUDA_CFLAGS)
+bin_pg_puremd_LDFLAGS += $(CUDA_LIBS)
 endif
--- a/puremd_rc_1003/PG-PuReMD/src/.gitignore
+++ b/puremd_rc_1003/PG-PuReMD/src/.gitignore
--- a/puremd_rc_1003/PuReMD-GPU/Makefile.am
+++ b/puremd_rc_1003/PuReMD-GPU/Makefile.am
+SUFFIXES = .cu
+include ../cuda.am
+
+AM_CFLAGS = -Wall -O3 -funroll-loops -fstrict-aliasing
+AM_CPPFLAGS =
+AM_LDFLAGS =
+
+# default CUDA nvcc flags
+#   Note: cc 13 for Tesla
+#   Note: cc 20 for Fermi
+#   Note: cc 30 for Kepler K10
+#   Note: cc 35 for Kepler K20
+NVCCFLAGS += -use_fast_math 
+NVCCFLAGS += -gencode arch=compute_35,code=sm_35
+NVCCFLAGS += --compiler-options "$(DEFS) -D__SM_35__ -O3 -funroll-loops -fstrict-aliasing"
+#NVCCFLAGS += --ptxas-options -v
+
+bin_PROGRAMS = bin/puremd-gpu
+bin_puremd_gpu_SOURCES = src/analyze.c src/print_utils.c src/reset_utils.c src/param.c src/pdb_tools.c \
+	src/GMRES.cu src/QEq.cu src/allocate.cu src/bond_orders.cu \
+	src/box.cu src/forces.cu src/four_body_interactions.cu \
+	src/grid.cu src/init_md.cu src/integrate.cu src/list.cu \
+	src/lookup.cu src/neighbors.cu \
+	src/restart.cu src/single_body_interactions.cu \
+	src/system_props.cu src/three_body_interactions.cu \
+	src/traj.cu src/two_body_interactions.cu src/vector.cu \
+	src/testmd.cu \
+	src/cuda_utils.cu src/cuda_copy.cu src/cuda_init.cu src/reduction.cu \
+	src/center_mass.cu src/helpers.cu src/validation.cu src/matvec.cu
+
+# dummy source to cause C linking
+nodist_EXTRA_bin_puremd_gpu_SOURCES = src/dummy.c
+
+bin_puremd_gpu_CFLAGS = $(AM_CFLAGS) $(CFLAGS) $(CUDA_CFLAGS)
+bin_puremd_gpu_CPPFLAGS = $(AM_CPPFLAGS) $(CPPFLAGS)
+bin_puremd_gpu_LDFLAGS = $(AM_LDFLAGS) $(LDFLAGS) $(CUDA_LIBS)
--- a/puremd_rc_1003/PuReMD-GPU/aclocal.m4
+++ b/puremd_rc_1003/PuReMD-GPU/aclocal.m4
--- a/puremd_rc_1003/PuReMD-GPU/configure.ac
+++ b/puremd_rc_1003/PuReMD-GPU/configure.ac
@@ -4,15 +4,24 @@
 AC_PREREQ([2.69])

 AC_INIT([PuReMD-GPU], [1.0], [ohearnku@msu.edu hma@msu.edu])
-#AM_INIT_AUTOMAKE([1.15])
-LT_PREREQ([2.2])
-LT_INIT([dlopen])
+AM_INIT_AUTOMAKE([1.15 subdir-objects -Wall -Werror foreign])
+AM_SILENT_RULES([yes])
+#LT_PREREQ([2.2])
+#LT_INIT([dlopen])
+
+AC_CONFIG_MACRO_DIR([../m4])

 AC_LANG([C])

 AC_CONFIG_SRCDIR([src/analyze.c])
 AC_CONFIG_HEADERS([src/config.h])

+# Headline formatter
+AC_DEFUN([CONFIGURE_HEADLINE],
+[
+        echo; echo "+++ $1 +++"
+])
+
 # Checks for programs.
 AC_PROG_CC
 AC_PROG_CPP
@@ -51,22 +60,38 @@ AC_C_INLINE
 AC_TYPE_SIZE_T
 AC_CHECK_TYPES([gzFile], [], 
 	       [AC_MSG_FAILURE([gzFile type not found in zlib.h], [1])], [#include<zlib.h>])
+
+# Checks for library functions.
+AC_FUNC_MALLOC
+AC_FUNC_STRTOD
+AC_CHECK_FUNCS([memset pow sqrt])
+
+# Check for CUDA support.
+CONFIGURE_HEADLINE([ CUDA support ])
+AX_CUDA
+NVCCFLAGS=
+if test "BUILD_DEBUG" = "true"
+then
+	NVCCFLAGS+=" -g -G"
+fi
+AC_DEFINE([HAVE_CUDA], [1], [Define to 1 if you have CUDA support enabled.])
+
+if test "BUILD_PROF" = "true"
+then
+	NVCCFLAGS+=" --compiler-options ${gprof_flags}"
+fi
+
 AC_CHECK_TYPES([cublasHandle_t], [], 
 	       [AC_MSG_FAILURE([cublasHandle_t type not found in cublas.h], [1])], [#include<cublas_v2.h>])
 AC_CHECK_TYPES([cusparseHandle_t], [], 
 	       [AC_MSG_FAILURE([cusparseHandle_t type not found in cusparse.h], [1])], [#include<cusparse_v2.h>])
 AC_CHECK_TYPES([cusparseMatDescr_t], [], 
 	       [AC_MSG_FAILURE([cusparseMatDescr_t type not found in cusparse.h], [1])], [#include<cusparse_v2.h>])
-AC_CHECK_TYPES([CUSPARSE_MATRIX_TYPE_GENERAL], [], 
-	       [AC_MSG_FAILURE([CUSPARSE_MATRIX_TYPE_GENERAL type not found in cusparse.h], [1])], [#include<cusparse_v2.h>])
-AC_CHECK_TYPES([CUSPARSE_INDEX_BASE_ZERO], [], 
-	       [AC_MSG_FAILURE([CUSPARSE_INDEX_BASE_ZERO type not found in cusparse.h], [1])], [#include<cusparse_v2.h>])
-
-# Checks for library functions.
-AC_FUNC_MALLOC
-AC_FUNC_STRTOD
-AC_CHECK_FUNCS([memset pow sqrt])
+#AC_CHECK_TYPES([CUSPARSE_MATRIX_TYPE_GENERAL], [], 
+#	       [AC_MSG_FAILURE([CUSPARSE_MATRIX_TYPE_GENERAL type not found in cusparse.h], [1])], [#include<cusparse_v2.h>])
+#AC_CHECK_TYPES([CUSPARSE_INDEX_BASE_ZERO], [], 
+#	       [AC_MSG_FAILURE([CUSPARSE_INDEX_BASE_ZERO type not found in cusparse.h], [1])], [#include<cusparse_v2.h>])

-AC_CONFIG_FILES([Makefile src/Makefile])
+AC_CONFIG_FILES([Makefile])

 AC_OUTPUT
--- a/puremd_rc_1003/PuReMD-GPU/src/Makefile.in
+++ b/puremd_rc_1003/PuReMD-GPU/src/Makefile.in
-BINDIR = ./bin
-
-CC = gcc
-NVCC = nvcc
-
-LIBS = -L/opt/cuda/lib64 -lm -lz -lcuda -lcudart -lcublas -lcusparse -m64
-#LIBS=-L/opt/cuda/lib64 -lm -lz -lcuda -lcudart
-
-#Debug Options
-#__CUDA_MEM__ Prints the memory allocated to the executable
-#__DEBUG_CUDA__ Prints debug information in CUDA
-#__BUILD_DEBUG__ builds a debug version, which runs serial and gpu code at the same time for 
-#					  every time step and validates the results 
-
-NVCCFLAGS = -I. -I/opt/cuda/include -D__USE_GPU__ -arch=sm_20 -O3 -Xptxas="-O3"
-CFLAGS = -I. -Wall -funroll-loops -fstrict-aliasing -O3
-
-DEFS = $(CFLAGS)
-NVCCDEFS = $(NVCCFLAGS)
-
-FLAG = $(DEFS) $(INCS) $(LIBS)
-NVCCFLAG = $(NVCCDEFS) $(LIBS)
-
-OBJ = GMRES.o QEq.o allocate.o analyze.o bond_orders.o \
-      box.o forces.o four_body_interactions.o \
-      grid.o init_md.o integrate.o list.o \
-      lookup.o neighbors.o param.o pdb_tools.o \
-      print_utils.o reset_utils.o \
-      restart.o single_body_interactions.o \
-      system_props.o three_body_interactions.o \
-      traj.o two_body_interactions.o vector.o \
-      testmd.o \
-      cuda_utils.o cuda_copy.o cuda_init.o reduction.o \
-      center_mass.o helpers.o validation.o matvec.o
-
-all: gpu 
-
-#
-#build the executable here
-#
-
-gpu: $(OBJ) Makefile
-	$(NVCC) $(NVCCFLAG) $(OBJ) -o puremd-gpu 
-
-#
-#Existing C code
-#
-#
-
-param.o: param.c param.h mytypes.h traj.o
-	$(CC) $(DEFS) -c param.c
-
-restart.o: restart.c restart.h mytypes.h box.h
-	$(CC) $(DEFS) -c restart.c
-
-pdb_tools.o: pdb_tools.c pdb_tools.h mytypes.h box.h list.h restart.h param.h
-	$(CC) $(DEFS) -c pdb_tools.c
-
-analyze.o: analyze.h analyze.c
-	$(CC) $(DEFS) -c analyze.c
-
-print_utils.o: print_utils.h print_utils.c
-	$(CC) $(DEFS) -c print_utils.c
-
-
-#
-# Code converted to cuda
-#
-
-traj.o: traj.cu traj.h mytypes.h 
-	$(NVCC) $(NVCCDEFS) -c traj.cu
-
-grid.o: grid.h grid.cu
-	$(NVCC) $(NVCCDEFS) -c grid.cu
-
-integrate.o: integrate.h integrate.cu
-	$(NVCC) $(NVCCDEFS) -c integrate.cu
-
-vector.o: vector.h vector.cu
-	$(NVCC) $(NVCCDEFS) -c vector.cu
-
-system_props.o: system_props.h system_props.cu
-	$(NVCC) $(NVCCDEFS) -c system_props.cu
-
-cuda_copy.o: cuda_copy.h cuda_copy.cu
-	$(NVCC) $(NVCCDEFS) -c cuda_copy.cu
-
-cuda_utils.o: cuda_utils.h cuda_utils.cu
-	$(NVCC) $(NVCCDEFS) -c cuda_utils.cu
-
-cuda_init.o: cuda_init.h cuda_init.cu
-	$(NVCC) $(NVCCDEFS) -c cuda_init.cu
-
-reduction.o: reduction.h reduction.cu
-	$(NVCC) $(NVCCDEFS) -c reduction.cu
-
-center_mass.o: center_mass.h center_mass.cu
-	$(NVCC) $(NVCCDEFS) -c center_mass.cu
-
-box.o: box.h
-	$(NVCC) $(NVCCDEFS) -c box.cu
-
-init_md.o: init_md.h init_md.cu
-	$(NVCC) $(NVCCDEFS) -c init_md.cu
-
-helpers.o: helpers.h helpers.cu
-	$(NVCC) $(NVCCDEFS) -c helpers.cu
-
-GMRES.o: GMRES.h GMRES.cu
-	$(NVCC) $(NVCCDEFS) -c GMRES.cu
-
-neighbors.o: neighbors.cu neighbors.h
-	$(NVCC) $(NVCCDEFS) -c neighbors.cu
-
-reset_utils.o: reset_utils.h reset_utils.cu mytypes.h list.h vector.h
-	$(NVCC) $(NVCCDEFS) -c reset_utils.cu
-
-list.o: list.h 
-	$(NVCC) $(NVCCDEFS) -c list.cu
-
-forces.o: forces.h forces.cu
-	$(NVCC) $(NVCCDEFS) -c forces.cu
-
-allocate.o: allocate.h allocate.cu
-	$(NVCC) $(NVCCDEFS) -c allocate.cu
-
-lookup.o: lookup.h lookup.cu
-	$(NVCC) $(NVCCDEFS) -c lookup.cu
-
-two_body_interactions.o: two_body_interactions.h two_body_interactions.cu
-	$(NVCC) $(NVCCDEFS) -c two_body_interactions.cu
-
-bond_orders.o: bond_orders.h bond_orders.cu
-	$(NVCC) $(NVCCDEFS) -c bond_orders.cu
-
-single_body_interactions.o: single_body_interactions.h single_body_interactions.cu
-	$(NVCC) $(NVCCDEFS) -c single_body_interactions.cu
-
-three_body_interactions.o: three_body_interactions.h three_body_interactions.cu
-	$(NVCC) $(NVCCDEFS) -c three_body_interactions.cu
-
-four_body_interactions.o: four_body_interactions.h four_body_interactions.cu
-	$(NVCC) $(NVCCDEFS) -c four_body_interactions.cu
-
-validation.o: validation.h validation.cu
-	$(NVCC) $(NVCCDEFS) -c validation.cu
-
-QEq.o: QEq.h QEq.cu
-	$(NVCC) $(NVCCDEFS) -c QEq.cu
-
-matvec.o: matvec.h matvec.cu
-	$(NVCC) $(NVCCDEFS) -c matvec.cu
-
-testmd.o: testmd.cu mytypes.h param.o traj.o restart.o pdb_tools.o list.o vector.o 
-	$(NVCC) $(NVCCDEFS) -c testmd.cu
-
-#
-# Clean up here
-#
-
-clean:
-	rm -f *.o *~ core 
--- a/puremd_rc_1003/PuReMD-GPU/src/config.h.in
+++ b/puremd_rc_1003/PuReMD-GPU/src/config.h.in
-/* src/config.h.in.  Generated from configure.ac by autoheader.  */
-
-/* Define to 1 if the system has the type `cublasHandle_t'. */
-#undef HAVE_CUBLASHANDLE_T
-
-/* Define to 1 if the system has the type `cusparseHandle_t'. */
-#undef HAVE_CUSPARSEHANDLE_T
-
-/* Define to 1 if the system has the type `cusparseMatDescr_t'. */
-#undef HAVE_CUSPARSEMATDESCR_T
-
-/* Define to 1 if the system has the type `CUSPARSE_INDEX_BASE_ZERO'. */
-#undef HAVE_CUSPARSE_INDEX_BASE_ZERO
-
-/* Define to 1 if the system has the type `CUSPARSE_MATRIX_TYPE_GENERAL'. */
-#undef HAVE_CUSPARSE_MATRIX_TYPE_GENERAL
-
-/* Define to 1 if you have the <dlfcn.h> header file. */
-#undef HAVE_DLFCN_H
-
-/* Define to 1 if the system has the type `gzFile'. */
-#undef HAVE_GZFILE
-
-/* Define to 1 if you have the <inttypes.h> header file. */
-#undef HAVE_INTTYPES_H
-
-/* Define to 1 if your system has a GNU libc compatible `malloc' function, and
-   to 0 otherwise. */
-#undef HAVE_MALLOC
-
-/* Define to 1 if you have the <memory.h> header file. */
-#undef HAVE_MEMORY_H
-
-/* Define to 1 if you have the `memset' function. */
-#undef HAVE_MEMSET
-
-/* Define to 1 if you have the `pow' function. */
-#undef HAVE_POW
-
-/* Define to 1 if you have the `sqrt' function. */
-#undef HAVE_SQRT
-
-/* Define to 1 if you have the <stdint.h> header file. */
-#undef HAVE_STDINT_H
-
-/* Define to 1 if you have the <stdlib.h> header file. */
-#undef HAVE_STDLIB_H
-
-/* Define to 1 if you have the <strings.h> header file. */
-#undef HAVE_STRINGS_H
-
-/* Define to 1 if you have the <string.h> header file. */
-#undef HAVE_STRING_H
-
-/* Define to 1 if you have the <sys/stat.h> header file. */
-#undef HAVE_SYS_STAT_H
-
-/* Define to 1 if you have the <sys/types.h> header file. */
-#undef HAVE_SYS_TYPES_H
-
-/* Define to 1 if you have the <unistd.h> header file. */
-#undef HAVE_UNISTD_H
-
-/* Define to 1 if the system has the type `_Bool'. */
-#undef HAVE__BOOL
-
-/* Define to the sub-directory in which libtool stores uninstalled libraries.
-   */
-#undef LT_OBJDIR
-
-/* Define to the address where bug reports for this package should be sent. */
-#undef PACKAGE_BUGREPORT
-
-/* Define to the full name of this package. */
-#undef PACKAGE_NAME
-
-/* Define to the full name and version of this package. */
-#undef PACKAGE_STRING
-
-/* Define to the one symbol short name of this package. */
-#undef PACKAGE_TARNAME
-
-/* Define to the home page for this package. */
-#undef PACKAGE_URL
-
-/* Define to the version of this package. */
-#undef PACKAGE_VERSION
-
-/* Define to 1 if you have the ANSI C header files. */
-#undef STDC_HEADERS
-
-/* Define to `__inline__' or `__inline' if that's what the C compiler
-   calls it, or to nothing if 'inline' is not supported under any name.  */
-#ifndef __cplusplus
-#undef inline
-#endif
-
-/* Define to rpl_malloc if the replacement function should be used. */
-#undef malloc
-
-/* Define to `unsigned int' if <sys/types.h> does not define. */
-#undef size_t
--- a/puremd_rc_1003/PuReMD/Makefile.am
+++ b/puremd_rc_1003/PuReMD/Makefile.am
-SUBDIRS = src
+AM_CFLAGS = -Wall -O3 -funroll-loops -fstrict-aliasing #-finline-functions -finline-limit=15 -qhot
+
+bin_PROGRAMS = bin/puremd
+bin_puremd_SOURCES = src/allocate.c src/basic_comm.c src/ffield.c src/grid.c src/list.c src/lookup.c \
+      src/io_tools.c src/reset_tools.c src/restart.c src/random.c src/tool_box.c src/traj.c \
+      src/vector.c src/analyze.c src/box.c src/system_props.c src/control.c src/comm_tools.c \
+      src/geo_tools.c src/linear_solvers.c src/neighbors.c src/qEq.c src/bond_orders.c src/multi_body.c \
+      src/bonds.c src/valence_angles.c src/hydrogen_bonds.c src/torsion_angles.c src/nonbonded.c src/forces.c \
+      src/integrate.c src/init_md.c src/parallelreax.c
+
+bin_puremd_CFLAGS = $(AM_CFLAGS) $(MPI_CFLAGS)
+bin_puremd_LDFLAGS = $(AM_LDFLAGS) $(MPI_LDFLAGS)
--- a/puremd_rc_1003/PuReMD/src/.gitignore
+++ b/puremd_rc_1003/PuReMD/src/.gitignore
--- a/puremd_rc_1003/PuReMD/configure.ac
+++ b/puremd_rc_1003/PuReMD/configure.ac
@@ -4,7 +4,7 @@
 AC_PREREQ([2.69])

 AC_INIT([PuReMD], [1.0], [ohearnku@msu.edu hma@msu.edu])
-AM_INIT_AUTOMAKE([1.15 -Wall -Werror foreign])
+AM_INIT_AUTOMAKE([1.15 subdir-objects -Wall -Werror foreign])
 AM_SILENT_RULES([yes])
 #LT_PREREQ([2.2])
 #LT_INIT([dlopen])
@@ -107,6 +107,6 @@ fi
 AC_SUBST(MPI_CFLAGS)
 AC_SUBST(MPI_LDFLAGS)

-AC_CONFIG_FILES([Makefile src/Makefile])
+AC_CONFIG_FILES([Makefile])

 AC_OUTPUT
--- a/puremd_rc_1003/PuReMD/src/Makefile.am
+++ b/puremd_rc_1003/PuReMD/src/Makefile.am
-AM_CFLAGS = -Wall -O3 -funroll-loops -fstrict-aliasing #-finline-functions -finline-limit=15 -qhot
-
-bin_PROGRAMS = puremd
-puremd_SOURCES = allocate.c basic_comm.c ffield.c grid.c list.c lookup.c \
-      io_tools.c reset_tools.c restart.c random.c tool_box.c traj.c \
-      vector.c analyze.c box.c system_props.c control.c comm_tools.c \
-      geo_tools.c linear_solvers.c neighbors.c qEq.c bond_orders.c multi_body.c \
-      bonds.c valence_angles.c hydrogen_bonds.c torsion_angles.c nonbonded.c forces.c \
-      integrate.c init_md.c parallelreax.c
-
-puremd_CFLAGS = $(AM_CFLAGS) $(MPI_CFLAGS)
-puremd_LDFLAGS = $(AM_LDFLAGS) $(MPI_LDFLAGS)
--- a/puremd_rc_1003/PG-PuReMD/cuda.am
+++ b/puremd_rc_1003/PG-PuReMD/cuda.am
--- a/puremd_rc_1003/data/script/command.txt
+++ b/puremd_rc_1003/data/script/command.txt
-###
-# 1. Convert the pdb file to custom format which is an intermediate format
-#    below is the awk command. Paste this command on the command line and 
-#     change the file names appropriately.
-###
-awk '{if($1=="CRYST1") print "BOXGEO", $2, $3, $4, $5, $6, $7; if($1=="ATOM")
-print $2, $3, $12, $6, $7, $8;}' <input-file>.pdb >& <output-file>.cus
-
-
-###
-#
-# 2. Convert the custom format to geo format with the following command
-#     replicate_geo.awk script can also be used to replicate the box in 
-#     any of the x, y, z directions. They are set as 1, 1, 1 for now. 
-#     If you want to replicate it, just change these numbers at the beginning
-#    of the replicate_geo.awk file.
-###
-
-awk -f replicate_geo.awk <output-file>.cus > <output-flie>.water.geo
-
-
-###
-#
-# 3. Open the geo file and insert a line below the BOXGEO line
-#     BOXGEO is the very first line which contains the BOX geometry
-#    The new line to be inserted contains the number of atoms in the
-#     newly created geo file. This number should be equal to the 
-#     total number of lines in the geo file - (2). one is the first line
-#     which is the BOXGEO line and second one is for the newly inserted line.
-###
--- a/puremd_rc_1003/sPuReMD/Makefile.am
+++ b/puremd_rc_1003/sPuReMD/Makefile.am
-SUBDIRS = src
+AM_CFLAGS += -Wall -O3 -funroll-loops -fstrict-aliasing
+
+bin_PROGRAMS = bin/spuremd
+bin_spuremd_SOURCES = src/grid.c src/list.c src/lookup.c src/print_utils.c \
+		  src/reset_utils.c src/restart.c src/random.c src/traj.c \
+		  src/vector.c src/allocate.c src/analyze.c src/box.c src/system_props.c \
+		  src/param.c src/pdb_tools.c src/neighbors.c src/GMRES.c src/QEq.c src/bond_orders.c \
+		  src/single_body_interactions.c src/two_body_interactions.c \
+		  src/three_body_interactions.c src/four_body_interactions.c src/forces.c \
+		  src/integrate.c src/init_md.c src/testmd.c 
--- a/puremd_rc_1003/sPuReMD/src/.gitignore
+++ b/puremd_rc_1003/sPuReMD/src/.gitignore
--- a/puremd_rc_1003/sPuReMD/configure.ac
+++ b/puremd_rc_1003/sPuReMD/configure.ac
@@ -4,7 +4,7 @@
 AC_PREREQ([2.69])

 AC_INIT([sPuReMD], [1.0], [ohearnku@msu.edu hma@msu.edu])
-AM_INIT_AUTOMAKE([1.15 -Wall -Werror foreign])
+AM_INIT_AUTOMAKE([1.15 subdir-objects -Wall -Werror foreign])
 AM_SILENT_RULES([yes])
 #LT_PREREQ([2.2])
 #LT_INIT([dlopen])
@@ -57,7 +57,6 @@ if test "x$BUILD_OPENMP" = "xyes"; then
 	fi
 fi

-AC_CONFIG_FILES([Makefile
-                 src/Makefile])
+AC_CONFIG_FILES([Makefile])

 AC_OUTPUT
--- a/puremd_rc_1003/sPuReMD/src/Makefile.am
+++ b/puremd_rc_1003/sPuReMD/src/Makefile.am
-AM_CFLAGS += -Wall -O3 -funroll-loops -fstrict-aliasing
-
-bin_PROGRAMS = spuremd
-spuremd_SOURCES = grid.c list.c lookup.c print_utils.c \
-		  reset_utils.c restart.c random.c traj.c \
-		  vector.c allocate.c analyze.c box.c system_props.c \
-		  param.c pdb_tools.c neighbors.c GMRES.c QEq.c bond_orders.c \
-		  single_body_interactions.c two_body_interactions.c \
-		  three_body_interactions.c four_body_interactions.c forces.c \
-		  integrate.c init_md.c testmd.c 
--- a/puremd_rc_1003/data/script/replicate.bash
+++ b/puremd_rc_1003/data/script/replicate.bash
--- a/puremd_rc_1003/data/script/replicate_geo.awk
+++ b/puremd_rc_1003/data/script/replicate_geo.awk