PuReMD: backport build system updates from branch full-far-nbrs-list-charge-matrix.

PuReMD/Makefile.am

 ACLOCAL_AMFLAGS = -I ../m4
 
-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
-
-include_HEADERS = src/reax_defs.h src/reax_types.h \
+      src/integrate.c src/init_md.c src/parallelreax.c \
+      src/reax_defs.h src/reax_types.h \
       src/allocate.h src/basic_comm.h src/ffield.h src/grid.h src/list.h src/lookup.h \
       src/io_tools.h src/reset_tools.h src/restart.h src/random.h src/tool_box.h src/traj.h \
       src/vector.h src/analyze.h src/box.h src/system_props.h src/control.h src/comm_tools.h \
@@ -18,5 +15,5 @@ include_HEADERS = src/reax_defs.h src/reax_types.h \
       src/bonds.h src/valence_angles.h src/hydrogen_bonds.h src/torsion_angles.h src/nonbonded.h src/forces.h \
       src/integrate.h src/init_md.h
 
-bin_puremd_CFLAGS = $(AM_CFLAGS) $(MPI_CFLAGS)
-bin_puremd_LDFLAGS = $(AM_LDFLAGS) $(MPI_LDFLAGS)
+bin_puremd_CFLAGS = $(MPI_CFLAGS)
+bin_puremd_LDADD = $(MPI_LIBS)

PuReMD/configure.ac

@@ -4,6 +4,8 @@
 AC_PREREQ([2.69])
 
 AC_INIT([PuReMD], [1.0], [ohearnku@msu.edu hma@msu.edu])
+# Do not allow AC_PROG_CC to set CFLAGS (this line must be after AC_INIT but before AC_PROG_CC)
+save_CFLAGS="${CFLAGS}"
 : ${CFLAGS=""}
 AM_INIT_AUTOMAKE([1.15 subdir-objects -Wall -Werror foreign])
 # Enable silent build rules by default.
@@ -13,20 +15,21 @@ m4_ifdef([AM_SILENT_RULES], [AM_SILENT_RULES([yes])], [AC_SUBST([AM_DEFAULT_VERB
 
 AC_CONFIG_MACRO_DIR([../m4])
 
-AC_LANG([C])
-
-AC_CONFIG_SRCDIR([src/torsion_angles.h])
-AC_CONFIG_HEADERS([src/config.h])
-
 # Headline formatter
 AC_DEFUN([CONFIGURE_HEADLINE],
 [
         echo; echo "+++ $1 +++"
 ])
 
+AC_LANG([C])
+
 # Checks for programs.
 AC_PROG_CC([cc icc gcc])
 AC_PROG_CPP
+CFLAGS="${save_CFLAGS}"
+
+AC_CONFIG_SRCDIR([src/torsion_angles.h])
+AC_CONFIG_HEADERS([src/config.h])
 
 # Checks for libraries.
 AC_SEARCH_LIBS([exp], [m])
@@ -47,69 +50,122 @@ AC_FUNC_REALLOC
 AC_FUNC_STRTOD
 AC_CHECK_FUNCS([gettimeofday memset pow sqrt])
 
-# Check for MPI support.
+# Check for compiler vendor. If the compiler is recognized,
+#   the variable ax_cv_c_compiler_vendor is set accordingly.
+AX_COMPILER_VENDOR
+if test "x${ax_cv_c_compiler_vendor}" = "xgnu"; then
+	if test "x${BUILD_DEBUG}" = "x"; then
+		CFLAGS="-Wall -O2 -funroll-loops"
+	else
+		CFLAGS="-Wall -O0 -g2 -D_GLIBCXX_DEBUG"
+	fi
+elif test "x${ax_cv_c_compiler_vendor}" = "xintel"; then
+	if test "x${BUILD_DEBUG}" = "x"; then
+		CFLAGS="-Wall -O2 -funroll-loops"
+	else
+		CFLAGS="-Wall -O0"
+	fi
+fi
+
+# Check for MPI support. If found, sets the following variables:
+#   Compiler-related: MPICC, MPICXX, MPIF77
+#   Library linking: MPILIBS
+#   Compilation support (via preprocessor def): HAVE_MPI
 CONFIGURE_HEADLINE([ MPI compiler ])
 ACX_MPI([], [AC_MSG_ERROR([could not find mpi library])])
 AC_CHECK_PROG(MPIRUN, mpirun, mpirun)
-AC_SUBST(MPIRUN)
 
 # try to find if we are using OpenMPI / MPICH by looking inside mpi.h
-sav_CC="$CC"
-sav_CFLAGS="$CFLAGS"
-CC="$MPICC"
-CFLAGS="$CFLAGS"
+save_CC="${CC}"
+save_CFLAGS="${CFLAGS}"
+CC="${MPICC}"
+CFLAGS=""
 AC_CHECK_DECL([OPEN_MPI], [mpi_vendor="OpenMPI"],
 	     [], [#include "mpi.h"])
+# MPICH v2
 AC_CHECK_DECL([MPICH2], [mpi_vendor="MPICH2"],
 	     [], [#include "mpi.h"])
+# MPICH v3
 AC_CHECK_DECL([MPICH_VERSION], [mpi_vendor="MPICH3"],
 	     [], [#include "mpi.h"])
-CC="$sav_CC"
-CFLAGS="$sav_CFLAGS"
+CC="${save_CC}"
+CFLAGS="${save_CFLAGS}"
 
-#
-# try to set MPI_CFLAGS and MPI_LDFLAGS
-#
+# try to set MPI_CFLAGS and MPI_LIBS
 MPI_CFLAGS=
-MPI_LDFLAGS=
-if test "x$mpi_vendor" = "xOpenMPI"
+MPI_LIBS=
+if test "x${mpi_vendor}" = "xOpenMPI"
 then 
-	MPI_CFLAGS=`$MPICC --showme:compile`
-	MPI_LDFLAGS=`$MPICC --showme:link`
+	MPI_CFLAGS=`${MPICC} --showme:compile`
+	MPI_LIBS=`${MPICC} --showme:link`
 	AC_MSG_NOTICE([OpenMPI found])
-	AC_MSG_NOTICE([MPI_CFLAGS=$MPI_CFLAGS])
-	AC_MSG_NOTICE([MPI_LDFLAGS=$MPI_LDFLAGS])
-elif test "x$mpi_vendor" = "xMPICH2" || test "x$mpi_vendor" = "xMPICH3"
+	AC_MSG_NOTICE([MPI_CFLAGS=${MPI_CFLAGS}])
+	AC_MSG_NOTICE([MPI_LIBS=${MPI_LIBS}])
+elif test "x${mpi_vendor}" = "xMPICH2" || test "x${mpi_vendor}" = "xMPICH3"
 then
 	# build MPI_CFLAGS
-	tmp=`$MPICC -compile-info | awk '{$1=""; print $0 }'`
+	tmp=`${MPICC} -compile-info | awk '{$1=""; print $0 }'`
 	MPI_CFLAGS=
 	for i in $tmp
 	do 
-		case $i in 
+		case ${i} in 
 			-[[DIUbi]]*)
-				MPI_CFLAGS="$MPI_CFLAGS $i"
+				MPI_CFLAGS="${MPI_CFLAGS} ${i}"
 				;;
 		esac
 	done
-	# build MPI_LDFLAGS
-	tmp=`$MPICC -link-info | awk '{$1=""; print $0 }'`
+	# build MPI_LIBS
+	tmp=`${MPICC} -link-info | awk '{$1=""; print $0 }'`
 	for i in $tmp
 	do 
-		case $i in 
+		case ${i} in 
 			[[\\/]]*.a | ?:[[\\/]]*.a | -[[lLRu]]* | -Wl* )
-				MPI_LDFLAGS="$MPI_LDFLAGS $i"
+				MPI_LIBS="${MPI_LIBS} ${i}"
 				;;
 		esac
 	done
 	AC_MSG_NOTICE([MPICH found])
-	AC_MSG_NOTICE([MPI_CFLAGS=$MPI_CFLAGS])
-	AC_MSG_NOTICE([MPI_LDFLAGS=$MPI_LDFLAGS])
+	AC_MSG_NOTICE([MPI_CFLAGS=${MPI_CFLAGS}])
+	AC_MSG_NOTICE([MPI_LIBS=${MPI_LIBS}])
 else
 	AC_MSG_WARN([Neither OpenMPI and MPICH have been recognized...])
 fi
 AC_SUBST(MPI_CFLAGS)
-AC_SUBST(MPI_LDFLAGS)
+AC_SUBST(MPI_LIBS)
+
+# Check for LAPACKE
+AC_CHECK_HEADERS([mkl.h], [MKL_FOUND_HEADERS="yes"])
+if test "x${MKL_FOUND_HEADERS}" = "xyes"
+then
+	AC_SEARCH_LIBS([LAPACKE_dgels], [mkl_intel_ilp64],
+		       [MKL_FOUND_LIBS="yes"], [MKL_FOUND_LIBS="no"],
+		       [-lmkl_sequential -lmkl_core -lpthread -lm -ldl])
+	AS_IF([test "x${MKL_FOUND_LIBS}" != "xyes"],
+	      [AC_MSG_ERROR([Unable to find MKL LAPACKE library.])])
+	# dynamic linking
+	#LIBS="${LIBS} -lmkl_intel_ilp64 -lmkl_sequential -lmkl_core -lpthread -lm -ldl"
+	# static linking
+	LIBS="${LIBS} -Wl,--start-group ${MKLROOT}/lib/intel64/libmkl_intel_ilp64.a ${MKLROOT}/lib/intel64/libmkl_sequential.a ${MKLROOT}/lib/intel64/libmkl_core.a -Wl,--end-group -lpthread -lm -ldl"
+	AC_DEFINE([HAVE_LAPACKE_MKL], [1], [Define to 1 if you have MKL LAPACKE support enabled.])
+else
+	AC_CHECK_HEADERS([lapacke.h], [LAPACKE_FOUND_HEADERS="yes"])
+	if test "x${LAPACKE_FOUND_HEADERS}" = "xyes"
+	then
+		AC_SEARCH_LIBS([LAPACKE_dgels], [lapacke],
+			       [LAPACKE_FOUND_LIBS="yes"], [LAPACKE_FOUND_LIBS="no"],
+			       [-llapack])
+		AS_IF([test "x${LAPACKE_FOUND_LIBS}" != "xyes"],
+		      [AC_MSG_ERROR([Unable to find LAPACKE library.])])
+		LIBS="${LIBS} -llapack"
+		AC_DEFINE([HAVE_LAPACKE], [1], [Define to 1 if you have LAPACKE support enabled.])
+	else
+		AC_MSG_WARN([
+  -----------------------------------------------
+   Unable to find LAPACKE on this system.
+   Disabling support for dependent methods.
+  -----------------------------------------------])
+	fi
+fi
 
 AC_CONFIG_FILES([Makefile])
 

configure.ac

@@ -84,9 +84,7 @@ if test "x${DEBUG}" = "xyes"
 then
 #	#TODO: fix exporting to subdirs
 #	# See: http://stackoverflow.com/questions/34124337/changing-flags-in-configure-ac-vs-caching-with-subprojects
-#	CFLAGS="-g3 -O0 -D_GLIBCXX_DEBUG ${CFLAGS}"
-	export BUILD_DEBUG="true"
-	export DEBUG_FLAGS="-g2 -O0 -D_GLIBCXX_DEBUG"
+	export BUILD_DEBUG="yes"
 fi
 
 # gprof flags.