diff --git a/Makefile.am b/Makefile.am
index 0baa2db6e9283fd6a0901199102f9f4709914683..a0d5bd01517b05b374bb56c71267e402bc41c55e 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -4,25 +4,478 @@ SUBDIRS =
DIST_SUBDIRS =
EXTRA_DIST = data environ tools
+# sPuReMD
if BUILD_S_OMP
-SUBDIRS += sPuReMD
-DIST_SUBDIRS += sPuReMD
+lib_LTLIBRARIES = sPuReMD/lib/libspuremd.la
+sPuReMD_lib_libspuremd_la_SOURCES = sPuReMD/src/allocate.c \
+ sPuReMD/src/allocate.h \
+ sPuReMD/src/analyze.c \
+ sPuReMD/src/analyze.h \
+ sPuReMD/src/bond_orders.c \
+ sPuReMD/src/bond_orders.h \
+ sPuReMD/src/box.c \
+ sPuReMD/src/box.h \
+ sPuReMD/src/charges.c \
+ sPuReMD/src/charges.h \
+ sPuReMD/src/control.c \
+ sPuReMD/src/control.h \
+ sPuReMD/src/ffield.c \
+ sPuReMD/src/ffield.h \
+ sPuReMD/src/forces.c \
+ sPuReMD/src/forces.h \
+ sPuReMD/src/four_body_interactions.c \
+ sPuReMD/src/four_body_interactions.h \
+ sPuReMD/src/geo_tools.c \
+ sPuReMD/src/geo_tools.h \
+ sPuReMD/src/grid.c \
+ sPuReMD/src/grid.h \
+ sPuReMD/src/init_md.c \
+ sPuReMD/src/init_md.h \
+ sPuReMD/src/integrate.c \
+ sPuReMD/src/integrate.h \
+ sPuReMD/src/lin_alg.c \
+ sPuReMD/src/lin_alg.h \
+ sPuReMD/src/list.c \
+ sPuReMD/src/list.h \
+ sPuReMD/src/lookup.c \
+ sPuReMD/src/lookup.h \
+ sPuReMD/src/neighbors.c \
+ sPuReMD/src/neighbors.h \
+ sPuReMD/src/print_utils.c \
+ sPuReMD/src/print_utils.h \
+ sPuReMD/src/random.c \
+ sPuReMD/src/random.h \
+ sPuReMD/src/reax_types.h \
+ sPuReMD/src/reset_utils.c \
+ sPuReMD/src/reset_utils.h \
+ sPuReMD/src/restart.c \
+ sPuReMD/src/restart.h \
+ sPuReMD/src/single_body_interactions.c \
+ sPuReMD/src/single_body_interactions.h \
+ sPuReMD/src/spuremd.c \
+ sPuReMD/src/spuremd.h \
+ sPuReMD/src/system_props.c \
+ sPuReMD/src/system_props.h \
+ sPuReMD/src/three_body_interactions.c \
+ sPuReMD/src/three_body_interactions.h \
+ sPuReMD/src/tool_box.c \
+ sPuReMD/src/tool_box.h \
+ sPuReMD/src/traj.c \
+ sPuReMD/src/traj.h \
+ sPuReMD/src/two_body_interactions.c \
+ sPuReMD/src/two_body_interactions.h \
+ sPuReMD/src/vector.c \
+ sPuReMD/src/vector.h
+sPuReMD_lib_libspuremd_la_CFLAGS = @DFT_CFLAGS@ @OMP_CFLAGS@
+sPuReMD_lib_libspuremd_la_CPPFLAGS = -I sPuReMD/src
+sPuReMD_lib_libspuremd_la_LDFLAGS = -version-info 1:0:0
+sPuReMD_lib_libspuremd_la_LIBADD = @OMP_LIBS@ @L_LIBS@
+
+bin_PROGRAMS = sPuReMD/bin/spuremd
+sPuReMD_bin_spuremd_SOURCES = sPuReMD/src/driver.c
+sPuReMD_bin_spuremd_CFLAGS = @DFT_CFLAGS@ @OMP_CFLAGS@
+sPuReMD_bin_spuremd_CPPFLAGS = -I sPuReMD/src
+sPuReMD_bin_spuremd_LDADD = sPuReMD/lib/libspuremd.la @OMP_LIBS@ @L_LIBS@
+
+check_PROGRAMS =
+TESTS =
+
+if BUILD_TEST
+check_PROGRAMS += sPuReMD/tests/test_spuremd
+check_PROGRAMS += sPuReMD/tests/test_lin_alg
+check_PROGRAMS += sPuReMD/tests/test_vector
+TESTS += $(check_PROGRAMS)
+
+sPuReMD_tests_test_spuremd_SOURCES = sPuReMD/tests/test_spuremd.cpp
+sPuReMD_tests_test_spuremd_CPPFLAGS = -I sPuReMD/src $(GTEST_CPPFLAGS)
+sPuReMD_tests_test_spuremd_CXXFLAGS = $(GTEST_CXXFLAGS)
+sPuReMD_tests_test_spuremd_LDFLAGS = $(GTEST_LDFLAGS) $(GTEST_LIBS)
+sPuReMD_tests_test_spuremd_LDADD = sPuReMD/lib/libspuremd.la -lgtest
+
+sPuReMD_tests_test_lin_alg_SOURCES = sPuReMD/tests/test_lin_alg.cpp
+sPuReMD_tests_test_lin_alg_CPPFLAGS = -I sPuReMD/src $(GTEST_CPPFLAGS)
+sPuReMD_tests_test_lin_alg_CXXFLAGS = $(GTEST_CXXFLAGS)
+sPuReMD_tests_test_lin_alg_LDFLAGS = $(GTEST_LDFLAGS) $(GTEST_LIBS)
+sPuReMD_tests_test_lin_alg_LDADD = -lgtest
+
+sPuReMD_tests_test_vector_SOURCES = sPuReMD/tests/test_vector.cpp
+sPuReMD_tests_test_vector_CPPFLAGS = -I sPuReMD/src $(GTEST_CPPFLAGS)
+sPuReMD_tests_test_vector_CXXFLAGS = $(GTEST_CXXFLAGS)
+sPuReMD_tests_test_vector_LDFLAGS = $(GTEST_LDFLAGS) $(GTEST_LIBS)
+sPuReMD_tests_test_vector_LDADD = -lgtest
+endif
endif
+
if BUILD_MPI
-SUBDIRS += PuReMD
-DIST_SUBDIRS += PuReMD
+bin_PROGRAMS = PuReMD/bin/puremd
+PuReMD_bin_puremd_SOURCES = PuReMD/src/allocate.c \
+ PuReMD/src/allocate.h \
+ PuReMD/src/analyze.c \
+ PuReMD/src/analyze.h \
+ PuReMD/src/basic_comm.c \
+ PuReMD/src/basic_comm.h \
+ PuReMD/src/bond_orders.c \
+ PuReMD/src/bond_orders.h \
+ PuReMD/src/bonds.c \
+ PuReMD/src/bonds.h \
+ PuReMD/src/box.c \
+ PuReMD/src/box.h \
+ PuReMD/src/comm_tools.c \
+ PuReMD/src/comm_tools.h \
+ PuReMD/src/control.c \
+ PuReMD/src/control.h \
+ PuReMD/src/ffield.c \
+ PuReMD/src/ffield.h \
+ PuReMD/src/forces.c \
+ PuReMD/src/forces.h \
+ PuReMD/src/geo_tools.c \
+ PuReMD/src/geo_tools.h \
+ PuReMD/src/grid.c \
+ PuReMD/src/grid.h \
+ PuReMD/src/hydrogen_bonds.c \
+ PuReMD/src/hydrogen_bonds.h \
+ PuReMD/src/init_md.c \
+ PuReMD/src/init_md.h \
+ PuReMD/src/integrate.c \
+ PuReMD/src/integrate.h \
+ PuReMD/src/io_tools.c \
+ PuReMD/src/io_tools.h \
+ PuReMD/src/linear_solvers.c \
+ PuReMD/src/linear_solvers.h \
+ PuReMD/src/list.c \
+ PuReMD/src/list.h \
+ PuReMD/src/lookup.c \
+ PuReMD/src/lookup.h \
+ PuReMD/src/multi_body.c \
+ PuReMD/src/multi_body.h \
+ PuReMD/src/neighbors.c \
+ PuReMD/src/neighbors.h \
+ PuReMD/src/nonbonded.c \
+ PuReMD/src/nonbonded.h \
+ PuReMD/src/parallelreax.c \
+ PuReMD/src/qEq.c \
+ PuReMD/src/qEq.h \
+ PuReMD/src/random.c \
+ PuReMD/src/random.h \
+ PuReMD/src/reax_defs.h \
+ PuReMD/src/reax_types.h \
+ PuReMD/src/reset_tools.c \
+ PuReMD/src/reset_tools.h \
+ PuReMD/src/restart.c \
+ PuReMD/src/restart.h \
+ PuReMD/src/system_props.c \
+ PuReMD/src/system_props.h \
+ PuReMD/src/tool_box.c \
+ PuReMD/src/tool_box.h \
+ PuReMD/src/torsion_angles.c \
+ PuReMD/src/torsion_angles.h \
+ PuReMD/src/traj.c \
+ PuReMD/src/traj.h \
+ PuReMD/src/valence_angles.c \
+ PuReMD/src/valence_angles.h \
+ PuReMD/src/vector.c \
+ PuReMD/src/vector.h
+
+PuReMD_bin_puremd_CFLAGS = @DFT_CFLAGS@ @M_CFLAGS@
+PuReMD_bin_puremd_CPPFLAGS = -I PuReMD/src
+PuReMD_bin_puremd_LDADD = @M_LIBS@ @L_LIBS@
endif
+
if BUILD_GPU
-SUBDIRS += PuReMD-GPU
-DIST_SUBDIRS += PuReMD-GPU
+if USE_CUDA
+SUFFIXES = .cu
+include cuda.am
+endif
+
+if USE_CUDA
+# flags for CUDA compilation via NVCC (see cuda.am)
+# Note: cc 13 for Tesla, cc 20 for Fermi, cc 30 for Kepler K10, cc 35 for Kepler K20/K40, etc.
+#NVCCFLAGS += -gencode arch=compute_35,code=sm_35
+NVCCFLAGS += $(NVCC_OPT_CODE)
+NVCCFLAGS += --compiler-options "$(DEFS) $(NVCC_OPT_CODE_DEFS) @DFT_CFLAGS@"
+#NVCCFLAGS += --ptxas-options -v
+endif
+
+bin_PROGRAMS = PuReMD-GPU/bin/spuremd
+PuReMD_GPU_bin_spuremd_SOURCES = PuReMD-GPU/src/allocate.c \
+ PuReMD-GPU/src/allocate.h \
+ PuReMD-GPU/src/analyze.c \
+ PuReMD-GPU/src/analyze.h \
+ PuReMD-GPU/src/bond_orders.c \
+ PuReMD-GPU/src/bond_orders.h \
+ PuReMD-GPU/src/box.c \
+ PuReMD-GPU/src/box.h \
+ PuReMD-GPU/src/control.c \
+ PuReMD-GPU/src/control.h \
+ PuReMD-GPU/src/ffield.c \
+ PuReMD-GPU/src/ffield.c \
+ PuReMD-GPU/src/forces.c \
+ PuReMD-GPU/src/forces.h \
+ PuReMD-GPU/src/four_body_interactions.c \
+ PuReMD-GPU/src/four_body_interactions.h \
+ PuReMD-GPU/src/geo_tools.c \
+ PuReMD-GPU/src/geo_tools.h \
+ PuReMD-GPU/src/grid.c \
+ PuReMD-GPU/src/grid.h \
+ PuReMD-GPU/src/init_md.c \
+ PuReMD-GPU/src/init_md.h \
+ PuReMD-GPU/src/integrate.c \
+ PuReMD-GPU/src/integrate.h \
+ PuReMD-GPU/src/lin_alg.c \
+ PuReMD-GPU/src/lin_alg.h \
+ PuReMD-GPU/src/list.c \
+ PuReMD-GPU/src/list.h \
+ PuReMD-GPU/src/lookup.c \
+ PuReMD-GPU/src/lookup.h \
+ PuReMD-GPU/src/mytypes.h \
+ PuReMD-GPU/src/neighbors.c \
+ PuReMD-GPU/src/neighbors.h \
+ PuReMD-GPU/src/print_utils.c \
+ PuReMD-GPU/src/print_utils.h \
+ PuReMD-GPU/src/qeq.c \
+ PuReMD-GPU/src/qeq.h \
+ PuReMD-GPU/src/reset_utils.c \
+ PuReMD-GPU/src/reset_utils.h \
+ PuReMD-GPU/src/restart.c \
+ PuReMD-GPU/src/restart.h \
+ PuReMD-GPU/src/single_body_interactions.c \
+ PuReMD-GPU/src/single_body_interactions.h \
+ PuReMD-GPU/src/system_props.c \
+ PuReMD-GPU/src/system_props.h \
+ PuReMD-GPU/src/testmd.c \
+ PuReMD-GPU/src/three_body_interactions.c \
+ PuReMD-GPU/src/three_body_interactions.h \
+ PuReMD-GPU/src/tool_box.c \
+ PuReMD-GPU/src/tool_box.c \
+ PuReMD-GPU/src/traj.c \
+ PuReMD-GPU/src/traj.h \
+ PuReMD-GPU/src/two_body_interactions.c \
+ PuReMD-GPU/src/two_body_interactions.h \
+ PuReMD-GPU/src/vector.c \
+ PuReMD-GPU/src/vector.h
+if USE_CUDA
+PuReMD_GPU_bin_spuremd_SOURCES += PuReMD-GPU/src/cuda_allocate.cu \
+ PuReMD-GPU/src/cuda_allocate.h \
+ PuReMD-GPU/src/cuda_bond_orders.cu \
+ PuReMD-GPU/src/cuda_bond_orders.h \
+ PuReMD-GPU/src/cuda_box.cu \
+ PuReMD-GPU/src/cuda_box.h \
+ PuReMD-GPU/src/cuda_center_mass.cu \
+ PuReMD-GPU/src/cuda_center_mass.h \
+ PuReMD-GPU/src/cuda_copy.cu \
+ PuReMD-GPU/src/cuda_copy.h \
+ PuReMD-GPU/src/cuda_environment.cu \
+ PuReMD-GPU/src/cuda_environment.h \
+ PuReMD-GPU/src/cuda_forces.cu \
+ PuReMD-GPU/src/cuda_forces.h \
+ PuReMD-GPU/src/cuda_four_body_interactions.cu \
+ PuReMD-GPU/src/cuda_four_body_interactions.h \
+ PuReMD-GPU/src/cuda_grid.cu \
+ PuReMD-GPU/src/cuda_grid.h \
+ PuReMD-GPU/src/cuda_init.cu \
+ PuReMD-GPU/src/cuda_init.h \
+ PuReMD-GPU/src/cuda_init_md.cu \
+ PuReMD-GPU/src/cuda_init_md.h \
+ PuReMD-GPU/src/cuda_integrate.cu \
+ PuReMD-GPU/src/cuda_integrate.h \
+ PuReMD-GPU/src/cuda_lin_alg.cu \
+ PuReMD-GPU/src/cuda_lin_alg.h \
+ PuReMD-GPU/src/cuda_list.cu \
+ PuReMD-GPU/src/cuda_list.h \
+ PuReMD-GPU/src/cuda_lookup.cu \
+ PuReMD-GPU/src/cuda_lookup.h \
+ PuReMD-GPU/src/cuda_neighbors.cu \
+ PuReMD-GPU/src/cuda_neighbors.h \
+ PuReMD-GPU/src/cuda_post_evolve.cu \
+ PuReMD-GPU/src/cuda_post_evolve.h \
+ PuReMD-GPU/src/cuda_qeq.cu \
+ PuReMD-GPU/src/cuda_qeq.h \
+ PuReMD-GPU/src/cuda_reduction.cu \
+ PuReMD-GPU/src/cuda_reduction.h \
+ PuReMD-GPU/src/cuda_reset_utils.cu \
+ PuReMD-GPU/src/cuda_reset_utils.h \
+ PuReMD-GPU/src/cuda_single_body_interactions.cu \
+ PuReMD-GPU/src/cuda_single_body_interactions.h \
+ PuReMD-GPU/src/cuda_system_props.cu \
+ PuReMD-GPU/src/cuda_system_props.h \
+ PuReMD-GPU/src/cuda_three_body_interactions.cu \
+ PuReMD-GPU/src/cuda_three_body_interactions.h \
+ PuReMD-GPU/src/cuda_two_body_interactions.cu \
+ PuReMD-GPU/src/cuda_two_body_interactions.h \
+ PuReMD-GPU/src/cuda_utils.cu \
+ PuReMD-GPU/src/cuda_utils.h \
+ PuReMD-GPU/src/cuda_validation.cu \
+ PuReMD-GPU/src/cuda_validation.h
+# dummy source to cause C linking
+nodist_EXTRA_PuReMD_GPU_bin_spuremd_SOURCES = PuReMD-GPU/src/dummy.c
endif
+PuReMD_GPU_bin_spuremd_CFLAGS = @DFT_CFLAGS@
+PuReMD_GPU_bin_spuremd_CPPFLAGS = -I PuReMD-GPU/src
+
+if USE_CUDA
+PuReMD_GPU_bin_spuremd_CFLAGS += @CUDA_CFLAGS@
+PuReMD_GPU_bin_spuremd_LDFLAGS = @CUDA_LIBS@
+endif
+endif
+
+
if BUILD_MPI_GPU
-SUBDIRS += PG-PuReMD
-DIST_SUBDIRS += PG-PuReMD
EXTRA_DIST += PG-PuReMD/src/cub
+
+if USE_CUDA
+SUFFIXES = .cu
+include cuda.am
+endif
+
+if USE_CUDA
+# flags for CUDA compilation via NVCC (see cuda.am)
+# Note: cc 13 for Tesla, cc 20 for Fermi, cc 30 for Kepler K10, cc 35 for Kepler K20/K40, etc.
+#NVCCFLAGS += -gencode arch=compute_35,code=sm_35
+NVCCFLAGS += $(NVCC_OPT_CODE)
+NVCCFLAGS += --compiler-options "$(DEFS) $(NVCC_OPT_CODE_DEFS) @DFT_CFLAGS@ @M_CFLAGS@"
+#NVCCFLAGS += --ptxas-options -v
+endif
+
+bin_PROGRAMS = PG-PuReMD/bin/pg-puremd
+PG_PuReMD_bin_pg_puremd_SOURCES = PG-PuReMD/src/allocate.c \
+ PG-PuReMD/src/allocate.h \
+ PG-PuReMD/src/analyze.c \
+ PG-PuReMD/src/analyze.h \
+ PG-PuReMD/src/basic_comm.c \
+ PG-PuReMD/src/basic_comm.h \
+ PG-PuReMD/src/bond_orders.c \
+ PG-PuReMD/src/bond_orders.h \
+ PG-PuReMD/src/bonds.c \
+ PG-PuReMD/src/bonds.h \
+ PG-PuReMD/src/box.c \
+ PG-PuReMD/src/box.h \
+ PG-PuReMD/src/charges.c \
+ PG-PuReMD/src/charges.h \
+ PG-PuReMD/src/comm_tools.c \
+ PG-PuReMD/src/comm_tools.h \
+ PG-PuReMD/src/control.c \
+ PG-PuReMD/src/control.h \
+ PG-PuReMD/src/driver.c \
+ PG-PuReMD/src/ffield.c \
+ PG-PuReMD/src/ffield.h \
+ PG-PuReMD/src/forces.c \
+ PG-PuReMD/src/forces.h \
+ PG-PuReMD/src/geo_tools.c \
+ PG-PuReMD/src/geo_tools.h \
+ PG-PuReMD/src/grid.c \
+ PG-PuReMD/src/grid.h \
+ PG-PuReMD/src/hydrogen_bonds.c \
+ PG-PuReMD/src/hydrogen_bonds.h \
+ PG-PuReMD/src/index_utils.h \
+ PG-PuReMD/src/init_md.c \
+ PG-PuReMD/src/init_md.h \
+ PG-PuReMD/src/integrate.c \
+ PG-PuReMD/src/integrate.h \
+ PG-PuReMD/src/io_tools.c \
+ PG-PuReMD/src/io_tools.h \
+ PG-PuReMD/src/lin_alg.c \
+ PG-PuReMD/src/lin_alg.h \
+ PG-PuReMD/src/list.c \
+ PG-PuReMD/src/list.h \
+ PG-PuReMD/src/lookup.c \
+ PG-PuReMD/src/lookup.h \
+ PG-PuReMD/src/multi_body.c \
+ PG-PuReMD/src/multi_body.h \
+ PG-PuReMD/src/neighbors.c \
+ PG-PuReMD/src/neighbors.h \
+ PG-PuReMD/src/nonbonded.c \
+ PG-PuReMD/src/nonbonded.h \
+ PG-PuReMD/src/puremd.c \
+ PG-PuReMD/src/random.c \
+ PG-PuReMD/src/random.h \
+ PG-PuReMD/src/reax_types.h \
+ PG-PuReMD/src/reset_tools.c \
+ PG-PuReMD/src/reset_tools.h \
+ PG-PuReMD/src/restart.c \
+ PG-PuReMD/src/restart.h \
+ PG-PuReMD/src/system_props.c \
+ PG-PuReMD/src/system_props.h \
+ PG-PuReMD/src/tool_box.c \
+ PG-PuReMD/src/tool_box.h \
+ PG-PuReMD/src/torsion_angles.c \
+ PG-PuReMD/src/torsion_angles.h \
+ PG-PuReMD/src/traj.c \
+ PG-PuReMD/src/traj.h \
+ PG-PuReMD/src/valence_angles.c \
+ PG-PuReMD/src/valence_angles.h \
+ PG-PuReMD/src/vector.h
+if USE_CUDA
+PG_PuReMD_bin_pg_puremd_SOURCES += PG-PuReMD/src/cuda/cuda_allocate.cu \
+ PG-PuReMD/src/cuda/cuda_allocate.h \
+ PG-PuReMD/src/cuda/cuda_bond_orders.cu \
+ PG-PuReMD/src/cuda/cuda_bond_orders.h \
+ PG-PuReMD/src/cuda/cuda_bonds.cu \
+ PG-PuReMD/src/cuda/cuda_bonds.h \
+ PG-PuReMD/src/cuda/cuda_box.cu \
+ PG-PuReMD/src/cuda/cuda_box.h \
+ PG-PuReMD/src/cuda/cuda_charges.cu \
+ PG-PuReMD/src/cuda/cuda_charges.h \
+ PG-PuReMD/src/cuda/cuda_copy.cu \
+ PG-PuReMD/src/cuda/cuda_copy.h \
+ PG-PuReMD/src/cuda/cuda_environment.cu \
+ PG-PuReMD/src/cuda/cuda_environment.h \
+ PG-PuReMD/src/cuda/cuda_forces.cu \
+ PG-PuReMD/src/cuda/cuda_forces.h \
+ PG-PuReMD/src/cuda/cuda_helpers.h \
+ PG-PuReMD/src/cuda/cuda_hydrogen_bonds.cu \
+ PG-PuReMD/src/cuda/cuda_hydrogen_bonds.h \
+ PG-PuReMD/src/cuda/cuda_init_md.cu \
+ PG-PuReMD/src/cuda/cuda_init_md.h \
+ PG-PuReMD/src/cuda/cuda_integrate.cu \
+ PG-PuReMD/src/cuda/cuda_integrate.h \
+ PG-PuReMD/src/cuda/cuda_lin_alg.cu \
+ PG-PuReMD/src/cuda/cuda_lin_alg.h \
+ PG-PuReMD/src/cuda/cuda_list.cu \
+ PG-PuReMD/src/cuda/cuda_list.h \
+ PG-PuReMD/src/cuda/cuda_lookup.cu \
+ PG-PuReMD/src/cuda/cuda_lookup.h \
+ PG-PuReMD/src/cuda/cuda_multi_body.cu \
+ PG-PuReMD/src/cuda/cuda_multi_body.h \
+ PG-PuReMD/src/cuda/cuda_neighbors.cu \
+ PG-PuReMD/src/cuda/cuda_neighbors.h \
+ PG-PuReMD/src/cuda/cuda_nonbonded.cu \
+ PG-PuReMD/src/cuda/cuda_nonbonded.h \
+ PG-PuReMD/src/cuda/cuda_post_evolve.cu \
+ PG-PuReMD/src/cuda/cuda_post_evolve.h \
+ PG-PuReMD/src/cuda/cuda_random.cu \
+ PG-PuReMD/src/cuda/cuda_random.h \
+ PG-PuReMD/src/cuda/cuda_reduction.cu \
+ PG-PuReMD/src/cuda/cuda_reduction.h \
+ PG-PuReMD/src/cuda/cuda_reset_tools.cu \
+ PG-PuReMD/src/cuda/cuda_reset_tools.h \
+ PG-PuReMD/src/cuda/cuda_shuffle.h \
+ PG-PuReMD/src/cuda/cuda_system_props.cu \
+ PG-PuReMD/src/cuda/cuda_system_props.h \
+ PG-PuReMD/src/cuda/cuda_torsion_angles.cu \
+ PG-PuReMD/src/cuda/cuda_torsion_angles.h \
+ PG-PuReMD/src/cuda/cuda_utils.cu \
+ PG-PuReMD/src/cuda/cuda_utils.h \
+ PG-PuReMD/src/cuda/cuda_valence_angles.cu \
+ PG-PuReMD/src/cuda/cuda_valence_angles.h \
+ PG-PuReMD/src/cuda/cuda_vector.h
+if CUDA_DEBUG
+PG_PuReMD_bin_pg_puremd_SOURCES += PG-PuReMD/src/cuda/cuda_validation.cu \
+ PG-PuReMD/src/cuda/cuda_validation.h
+endif
+# dummy source to trigger C linking
+nodist_EXTRA_PG_PuReMD_bin_pg_puremd_SOURCES = src/dummy.c
+endif
+
+PG_PuReMD_bin_pg_puremd_CFLAGS = @DFT_CFLAGS@ @M_CFLAGS@
+PG_PuReMD_bin_pg_puremd_CPPFLAGS = -I PG-PuReMD/src
+PG_PuReMD_bin_pg_puremd_LDADD = @M_LIBS@ @L_LIBS@ -lstdc++
+if USE_CUDA
+PG_PuReMD_bin_pg_puremd_CFLAGS += @CUDA_CFLAGS@
+PG_PuReMD_bin_pg_puremd_LDADD += @CUDA_LIBS@
+endif
endif
if BUILD_DOC
diff --git a/PG-PuReMD/Makefile.am b/PG-PuReMD/Makefile.am
deleted file mode 100644
index 2c878ef102e146c55c41fe9c4d852cf2f20701d7..0000000000000000000000000000000000000000
--- a/PG-PuReMD/Makefile.am
+++ /dev/null
@@ -1,70 +0,0 @@
-ACLOCAL_AMFLAGS = -I ../m4
-
-if USE_CUDA
-SUFFIXES = .cu
-include ../cuda.am
-endif
-
-if USE_CUDA
-# flags for CUDA compilation via NVCC (see cuda.am)
-# Note: cc 13 for Tesla, cc 20 for Fermi, cc 30 for Kepler K10, cc 35 for Kepler K20/K40, etc.
-#NVCCFLAGS += -use_fast_math -gencode arch=compute_35,code=sm_35
-NVCCFLAGS += -use_fast_math $(NVCC_OPT_CODE)
-NVCCFLAGS += --compiler-options "$(DEFS) $(NVCC_OPT_CODE_DEFS) -O2 -funroll-loops $(MPI_CFLAGS)"
-#NVCCFLAGS += --ptxas-options -v
-endif
-
-
-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/lin_alg.c src/neighbors.c \
- src/charges.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/puremd.c \
- src/driver.c \
- src/reax_types.h src/index_utils.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/vector.h \
- src/tool_box.h src/traj.h src/analyze.h src/box.h src/system_props.h \
- src/control.h src/comm_tools.h src/geo_tools.h src/lin_alg.h src/neighbors.h \
- src/charges.h src/bond_orders.h src/multi_body.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
-if USE_CUDA
-bin_pg_puremd_SOURCES += src/cuda/cuda_utils.cu src/cuda/cuda_allocate.cu src/cuda/cuda_environment.cu \
- src/cuda/cuda_system_props.cu src/cuda/cuda_reduction.cu src/cuda/cuda_box.cu src/cuda/cuda_list.cu \
- src/cuda/cuda_copy.cu src/cuda/cuda_reset_tools.cu src/cuda/cuda_random.cu \
- src/cuda/cuda_neighbors.cu src/cuda/cuda_bond_orders.cu src/cuda/cuda_bonds.cu \
- src/cuda/cuda_multi_body.cu src/cuda/cuda_valence_angles.cu \
- src/cuda/cuda_torsion_angles.cu src/cuda/cuda_hydrogen_bonds.cu src/cuda/cuda_forces.cu \
- src/cuda/cuda_charges.cu src/cuda/cuda_lin_alg.cu \
- src/cuda/cuda_nonbonded.cu src/cuda/cuda_integrate.cu src/cuda/cuda_post_evolve.cu \
- src/cuda/cuda_init_md.cu src/cuda/cuda_lookup.cu \
- src/cuda/cuda_helpers.h src/cuda/cuda_shuffle.h \
- src/cuda/cuda_utils.h src/cuda/cuda_allocate.h src/cuda/cuda_environment.h \
- src/cuda/cuda_system_props.h src/cuda/cuda_reduction.h src/cuda/cuda_box.h src/cuda/cuda_list.h \
- src/cuda/cuda_copy.h src/cuda/cuda_reset_tools.h src/cuda/cuda_random.h src/cuda/cuda_vector.h \
- src/cuda/cuda_neighbors.h src/cuda/cuda_bond_orders.h src/cuda/cuda_bonds.h \
- src/cuda/cuda_multi_body.h src/cuda/cuda_valence_angles.h \
- src/cuda/cuda_torsion_angles.h src/cuda/cuda_hydrogen_bonds.h src/cuda/cuda_forces.h \
- src/cuda/cuda_charges.h src/cuda/cuda_lin_alg.h \
- src/cuda/cuda_nonbonded.h src/cuda/cuda_integrate.h src/cuda/cuda_post_evolve.h \
- src/cuda/cuda_init_md.h src/cuda/cuda_lookup.h
-if DEBUG
-bin_pg_puremd_SOURCES += src/cuda/cuda_validation.cu \
- src/cuda/cuda_validation.h
-endif
-# dummy source to trigger C linking
-nodist_EXTRA_bin_pg_puremd_SOURCES = src/dummy.c
-endif
-
-bin_pg_puremd_CFLAGS = $(AM_CFLAGS) $(MPI_CFLAGS) $(CFLAGS)
-bin_pg_puremd_CPPFLAGS = $(AM_CPPFLAGS) $(CPPFLAGS)
-bin_pg_puremd_LDADD = $(AM_LDADD) $(MPI_LIBS) $(LDADD) -lstdc++
-if USE_CUDA
-bin_pg_puremd_CFLAGS += $(CUDA_CFLAGS)
-bin_pg_puremd_LDADD += $(CUDA_LIBS)
-endif
diff --git a/PG-PuReMD/aclocal.m4 b/PG-PuReMD/aclocal.m4
deleted file mode 100644
index e1a7adedccfa9f18035be1d931ad439b6df5dc38..0000000000000000000000000000000000000000
--- a/PG-PuReMD/aclocal.m4
+++ /dev/null
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-m4_include([../m4/acx_mpi.m4])
-m4_include([../m4/ax_compiler_vendor.m4])
-m4_include([../m4/ax_cuda.m4])
diff --git a/PG-PuReMD/configure.ac b/PG-PuReMD/configure.ac
deleted file mode 100644
index 9545d8e673dfa6d61cad7f099a98df2701c5c40c..0000000000000000000000000000000000000000
--- a/PG-PuReMD/configure.ac
+++ /dev/null
@@ -1,209 +0,0 @@
-# -*- Autoconf -*-
-# Process this file with autoconf to produce a configure script.
-
-AC_PREREQ([2.69])
-
-AC_INIT([PG-PuReMD], [1.0], [ohearnku@msu.edu hma@msu.edu])
-# Do not allow AC_PROG_CC to set CFLAGS (this line must be after AC_INIT but before AC_PROG_CC)
-save_CFLAGS="$CFLAGS"
-: ${CFLAGS=""}
-AM_INIT_AUTOMAKE([1.15 subdir-objects -Wall -Werror foreign])
-# Enable silent build rules by default.
-m4_ifdef([AM_SILENT_RULES], [AM_SILENT_RULES([yes])], [AC_SUBST([AM_DEFAULT_VERBOSITY],[1])])
-#AM_PROG_AR
-#LT_PREREQ([2.2])
-#LT_INIT([dlopen])
-
-AC_CONFIG_MACRO_DIR([../m4])
-
-# Headline formatter
-AC_DEFUN([CONFIGURE_HEADLINE],
-[
- echo; echo "+++ $1 +++"
-])
-
-AC_LANG([C])
-
-AC_CONFIG_SRCDIR([src/torsion_angles.h])
-AC_CONFIG_HEADERS([src/config.h])
-
-# Checks for programs.
-AC_PROG_CC([icc gcc clang cc])
-AC_PROG_CPP
-CFLAGS="${save_CFLAGS}"
-
-# Checks for libraries.
-AC_SEARCH_LIBS([exp], [m])
-AC_SEARCH_LIBS([sqrt], [m])
-AC_SEARCH_LIBS([pow], [m])
-AC_SEARCH_LIBS([acos], [m])
-AC_SEARCH_LIBS([cos], [m])
-AC_SEARCH_LIBS([sin], [m])
-AC_SEARCH_LIBS([tan], [m])
-AC_SEARCH_LIBS([fabs], [m])
-
-# Checks for typedefs, structures, and compiler characteristics.
-AC_CHECK_HEADER_STDBOOL
-AC_C_INLINE
-AC_TYPE_SIZE_T
-
-# Checks for library functions.
-AC_FUNC_MALLOC
-AC_FUNC_REALLOC
-AC_FUNC_STRTOD
-AC_CHECK_FUNCS([gettimeofday memset])
-
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-# 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}" = "xyes"; then
- CFLAGS="-Wall -O0 -g2 -D_GLIBCXX_DEBUG"
- else
- CFLAGS="-Wall -O2 -funroll-loops"
- fi
- if test "x${BUILD_GPROF}" = "xyes"; then
- CFLAGS="${CFLAGS} -pg"
- fi
-elif test "x${ax_cv_c_compiler_vendor}" = "xintel"; then
- if test "x${BUILD_DEBUG}" = "xyes"; then
- CFLAGS="-Wall -O0"
- else
- CFLAGS="-Wall -O2 -funroll-loops"
- fi
- if test "x${BUILD_GPROF}" = "xyes"; then
- CFLAGS="${CFLAGS} -p"
- fi
-fi
-
-# Check for MPI support.
-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
-save_CC="${CC}"
-save_CFLAGS="${CFLAGS}"
-CC="${MPICC}"
-CFLAGS="${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="${save_CC}"
-CFLAGS="${save_CFLAGS}"
-
-# try to set MPI_CFLAGS and MPI_LIBS
-MPI_CFLAGS=
-MPI_LIBS=
-if test "x${mpi_vendor}" = "xOpenMPI"
-then
- MPI_CFLAGS=`${MPICC} --showme:compile`
- MPI_LIBS=`${MPICC} --showme:link`
- AC_MSG_NOTICE([OpenMPI found])
- AC_MSG_NOTICE([MPI_CFLAGS=${MPI_CFLAGS}])
- AC_MSG_NOTICE([MPI_LIBS=${MPI_LIBS}])
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-then
- # build MPI_CFLAGS
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- do
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- -[[DIUbi]]*)
- MPI_CFLAGS="${MPI_CFLAGS} ${i}"
- ;;
- esac
- done
- # build MPI_LIBS
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- for i in ${tmp}
- do
- case ${i} in
- [[\\/]]*.a | ?:[[\\/]]*.a | -[[lLRu]]* | -Wl* )
- MPI_LIBS="${MPI_LIBS} ${i}"
- ;;
- esac
- done
- AC_MSG_NOTICE([MPICH found])
- AC_MSG_NOTICE([MPI_CFLAGS=${MPI_CFLAGS}])
- AC_MSG_NOTICE([MPI_LIBS=${MPI_LIBS}])
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- AC_MSG_WARN([Neither OpenMPI and MPICH have been recognized...])
-fi
-AC_SUBST(MPI_CFLAGS)
-AC_SUBST(MPI_LIBS)
-
-# Check for LAPACKE
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-if test "x${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${MKL_FOUND_LIBS}" != "xyes"],
- [AC_MSG_ERROR([Unable to find MKL LAPACKE library.])])
- LIBS="${LIBS} -lmkl_intel_ilp64 -lmkl_sequential -lmkl_core -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${LAPACKE_FOUND_HEADERS}" = "xyes"
- then
- AC_SEARCH_LIBS([LAPACKE_dgels], [lapacke],
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- -----------------------------------------------
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-
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-
-# Checks for programs.
-AC_PROG_CXX([icpc g++ clang++ c++])
-AC_PROG_CXXCPP
-
-# Check for CUDA support.
-if test "x${BUILD_GPU}" = "xyes"; then
- CONFIGURE_HEADLINE([ CUDA support ])
- AX_CUDA
-
- NVCCFLAGS=
- NVCCFLAGS+=" -ccbin=${CXX}"
- if test "x${BUILD_DEBUG}" = "xyes"
- then
- NVCCFLAGS+=" -g -G"
-
- fi
- AC_DEFINE([HAVE_CUDA], [1], [Define to 1 if you have CUDA support enabled.])
-else
- AM_CONDITIONAL(USE_CUDA, test "x" = "xyes")
-fi
-AM_CONDITIONAL(DEBUG, test "x${BUILD_DEBUG}" = "xyes")
-
-if test "x${BUILD_GPROF}" = "xyes"
-then
- if test "x${BUILD_GPU}" = "xyes"; then
- NVCCFLAGS+=" --compiler-options ${gprof_flags}"
- else
- CFLAGS+=" ${gprof_flags}"
- fi
-fi
-
-AC_CONFIG_FILES([Makefile])
-
-AC_OUTPUT
diff --git a/PuReMD-GPU/Makefile.am b/PuReMD-GPU/Makefile.am
deleted file mode 100644
index 90d70db89f88125526397044c497f23799528212..0000000000000000000000000000000000000000
--- a/PuReMD-GPU/Makefile.am
+++ /dev/null
@@ -1,72 +0,0 @@
-ACLOCAL_AMFLAGS = -I ../m4
-
-if USE_CUDA
-SUFFIXES = .cu
-include ../cuda.am
-endif
-
-# flags for CUDA compilation via NVCC (see cuda.am)
-# Note: cc 13 for Tesla, cc 20 for Fermi, cc 30 for Kepler K10, cc 35 for Kepler K20/K40, etc.
-#NVCCFLAGS += -use_fast_math -gencode arch=compute_35,code=sm_35
-NVCCFLAGS += -use_fast_math $(NVCC_OPT_CODE)
-NVCCFLAGS += --compiler-options "$(DEFS) $(NVCC_OPT_CODE_DEFS) -O2 -funroll-loops"
-#NVCCFLAGS += --ptxas-options -v
-
-bin_PROGRAMS = bin/spuremd
-bin_spuremd_SOURCES = src/analyze.c src/print_utils.c \
- src/restart.c src/tool_box.c src/control.c src/ffield.c \
- src/geo_tools.c src/box.c \
- src/lin_alg.c src/qeq.c src/allocate.c src/bond_orders.c \
- src/forces.c src/four_body_interactions.c \
- src/grid.c src/init_md.c src/integrate.c src/list.c \
- src/lookup.c src/neighbors.c \
- src/reset_utils.c src/single_body_interactions.c \
- src/system_props.c src/three_body_interactions.c \
- src/traj.c src/two_body_interactions.c src/vector.c \
- src/testmd.c \
- src/mytypes.h src/analyze.h src/print_utils.h \
- src/restart.h src/tool_box.c src/control.h src/ffield.c \
- src/geo_tools.h src/box.h \
- src/lin_alg.h src/qeq.h src/allocate.h src/bond_orders.h \
- src/forces.h src/four_body_interactions.h \
- src/grid.h src/init_md.h src/integrate.h src/list.h \
- src/lookup.h src/neighbors.h \
- src/reset_utils.h src/single_body_interactions.h \
- src/system_props.h src/three_body_interactions.h \
- src/traj.h src/two_body_interactions.h src/vector.h
-
-if USE_CUDA
-bin_spuremd_SOURCES += src/cuda_utils.cu src/cuda_copy.cu \
- src/cuda_init.cu src/cuda_reduction.cu \
- src/cuda_center_mass.cu src/cuda_box.cu src/cuda_validation.cu \
- src/cuda_allocate.cu src/cuda_bond_orders.cu \
- src/cuda_lin_alg.cu src/cuda_qeq.cu \
- src/cuda_forces.cu src/cuda_four_body_interactions.cu \
- src/cuda_grid.cu src/cuda_init_md.cu src/cuda_integrate.cu src/cuda_list.cu \
- src/cuda_lookup.cu src/cuda_neighbors.cu \
- src/cuda_reset_utils.cu src/cuda_single_body_interactions.cu \
- src/cuda_system_props.cu src/cuda_three_body_interactions.cu \
- src/cuda_two_body_interactions.cu src/cuda_environment.cu \
- src/cuda_post_evolve.cu \
- src/cuda_utils.h src/cuda_copy.h \
- src/cuda_init.h src/cuda_reduction.h \
- src/cuda_center_mass.h src/cuda_box.h src/cuda_validation.h \
- src/cuda_allocate.h src/cuda_bond_orders.h \
- src/cuda_lin_alg.h src/cuda_qeq.h \
- src/cuda_forces.h src/cuda_four_body_interactions.h \
- src/cuda_grid.h src/cuda_init_md.h src/cuda_integrate.h src/cuda_list.h \
- src/cuda_lookup.h src/cuda_neighbors.h \
- src/cuda_reset_utils.h src/cuda_single_body_interactions.h \
- src/cuda_system_props.h src/cuda_three_body_interactions.h \
- src/cuda_two_body_interactions.h src/cuda_environment.h \
- src/cuda_post_evolve.h
-
-# dummy source to cause C linking
-nodist_EXTRA_bin_spuremd_SOURCES = src/dummy.c
-
-endif
-
-if USE_CUDA
-bin_spuremd_CFLAGS = $(CUDA_CFLAGS)
-bin_spuremd_LDFLAGS = $(CUDA_LIBS)
-endif
diff --git a/PuReMD-GPU/aclocal.m4 b/PuReMD-GPU/aclocal.m4
deleted file mode 100644
index d6bf5baa543b24a4c3d8f9fc06ee2020a1d3f9bf..0000000000000000000000000000000000000000
--- a/PuReMD-GPU/aclocal.m4
+++ /dev/null
@@ -1,1154 +0,0 @@
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deleted file mode 100644
index 07c96867b29474d57b94ae9a0a96099bac8d98e3..0000000000000000000000000000000000000000
--- a/PuReMD-GPU/configure.ac
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diff --git a/PuReMD/Makefile.am b/PuReMD/Makefile.am
deleted file mode 100644
index c657b37a7bde1349eaa877de14d82b8d8bf727cd..0000000000000000000000000000000000000000
--- a/PuReMD/Makefile.am
+++ /dev/null
@@ -1,19 +0,0 @@
-ACLOCAL_AMFLAGS = -I ../m4
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-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 \
- 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 \
- src/geo_tools.h src/linear_solvers.h src/neighbors.h src/qEq.h src/bond_orders.h src/multi_body.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
-
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diff --git a/PuReMD/aclocal.m4 b/PuReMD/aclocal.m4
deleted file mode 100644
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-# We'll loop over all known methods to create a tar archive until one works.
-_am_tools='gnutar m4_if([$1], [ustar], [plaintar]) pax cpio none'
-
-m4_if([$1], [v7],
- [am__tar='$${TAR-tar} chof - "$$tardir"' am__untar='$${TAR-tar} xf -'],
-
- [m4_case([$1],
- [ustar],
- [# The POSIX 1988 'ustar' format is defined with fixed-size fields.
- # There is notably a 21 bits limit for the UID and the GID. In fact,
- # the 'pax' utility can hang on bigger UID/GID (see automake bug#8343
- # and bug#13588).
- am_max_uid=2097151 # 2^21 - 1
- am_max_gid=$am_max_uid
- # The $UID and $GID variables are not portable, so we need to resort
- # to the POSIX-mandated id(1) utility. Errors in the 'id' calls
- # below are definitely unexpected, so allow the users to see them
- # (that is, avoid stderr redirection).
- am_uid=`id -u || echo unknown`
- am_gid=`id -g || echo unknown`
- AC_MSG_CHECKING([whether UID '$am_uid' is supported by ustar format])
- if test $am_uid -le $am_max_uid; then
- AC_MSG_RESULT([yes])
- else
- AC_MSG_RESULT([no])
- _am_tools=none
- fi
- AC_MSG_CHECKING([whether GID '$am_gid' is supported by ustar format])
- if test $am_gid -le $am_max_gid; then
- AC_MSG_RESULT([yes])
- else
- AC_MSG_RESULT([no])
- _am_tools=none
- fi],
-
- [pax],
- [],
-
- [m4_fatal([Unknown tar format])])
-
- AC_MSG_CHECKING([how to create a $1 tar archive])
-
- # Go ahead even if we have the value already cached. We do so because we
- # need to set the values for the 'am__tar' and 'am__untar' variables.
- _am_tools=${am_cv_prog_tar_$1-$_am_tools}
-
- for _am_tool in $_am_tools; do
- case $_am_tool in
- gnutar)
- for _am_tar in tar gnutar gtar; do
- AM_RUN_LOG([$_am_tar --version]) && break
- done
- am__tar="$_am_tar --format=m4_if([$1], [pax], [posix], [$1]) -chf - "'"$$tardir"'
- am__tar_="$_am_tar --format=m4_if([$1], [pax], [posix], [$1]) -chf - "'"$tardir"'
- am__untar="$_am_tar -xf -"
- ;;
- plaintar)
- # Must skip GNU tar: if it does not support --format= it doesn't create
- # ustar tarball either.
- (tar --version) >/dev/null 2>&1 && continue
- am__tar='tar chf - "$$tardir"'
- am__tar_='tar chf - "$tardir"'
- am__untar='tar xf -'
- ;;
- pax)
- am__tar='pax -L -x $1 -w "$$tardir"'
- am__tar_='pax -L -x $1 -w "$tardir"'
- am__untar='pax -r'
- ;;
- cpio)
- am__tar='find "$$tardir" -print | cpio -o -H $1 -L'
- am__tar_='find "$tardir" -print | cpio -o -H $1 -L'
- am__untar='cpio -i -H $1 -d'
- ;;
- none)
- am__tar=false
- am__tar_=false
- am__untar=false
- ;;
- esac
-
- # If the value was cached, stop now. We just wanted to have am__tar
- # and am__untar set.
- test -n "${am_cv_prog_tar_$1}" && break
-
- # tar/untar a dummy directory, and stop if the command works.
- rm -rf conftest.dir
- mkdir conftest.dir
- echo GrepMe > conftest.dir/file
- AM_RUN_LOG([tardir=conftest.dir && eval $am__tar_ >conftest.tar])
- rm -rf conftest.dir
- if test -s conftest.tar; then
- AM_RUN_LOG([$am__untar <conftest.tar])
- AM_RUN_LOG([cat conftest.dir/file])
- grep GrepMe conftest.dir/file >/dev/null 2>&1 && break
- fi
- done
- rm -rf conftest.dir
-
- AC_CACHE_VAL([am_cv_prog_tar_$1], [am_cv_prog_tar_$1=$_am_tool])
- AC_MSG_RESULT([$am_cv_prog_tar_$1])])
-
-AC_SUBST([am__tar])
-AC_SUBST([am__untar])
-]) # _AM_PROG_TAR
-
-m4_include([../m4/acx_mpi.m4])
diff --git a/PuReMD/configure.ac b/PuReMD/configure.ac
deleted file mode 100644
index 6a1bb0a187736d4baf0207f537e2d224758a3901..0000000000000000000000000000000000000000
--- a/PuReMD/configure.ac
+++ /dev/null
@@ -1,172 +0,0 @@
-# -*- Autoconf -*-
-# Process this file with autoconf to produce a configure script.
-
-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.
-m4_ifdef([AM_SILENT_RULES], [AM_SILENT_RULES([yes])], [AC_SUBST([AM_DEFAULT_VERBOSITY],[1])])
-#LT_PREREQ([2.2])
-#LT_INIT([dlopen])
-
-AC_CONFIG_MACRO_DIR([../m4])
-
-# 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])
-AC_SEARCH_LIBS([sqrt], [m])
-AC_SEARCH_LIBS([pow], [m])
-AC_SEARCH_LIBS([acos], [m])
-AC_SEARCH_LIBS([cos], [m])
-AC_SEARCH_LIBS([sin], [m])
-AC_SEARCH_LIBS([tan], [m])
-AC_SEARCH_LIBS([fabs], [m])
-
-# Checks for typedefs, structures, and compiler characteristics.
-AC_C_INLINE
-
-# Checks for library functions.
-AC_FUNC_MALLOC
-AC_FUNC_REALLOC
-AC_FUNC_STRTOD
-AC_CHECK_FUNCS([gettimeofday memset pow sqrt])
-
-# 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)
-
-# try to find if we are using OpenMPI / MPICH by looking inside mpi.h
-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="${save_CC}"
-CFLAGS="${save_CFLAGS}"
-
-# try to set MPI_CFLAGS and MPI_LIBS
-MPI_CFLAGS=
-MPI_LIBS=
-if test "x${mpi_vendor}" = "xOpenMPI"
-then
- 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_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 }'`
- MPI_CFLAGS=
- for i in $tmp
- do
- case ${i} in
- -[[DIUbi]]*)
- MPI_CFLAGS="${MPI_CFLAGS} ${i}"
- ;;
- esac
- done
- # build MPI_LIBS
- tmp=`${MPICC} -link-info | awk '{$1=""; print $0 }'`
- for i in $tmp
- do
- case ${i} in
- [[\\/]]*.a | ?:[[\\/]]*.a | -[[lLRu]]* | -Wl* )
- MPI_LIBS="${MPI_LIBS} ${i}"
- ;;
- esac
- done
- AC_MSG_NOTICE([MPICH found])
- 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_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])
-
-AC_OUTPUT
diff --git a/aclocal.m4 b/aclocal.m4
index 3610979edf04a670e7960e14a83759c6d6799abf..68021b8b585459e3cc87f5cc44c3220f9efc9fad 100644
--- a/aclocal.m4
+++ b/aclocal.m4
@@ -56,6 +56,66 @@ m4_ifndef([AC_AUTOCONF_VERSION],
[m4_copy([m4_PACKAGE_VERSION], [AC_AUTOCONF_VERSION])])dnl
_AM_AUTOCONF_VERSION(m4_defn([AC_AUTOCONF_VERSION]))])
+# Copyright (C) 2011-2017 Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# AM_PROG_AR([ACT-IF-FAIL])
+# -------------------------
+# Try to determine the archiver interface, and trigger the ar-lib wrapper
+# if it is needed. If the detection of archiver interface fails, run
+# ACT-IF-FAIL (default is to abort configure with a proper error message).
+AC_DEFUN([AM_PROG_AR],
+[AC_BEFORE([$0], [LT_INIT])dnl
+AC_BEFORE([$0], [AC_PROG_LIBTOOL])dnl
+AC_REQUIRE([AM_AUX_DIR_EXPAND])dnl
+AC_REQUIRE_AUX_FILE([ar-lib])dnl
+AC_CHECK_TOOLS([AR], [ar lib "link -lib"], [false])
+: ${AR=ar}
+
+AC_CACHE_CHECK([the archiver ($AR) interface], [am_cv_ar_interface],
+ [AC_LANG_PUSH([C])
+ am_cv_ar_interface=ar
+ AC_COMPILE_IFELSE([AC_LANG_SOURCE([[int some_variable = 0;]])],
+ [am_ar_try='$AR cru libconftest.a conftest.$ac_objext >&AS_MESSAGE_LOG_FD'
+ AC_TRY_EVAL([am_ar_try])
+ if test "$ac_status" -eq 0; then
+ am_cv_ar_interface=ar
+ else
+ am_ar_try='$AR -NOLOGO -OUT:conftest.lib conftest.$ac_objext >&AS_MESSAGE_LOG_FD'
+ AC_TRY_EVAL([am_ar_try])
+ if test "$ac_status" -eq 0; then
+ am_cv_ar_interface=lib
+ else
+ am_cv_ar_interface=unknown
+ fi
+ fi
+ rm -f conftest.lib libconftest.a
+ ])
+ AC_LANG_POP([C])])
+
+case $am_cv_ar_interface in
+ar)
+ ;;
+lib)
+ # Microsoft lib, so override with the ar-lib wrapper script.
+ # FIXME: It is wrong to rewrite AR.
+ # But if we don't then we get into trouble of one sort or another.
+ # A longer-term fix would be to have automake use am__AR in this case,
+ # and then we could set am__AR="$am_aux_dir/ar-lib \$(AR)" or something
+ # similar.
+ AR="$am_aux_dir/ar-lib $AR"
+ ;;
+unknown)
+ m4_default([$1],
+ [AC_MSG_ERROR([could not determine $AR interface])])
+ ;;
+esac
+AC_SUBST([AR])dnl
+])
+
# AM_AUX_DIR_EXPAND -*- Autoconf -*-
# Copyright (C) 2001-2017 Free Software Foundation, Inc.
@@ -1150,6 +1210,11 @@ AC_SUBST([am__tar])
AC_SUBST([am__untar])
]) # _AM_PROG_TAR
+m4_include([m4/acx_mpi.m4])
+m4_include([m4/acx_pthread.m4])
+m4_include([m4/ax_compiler_vendor.m4])
+m4_include([m4/ax_cuda.m4])
+m4_include([m4/ax_openmp.m4])
m4_include([m4/libtool.m4])
m4_include([m4/ltoptions.m4])
m4_include([m4/ltsugar.m4])
diff --git a/compile b/compile
index 2ab71e4ea13e0e902ec8a5357546f0a10d3f67ea..de0005d4f9f4018db22e6fd9665d589f3c626dde 100755
--- a/compile
+++ b/compile
@@ -1,4 +1,4 @@
-#! /bin/sh
+#!/bin/sh
# Wrapper for compilers which do not understand '-c -o'.
scriptversion=2016-01-11.22; # UTC
diff --git a/configure.ac b/configure.ac
index 8d0243d4094d01001ff4e333459b478a1f4c5405..a7f54a52b654d5061905adecae57cc9faf7453a8 100644
--- a/configure.ac
+++ b/configure.ac
@@ -4,14 +4,24 @@
AC_PREREQ([2.69])
AC_INIT([PuReMD], [1.0], [ohearnku@msu.edu hma@msu.edu])
-AM_INIT_AUTOMAKE([1.15 -Wall -Werror])
+# 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])
# Enable silent build rules by default.
m4_ifdef([AM_SILENT_RULES], [AM_SILENT_RULES([yes])], [AC_SUBST([AM_DEFAULT_VERBOSITY],[1])])
+AM_PROG_AR
LT_PREREQ([2.2])
LT_INIT([dlopen])
AC_CONFIG_MACRO_DIR([m4])
+# Headline formatter
+AC_DEFUN([CONFIGURE_HEADLINE],
+[
+ echo; echo "+++ $1 +++"
+])
+
AC_DEFUN([AC_PROG_PDFLATEX],
[AC_ARG_VAR([PDFLATEX], [LaTeX PDF generation program])dnl
AC_CHECK_PROGS([PDFLATEX], [pdflatex])
@@ -45,35 +55,6 @@ AC_ARG_ENABLE([mpi-gpu],
[enable MPI+CUDA (multi GPU) support @<:@default: no@:>@])],
[pack_mpi_gpu_enabled=${enableval}], [pack_mpi_gpu_enabled=no])
-if test "x${pack_serial_enabled}" = "xyes" || test "x${pack_openmp_enabled}" = "xyes" || test "x${pack_gpu_enabled}" = "xyes"; then
- AC_CONFIG_SUBDIRS([sPuReMD])
- if test "x${pack_serial_enabled}" = "xyes" || test "x${pack_openmp_enabled}" != "xyes"; then
- export BUILD_OPENMP="no"
- else
- if test "x${pack_gpu_enabled}" = "xyes"; then
- export BUILD_GPU="yes"
- else
- export BUILD_OPENMP="yes"
- fi
- fi
-fi
-AM_CONDITIONAL([BUILD_S_OMP], [test "x${pack_serial_enabled}" = "xyes" || test "x${pack_openmp_enabled}" = "xyes"])
-AM_CONDITIONAL([BUILD_GPU], [test "x${pack_gpu_enabled}" = "xyes"])
-
-if test "x${pack_mpi_old_enabled}" = "xyes"; then
- AC_CONFIG_SUBDIRS([PuReMD])
-fi
-AM_CONDITIONAL([BUILD_MPI], [test "x${pack_mpi_old_enabled}" = "xyes"])
-if test "x${pack_mpi_enabled}" = "xyes" || test "x${pack_mpi_gpu_enabled}" = "xyes"; then
- AC_CONFIG_SUBDIRS([PG-PuReMD])
- if test "x${pack_mpi_enabled}" = "xyes" || test "x${pack_mpi_gpu_enabled}" != "xyes"; then
- export BUILD_GPU="no"
- else
- export BUILD_GPU="yes"
- fi
-fi
-AM_CONDITIONAL([BUILD_MPI_GPU], [test "x${pack_mpi_enabled}" = "xyes" || test "x${pack_mpi_gpu_enabled}" = "xyes"])
-
# Provides debug compilation mode.
AC_ARG_ENABLE([debug],
[AS_HELP_STRING([--enable-debug],
@@ -124,6 +105,638 @@ if test "x${pack_doc_enabled}" = "xyes"; then
AC_CONFIG_SUBDIRS([doc])
fi
+
+# Checks for compilers.
+AC_LANG([C])
+AC_PROG_CC([icc gcc clang cc])
+AC_PROG_CPP
+CFLAGS="${save_CFLAGS}"
+
+AC_LANG([C++])
+AC_PROG_CXX([icpc g++ clang++ CC c++])
+AC_PROG_CXXCPP
+
+
+# sPuReMD
+if test "x${pack_serial_enabled}" = "xyes" || test "x${pack_openmp_enabled}" = "xyes"; then
+ if test "x${pack_serial_enabled}" = "xyes" || test "x${pack_openmp_enabled}" != "xyes"; then
+ BUILD_OPENMP="no"
+ else
+ BUILD_OPENMP="yes"
+ fi
+
+ AC_LANG_PUSH([C])
+
+ AC_CONFIG_SRCDIR([sPuReMD/src/traj.h])
+ AC_CONFIG_HEADERS([sPuReMD/src/config.h])
+
+ # Checks for libraries.
+ AC_SEARCH_LIBS([exp], [m])
+ AC_SEARCH_LIBS([sqrt], [m])
+ AC_SEARCH_LIBS([pow], [m])
+ AC_SEARCH_LIBS([acos], [m])
+ AC_SEARCH_LIBS([cos], [m])
+ AC_SEARCH_LIBS([sin], [m])
+ AC_SEARCH_LIBS([tan], [m])
+ AC_SEARCH_LIBS([fabs], [m])
+ AC_SEARCH_LIBS([gzopen], [z])
+ AC_SEARCH_LIBS([gzeof], [z])
+ AC_SEARCH_LIBS([gzgets], [z])
+ AC_SEARCH_LIBS([gzseek], [z])
+ AC_SEARCH_LIBS([gzclose], [z])
+
+ # Checks for typedefs, structures, and compiler characteristics.
+ AC_C_INLINE
+ 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_REALLOC
+ AC_FUNC_STRTOD
+ AC_CHECK_FUNCS([gettimeofday memset])
+
+ # 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}" = "xyes"; then
+ DEFAULT_CFLAGS="-Wall -O0 -g2 -D_GLIBCXX_DEBUG"
+ else
+ DEFAULT_CFLAGS="-Wall -O3"
+ fi
+ if test "x${BUILD_GPROF}" = "xyes"; then
+ DEFAULT_CFLAGS+=" -pg"
+ fi
+ elif test "x${ax_cv_c_compiler_vendor}" = "xintel"; then
+ if test "x${BUILD_DEBUG}" = "xyes"; then
+ DEFAULT_CFLAGS="-Wall -O0"
+ else
+ DEFAULT_CFLAGS="-Wall -O3"
+ fi
+ if test "x${BUILD_GPROF}" = "xyes"; then
+ DEFAULT_CFLAGS+=" -p"
+ fi
+ fi
+ AC_SUBST([DFT_CFLAGS], ["${DEFAULT_CFLAGS}"])
+
+ # Check for OpenMP support.
+ if test "x${BUILD_OPENMP}" = "xyes"; then
+ AX_OPENMP
+
+ if test "x${OPENMP_CFLAGS}" = "x"; then
+ AC_MSG_WARN([
+-----------------------------------------------
+ Unable to find OpenMP support on this system.
+ Building a single-threaded version.
+-----------------------------------------------])
+ else
+ # bug due to recent Intel compiler change (?)
+ if test "x${ax_cv_c_compiler_vendor}" = "xintel"; then
+ OPENMP_CFLAGS="-qopenmp"
+ fi
+ OPENMP_LIBS="-lgomp"
+ fi
+
+ # AC_MSG_NOTICE([OPENMP_CFLAGS=${OPENMP_CFLAGS}])
+ # AC_MSG_NOTICE([OPENMP_LIBS=${OPENMP_LIBS}])
+ AC_SUBST([OMP_CFLAGS], ["${OPENMP_CFLAGS}"])
+ AC_SUBST([OMP_LIBS], ["${OPENMP_LIBS}"])
+ fi
+
+ # Check for LAPACKE
+ LAPACKE_LIBS=
+ 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.])])
+ LAPACKE_LIBS="-lmkl_intel_ilp64 -lmkl_sequential -lmkl_core -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.])])
+ LAPACKE_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_SUBST([L_LIBS], ["${LAPACKE_LIBS}"])
+
+ AC_LANG_POP([C])
+fi
+AM_CONDITIONAL([BUILD_S_OMP], [test "x${pack_serial_enabled}" = "xyes" || test "x${pack_openmp_enabled}" = "xyes"])
+
+
+# PuReMD-GPU
+if test "x${pack_gpu_enabled}" = "xyes"; then
+ BUILD_GPU="yes"
+
+ AC_LANG_PUSH([C])
+
+ AC_CONFIG_SRCDIR([PuReMD-GPU/src/analyze.c])
+ AC_CONFIG_HEADERS([PuReMD-GPU/src/config.h])
+
+ # Checks for libraries.
+ AC_SEARCH_LIBS([exp], [m])
+ AC_SEARCH_LIBS([sqrt], [m])
+ AC_SEARCH_LIBS([pow], [m])
+ AC_SEARCH_LIBS([acos], [m])
+ AC_SEARCH_LIBS([cos], [m])
+ AC_SEARCH_LIBS([sin], [m])
+ AC_SEARCH_LIBS([tan], [m])
+ AC_SEARCH_LIBS([fabs], [m])
+ AC_SEARCH_LIBS([gzopen], [z])
+ AC_SEARCH_LIBS([gzeof], [z])
+ AC_SEARCH_LIBS([gzgets], [z])
+ AC_SEARCH_LIBS([gzseek], [z])
+ AC_SEARCH_LIBS([gzclose, [z]])
+
+ # Checks for typedefs, structures, and compiler characteristics.
+ AC_CHECK_HEADER_STDBOOL
+ 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_REALLOC
+ AC_FUNC_STRTOD
+ AC_CHECK_FUNCS([gettimeofday memset])
+
+ # 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}" = "xyes"; then
+ DEFAULT_CFLAGS="-Wall -O0 -g2 -D_GLIBCXX_DEBUG"
+ else
+ DEFAULT_CFLAGS="-Wall -O3"
+ fi
+ if test "x${BUILD_GPROF}" = "xyes"; then
+ DEFAULT_CFLAGS+=" -pg"
+ fi
+ elif test "x${ax_cv_c_compiler_vendor}" = "xintel"; then
+ if test "x${BUILD_DEBUG}" = "xyes"; then
+ DEFAULT_CFLAGS="-Wall -O0"
+ else
+ DEFAULT_CFLAGS="-Wall -O3"
+ fi
+ if test "x${BUILD_GPROF}" = "xyes"; then
+ DEFAULT_CFLAGS+=" -p"
+ fi
+ fi
+
+ # Check for CUDA support.
+ CONFIGURE_HEADLINE([ CUDA support ])
+ AX_CUDA
+ NVCCFLAGS=
+ if test "x${BUILD_DEBUG}" = "xyes"
+ then
+ NVCCFLAGS="-g -G"
+ fi
+ if test "x${BUILD_GPROF}" = "xtrue"
+ then
+ NVCCFLAGS+=" --compiler-options ${gprof_flags}"
+ fi
+ AC_DEFINE([HAVE_CUDA], [1], [Define to 1 if you have CUDA support enabled.])
+
+ AC_CHECK_LIB([cuda], [cuGetErrorString])
+ AC_CHECK_LIB([cudart], [cudaMalloc])
+ AC_CHECK_LIB([cublas], [cublasDnrm2])
+ AC_CHECK_LIB([cusparse], [cusparseCreateMatDescr])
+# AC_SEARCH_LIBS([cublasDaxpy], [cublas])
+# AC_SEARCH_LIBS([cublasDscal], [cublas])
+# AC_SEARCH_LIBS([cublasDdot], [cublas])
+# AC_SEARCH_LIBS([cudaThreadSynchronize], [cudart])
+# AC_SEARCH_LIBS([cudaGetLastError], [cudart])
+# AC_SEARCH_LIBS([cusparseCreateMatDescr], [cusparse])
+# AC_SEARCH_LIBS([cusparseSetMatType], [cusparse])
+# AC_SEARCH_LIBS([cusparseSetMatIndexBase], [cusparse])
+#
+# AC_SEARCH_LIBS([cublasDnrm2], [cublas],
+# [CUBLAS_FOUND_LIBS="yes"], [CUBLAS_FOUND_LIBS="no"], [-lcublas])
+# AS_IF([test "x${CUBLAS_FOUND_LIBS}" != "xyes"],
+# [AC_MSG_ERROR([Unable to find CUBLAS library.])])
+#
+# AC_SEARCH_LIBS([cusparseSetMatType], [cusparse],
+# [CUSPARSE_FOUND_LIBS="yes"], [CUSPARSE_FOUND_LIBS="no"], [-lcusparse])
+# AS_IF([test "x${CUSPARSE_FOUND_LIBS}" != "xyes"],
+# [AC_MSG_ERROR([Unable to find CUSPARSE library.])])
+#
+# 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_LANG_POP([C])
+fi
+AM_CONDITIONAL([BUILD_GPU], [test "x${pack_gpu_enabled}" = "xyes"])
+
+
+# PuReMD
+if test "x${pack_mpi_old_enabled}" = "xyes"; then
+ AC_LANG_PUSH([C])
+
+ AC_CONFIG_SRCDIR([PuReMD/src/torsion_angles.h])
+ AC_CONFIG_HEADERS([PuReMD/src/config.h])
+
+ # Checks for libraries.
+ AC_SEARCH_LIBS([exp], [m])
+ AC_SEARCH_LIBS([sqrt], [m])
+ AC_SEARCH_LIBS([pow], [m])
+ AC_SEARCH_LIBS([acos], [m])
+ AC_SEARCH_LIBS([cos], [m])
+ AC_SEARCH_LIBS([sin], [m])
+ AC_SEARCH_LIBS([tan], [m])
+ AC_SEARCH_LIBS([fabs], [m])
+
+ # Checks for typedefs, structures, and compiler characteristics.
+ AC_C_INLINE
+
+ # Checks for library functions.
+ AC_FUNC_MALLOC
+ AC_FUNC_REALLOC
+ AC_FUNC_STRTOD
+ AC_CHECK_FUNCS([gettimeofday memset pow sqrt])
+
+ # 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}" = "xyes"; then
+ DEFAULT_CFLAGS="-Wall -O0 -g2 -D_GLIBCXX_DEBUG"
+ else
+ DEFAULT_CFLAGS="-Wall -O3"
+ fi
+ if test "x${BUILD_GPROF}" = "xyes"; then
+ DEFAULT_CFLAGS+=" -pg"
+ fi
+ elif test "x${ax_cv_c_compiler_vendor}" = "xintel"; then
+ if test "x${BUILD_DEBUG}" = "xyes"; then
+ DEFAULT_CFLAGS="-Wall -O0"
+ else
+ DEFAULT_CFLAGS="-Wall -O3"
+ fi
+ if test "x${BUILD_GPROF}" = "xyes"; then
+ DEFAULT_CFLAGS+=" -p"
+ fi
+ fi
+ AC_SUBST([DFT_CFLAGS], ["${DEFAULT_CFLAGS}"])
+
+ # 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)
+
+ # try to find if we are using OpenMPI / MPICH by looking inside mpi.h
+ 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="${save_CC}"
+ CFLAGS="${save_CFLAGS}"
+
+ # try to set MPI_CFLAGS and MPI_LIBS
+ MPI_CFLAGS=
+ MPI_LIBS=
+ if test "x${mpi_vendor}" = "xOpenMPI"
+ then
+ MPI_CFLAGS=`${MPICC} --showme:compile`
+ MPI_LIBS=`${MPICC} --showme:link`
+ AC_MSG_NOTICE([OpenMPI support found])
+ 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 }'`
+ MPI_CFLAGS=
+ for i in $tmp
+ do
+ case ${i} in
+ -[[DIUbi]]*)
+ MPI_CFLAGS="${MPI_CFLAGS} ${i}"
+ ;;
+ esac
+ done
+ # build MPI_LIBS
+ tmp=`${MPICC} -link-info | awk '{$1=""; print $0 }'`
+ for i in $tmp
+ do
+ case ${i} in
+ [[\\/]]*.a | ?:[[\\/]]*.a | -[[lLRu]]* | -Wl* )
+ MPI_LIBS="${MPI_LIBS} ${i}"
+ ;;
+ esac
+ done
+ AC_MSG_NOTICE([MPICH support found])
+ AC_MSG_NOTICE([MPI_CFLAGS=${MPI_CFLAGS}])
+ AC_MSG_NOTICE([MPI_LIBS=${MPI_LIBS}])
+ else
+ AC_MSG_WARN([Neither OpenMPI and MPICH support recognized...])
+ fi
+ AC_SUBST([M_CFLAGS], ["${MPI_CFLAGS}"])
+ AC_SUBST([M_LIBS], ["${MPI_LIBS}"])
+
+ # Check for LAPACKE
+ LAPACKE_LIBS=
+ 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
+ #LAPACKE_LIBS="-lmkl_intel_ilp64 -lmkl_sequential -lmkl_core -lpthread -lm -ldl"
+ # static linking
+ LAPACKE_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.])])
+ LAPACKE_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_SUBST([L_LIBS], ["${LAPACKE_LIBS}"])
+fi
+
+ AC_LANG_POP([C])
+AM_CONDITIONAL([BUILD_MPI], [test "x${pack_mpi_old_enabled}" = "xyes"])
+
+
+# PG-PuReMD
+if test "x${pack_mpi_enabled}" = "xyes" || test "x${pack_mpi_gpu_enabled}" = "xyes"; then
+ if test "x${pack_mpi_enabled}" = "xyes" || test "x${pack_mpi_gpu_enabled}" != "xyes"; then
+ export BUILD_GPU="no"
+ else
+ export BUILD_GPU="yes"
+ fi
+
+ AC_LANG_PUSH([C])
+
+ AC_CONFIG_SRCDIR([PG-PuReMD/src/torsion_angles.h])
+ AC_CONFIG_HEADERS([PG-PuReMD/src/config.h])
+
+ # Checks for libraries.
+ AC_SEARCH_LIBS([exp], [m])
+ AC_SEARCH_LIBS([sqrt], [m])
+ AC_SEARCH_LIBS([pow], [m])
+ AC_SEARCH_LIBS([acos], [m])
+ AC_SEARCH_LIBS([cos], [m])
+ AC_SEARCH_LIBS([sin], [m])
+ AC_SEARCH_LIBS([tan], [m])
+ AC_SEARCH_LIBS([fabs], [m])
+
+ # Checks for typedefs, structures, and compiler characteristics.
+ AC_CHECK_HEADER_STDBOOL
+ AC_C_INLINE
+ AC_TYPE_SIZE_T
+
+ # Checks for library functions.
+ AC_FUNC_MALLOC
+ AC_FUNC_REALLOC
+ AC_FUNC_STRTOD
+ AC_CHECK_FUNCS([gettimeofday memset])
+
+ # 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}" = "xyes"; then
+ DEFAULT_CFLAGS="-Wall -O0 -g2 -D_GLIBCXX_DEBUG"
+ else
+ DEFAULT_CFLAGS="-Wall -O3"
+ fi
+ if test "x${BUILD_GPROF}" = "xyes"; then
+ DEFAULT_CFLAGS+=" -pg"
+ fi
+ elif test "x${ax_cv_c_compiler_vendor}" = "xintel"; then
+ if test "x${BUILD_DEBUG}" = "xyes"; then
+ DEFAULT_CFLAGS="-Wall -O0"
+ else
+ DEFAULT_CFLAGS="-Wall -O3"
+ fi
+ if test "x${BUILD_GPROF}" = "xyes"; then
+ DEFAULT_CFLAGS+=" -p"
+ fi
+ fi
+ AC_SUBST([DFT_CFLAGS], ["${DEFAULT_CFLAGS}"])
+
+ # Check for MPI support.
+ 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
+ save_CC="${CC}"
+ save_CFLAGS="${CFLAGS}"
+ CC="${MPICC}"
+ CFLAGS="${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="${save_CC}"
+ CFLAGS="${save_CFLAGS}"
+
+ # try to set MPI_CFLAGS and MPI_LIBS
+ MPI_CFLAGS=
+ MPI_LIBS=
+ if test "x${mpi_vendor}" = "xOpenMPI"
+ then
+ 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_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 }'`
+ MPI_CFLAGS=
+ for i in ${tmp}
+ do
+ case ${i} in
+ -[[DIUbi]]*)
+ MPI_CFLAGS="${MPI_CFLAGS} ${i}"
+ ;;
+ esac
+ done
+ # build MPI_LIBS
+ tmp=`${MPICC} -link-info | awk '{$1=""; print $0 }'`
+ for i in ${tmp}
+ do
+ case ${i} in
+ [[\\/]]*.a | ?:[[\\/]]*.a | -[[lLRu]]* | -Wl* )
+ MPI_LIBS="${MPI_LIBS} ${i}"
+ ;;
+ esac
+ done
+ AC_MSG_NOTICE([MPICH found])
+ 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([M_CFLAGS], ["${MPI_CFLAGS}"])
+ AC_SUBST([M_LIBS], ["${MPI_LIBS}"])
+
+ # Check for LAPACKE
+ LAPACKE_LIBS=
+ 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.])])
+ LAPACKE_LIBS="-lmkl_intel_ilp64 -lmkl_sequential -lmkl_core -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.])])
+ LAPACKE_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_SUBST([L_LIBS], ["${LAPACKE_LIBS}"])
+
+ AC_LANG_POP([C])
+
+ AC_LANG_PUSH([C++])
+
+ # Check for CUDA support.
+ if test "x${BUILD_GPU}" = "xyes"; then
+ CONFIGURE_HEADLINE([ CUDA support ])
+ AX_CUDA
+
+ NVCCFLAGS=
+ NVCCFLAGS+=" -ccbin=${CXX}"
+ if test "x${BUILD_DEBUG}" = "xyes"
+ then
+ NVCCFLAGS+=" -g -G"
+
+ fi
+ AC_DEFINE([HAVE_CUDA], [1], [Define to 1 if you have CUDA support enabled.])
+ else
+ AM_CONDITIONAL(USE_CUDA, test "x" = "xyes")
+ fi
+
+ if test "x${BUILD_GPROF}" = "xyes"
+ then
+ if test "x${BUILD_GPU}" = "xyes"; then
+ NVCCFLAGS+=" --compiler-options ${gprof_flags}"
+ else
+ CFLAGS+=" ${gprof_flags}"
+ fi
+ fi
+
+ AC_LANG_POP([C++])
+fi
+AM_CONDITIONAL([BUILD_MPI_GPU], [test "x${pack_mpi_enabled}" = "xyes" || test "x${pack_mpi_gpu_enabled}" = "xyes"])
+# Moved from m4/ax_cuda.am to avoid conditionally calling inside AX_CUDA
+AM_CONDITIONAL(USE_CUDA, [test "x${pack_gpu_enabled}" = "xyes" || test "x${pack_mpi_gpu_enabled}" = "xyes"])
+AM_CONDITIONAL(CUDA_DEBUG, [(test "x${pack_gpu_enabled}" = "xyes" || test "x${pack_mpi_gpu_enabled}" = "xyes") && test "x${BUILD_DEBUG}" = "xyes"])
+
+
+# Tests using Google C++ testing framework (gtest)
+AC_LANG_PUSH([C++])
+AC_COMPILE_IFELSE([AC_LANG_PROGRAM(
+ [[#ifndef __cplusplus
+ #error "broken C++"
+ #endif]])],,
+ [CXX=;])
+if test "x${CXX}" != "x"
+then
+ AC_CHECK_HEADER([gtest/gtest.h], [HAVE_GTEST_H="yes"])
+ if test "x${HAVE_GTEST_H}" != "xyes"
+ then
+ AC_MSG_WARN([gtest.h not found. Unable to build tests. Continuing...])
+ else
+ ACX_PTHREAD([have_pthread=yes])
+
+ # define gtest variables
+ if test "x${have_pthread}" = "xyes"; then
+ GTEST_CPPFLAGS="-DGTEST_HAS_PTHREAD=1"
+ GTEST_CXXFLAGS="${PTHREAD_CFLAGS}"
+ GTEST_LDFLAGS=
+ GTEST_LIBS="${PTHREAD_LIBS}"
+ else
+ GTEST_CPPFLAGS="-DGTEST_HAS_PTHREAD=0"
+ GTEST_CXXFLAGS=
+ GTEST_LDFLAGS=
+ GTEST_LIBS=
+ fi
+ fi
+else
+ AC_MSG_WARN([C++ compiler not found. Unable to build tests. Continuing...])
+fi
+AM_CONDITIONAL([BUILD_TEST], [test "x${HAVE_GTEST_H}" = "xyes"])
+AC_LANG_POP([C++])
+
+
AC_CONFIG_FILES([Makefile])
AC_OUTPUT
diff --git a/ltmain.sh b/ltmain.sh
index 0f0a2da3f9dd10627626bf9725b332d95f314393..30be9c82c07013c35ae65542561f1f1ffd87c72c 100644
--- a/ltmain.sh
+++ b/ltmain.sh
@@ -7272,10 +7272,12 @@ func_mode_link ()
# -tp=* Portland pgcc target processor selection
# --sysroot=* for sysroot support
# -O*, -g*, -flto*, -fwhopr*, -fuse-linker-plugin GCC link-time optimization
+ # -specs=* GCC specs files
# -stdlib=* select c++ std lib with clang
-64|-mips[0-9]|-r[0-9][0-9]*|-xarch=*|-xtarget=*|+DA*|+DD*|-q*|-m*| \
-t[45]*|-txscale*|-p|-pg|--coverage|-fprofile-*|-F*|@*|-tp=*|--sysroot=*| \
- -O*|-g*|-flto*|-fwhopr*|-fuse-linker-plugin|-fstack-protector*|-stdlib=*)
+ -O*|-g*|-flto*|-fwhopr*|-fuse-linker-plugin|-fstack-protector*|-stdlib=*| \
+ -specs=*)
func_quote_for_eval "$arg"
arg=$func_quote_for_eval_result
func_append compile_command " $arg"
diff --git a/m4/ax_cuda.m4 b/m4/ax_cuda.m4
index d69205a3f410f34e913116cf2e76806c39d55db9..169632e774aa187ed9c67f877518eb7d843a10cb 100644
--- a/m4/ax_cuda.m4
+++ b/m4/ax_cuda.m4
@@ -61,7 +61,7 @@ AC_ARG_WITH([cuda],
want_cuda="yes"
])
-AM_CONDITIONAL(USE_CUDA, test "x${want_cuda}" = xyes)
+#AM_CONDITIONAL(USE_CUDA, test "x${want_cuda}" = xyes)
if test "$want_cuda" = "yes"
then
@@ -215,7 +215,7 @@ if test x$EMULATION = xtrue
then
NVCCFLAGS=" -deviceemu"
fi
-#
+
#AS_IF([test "x$want_cuda" = xyes],
# [AS_IF([test "x$NVCCFLAGS" = x],
# [dnl generate CUDA code for broad spectrum of devices
diff --git a/missing b/missing
index c6e379584baf766f931c6ec18292a2c3dbe0eb90..b7e571efa44e300f6b9cc30b168a135f61e49c75 100755
--- a/missing
+++ b/missing
@@ -1,4 +1,4 @@
-#! /bin/sh
+#!/bin/sh
# Common wrapper for a few potentially missing GNU programs.
scriptversion=2016-01-11.22; # UTC
diff --git a/sPuReMD/Makefile.am b/sPuReMD/Makefile.am
deleted file mode 100644
index 392170679cfcf8b18bdf5a7416a3c181f287e258..0000000000000000000000000000000000000000
--- a/sPuReMD/Makefile.am
+++ /dev/null
@@ -1,52 +0,0 @@
-ACLOCAL_AMFLAGS = -I ../m4
-
-lib_LTLIBRARIES = lib/libspuremd.la
-lib_libspuremd_la_SOURCES = src/ffield.c src/grid.c src/list.c src/lookup.c src/print_utils.c \
- src/reset_utils.c src/restart.c src/random.c src/tool_box.c src/traj.c \
- src/vector.c src/allocate.c src/analyze.c src/box.c src/system_props.c src/control.c \
- src/geo_tools.c src/neighbors.c src/lin_alg.c src/charges.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/spuremd.c \
- src/ffield.h src/grid.h src/list.h src/lookup.h src/print_utils.h \
- src/reset_utils.h src/restart.h src/random.h src/tool_box.h src/traj.h \
- src/vector.h src/allocate.h src/analyze.h src/box.h src/system_props.h src/control.h \
- src/geo_tools.h src/neighbors.h src/lin_alg.h src/charges.h src/bond_orders.h \
- src/single_body_interactions.h src/two_body_interactions.h \
- src/three_body_interactions.h src/four_body_interactions.h src/forces.h \
- src/integrate.h src/init_md.h src/spuremd.h src/reax_types.h
-lib_libspuremd_la_CFLAGS = -I src
-lib_libspuremd_la_LDFLAGS = -version-info 1:0:0
-
-bin_PROGRAMS = bin/spuremd
-bin_spuremd_SOURCES = src/driver.c
-bin_spuremd_CPPFLAGS = -I src
-bin_spuremd_LDADD = lib/libspuremd.la
-
-check_PROGRAMS =
-TESTS =
-
-if BUILD_TEST
-check_PROGRAMS += tests/test_spuremd
-check_PROGRAMS += tests/test_lin_alg
-check_PROGRAMS += tests/test_vector
-TESTS += $(check_PROGRAMS)
-
-tests_test_spuremd_SOURCES = tests/test_spuremd.cpp
-tests_test_spuremd_CPPFLAGS = -Isrc $(GTEST_CPPFLAGS)
-tests_test_spuremd_CXXFLAGS = $(GTEST_CXXFLAGS)
-tests_test_spuremd_LDFLAGS = $(GTEST_LDFLAGS) $(GTEST_LIBS)
-tests_test_spuremd_LDADD = lib/libspuremd.la -lgtest
-
-tests_test_lin_alg_SOURCES = tests/test_lin_alg.cpp
-tests_test_lin_alg_CPPFLAGS = -Isrc $(GTEST_CPPFLAGS)
-tests_test_lin_alg_CXXFLAGS = $(GTEST_CXXFLAGS)
-tests_test_lin_alg_LDFLAGS = $(GTEST_LDFLAGS) $(GTEST_LIBS)
-tests_test_lin_alg_LDADD = -lgtest
-
-tests_test_vector_SOURCES = tests/test_vector.cpp
-tests_test_vector_CPPFLAGS = -Isrc $(GTEST_CPPFLAGS)
-tests_test_vector_CXXFLAGS = $(GTEST_CXXFLAGS)
-tests_test_vector_LDFLAGS = $(GTEST_LDFLAGS) $(GTEST_LIBS)
-tests_test_vector_LDADD = -lgtest
-endif
diff --git a/sPuReMD/aclocal.m4 b/sPuReMD/aclocal.m4
deleted file mode 100644
index 4bdae0816eee72bd92b6e9398344d7436c1aa0a1..0000000000000000000000000000000000000000
--- a/sPuReMD/aclocal.m4
+++ /dev/null
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-# AM_SUBST_NOTMAKE(VARIABLE)
-# --------------------------
-# Public sister of _AM_SUBST_NOTMAKE.
-AC_DEFUN([AM_SUBST_NOTMAKE], [_AM_SUBST_NOTMAKE($@)])
-
-# Check how to create a tarball. -*- Autoconf -*-
-
-# Copyright (C) 2004-2017 Free Software Foundation, Inc.
-#
-# This file is free software; the Free Software Foundation
-# gives unlimited permission to copy and/or distribute it,
-# with or without modifications, as long as this notice is preserved.
-
-# _AM_PROG_TAR(FORMAT)
-# --------------------
-# Check how to create a tarball in format FORMAT.
-# FORMAT should be one of 'v7', 'ustar', or 'pax'.
-#
-# Substitute a variable $(am__tar) that is a command
-# writing to stdout a FORMAT-tarball containing the directory
-# $tardir.
-# tardir=directory && $(am__tar) > result.tar
-#
-# Substitute a variable $(am__untar) that extract such
-# a tarball read from stdin.
-# $(am__untar) < result.tar
-#
-AC_DEFUN([_AM_PROG_TAR],
-[# Always define AMTAR for backward compatibility. Yes, it's still used
-# in the wild :-( We should find a proper way to deprecate it ...
-AC_SUBST([AMTAR], ['$${TAR-tar}'])
-
-# We'll loop over all known methods to create a tar archive until one works.
-_am_tools='gnutar m4_if([$1], [ustar], [plaintar]) pax cpio none'
-
-m4_if([$1], [v7],
- [am__tar='$${TAR-tar} chof - "$$tardir"' am__untar='$${TAR-tar} xf -'],
-
- [m4_case([$1],
- [ustar],
- [# The POSIX 1988 'ustar' format is defined with fixed-size fields.
- # There is notably a 21 bits limit for the UID and the GID. In fact,
- # the 'pax' utility can hang on bigger UID/GID (see automake bug#8343
- # and bug#13588).
- am_max_uid=2097151 # 2^21 - 1
- am_max_gid=$am_max_uid
- # The $UID and $GID variables are not portable, so we need to resort
- # to the POSIX-mandated id(1) utility. Errors in the 'id' calls
- # below are definitely unexpected, so allow the users to see them
- # (that is, avoid stderr redirection).
- am_uid=`id -u || echo unknown`
- am_gid=`id -g || echo unknown`
- AC_MSG_CHECKING([whether UID '$am_uid' is supported by ustar format])
- if test $am_uid -le $am_max_uid; then
- AC_MSG_RESULT([yes])
- else
- AC_MSG_RESULT([no])
- _am_tools=none
- fi
- AC_MSG_CHECKING([whether GID '$am_gid' is supported by ustar format])
- if test $am_gid -le $am_max_gid; then
- AC_MSG_RESULT([yes])
- else
- AC_MSG_RESULT([no])
- _am_tools=none
- fi],
-
- [pax],
- [],
-
- [m4_fatal([Unknown tar format])])
-
- AC_MSG_CHECKING([how to create a $1 tar archive])
-
- # Go ahead even if we have the value already cached. We do so because we
- # need to set the values for the 'am__tar' and 'am__untar' variables.
- _am_tools=${am_cv_prog_tar_$1-$_am_tools}
-
- for _am_tool in $_am_tools; do
- case $_am_tool in
- gnutar)
- for _am_tar in tar gnutar gtar; do
- AM_RUN_LOG([$_am_tar --version]) && break
- done
- am__tar="$_am_tar --format=m4_if([$1], [pax], [posix], [$1]) -chf - "'"$$tardir"'
- am__tar_="$_am_tar --format=m4_if([$1], [pax], [posix], [$1]) -chf - "'"$tardir"'
- am__untar="$_am_tar -xf -"
- ;;
- plaintar)
- # Must skip GNU tar: if it does not support --format= it doesn't create
- # ustar tarball either.
- (tar --version) >/dev/null 2>&1 && continue
- am__tar='tar chf - "$$tardir"'
- am__tar_='tar chf - "$tardir"'
- am__untar='tar xf -'
- ;;
- pax)
- am__tar='pax -L -x $1 -w "$$tardir"'
- am__tar_='pax -L -x $1 -w "$tardir"'
- am__untar='pax -r'
- ;;
- cpio)
- am__tar='find "$$tardir" -print | cpio -o -H $1 -L'
- am__tar_='find "$tardir" -print | cpio -o -H $1 -L'
- am__untar='cpio -i -H $1 -d'
- ;;
- none)
- am__tar=false
- am__tar_=false
- am__untar=false
- ;;
- esac
-
- # If the value was cached, stop now. We just wanted to have am__tar
- # and am__untar set.
- test -n "${am_cv_prog_tar_$1}" && break
-
- # tar/untar a dummy directory, and stop if the command works.
- rm -rf conftest.dir
- mkdir conftest.dir
- echo GrepMe > conftest.dir/file
- AM_RUN_LOG([tardir=conftest.dir && eval $am__tar_ >conftest.tar])
- rm -rf conftest.dir
- if test -s conftest.tar; then
- AM_RUN_LOG([$am__untar <conftest.tar])
- AM_RUN_LOG([cat conftest.dir/file])
- grep GrepMe conftest.dir/file >/dev/null 2>&1 && break
- fi
- done
- rm -rf conftest.dir
-
- AC_CACHE_VAL([am_cv_prog_tar_$1], [am_cv_prog_tar_$1=$_am_tool])
- AC_MSG_RESULT([$am_cv_prog_tar_$1])])
-
-AC_SUBST([am__tar])
-AC_SUBST([am__untar])
-]) # _AM_PROG_TAR
-
-m4_include([../m4/acx_pthread.m4])
-m4_include([../m4/ax_compiler_vendor.m4])
-m4_include([../m4/libtool.m4])
-m4_include([../m4/ltoptions.m4])
-m4_include([../m4/ltsugar.m4])
-m4_include([../m4/ltversion.m4])
-m4_include([../m4/lt~obsolete.m4])
diff --git a/sPuReMD/configure.ac b/sPuReMD/configure.ac
deleted file mode 100644
index 2e0fe8795620cb1d1677fbba0446240a62de5e70..0000000000000000000000000000000000000000
--- a/sPuReMD/configure.ac
+++ /dev/null
@@ -1,177 +0,0 @@
-# -*- Autoconf -*-
-# Process this file with autoconf to produce a configure script.
-
-AC_PREREQ([2.69])
-
-AC_INIT([sPuReMD], [1.0], [ohearnku@msu.edu hma@msu.edu])
-# Do not allow AC_PROG_CC to set CFLAGS (this line must be after AC_INIT but before AC_PROG_CC)
-save_CFLAGS="${CFLAGS}"
-: ${CFLAGS=""}
-AM_INIT_AUTOMAKE([1.15 subdir-objects -Wall -Werror foreign])
-# Enable silent build rules by default.
-m4_ifdef([AM_SILENT_RULES], [AM_SILENT_RULES([yes])], [AC_SUBST([AM_DEFAULT_VERBOSITY],[1])])
-AM_PROG_AR
-LT_PREREQ([2.2])
-LT_INIT([dlopen])
-
-AC_CONFIG_MACRO_DIR([../m4])
-
-# Headline formatter
-AC_DEFUN([CONFIGURE_HEADLINE],
-[
- echo; echo "+++ $1 +++"
-])
-
-AC_LANG([C])
-
-AC_CONFIG_SRCDIR([src/traj.h])
-AC_CONFIG_HEADERS([src/config.h])
-
-# Checks for programs.
-AC_PROG_CC([icc gcc cc])
-AC_PROG_CPP
-CFLAGS="${save_CFLAGS}"
-
-# Checks for libraries.
-AC_SEARCH_LIBS([exp], [m])
-AC_SEARCH_LIBS([sqrt], [m])
-AC_SEARCH_LIBS([pow], [m])
-AC_SEARCH_LIBS([acos], [m])
-AC_SEARCH_LIBS([cos], [m])
-AC_SEARCH_LIBS([sin], [m])
-AC_SEARCH_LIBS([tan], [m])
-AC_SEARCH_LIBS([fabs], [m])
-AC_SEARCH_LIBS([gzopen], [z])
-AC_SEARCH_LIBS([gzeof], [z])
-AC_SEARCH_LIBS([gzgets], [z])
-AC_SEARCH_LIBS([gzseek], [z])
-AC_SEARCH_LIBS([gzclose], [z])
-
-# Checks for typedefs, structures, and compiler characteristics.
-AC_C_INLINE
-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_REALLOC
-AC_FUNC_STRTOD
-AC_CHECK_FUNCS([gettimeofday memset])
-
-# 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}" = "xyes"; then
- CFLAGS="-Wall -O0 -g2 -D_GLIBCXX_DEBUG"
- else
- CFLAGS="-Wall -O2 -funroll-loops"
- fi
- if test "x${BUILD_GPROF}" = "xyes"; then
- CFLAGS="${CFLAGS} -pg"
- fi
-elif test "x${ax_cv_c_compiler_vendor}" = "xintel"; then
- if test "x${BUILD_DEBUG}" = "xyes"; then
- CFLAGS="-Wall -O0"
- else
- CFLAGS="-Wall -O2 -funroll-loops"
- fi
- if test "x${BUILD_GPROF}" = "xyes"; then
- CFLAGS="${CFLAGS} -p"
- fi
-fi
-
-# Check for OpenMP support.
-if test "x${BUILD_OPENMP}" = "xyes"; then
- AC_OPENMP
- if test "x${OPENMP_CFLAGS}" = "x"; then
- AC_MSG_WARN([
- -----------------------------------------------
- Unable to find OpenMP support on this system.
- Building a single-threaded version.
- -----------------------------------------------])
- else
- # bug due to recent Intel compiler change (?)
- if test "x${ax_cv_c_compiler_vendor}" = "xintel"; then
- OPENMP_CFLAGS="-qopenmp"
- fi
- AC_SUBST(AM_CFLAGS, "${OPENMP_CFLAGS}")
- AC_SUBST(AM_CPPFLAGS, "${OPENMP_CFLAGS}")
- LIBS="${LIBS} -lgomp"
- fi
-fi
-
-# 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.])])
- LIBS="${LIBS} -lmkl_intel_ilp64 -lmkl_sequential -lmkl_core -lpthread -lm -ldl"
- AC_DEFINE([HAVE_LAPACKE_MKL], [1], [Define to 1 if you have MKL LAPACKE support enabled.])
-else
- AC_CHECK_HEADERS([lapacke.h], [LAPACKE_FOUND_HEADERS="yes"])
- if test "x${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
-
-# Tests using Google C++ testing framework (gtest)
-AC_LANG_PUSH([C++])
-AC_PROG_CXX([icpc g++ clang++ CC])
-AC_COMPILE_IFELSE([AC_LANG_PROGRAM(
- [[#ifndef __cplusplus
- #error "broken C++"
- #endif]])],,
- [CXX=;])
-if test "x${CXX}" != "x"
-then
- AC_CHECK_HEADER([gtest/gtest.h], [HAVE_GTEST_H="yes"])
- if test "x${HAVE_GTEST_H}" != "xyes"
- then
- AC_MSG_WARN([gtest.h not found. Unable to build tests. Continuing...])
- else
- ACX_PTHREAD([have_pthread=yes])
-
- # define gtest variables
- if test "x${have_pthread}" = "xyes"; then
- GTEST_CPPFLAGS="-DGTEST_HAS_PTHREAD=1"
- GTEST_CXXFLAGS="$PTHREAD_CFLAGS"
- GTEST_LDFLAGS=
- GTEST_LIBS="$PTHREAD_LIBS"
- else
- GTEST_CPPFLAGS="-DGTEST_HAS_PTHREAD=0"
- GTEST_CXXFLAGS=
- GTEST_LDFLAGS=
- GTEST_LIBS=
- fi
- AC_SUBST([GTEST_CPPFLAGS])
- AC_SUBST([GTEST_CXXFLAGS])
- AC_SUBST([GTEST_LDFLAGS])
- AC_SUBST([GTEST_LIBS])
- fi
-else
- AC_MSG_WARN([C++ compiler not found. Unable to build tests. Continuing...])
-fi
-AM_CONDITIONAL([BUILD_TEST], [test "x${HAVE_GTEST_H}" = "xyes"])
-AC_LANG_POP([C++])
-
-AC_CONFIG_FILES([Makefile])
-
-AC_OUTPUT