Merge branch 'master' into mc-fix-bond-create-angle (d7ef1b00) · Commits · 郑智淋 / lammps

cmake/CMakeLists.txt

+1 −1

Original line number	Original line	Diff line number	Diff line
	@@ -193,7 +193,7 @@ if(NOT ${LAMMPS_MEMALIGN} STREQUAL "0")
	target_compile_definitions(lammps PRIVATE -DLAMMPS_MEMALIGN=${LAMMPS_MEMALIGN})		target_compile_definitions(lammps PRIVATE -DLAMMPS_MEMALIGN=${LAMMPS_MEMALIGN})
	endif()		endif()

	option(LAMMPS_EXCEPTIONS "enable the use of C++ exceptions for error messages (useful for library interface)" OFF)		option(LAMMPS_EXCEPTIONS "enable the use of C++ exceptions for error messages (useful for library interface)" ${ENABLE_TESTING})
	if(LAMMPS_EXCEPTIONS)		if(LAMMPS_EXCEPTIONS)
	target_compile_definitions(lammps PUBLIC -DLAMMPS_EXCEPTIONS)		target_compile_definitions(lammps PUBLIC -DLAMMPS_EXCEPTIONS)
	endif()		endif()

cmake/Modules/Packages/GPU.cmake

+50 −28

Original line number	Original line	Diff line number	Diff line
	@@ -66,29 +66,40 @@ if(GPU_API STREQUAL "CUDA")
	# --arch translates directly instead of JIT, so this should be for the preferred or most common architecture		# --arch translates directly instead of JIT, so this should be for the preferred or most common architecture
	set(GPU_CUDA_GENCODE "-arch=${GPU_ARCH}")		set(GPU_CUDA_GENCODE "-arch=${GPU_ARCH}")
	# Fermi (GPU Arch 2.x) is supported by CUDA 3.2 to CUDA 8.0		# Fermi (GPU Arch 2.x) is supported by CUDA 3.2 to CUDA 8.0
	if((CUDA_VERSION VERSION_GREATER "3.1") AND (CUDA_VERSION VERSION_LESS "9.0"))		if((CUDA_VERSION VERSION_GREATER_EQUAL "3.2") AND (CUDA_VERSION VERSION_LESS "9.0"))
	string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_20,code=[sm_20,compute_20] ")		string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_20,code=[sm_20,compute_20] ")
	endif()		endif()
	# Kepler (GPU Arch 3.x) is supported by CUDA 5 and later		# Kepler (GPU Arch 3.0) is supported by CUDA 5 to CUDA 10.2
	if(CUDA_VERSION VERSION_GREATER "4.9")		if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "11.0"))
			string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_30,code=[sm_30,compute_30] ")
			endif()
			# Kepler (GPU Arch 3.5) is supported by CUDA 5 to CUDA 11
			if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "12.0"))
	string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_30,code=[sm_30,compute_30] -gencode arch=compute_35,code=[sm_35,compute_35]")		string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_30,code=[sm_30,compute_30] -gencode arch=compute_35,code=[sm_35,compute_35]")
	endif()		endif()
	# Maxwell (GPU Arch 5.x) is supported by CUDA 6 and later		# Maxwell (GPU Arch 5.x) is supported by CUDA 6 and later
	if(CUDA_VERSION VERSION_GREATER "5.9")		if(CUDA_VERSION VERSION_GREATER_EQUAL "6.0")
	string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_50,code=[sm_50,compute_50] -gencode arch=compute_52,code=[sm_52,compute_52]")		string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_50,code=[sm_50,compute_50] -gencode arch=compute_52,code=[sm_52,compute_52]")
	endif()		endif()
	# Pascal (GPU Arch 6.x) is supported by CUDA 8 and later		# Pascal (GPU Arch 6.x) is supported by CUDA 8 and later
	if(CUDA_VERSION VERSION_GREATER "7.9")		if(CUDA_VERSION VERSION_GREATER_EQUAL "8.0")
	string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_60,code=[sm_60,compute_60] -gencode arch=compute_61,code=[sm_61,compute_61]")		string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_60,code=[sm_60,compute_60] -gencode arch=compute_61,code=[sm_61,compute_61]")
	endif()		endif()
	# Volta (GPU Arch 7.0) is supported by CUDA 9 and later		# Volta (GPU Arch 7.0) is supported by CUDA 9 and later
	if(CUDA_VERSION VERSION_GREATER "8.9")		if(CUDA_VERSION VERSION_GREATER_EQUAL "9.0")
	string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_70,code=[sm_70,compute_70]")		string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_70,code=[sm_70,compute_70]")
	endif()		endif()
	# Turing (GPU Arch 7.5) is supported by CUDA 10 and later		# Turing (GPU Arch 7.5) is supported by CUDA 10 and later
	if(CUDA_VERSION VERSION_GREATER "9.9")		if(CUDA_VERSION VERSION_GREATER_EQUAL "10.0")
	string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_75,code=[sm_75,compute_75]")		string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_75,code=[sm_75,compute_75]")
	endif()		endif()
			# Ampere (GPU Arch 8.0) is supported by CUDA 11 and later
			if(CUDA_VERSION VERSION_GREATER_EQUAL "11.0")
			string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_80,code=[sm_80,compute_80]")
			endif()
			if(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
			message(WARNING "Unsupported CUDA version. Use at your own risk.")
			endif()

	cuda_compile_fatbin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS ${CUDA_REQUEST_PIC}		cuda_compile_fatbin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS ${CUDA_REQUEST_PIC}
	-DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DNV_KERNEL -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING})		-DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DNV_KERNEL -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING})
	@@ -228,29 +239,40 @@ elseif(GPU_API STREQUAL "HIP")
	# --arch translates directly instead of JIT, so this should be for the preferred or most common architecture		# --arch translates directly instead of JIT, so this should be for the preferred or most common architecture
	set(HIP_CUDA_GENCODE "-arch=${HIP_ARCH}")		set(HIP_CUDA_GENCODE "-arch=${HIP_ARCH}")
	# Fermi (GPU Arch 2.x) is supported by CUDA 3.2 to CUDA 8.0		# Fermi (GPU Arch 2.x) is supported by CUDA 3.2 to CUDA 8.0
	if((CUDA_VERSION VERSION_GREATER "3.1") AND (CUDA_VERSION VERSION_LESS "9.0"))		if((CUDA_VERSION VERSION_GREATER_EQUAL "3.2") AND (CUDA_VERSION VERSION_LESS "9.0"))
	string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_20,code=[sm_20,compute_20]")		string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_20,code=[sm_20,compute_20]")
	endif()		endif()
	# Kepler (GPU Arch 3.x) is supported by CUDA 5 and later		# Kepler (GPU Arch 3.0) is supported by CUDA 5 to CUDA 10.2
	if(CUDA_VERSION VERSION_GREATER "4.9")		if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "11.0"))
	string(APPEND HIP_CUDA_GENCODE "-gencode arch=compute_30,code=[sm_30,compute_30] -gencode arch=compute_35,code=[sm_35,compute_35] ")		string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_30,code=[sm_30,compute_30]")
			endif()
			# Kepler (GPU Arch 3.5) is supported by CUDA 5 to CUDA 11.0
			if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "12.0"))
			string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_35,code=[sm_35,compute_35]")
	endif()		endif()
	# Maxwell (GPU Arch 5.x) is supported by CUDA 6 and later		# Maxwell (GPU Arch 5.x) is supported by CUDA 6 and later
	if(CUDA_VERSION VERSION_GREATER "5.9")		if(CUDA_VERSION VERSION_GREATER_EQUAL "6.0")
	string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_50,code=[sm_50,compute_50] -gencode arch=compute_52,code=[sm_52,compute_52]")		string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_50,code=[sm_50,compute_50] -gencode arch=compute_52,code=[sm_52,compute_52]")
	endif()		endif()
	# Pascal (GPU Arch 6.x) is supported by CUDA 8 and later		# Pascal (GPU Arch 6.x) is supported by CUDA 8 and later
	if(CUDA_VERSION VERSION_GREATER "7.9")		if(CUDA_VERSION VERSION_GREATER_EQUAL "8.0")
	string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_60,code=[sm_60,compute_60] -gencode arch=compute_61,code=[sm_61,compute_61]")		string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_60,code=[sm_60,compute_60] -gencode arch=compute_61,code=[sm_61,compute_61]")
	endif()		endif()
	# Volta (GPU Arch 7.0) is supported by CUDA 9 and later		# Volta (GPU Arch 7.0) is supported by CUDA 9 and later
	if(CUDA_VERSION VERSION_GREATER "8.9")		if(CUDA_VERSION VERSION_GREATER_EQUAL "9.0")
	string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_70,code=[sm_70,compute_70]")		string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_70,code=[sm_70,compute_70]")
	endif()		endif()
	# Turing (GPU Arch 7.5) is supported by CUDA 10 and later		# Turing (GPU Arch 7.5) is supported by CUDA 10 and later
	if(CUDA_VERSION VERSION_GREATER "9.9")		if(CUDA_VERSION VERSION_GREATER_EQUAL "10.0")
	string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_75,code=[sm_75,compute_75]")		string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_75,code=[sm_75,compute_75]")
	endif()		endif()
			# Ampere (GPU Arch 8.0) is supported by CUDA 11 and later
			if(CUDA_VERSION VERSION_GREATER_EQUAL "11.0")
			string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_80,code=[sm_80,compute_80]")
			endif()
			if(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
			message(WARNING "Unsupported CUDA version. Use at your own risk.")
			endif()
	endif()		endif()

	file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.].cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/[^.].cu)		file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.].cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/[^.].cu)

doc/src/Build_extras.rst

+11 −2

Original line number	Original line	Diff line number	Diff line
	@@ -105,10 +105,10 @@ CMake build
	# generic (default) or intel (Intel CPU) or fermi, kepler, cypress (NVIDIA)		# generic (default) or intel (Intel CPU) or fermi, kepler, cypress (NVIDIA)
	-D GPU_ARCH=value # primary GPU hardware choice for GPU_API=cuda		-D GPU_ARCH=value # primary GPU hardware choice for GPU_API=cuda
	# value = sm_XX, see below		# value = sm_XX, see below
	# default is sm_30		# default is sm_50
	-D HIP_ARCH=value # primary GPU hardware choice for GPU_API=hip		-D HIP_ARCH=value # primary GPU hardware choice for GPU_API=hip
	# value depends on selected HIP_PLATFORM		# value depends on selected HIP_PLATFORM
	# default is 'gfx906' for HIP_PLATFORM=hcc and 'sm_30' for HIP_PLATFORM=nvcc		# default is 'gfx906' for HIP_PLATFORM=hcc and 'sm_50' for HIP_PLATFORM=nvcc
	-D HIP_USE_DEVICE_SORT=value # enables GPU sorting		-D HIP_USE_DEVICE_SORT=value # enables GPU sorting
	# value = yes (default) or no		# value = yes (default) or no
	-D CUDPP_OPT=value # optimization setting for GPU_API=cuda		-D CUDPP_OPT=value # optimization setting for GPU_API=cuda
	@@ -1255,6 +1255,15 @@ also typically :ref:`install the USER-OMP package <user-omp>`, as it can be
	used in tandem with the USER-INTEL package to good effect, as explained		used in tandem with the USER-INTEL package to good effect, as explained
	on the :doc:`Speed intel <Speed_intel>` doc page.		on the :doc:`Speed intel <Speed_intel>` doc page.

			When using Intel compilers version 16.0 or later is required. You can
			also use the GNU or Clang compilers and they will provide performance
			improvements over regular styles and USER-OMP styles, but less so than
			with the Intel compilers. Please also note, that some compilers have
			been found to apply memory alignment constraints incompletely or
			incorrectly and thus can cause segmentation faults in otherwise correct
			code when using features from the USER-INTEL package.


	CMake build		CMake build
	^^^^^^^^^^^		^^^^^^^^^^^

doc/src/Commands_all.rst

+2 −8

Original line number	Original line	Diff line number	Diff line
	@@ -46,13 +46,6 @@ An alphabetic list of all general LAMMPS commands.
	* :doc:`dimension <dimension>`		* :doc:`dimension <dimension>`
	* :doc:`displace_atoms <displace_atoms>`		* :doc:`displace_atoms <displace_atoms>`
	* :doc:`dump <dump>`		* :doc:`dump <dump>`
	* :doc:`dump atom/adios <dump_adios>`
	* :doc:`dump custom/adios <dump_adios>`
	* :doc:`dump image <dump_image>`
	* :doc:`dump movie <dump_image>`
	* :doc:`dump netcdf <dump_netcdf>`
	* :doc:`dump netcdf/mpiio <dump_netcdf>`
	* :doc:`dump vtk <dump_vtk>`
	* :doc:`dump_modify <dump_modify>`		* :doc:`dump_modify <dump_modify>`
	* :doc:`dynamical_matrix <dynamical_matrix>`		* :doc:`dynamical_matrix <dynamical_matrix>`
	* :doc:`echo <echo>`		* :doc:`echo <echo>`
	@@ -108,7 +101,8 @@ An alphabetic list of all general LAMMPS commands.
	* :doc:`region <region>`		* :doc:`region <region>`
	* :doc:`replicate <replicate>`		* :doc:`replicate <replicate>`
	* :doc:`rerun <rerun>`		* :doc:`rerun <rerun>`
	* :doc:`reset_ids <reset_ids>`		* :doc:`reset_atom_ids <reset_atom_ids>`
			* :doc:`reset_mol_ids <reset_mol_ids>`
	* :doc:`reset_timestep <reset_timestep>`		* :doc:`reset_timestep <reset_timestep>`
	* :doc:`restart <restart>`		* :doc:`restart <restart>`
	* :doc:`run <run>`		* :doc:`run <run>`

doc/src/Commands_compute.rst

+2 −0

Original line number	Original line	Diff line number	Diff line
	@@ -80,6 +80,7 @@ KOKKOS, o = USER-OMP, t = OPT.
	* :doc:`ke/eff <compute_ke_eff>`		* :doc:`ke/eff <compute_ke_eff>`
	* :doc:`ke/rigid <compute_ke_rigid>`		* :doc:`ke/rigid <compute_ke_rigid>`
	* :doc:`mesont <compute_mesont>`		* :doc:`mesont <compute_mesont>`
			* :doc:`mliap <compute_mliap>`
	* :doc:`momentum <compute_momentum>`		* :doc:`momentum <compute_momentum>`
	* :doc:`msd <compute_msd>`		* :doc:`msd <compute_msd>`
	* :doc:`msd/chunk <compute_msd_chunk>`		* :doc:`msd/chunk <compute_msd_chunk>`
	@@ -122,6 +123,7 @@ KOKKOS, o = USER-OMP, t = OPT.
	* :doc:`smd/tlsph/strain/rate <compute_smd_tlsph_strain_rate>`		* :doc:`smd/tlsph/strain/rate <compute_smd_tlsph_strain_rate>`
	* :doc:`smd/tlsph/stress <compute_smd_tlsph_stress>`		* :doc:`smd/tlsph/stress <compute_smd_tlsph_stress>`
	* :doc:`smd/triangle/vertices <compute_smd_triangle_vertices>`		* :doc:`smd/triangle/vertices <compute_smd_triangle_vertices>`
			* :doc:`smd/ulsph/effm <compute_smd_ulsph_effm>`
	* :doc:`smd/ulsph/num/neighs <compute_smd_ulsph_num_neighs>`		* :doc:`smd/ulsph/num/neighs <compute_smd_ulsph_num_neighs>`
	* :doc:`smd/ulsph/strain <compute_smd_ulsph_strain>`		* :doc:`smd/ulsph/strain <compute_smd_ulsph_strain>`
	* :doc:`smd/ulsph/strain/rate <compute_smd_ulsph_strain_rate>`		* :doc:`smd/ulsph/strain/rate <compute_smd_ulsph_strain_rate>`

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