Feb2021 GPU Package Update - Core LAMMPS Files

src/MAKE/OPTIONS/Makefile.g++_openmpi

@@ -7,12 +7,12 @@ SHELL = /bin/sh
 # specify flags and libraries needed for your compiler
 
 export OMPI_CXX = g++
-CC =		mpicxx
+CC =		mpicxx -std=c++11
 CCFLAGS =	-g -O3
 SHFLAGS =	-fPIC
 DEPFLAGS =	-M
 
-LINK =		mpicxx
+LINK =		mpicxx -std=c++11
 LINKFLAGS =	-g -O
 LIB = 
 SIZE =		size

src/MAKE/OPTIONS/Makefile.g++_serial

@@ -6,12 +6,12 @@ SHELL = /bin/sh
 # compiler/linker settings
 # specify flags and libraries needed for your compiler
 
-CC =		g++
+CC =		g++ -std=c++11
 CCFLAGS =	-g -O3
 SHFLAGS =	-fPIC
 DEPFLAGS =	-M
 
-LINK =		g++
+LINK =		g++ -std=c++11
 LINKFLAGS =	-g -O
 LIB = 
 SIZE =		size

src/MAKE/OPTIONS/Makefile.oneapi

@@ -0,0 +1,122 @@
+# oneapi = For Intel oneAPI builds with GPU package
+
+SHELL = /bin/sh
+
+# ---------------------------------------------------------------------
+# compiler/linker settings
+# specify flags and libraries needed for your compiler
+
+CC =		mpiicpc -std=c++11
+OPTFLAGS =      -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits
+CCFLAGS =	-qopenmp -qopenmp-simd -qno-offload -ansi-alias -restrict \
+                -DLMP_INTEL_USELRT -DLMP_USE_MKL_RNG $(OPTFLAGS) \
+                -I$(MKLROOT)/include
+SHFLAGS =	-fPIC
+DEPFLAGS =	-M
+
+LINK =		mpiicpc -std=c++11
+LINKFLAGS =	-qopenmp -qopenmp-simd $(OPTFLAGS) -L$(MKLROOT)/lib/intel64/
+LIB =           -ltbbmalloc -lmkl_intel_ilp64 -lmkl_sequential -lmkl_core	
+SIZE =		size
+
+ARCHIVE =	ar
+ARFLAGS =	-rc
+SHLIBFLAGS =	-shared
+
+# ---------------------------------------------------------------------
+# LAMMPS-specific settings, all OPTIONAL
+# specify settings for LAMMPS features you will use
+# if you change any -D setting, do full re-compile after "make clean"
+
+# LAMMPS ifdef settings
+# see possible settings in Section 3.5 of the manual
+
+LMP_INC =	-DLAMMPS_GZIP
+
+# MPI library
+# see discussion in Section 3.4 of the manual
+# MPI wrapper compiler/linker can provide this info
+# can point to dummy MPI library in src/STUBS as in Makefile.serial
+# use -D MPICH and OMPI settings in INC to avoid C++ lib conflicts
+# INC = path for mpi.h, MPI compiler settings
+# PATH = path for MPI library
+# LIB = name of MPI library
+
+MPI_INC =       -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1
+MPI_PATH = 
+MPI_LIB =
+
+# FFT library
+# see discussion in Section 3.5.2 of manual
+# can be left blank to use provided KISS FFT library
+# INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings
+# PATH = path for FFT library
+# LIB = name of FFT library
+
+FFT_INC =       -DFFT_MKL -DFFT_SINGLE
+FFT_PATH = 
+FFT_LIB =
+
+# JPEG and/or PNG library
+# see discussion in Section 3.5.4 of manual
+# only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC
+# INC = path(s) for jpeglib.h and/or png.h
+# PATH = path(s) for JPEG library and/or PNG library
+# LIB = name(s) of JPEG library and/or PNG library
+
+JPG_INC =
+JPG_PATH =
+JPG_LIB =
+
+# ---------------------------------------------------------------------
+# build rules and dependencies
+# do not edit this section
+
+include Makefile.package.settings
+include Makefile.package
+
+EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
+EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
+EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
+EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)
+EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)
+
+# Path to src files
+
+vpath %.cpp ..
+vpath %.h ..
+
+# Link target
+
+$(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
+	$(LINK) $(LINKFLAGS) main.o $(EXTRA_PATH) $(LMPLINK) $(EXTRA_LIB) $(LIB) -o $@
+	$(SIZE) $@
+
+# Library targets
+
+$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
+	@rm -f ../$(ARLIB)
+	$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
+	@rm -f $(ARLIB)
+	@ln -s ../$(ARLIB) $(ARLIB)
+
+$(SHLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
+	$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o ../$(SHLIB) \
+		$(OBJ) $(EXTRA_LIB) $(LIB)
+	@rm -f $(SHLIB)
+	@ln -s ../$(SHLIB) $(SHLIB)
+
+# Compilation rules
+
+%.o:%.cpp
+	$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
+
+# Individual dependencies
+
+depend : fastdep.exe $(SRC)
+	@./fastdep.exe $(EXTRA_INC) -- $^ > .depend || exit 1
+
+fastdep.exe: ../DEPEND/fastdep.c
+	cc -O -o $@ $<
+
+sinclude .depend

src/atom.cpp

@@ -40,6 +40,10 @@
 #include "neigh_request.h"
 #endif
 
+#ifdef LMP_GPU
+#include "fix_gpu.h"
+#endif
+
 using namespace LAMMPS_NS;
 using namespace MathConst;
 
@@ -2196,6 +2200,35 @@ void Atom::setup_sort_bins()
   }
   #endif
 
+  #ifdef LMP_GPU
+  if (userbinsize == 0.0) {
+    int ifix = modify->find_fix("package_gpu");
+    if (ifix >= 0) {
+      const double subx = domain->subhi[0] - domain->sublo[0];
+      const double suby = domain->subhi[1] - domain->sublo[1];
+      const double subz = domain->subhi[2] - domain->sublo[2];
+
+      FixGPU *fix = static_cast<FixGPU *>(modify->fix[ifix]);
+      binsize = fix->binsize(subx, suby, subz, atom->nlocal,
+                             neighbor->cutneighmax);
+      bininv = 1.0 / binsize;
+      
+      nbinx = static_cast<int> (ceil(subx * bininv));
+      nbiny = static_cast<int> (ceil(suby * bininv));
+      nbinz = static_cast<int> (ceil(subz * bininv));
+      if (domain->dimension == 2) nbinz = 1;
+
+      if (nbinx == 0) nbinx = 1;
+      if (nbiny == 0) nbiny = 1;
+      if (nbinz == 0) nbinz = 1;
+
+      bininvx = bininv;
+      bininvy = bininv;
+      bininvz = bininv;
+    }
+  }
+  #endif
+
   if (1.0*nbinx*nbiny*nbinz > INT_MAX)
     error->one(FLERR,"Too many atom sorting bins");
 

src/lammps.cpp

@@ -842,12 +842,12 @@ void LAMMPS::post_create()
     if (strcmp(suffix,"omp") == 0 && !modify->check_package("OMP"))
       error->all(FLERR,"Using suffix omp without USER-OMP package installed");
 
-    if (strcmp(suffix,"gpu") == 0) input->one("package gpu 1");
+    if (strcmp(suffix,"gpu") == 0) input->one("package gpu 0");
     if (strcmp(suffix,"intel") == 0) input->one("package intel 1");
     if (strcmp(suffix,"omp") == 0) input->one("package omp 0");
 
     if (suffix2) {
-      if (strcmp(suffix2,"gpu") == 0) input->one("package gpu 1");
+      if (strcmp(suffix2,"gpu") == 0) input->one("package gpu 0");
       if (strcmp(suffix2,"intel") == 0) input->one("package intel 1");
       if (strcmp(suffix2,"omp") == 0) input->one("package omp 0");
     }