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Merge branch 'master' into gpu-mem-leak-init

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This commit is contained in:
Axel Kohlmeyer
2020-01-08 14:26:03 -05:00
parent e119bffcca 97a798c776
commit 00dce6b198
2546 changed files with 185607 additions and 25976 deletions
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2
lib/gpu/Makefile.lammps.standard
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@ -7,5 +7,5 @@ endif
gpu_SYSINC =
gpu_SYSLIB = -lcudart -lcuda
gpu_SYSPATH = -L$(CUDA_HOME)/lib64
gpu_SYSPATH = -L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib64/stubs

2
lib/gpu/Makefile.linux
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@ -54,7 +54,7 @@ LMP_INC = -DLAMMPS_SMALLBIG
CUDA_PRECISION = -D_SINGLE_DOUBLE
CUDA_INCLUDE = -I$(CUDA_HOME)/include
CUDA_LIB = -L$(CUDA_HOME)/lib64
CUDA_LIB = -L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib64/stubs
CUDA_OPTS = -DUNIX -O3 --use_fast_math $(LMP_INC) -Xcompiler -fPIC
CUDR_CPP = mpicxx -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK -DOMPI_SKIP_MPICXX=1 -fPIC

2
lib/gpu/Makefile.linux.double
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@ -32,7 +32,7 @@ LMP_INC = -DLAMMPS_SMALLBIG
CUDA_PRECISION = -D_DOUBLE_DOUBLE
CUDA_INCLUDE = -I$(CUDA_HOME)/include
CUDA_LIB = -L$(CUDA_HOME)/lib64
CUDA_LIB = -L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib64/stubs
CUDA_OPTS = -DUNIX -O3 --use_fast_math
CUDR_CPP = mpic++ -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK

2
lib/gpu/Makefile.linux.mixed
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@ -32,7 +32,7 @@ LMP_INC = -DLAMMPS_SMALLBIG
CUDA_PRECISION = -D_SINGLE_DOUBLE
CUDA_INCLUDE = -I$(CUDA_HOME)/include
CUDA_LIB = -L$(CUDA_HOME)/lib64
CUDA_LIB = -L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib64/stubs
CUDA_OPTS = -DUNIX -O3 --use_fast_math
CUDR_CPP = mpic++ -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK

2
lib/gpu/Makefile.linux.single
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@ -32,7 +32,7 @@ LMP_INC = -DLAMMPS_SMALLBIG
CUDA_PRECISION = -D_SINGLE_SINGLE
CUDA_INCLUDE = -I$(CUDA_HOME)/include
CUDA_LIB = -L$(CUDA_HOME)/lib64
CUDA_LIB = -L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib64/stubs
CUDA_OPTS = -DUNIX -O3 --use_fast_math
CUDR_CPP = mpic++ -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK

2
lib/gpu/Makefile.linux_multi
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@ -40,7 +40,7 @@ LMP_INC = -DLAMMPS_SMALLBIG
CUDA_PRECISION = -D_SINGLE_DOUBLE
CUDA_INCLUDE = -I$(CUDA_HOME)/include
CUDA_LIB = -L$(CUDA_HOME)/lib64
CUDA_LIB = -L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib64/stubs
CUDA_OPTS = -DUNIX -O3 --use_fast_math $(LMP_INC) -Xcompiler "-fPIC -std=c++98"
CUDR_CPP = mpicxx -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK -DOMPI_SKIP_MPICXX=1 -fPIC

2
lib/gpu/Makefile.mac
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@ -14,7 +14,7 @@ NVCC = nvcc -m64
CUDA_ARCH = -arch=sm_11
CUDA_PRECISION = -D_SINGLE_SINGLE
CUDA_INCLUDE = -I$(CUDA_HOME)/include
CUDA_LIB = -L$(CUDA_HOME)/lib
CUDA_LIB = -L$(CUDA_HOME)/lib -L$(CUDA_HOME)/lib/stubs
CUDA_OPTS = -DUNIX -DUCL_NO_EXIT -O3 --use_fast_math
CUDR_CPP = mpic++ -m64

2
lib/gpu/Makefile.serial
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@ -34,7 +34,7 @@ LMP_INC = -DLAMMPS_SMALLBIG
CUDA_PRECISION = -D_SINGLE_DOUBLE
CUDA_INCLUDE = -I$(CUDA_HOME)/include
CUDA_LIB = -L$(CUDA_HOME)/lib64 -L../../src/STUBS -lmpi_stubs
CUDA_LIB = -L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib64/stubs -L../../src/STUBS -lmpi_stubs
CUDA_OPTS = -DUNIX -O3 --use_fast_math $(LMP_INC)
CUDR_CPP = g++ -DMPI_GERYON -DUCL_NO_EXIT -fPIC -I../../src/STUBS

2
lib/gpu/Makefile.shannon
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@ -32,7 +32,7 @@ LMP_INC = -DLAMMPS_SMALLBIG
CUDA_PRECISION = -D_DOUBLE_DOUBLE
CUDA_INCLUDE = -I$(CUDA_HOME)/include
CUDA_LIB = -L$(CUDA_HOME)/lib64
CUDA_LIB = -L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib64/stubs
CUDA_OPTS = -DUNIX -O3 --use_fast_math
CUDR_CPP = mpic++ -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK

2
lib/gpu/Makefile.xk7
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@ -14,7 +14,7 @@ CUDA_ARCH = -arch=sm_35
CUDA_PRECISION = -D_SINGLE_DOUBLE
CUDA_INCLUDE = -I$(CUDA_HOME)/include
CUDA_LIB = -L$(CUDA_HOME)/lib64
CUDA_LIB = -L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib64/stubs
CUDA_OPTS = -DUNIX -O3 --use_fast_math
CUDR_CPP = CC -DCUDA_PROXY -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK

5
lib/gpu/README
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@ -3,7 +3,7 @@
--------------------------------
W. Michael Brown (ORNL)
Trung Dac Nguyen (ORNL)
Trung Dac Nguyen (ORNL/Northwestern)
Peng Wang (NVIDIA)
Axel Kohlmeyer (Temple)
Steve Plimpton (SNL)
@ -129,7 +129,8 @@ that ships with the CUDA toolkit, but also with the CUDA driver library
on the head node of a GPU cluster, this library may not be installed,
so you may need to copy it over from one of the compute nodes (best into
this directory). Recent CUDA toolkits starting from CUDA 9 provide a dummy
libcuda.so library, that can be used for linking (but not for running).
libcuda.so library (typically under $(CUDA_HOME)/lib64/stubs), that can be used for
linking.
The gpu library supports 3 precision modes as determined by
the CUDA_PRECISION variable:

7
lib/gpu/lal_gayberne.cu
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@ -316,10 +316,9 @@ __kernel void k_gayberne(const __global numtyp4 *restrict x_,
numtyp tempv[3];
gpu_row_times3(iota,b1,tempv);
gpu_cross3(tempv,iota,tchi);
temp1 = (numtyp)-4.0*ir*ir;
tchi[0] *= temp1;
tchi[1] *= temp1;
tchi[2] *= temp1;
tchi[0] *= temp2;
tchi[1] *= temp2;
tchi[2] *= temp2;
}
numtyp temp2 = factor_lj*eta*chi;