From 65d8207b9afcd26054b66a9506c21220e8d8a822 Mon Sep 17 00:00:00 2001
From: "Kurt A. O'Hearn" <ohearnku@msu.edu>
Date: Mon, 5 Nov 2018 07:47:25 -0800
Subject: [PATCH] PuReMD: fix compilation error. Use safer default optimization
levels for compilation.
---
PuReMD/Makefile.am | 4 ++--
PuReMD/configure.ac | 42 ++++++++++++++++++++++++-----------------
PuReMD/src/reax_types.h | 2 +-
3 files changed, 28 insertions(+), 20 deletions(-)
diff --git a/PuReMD/Makefile.am b/PuReMD/Makefile.am
index 192ad0e9..718c453f 100644
--- a/PuReMD/Makefile.am
+++ b/PuReMD/Makefile.am
@@ -16,5 +16,5 @@ 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) $(CFLAGS)
-bin_puremd_LDADD = $(AM_LDADD) $(MPI_LIBS) $(LDADD)
+bin_puremd_CFLAGS = $(CFLAGS) $(MPI_CFLAGS)
+bin_puremd_LDADD = $(LDADD) $(MPI_LIBS)
diff --git a/PuReMD/configure.ac b/PuReMD/configure.ac
index 01682497..8833fc24 100644
--- a/PuReMD/configure.ac
+++ b/PuReMD/configure.ac
@@ -5,7 +5,7 @@ AC_PREREQ([2.69])
AC_INIT([PuReMD], [1.0], [ohearnku@msu.edu hma@msu.edu])
# Do not allow AC_PROG_CC to set CFLAGS (this line must be after AC_INIT but before AC_PROG_CC)
-sav_CFLAGS="${CFLAGS}"
+save_CFLAGS="${CFLAGS}"
: ${CFLAGS=""}
AM_INIT_AUTOMAKE([1.15 subdir-objects -Wall -Werror foreign])
# Enable silent build rules by default.
@@ -26,7 +26,7 @@ AC_LANG([C])
# Checks for programs.
AC_PROG_CC([cc icc gcc])
AC_PROG_CPP
-CFLAGS="${sav_CFLAGS}"
+CFLAGS="${save_CFLAGS}"
AC_CONFIG_SRCDIR([src/torsion_angles.h])
AC_CONFIG_HEADERS([src/config.h])
@@ -50,32 +50,37 @@ AC_FUNC_REALLOC
AC_FUNC_STRTOD
AC_CHECK_FUNCS([gettimeofday memset pow sqrt])
-# Check for compiler vendor
+# Check for compiler vendor. If the compiler is recognized,
+# the variable ax_cv_c_compiler_vendor is set accordingly.
AX_COMPILER_VENDOR
if test "x${ax_cv_c_compiler_vendor}" = "xgnu"; then
if test "x${BUILD_DEBUG}" = "x"; then
- CFLAGS="${CFLAGS} -Wall -O3 -funroll-loops"
+ CFLAGS="-Wall -O2 -funroll-loops"
else
- CFLAGS="${CFLAGS} -Wall -O0 -g"
+ CFLAGS="-Wall -O0 -g2 -D_GLIBCXX_DEBUG"
fi
-fi
-if test "x${ax_cv_c_compiler_vendor}" = "xintel"; then
+elif test "x${ax_cv_c_compiler_vendor}" = "xintel"; then
if test "x${BUILD_DEBUG}" = "x"; then
- CFLAGS="$CFLAGS -fast"
+ CFLAGS="-Wall -O2 -funroll-loops"
+ else
+ CFLAGS="-Wall -O0"
fi
fi
-# Check for MPI support.
+# Check for MPI support. If found, sets the following variables:
+# Compiler-related: MPICC, MPICXX, MPIF77
+# Library linking: MPILIBS
+# Compilation support (via preprocessor def): HAVE_MPI
CONFIGURE_HEADLINE([ MPI compiler ])
ACX_MPI([], [AC_MSG_ERROR([could not find mpi library])])
AC_CHECK_PROG(MPIRUN, mpirun, mpirun)
AC_SUBST(MPIRUN)
# try to find if we are using OpenMPI / MPICH by looking inside mpi.h
-sav_CC="${CC}"
-sav_CFLAGS="${CFLAGS}"
+save_CC="${CC}"
+save_CFLAGS="${CFLAGS}"
CC="${MPICC}"
-CFLAGS="${CFLAGS}"
+CFLAGS=""
AC_CHECK_DECL([OPEN_MPI], [mpi_vendor="OpenMPI"],
[], [#include "mpi.h"])
# MPICH v2
@@ -84,8 +89,8 @@ AC_CHECK_DECL([MPICH2], [mpi_vendor="MPICH2"],
# MPICH v3
AC_CHECK_DECL([MPICH_VERSION], [mpi_vendor="MPICH3"],
[], [#include "mpi.h"])
-CC="${sav_CC}"
-CFLAGS="${sav_CFLAGS}"
+CC="${save_CC}"
+CFLAGS="${save_CFLAGS}"
# try to set MPI_CFLAGS and MPI_LIBS
MPI_CFLAGS=
@@ -104,7 +109,7 @@ then
MPI_CFLAGS=
for i in $tmp
do
- case $i in
+ case ${i} in
-[[DIUbi]]*)
MPI_CFLAGS="${MPI_CFLAGS} ${i}"
;;
@@ -114,7 +119,7 @@ then
tmp=`${MPICC} -link-info | awk '{$1=""; print $0 }'`
for i in $tmp
do
- case $i in
+ case ${i} in
[[\\/]]*.a | ?:[[\\/]]*.a | -[[lLRu]]* | -Wl* )
MPI_LIBS="${MPI_LIBS} ${i}"
;;
@@ -138,7 +143,10 @@ then
[-lmkl_sequential -lmkl_core -lpthread -lm -ldl])
AS_IF([test "x${MKL_FOUND_LIBS}" != "xyes"],
[AC_MSG_ERROR([Unable to find MKL LAPACKE library.])])
- LIBS="${LIBS} -lmkl_intel_ilp64 -lmkl_sequential -lmkl_core -lpthread -lm -ldl"
+ # dynamic linking
+ #LIBS="${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"])
diff --git a/PuReMD/src/reax_types.h b/PuReMD/src/reax_types.h
index 7e3de437..17f3ee3f 100644
--- a/PuReMD/src/reax_types.h
+++ b/PuReMD/src/reax_types.h
@@ -209,7 +209,7 @@ typedef struct
mpi_out_data out_nt_buffers[REAX_MAX_NT_NBRS];
void *in1_buffer;
void *in2_buffer;
- void *in_nt_buffer[REAX_MAX_NT_NBRS]
+ void *in_nt_buffer[REAX_MAX_NT_NBRS];
} mpi_datatypes;
--
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