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Cleanup. Remove copyright year. Reformat.

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This commit is contained in:
Jan Eitzinger 2024-05-13 12:33:08 +02:00
parent a6a269703d
commit 9712d7e2c8
77 changed files with 959 additions and 648 deletions
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176
.clang-format Normal file
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@ -0,0 +1,176 @@
---
Language: Cpp
# BasedOnStyle: WebKit
AccessModifierOffset: -4
AlignAfterOpenBracket: DontAlign
AlignArrayOfStructures: None
AlignConsecutiveAssignments: Consecutive
AlignConsecutiveBitFields: None
AlignConsecutiveDeclarations: None
AlignConsecutiveMacros: Consecutive
AlignEscapedNewlines: Right
AlignOperands: Align
AlignTrailingComments: true
AllowAllArgumentsOnNextLine: false
AllowAllParametersOfDeclarationOnNextLine: true
AllowShortEnumsOnASingleLine: true
AllowShortBlocksOnASingleLine: Never
AllowShortCaseLabelsOnASingleLine: false
AllowShortFunctionsOnASingleLine: All
AllowShortLambdasOnASingleLine: All
AllowShortIfStatementsOnASingleLine: OnlyFirstIf
AllowShortLoopsOnASingleLine: false
AlwaysBreakAfterDefinitionReturnType: None
AlwaysBreakAfterReturnType: None
AlwaysBreakBeforeMultilineStrings: false
AlwaysBreakTemplateDeclarations: MultiLine
AttributeMacros:
- __capability
BinPackArguments: false
BinPackParameters: false
BraceWrapping:
AfterCaseLabel: false
AfterClass: false
AfterControlStatement: Never
AfterEnum: false
AfterFunction: true
AfterNamespace: false
AfterObjCDeclaration: false
AfterStruct: false
AfterUnion: false
AfterExternBlock: false
BeforeCatch: false
BeforeElse: false
BeforeLambdaBody: false
BeforeWhile: false
IndentBraces: false
SplitEmptyFunction: true
SplitEmptyRecord: true
SplitEmptyNamespace: true
BreakBeforeBinaryOperators: None
BreakBeforeBraces: WebKit
BreakBeforeInheritanceComma: false
BreakInheritanceList: BeforeColon
BreakBeforeTernaryOperators: true
BreakConstructorInitializersBeforeComma: false
BreakConstructorInitializers: BeforeComma
BreakAfterJavaFieldAnnotations: false
BreakStringLiterals: true
ColumnLimit: 90
CommentPragmas: '^ IWYU pragma:'
CompactNamespaces: false
ConstructorInitializerIndentWidth: 4
ContinuationIndentWidth: 4
Cpp11BracedListStyle: false
DeriveLineEnding: true
DerivePointerAlignment: false
DisableFormat: false
EmptyLineAfterAccessModifier: Never
EmptyLineBeforeAccessModifier: LogicalBlock
ExperimentalAutoDetectBinPacking: false
BasedOnStyle: ''
ConstructorInitializerAllOnOneLineOrOnePerLine: false
AllowAllConstructorInitializersOnNextLine: true
FixNamespaceComments: false
ForEachMacros:
- foreach
- Q_FOREACH
- BOOST_FOREACH
IfMacros:
- KJ_IF_MAYBE
IncludeBlocks: Preserve
IncludeCategories:
- Regex: '^"(llvm|llvm-c|clang|clang-c)/'
Priority: 2
SortPriority: 0
CaseSensitive: false
- Regex: '^(<|"(gtest|gmock|isl|json)/)'
Priority: 3
SortPriority: 0
CaseSensitive: false
- Regex: '.*'
Priority: 1
SortPriority: 0
CaseSensitive: false
IncludeIsMainRegex: '(Test)?$'
IncludeIsMainSourceRegex: ''
IndentAccessModifiers: false
IndentCaseLabels: false
IndentCaseBlocks: false
IndentGotoLabels: true
IndentPPDirectives: None
IndentExternBlock: AfterExternBlock
IndentWidth: 4
IndentWrappedFunctionNames: false
InsertTrailingCommas: None
JavaScriptQuotes: Leave
JavaScriptWrapImports: true
KeepEmptyLinesAtTheStartOfBlocks: true
LambdaBodyIndentation: Signature
MacroBlockBegin: ''
MacroBlockEnd: ''
MaxEmptyLinesToKeep: 1
NamespaceIndentation: Inner
ObjCBinPackProtocolList: Auto
ObjCBlockIndentWidth: 4
ObjCBreakBeforeNestedBlockParam: true
ObjCSpaceAfterProperty: true
ObjCSpaceBeforeProtocolList: true
PenaltyBreakAssignment: 200
PenaltyBreakBeforeFirstCallParameter: 19
PenaltyBreakComment: 300
PenaltyBreakFirstLessLess: 120
PenaltyBreakString: 1000
PenaltyBreakTemplateDeclaration: 10
PenaltyExcessCharacter: 1000000
PenaltyReturnTypeOnItsOwnLine: 60
PenaltyIndentedWhitespace: 0
PointerAlignment: Left
PPIndentWidth: -1
ReferenceAlignment: Pointer
ReflowComments: true
ShortNamespaceLines: 1
SortIncludes: CaseSensitive
SortJavaStaticImport: Before
SortUsingDeclarations: true
SpaceAfterCStyleCast: false
SpaceAfterLogicalNot: false
SpaceAfterTemplateKeyword: true
SpaceBeforeAssignmentOperators: true
SpaceBeforeCaseColon: false
SpaceBeforeCpp11BracedList: true
SpaceBeforeCtorInitializerColon: true
SpaceBeforeInheritanceColon: true
SpaceBeforeParens: ControlStatements
SpaceAroundPointerQualifiers: Default
SpaceBeforeRangeBasedForLoopColon: true
SpaceInEmptyBlock: false
SpaceInEmptyParentheses: false
SpacesBeforeTrailingComments: 1
SpacesInAngles: Never
SpacesInConditionalStatement: false
SpacesInContainerLiterals: true
SpacesInCStyleCastParentheses: false
SpacesInLineCommentPrefix:
Minimum: 1
Maximum: -1
SpacesInParentheses: false
SpacesInSquareBrackets: false
SpaceBeforeSquareBrackets: false
BitFieldColonSpacing: Both
Standard: Latest
StatementAttributeLikeMacros:
- Q_EMIT
StatementMacros:
- Q_UNUSED
- QT_REQUIRE_VERSION
TabWidth: 8
UseCRLF: false
UseTab: Never
WhitespaceSensitiveMacros:
- STRINGIZE
- PP_STRINGIZE
- BOOST_PP_STRINGIZE
- NS_SWIFT_NAME
- CF_SWIFT_NAME
...

14
.clang-tidy Normal file
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@ -0,0 +1,14 @@
---
Checks: 'clang-diagnostic-*,clang-analyzer-*,clang-bugprone-*,readability-identifier-naming'
WarningsAsErrors: true
HeaderFilterRegex: '.*'
AnalyzeTemporaryDtors: false
CheckOptions:
- key: readability-identifier-naming.StructCase
value: 'CamelCase'
- key: readability-identifier-naming.FunctionCase
value: 'camelBack'
- key: readability-identifier-naming.VariableCase
value: 'camelBack'
- key: readability-identifier-naming.GlobalConstantCase
value: 'UPPER_CASE'

3
.clangd Normal file
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@ -0,0 +1,3 @@
CompileFlags:
Add: [-I/Users/jan/prg/MD-Bench/verletlist/includes, -I/Users/jan/prg/MD-Bench/common/includes, -DALIGNMENT=64]
Compiler: clang

4
Makefile
View File

@ -98,10 +98,6 @@ ifeq ($(strip $(ENABLE_OMP_SIMD)),true)
DEFINES += -DENABLE_OMP_SIMD
endif
ifeq ($(strip $(USE_SIMD_KERNEL)),true)
DEFINES += -DUSE_SIMD_KERNEL
endif
VPATH = $(SRC_DIR) $(ASM_DIR) $(CUDA_DIR)
ASM = $(patsubst $(SRC_DIR)/%.c, $(BUILD_DIR)/%.s,$(wildcard $(SRC_DIR)/*.c))
OVERWRITE:= $(patsubst $(ASM_DIR)/%-new.s, $(BUILD_DIR)/%.o,$(wildcard $(ASM_DIR)/*-new.s))

2
gromacs/atom.c → clusterpair/atom.c
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@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.

2
gromacs/cuda/force_lj.cu → clusterpair/cuda/force_lj.cu
View File

@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.

2
gromacs/force_eam.c → clusterpair/force_eam.c
View File

@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.

2
gromacs/force_lj.c → clusterpair/force_lj.c
View File

@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.

2
gromacs/includes/atom.h → clusterpair/includes/atom.h
View File

@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.

2
gromacs/includes/integrate.h → clusterpair/includes/integrate.h
View File

@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.

2
gromacs/includes/neighbor.h → clusterpair/includes/neighbor.h
View File

@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.

2
gromacs/includes/pbc.h → clusterpair/includes/pbc.h
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@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.

2
gromacs/includes/stats.h → clusterpair/includes/stats.h
View File

@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.

2
gromacs/includes/tracing.h → clusterpair/includes/tracing.h
View File

@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.

2
gromacs/includes/vtk.h → clusterpair/includes/vtk.h
View File

@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.

2
gromacs/includes/xtc.h → clusterpair/includes/xtc.h
View File

@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.

2
gromacs/main-stub.c → clusterpair/main-stub.c
View File

@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.

2
gromacs/main.c → clusterpair/main.c
View File

@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.

2
gromacs/neighbor.c → clusterpair/neighbor.c
View File

@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.

2
gromacs/pbc.c → clusterpair/pbc.c
View File

@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.

2
gromacs/stats.c → clusterpair/stats.c
View File

@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.

2
gromacs/tracing.c → clusterpair/tracing.c
View File

@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.

2
gromacs/vtk.c → clusterpair/vtk.c
View File

@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.

2
gromacs/xtc.c → clusterpair/xtc.c
View File

@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.

2
common/allocate.c
View File

@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.

2
common/device.c
View File

@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.

2
common/eam_utils.c
View File

@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.

2
common/includes/allocate.h
View File

@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.

2
common/includes/device.h
View File

@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.

2
common/includes/eam.h
View File

@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.

2
common/includes/likwid-marker.h
View File

@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.

2
common/includes/parameter.h
View File

@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.

2
common/includes/simd.h
View File

@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.

2
common/includes/simd/avx2_double.h
View File

@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.

2
common/includes/simd/avx2_float.h
View File

@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.

2
common/includes/simd/avx512_double.h
View File

@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.

2
common/includes/simd/avx512_float.h
View File

@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.

2
common/includes/simd/avx_double.h
View File

@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.

2
common/includes/simd/avx_float.h
View File

@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.

2
common/includes/thermo.h
View File

@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.

2
common/includes/timers.h
View File

@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.

2
common/includes/timing.h
View File

@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.

27
common/includes/util.h
View File

@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.
@ -7,40 +7,41 @@
#ifndef __UTIL_H_
#define __UTIL_H_
#include <stdio.h>
#ifndef MIN
# define MIN(x,y) ((x)<(y)?(x):(y))
#define MIN(x, y) ((x) < (y) ? (x) : (y))
#endif
#ifndef MAX
# define MAX(x,y) ((x)>(y)?(x):(y))
#define MAX(x, y) ((x) > (y) ? (x) : (y))
#endif
#ifndef ABS
# define ABS(a) ((a) >= 0 ? (a) : -(a))
#define ABS(a) ((a) >= 0 ? (a) : -(a))
#endif
#define DEBUG_MESSAGE debug_printf
#ifndef MAXLINE
# define MAXLINE 4096
#define MAXLINE 4096
#endif
#define FF_LJ 0
#define FF_EAM 1
#define FF_DEM 2
#define FF_LJ 0
#define FF_EAM 1
#define FF_DEM 2
#if PRECISION == 1
# define PRECISION_STRING "single"
#define PRECISION_STRING "single"
#else
# define PRECISION_STRING "double"
#define PRECISION_STRING "double"
#endif
extern double myrandom(int*);
extern double myrandom(int *);
extern void random_reset(int *seed, int ibase, double *coord);
extern int str2ff(const char *string);
extern const char* ff2str(int ff);
extern const char *ff2str(int ff);
extern void readline(char *line, FILE *fp);
extern void debug_printf(const char *format, ...);
extern int get_cuda_num_threads();
extern int get_cuda_num_threads(void);
#endif

2
common/parameter.c
View File

@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.

2
common/thermo.c
View File

@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.

2
common/timing.c
View File

@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.

2
common/util.c
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@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.

14
config.mk
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@ -1,17 +1,17 @@
# Compiler tag (GCC/CLANG/ICC/ICX/ONEAPI/NVCC)
TAG ?= ICC
TAG ?= CLANG
# Instruction set (SSE/AVX/AVX_FMA/AVX2/AVX512)
ISA ?= AVX512
# Optimization scheme (lammps/gromacs/clusters_per_bin)
OPT_SCHEME ?= lammps
ISA ?= SSE
# Optimization scheme (verletlist/clusterpair/clusters_per_bin)
OPT_SCHEME ?= verletlist
# Enable likwid (true or false)
ENABLE_LIKWID ?= true
ENABLE_LIKWID ?= false
# SP or DP
DATA_TYPE ?= DP
# AOS or SOA
DATA_LAYOUT ?= AOS
# Assembly syntax to generate (ATT/INTEL)
ASM_SYNTAX ?= ATT
ASM_SYNTAX ?= INTEL
# Debug
DEBUG ?= false
@ -28,7 +28,7 @@ COMPUTE_STATS ?= true
# Configurations for lammps optimization scheme
# Use omp simd pragma when running with half neighbor-lists
ENABLE_OMP_SIMD ?= true
ENABLE_OMP_SIMD ?= false
# Use kernel with explicit SIMD intrinsics
USE_SIMD_KERNEL ?= false

278
lammps/force_lj.c
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@ -1,278 +0,0 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.
*/
#include <stdio.h>
#include <stdlib.h>
//---
#include <atom.h>
#include <likwid-marker.h>
#include <neighbor.h>
#include <parameter.h>
#include <stats.h>
#include <timing.h>
#ifdef __SIMD_KERNEL__
#include <simd.h>
#endif
double computeForceLJFullNeigh_plain_c(Parameter *param, Atom *atom, Neighbor *neighbor, Stats *stats) {
int Nlocal = atom->Nlocal;
int* neighs;
#ifndef EXPLICIT_TYPES
MD_FLOAT cutforcesq = param->cutforce * param->cutforce;
MD_FLOAT sigma6 = param->sigma6;
MD_FLOAT epsilon = param->epsilon;
#endif
const MD_FLOAT num1 = 1.0;
const MD_FLOAT num48 = 48.0;
const MD_FLOAT num05 = 0.5;
for(int i = 0; i < Nlocal; i++) {
atom_fx(i) = 0.0;
atom_fy(i) = 0.0;
atom_fz(i) = 0.0;
}
double S = getTimeStamp();
#pragma omp parallel
{
LIKWID_MARKER_START("force");
#pragma omp for schedule(runtime)
for(int i = 0; i < Nlocal; i++) {
neighs = &neighbor->neighbors[i * neighbor->maxneighs];
int numneighs = neighbor->numneigh[i];
MD_FLOAT xtmp = atom_x(i);
MD_FLOAT ytmp = atom_y(i);
MD_FLOAT ztmp = atom_z(i);
MD_FLOAT fix = 0;
MD_FLOAT fiy = 0;
MD_FLOAT fiz = 0;
#ifdef EXPLICIT_TYPES
const int type_i = atom->type[i];
#endif
for(int k = 0; k < numneighs; k++) {
int j = neighs[k];
MD_FLOAT delx = xtmp - atom_x(j);
MD_FLOAT dely = ytmp - atom_y(j);
MD_FLOAT delz = ztmp - atom_z(j);
MD_FLOAT rsq = delx * delx + dely * dely + delz * delz;
#ifdef EXPLICIT_TYPES
const int type_j = atom->type[j];
const int type_ij = type_i * atom->ntypes + type_j;
const MD_FLOAT cutforcesq = atom->cutforcesq[type_ij];
const MD_FLOAT sigma6 = atom->sigma6[type_ij];
const MD_FLOAT epsilon = atom->epsilon[type_ij];
#endif
if(rsq < cutforcesq) {
MD_FLOAT sr2 = num1 / rsq;
MD_FLOAT sr6 = sr2 * sr2 * sr2 * sigma6;
MD_FLOAT force = num48 * sr6 * (sr6 - num05) * sr2 * epsilon;
fix += delx * force;
fiy += dely * force;
fiz += delz * force;
#ifdef USE_REFERENCE_VERSION
addStat(stats->atoms_within_cutoff, 1);
} else {
addStat(stats->atoms_outside_cutoff, 1);
#endif
}
}
atom_fx(i) += fix;
atom_fy(i) += fiy;
atom_fz(i) += fiz;
#ifdef USE_REFERENCE_VERSION
if(numneighs % VECTOR_WIDTH > 0) {
addStat(stats->atoms_outside_cutoff, VECTOR_WIDTH - (numneighs % VECTOR_WIDTH));
}
#endif
addStat(stats->total_force_neighs, numneighs);
addStat(stats->total_force_iters, (numneighs + VECTOR_WIDTH - 1) / VECTOR_WIDTH);
}
LIKWID_MARKER_STOP("force");
}
double E = getTimeStamp();
return E-S;
}
double computeForceLJHalfNeigh(Parameter *param, Atom *atom, Neighbor *neighbor, Stats *stats) {
int Nlocal = atom->Nlocal;
int* neighs;
#ifndef EXPLICIT_TYPES
MD_FLOAT cutforcesq = param->cutforce * param->cutforce;
MD_FLOAT sigma6 = param->sigma6;
MD_FLOAT epsilon = param->epsilon;
#endif
const MD_FLOAT num1 = 1.0;
const MD_FLOAT num48 = 48.0;
const MD_FLOAT num05 = 0.5;
for(int i = 0; i < Nlocal; i++) {
atom_fx(i) = 0.0;
atom_fy(i) = 0.0;
atom_fz(i) = 0.0;
}
double S = getTimeStamp();
#pragma omp parallel
{
LIKWID_MARKER_START("forceLJ-halfneigh");
#pragma omp for schedule(runtime)
for(int i = 0; i < Nlocal; i++) {
neighs = &neighbor->neighbors[i * neighbor->maxneighs];
int numneighs = neighbor->numneigh[i];
MD_FLOAT xtmp = atom_x(i);
MD_FLOAT ytmp = atom_y(i);
MD_FLOAT ztmp = atom_z(i);
MD_FLOAT fix = 0;
MD_FLOAT fiy = 0;
MD_FLOAT fiz = 0;
#ifdef EXPLICIT_TYPES
const int type_i = atom->type[i];
#endif
// Pragma required to vectorize the inner loop
#ifdef ENABLE_OMP_SIMD
#pragma omp simd reduction(+: fix,fiy,fiz)
#endif
for(int k = 0; k < numneighs; k++) {
int j = neighs[k];
MD_FLOAT delx = xtmp - atom_x(j);
MD_FLOAT dely = ytmp - atom_y(j);
MD_FLOAT delz = ztmp - atom_z(j);
MD_FLOAT rsq = delx * delx + dely * dely + delz * delz;
#ifdef EXPLICIT_TYPES
const int type_j = atom->type[j];
const int type_ij = type_i * atom->ntypes + type_j;
const MD_FLOAT cutforcesq = atom->cutforcesq[type_ij];
const MD_FLOAT sigma6 = atom->sigma6[type_ij];
const MD_FLOAT epsilon = atom->epsilon[type_ij];
#endif
if(rsq < cutforcesq) {
MD_FLOAT sr2 = num1 / rsq;
MD_FLOAT sr6 = sr2 * sr2 * sr2 * sigma6;
MD_FLOAT force = num48 * sr6 * (sr6 - num05) * sr2 * epsilon;
fix += delx * force;
fiy += dely * force;
fiz += delz * force;
// We do not need to update forces for ghost atoms
if(j < Nlocal) {
atom_fx(j) -= delx * force;
atom_fy(j) -= dely * force;
atom_fz(j) -= delz * force;
}
}
}
atom_fx(i) += fix;
atom_fy(i) += fiy;
atom_fz(i) += fiz;
addStat(stats->total_force_neighs, numneighs);
addStat(stats->total_force_iters, (numneighs + VECTOR_WIDTH - 1) / VECTOR_WIDTH);
}
LIKWID_MARKER_STOP("forceLJ-halfneigh");
}
double E = getTimeStamp();
return E-S;
}
double computeForceLJFullNeigh_simd(Parameter *param, Atom *atom, Neighbor *neighbor, Stats *stats) {
int Nlocal = atom->Nlocal;
int* neighs;
MD_FLOAT cutforcesq = param->cutforce * param->cutforce;
MD_FLOAT sigma6 = param->sigma6;
MD_FLOAT epsilon = param->epsilon;
for(int i = 0; i < Nlocal; i++) {
atom_fx(i) = 0.0;
atom_fy(i) = 0.0;
atom_fz(i) = 0.0;
}
double S = getTimeStamp();
#ifndef __SIMD_KERNEL__
fprintf(stderr, "Error: SIMD kernel not implemented for specified instruction set!");
exit(-1);
#else
MD_SIMD_FLOAT cutforcesq_vec = simd_broadcast(cutforcesq);
MD_SIMD_FLOAT sigma6_vec = simd_broadcast(sigma6);
MD_SIMD_FLOAT eps_vec = simd_broadcast(epsilon);
MD_SIMD_FLOAT c48_vec = simd_broadcast(48.0);
MD_SIMD_FLOAT c05_vec = simd_broadcast(0.5);
#pragma omp parallel
{
LIKWID_MARKER_START("force");
#pragma omp for schedule(runtime)
for(int i = 0; i < Nlocal; i++) {
neighs = &neighbor->neighbors[i * neighbor->maxneighs];
int numneighs = neighbor->numneigh[i];
MD_SIMD_INT numneighs_vec = simd_int_broadcast(numneighs);
MD_SIMD_FLOAT xtmp = simd_broadcast(atom_x(i));
MD_SIMD_FLOAT ytmp = simd_broadcast(atom_y(i));
MD_SIMD_FLOAT ztmp = simd_broadcast(atom_z(i));
MD_SIMD_FLOAT fix = simd_zero();
MD_SIMD_FLOAT fiy = simd_zero();
MD_SIMD_FLOAT fiz = simd_zero();
for(int k = 0; k < numneighs; k += VECTOR_WIDTH) {
// If the last iteration of this loop is separated from the rest, this mask can be set only there
MD_SIMD_MASK mask_numneighs = simd_mask_int_cond_lt(simd_int_add(simd_int_broadcast(k), simd_int_seq()), numneighs_vec);
MD_SIMD_INT j = simd_int_mask_load(&neighs[k], mask_numneighs);
#ifdef AOS
MD_SIMD_INT j3 = simd_int_add(simd_int_add(j, j), j); // j * 3
MD_SIMD_FLOAT delx = xtmp - simd_gather(j3, &(atom->x[0]), sizeof(MD_FLOAT));
MD_SIMD_FLOAT dely = ytmp - simd_gather(j3, &(atom->x[1]), sizeof(MD_FLOAT));
MD_SIMD_FLOAT delz = ztmp - simd_gather(j3, &(atom->x[2]), sizeof(MD_FLOAT));
#else
MD_SIMD_FLOAT delx = xtmp - simd_gather(j, atom->x, sizeof(MD_FLOAT));
MD_SIMD_FLOAT dely = ytmp - simd_gather(j, atom->y, sizeof(MD_FLOAT));
MD_SIMD_FLOAT delz = ztmp - simd_gather(j, atom->z, sizeof(MD_FLOAT));
#endif
MD_SIMD_FLOAT rsq = simd_fma(delx, delx, simd_fma(dely, dely, simd_mul(delz, delz)));
MD_SIMD_MASK cutoff_mask = simd_mask_and(mask_numneighs, simd_mask_cond_lt(rsq, cutforcesq_vec));
MD_SIMD_FLOAT sr2 = simd_reciprocal(rsq);
MD_SIMD_FLOAT sr6 = simd_mul(sr2, simd_mul(sr2, simd_mul(sr2, sigma6_vec)));
MD_SIMD_FLOAT force = simd_mul(c48_vec, simd_mul(sr6, simd_mul(simd_sub(sr6, c05_vec), simd_mul(sr2, eps_vec))));
fix = simd_masked_add(fix, simd_mul(delx, force), cutoff_mask);
fiy = simd_masked_add(fiy, simd_mul(dely, force), cutoff_mask);
fiz = simd_masked_add(fiz, simd_mul(delz, force), cutoff_mask);
}
atom_fx(i) += simd_h_reduce_sum(fix);
atom_fy(i) += simd_h_reduce_sum(fiy);
atom_fz(i) += simd_h_reduce_sum(fiz);
}
LIKWID_MARKER_STOP("force");
}
#endif
double E = getTimeStamp();
return E-S;
}

171
lammps/pbc.c
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@ -1,171 +0,0 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.
*/
#include <stdbool.h>
#include <stdlib.h>
#include <stdio.h>
//---
#include <pbc.h>
#include <atom.h>
#include <allocate.h>
#define DELTA 20000
int NmaxGhost;
int *PBCx, *PBCy, *PBCz;
static void growPbc(Atom*);
/* exported subroutines */
void initPbc(Atom* atom) {
NmaxGhost = 0;
atom->border_map = NULL;
PBCx = NULL; PBCy = NULL; PBCz = NULL;
}
/* update coordinates of ghost atoms */
/* uses mapping created in setupPbc */
void updatePbc_cpu(Atom *atom, Parameter *param, bool doReneighbor) {
int *border_map = atom->border_map;
int nlocal = atom->Nlocal;
MD_FLOAT xprd = param->xprd;
MD_FLOAT yprd = param->yprd;
MD_FLOAT zprd = param->zprd;
for(int i = 0; i < atom->Nghost; i++) {
atom_x(nlocal + i) = atom_x(border_map[i]) + PBCx[i] * xprd;
atom_y(nlocal + i) = atom_y(border_map[i]) + PBCy[i] * yprd;
atom_z(nlocal + i) = atom_z(border_map[i]) + PBCz[i] * zprd;
}
}
/* relocate atoms that have left domain according
* to periodic boundary conditions */
void updateAtomsPbc_cpu(Atom *atom, Parameter *param) {
MD_FLOAT xprd = param->xprd;
MD_FLOAT yprd = param->yprd;
MD_FLOAT zprd = param->zprd;
for(int i = 0; i < atom->Nlocal; i++) {
if(atom_x(i) < 0.0) {
atom_x(i) += xprd;
} else if(atom_x(i) >= xprd) {
atom_x(i) -= xprd;
}
if(atom_y(i) < 0.0) {
atom_y(i) += yprd;
} else if(atom_y(i) >= yprd) {
atom_y(i) -= yprd;
}
if(atom_z(i) < 0.0) {
atom_z(i) += zprd;
} else if(atom_z(i) >= zprd) {
atom_z(i) -= zprd;
}
}
}
/* setup periodic boundary conditions by
* defining ghost atoms around domain
* only creates mapping and coordinate corrections
* that are then enforced in updatePbc */
#define ADDGHOST(dx,dy,dz) \
Nghost++; \
border_map[Nghost] = i; \
PBCx[Nghost] = dx; \
PBCy[Nghost] = dy; \
PBCz[Nghost] = dz; \
atom->type[atom->Nlocal + Nghost] = atom->type[i]
void setupPbc(Atom *atom, Parameter *param) {
int *border_map = atom->border_map;
MD_FLOAT xprd = param->xprd;
MD_FLOAT yprd = param->yprd;
MD_FLOAT zprd = param->zprd;
MD_FLOAT Cutneigh = param->cutneigh;
int Nghost = -1;
for(int i = 0; i < atom->Nlocal; i++) {
if (atom->Nlocal + Nghost + 7 >= atom->Nmax) {
growAtom(atom);
}
if (Nghost + 7 >= NmaxGhost) {
growPbc(atom);
border_map = atom->border_map;
}
MD_FLOAT x = atom_x(i);
MD_FLOAT y = atom_y(i);
MD_FLOAT z = atom_z(i);
/* Setup ghost atoms */
/* 6 planes */
if(param->pbc_x != 0) {
if (x < Cutneigh) { ADDGHOST(+1,0,0); }
if (x >= (xprd-Cutneigh)) { ADDGHOST(-1,0,0); }
}
if(param->pbc_y != 0) {
if (y < Cutneigh) { ADDGHOST(0,+1,0); }
if (y >= (yprd-Cutneigh)) { ADDGHOST(0,-1,0); }
}
if(param->pbc_z != 0) {
if (z < Cutneigh) { ADDGHOST(0,0,+1); }
if (z >= (zprd-Cutneigh)) { ADDGHOST(0,0,-1); }
}
/* 8 corners */
if(param->pbc_x != 0 && param->pbc_y != 0 && param->pbc_z != 0) {
if (x < Cutneigh && y < Cutneigh && z < Cutneigh) { ADDGHOST(+1,+1,+1); }
if (x < Cutneigh && y >= (yprd-Cutneigh) && z < Cutneigh) { ADDGHOST(+1,-1,+1); }
if (x < Cutneigh && y < Cutneigh && z >= (zprd-Cutneigh)) { ADDGHOST(+1,+1,-1); }
if (x < Cutneigh && y >= (yprd-Cutneigh) && z >= (zprd-Cutneigh)) { ADDGHOST(+1,-1,-1); }
if (x >= (xprd-Cutneigh) && y < Cutneigh && z < Cutneigh) { ADDGHOST(-1,+1,+1); }
if (x >= (xprd-Cutneigh) && y >= (yprd-Cutneigh) && z < Cutneigh) { ADDGHOST(-1,-1,+1); }
if (x >= (xprd-Cutneigh) && y < Cutneigh && z >= (zprd-Cutneigh)) { ADDGHOST(-1,+1,-1); }
if (x >= (xprd-Cutneigh) && y >= (yprd-Cutneigh) && z >= (zprd-Cutneigh)) { ADDGHOST(-1,-1,-1); }
}
/* 12 edges */
if(param->pbc_x != 0 && param->pbc_z != 0) {
if (x < Cutneigh && z < Cutneigh) { ADDGHOST(+1,0,+1); }
if (x < Cutneigh && z >= (zprd-Cutneigh)) { ADDGHOST(+1,0,-1); }
if (x >= (xprd-Cutneigh) && z < Cutneigh) { ADDGHOST(-1,0,+1); }
if (x >= (xprd-Cutneigh) && z >= (zprd-Cutneigh)) { ADDGHOST(-1,0,-1); }
}
if(param->pbc_y != 0 && param->pbc_z != 0) {
if (y < Cutneigh && z < Cutneigh) { ADDGHOST(0,+1,+1); }
if (y < Cutneigh && z >= (zprd-Cutneigh)) { ADDGHOST(0,+1,-1); }
if (y >= (yprd-Cutneigh) && z < Cutneigh) { ADDGHOST(0,-1,+1); }
if (y >= (yprd-Cutneigh) && z >= (zprd-Cutneigh)) { ADDGHOST(0,-1,-1); }
}
if(param->pbc_x != 0 && param->pbc_y != 0) {
if (y < Cutneigh && x < Cutneigh) { ADDGHOST(+1,+1,0); }
if (y < Cutneigh && x >= (xprd-Cutneigh)) { ADDGHOST(-1,+1,0); }
if (y >= (yprd-Cutneigh) && x < Cutneigh) { ADDGHOST(+1,-1,0); }
if (y >= (yprd-Cutneigh) && x >= (xprd-Cutneigh)) { ADDGHOST(-1,-1,0); }
}
}
// increase by one to make it the ghost atom count
atom->Nghost = Nghost + 1;
}
/* internal subroutines */
void growPbc(Atom* atom) {
int nold = NmaxGhost;
NmaxGhost += DELTA;
atom->border_map = (int*) reallocate(atom->border_map, ALIGNMENT, NmaxGhost * sizeof(int), nold * sizeof(int));
PBCx = (int*) reallocate(PBCx, ALIGNMENT, NmaxGhost * sizeof(int), nold * sizeof(int));
PBCy = (int*) reallocate(PBCy, ALIGNMENT, NmaxGhost * sizeof(int), nold * sizeof(int));
PBCz = (int*) reallocate(PBCz, ALIGNMENT, NmaxGhost * sizeof(int), nold * sizeof(int));
}

2
util/gather-bench/LICENSE
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@ -1,6 +1,6 @@
MIT License
Copyright (c) 2021 RRZE-HPC
Copyright (c) RRZE-HPC
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal

2
util/gather-bench/src/main-md-trace.c
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@ -2,7 +2,7 @@
* =======================================================================================
*
* Author: Jan Eitzinger (je), jan.eitzinger@fau.de
* Copyright (c) 2021 RRZE, University Erlangen-Nuremberg
* Copyright (c) RRZE, University Erlangen-Nuremberg
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal

2
util/gather-bench/src/main-md.c
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@ -2,7 +2,7 @@
* =======================================================================================
*
* Author: Jan Eitzinger (je), jan.eitzinger@fau.de
* Copyright (c) 2021 RRZE, University Erlangen-Nuremberg
* Copyright (c) RRZE, University Erlangen-Nuremberg
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal

2
util/gather-bench/src/main.c
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@ -2,7 +2,7 @@
* =======================================================================================
*
* Author: Jan Eitzinger (je), jan.eitzinger@fau.de
* Copyright (c) 2021 RRZE, University Erlangen-Nuremberg
* Copyright (c) RRZE, University Erlangen-Nuremberg
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal

2
util/mdBench.c
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@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.

2
lammps/atom.c → verletlist/atom.c
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@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.

2
lammps/cuda/force.cu → verletlist/cuda/force.cu
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@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.

2
lammps/cuda/neighbor.cu → verletlist/cuda/neighbor.cu
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@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.

2
lammps/cuda/pbc.cu → verletlist/cuda/pbc.cu
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@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.

2
lammps/device_spec.c → verletlist/device_spec.c
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@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.

2
lammps/force_dem.c → verletlist/force_dem.c
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@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.

2
lammps/force_eam.c → verletlist/force_eam.c
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@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.

298
verletlist/force_lj.c Normal file
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@ -0,0 +1,298 @@
/*
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.
*/
#include <stdio.h>
#include <stdlib.h>
//---
#include <atom.h>
#include <likwid-marker.h>
#include <neighbor.h>
#include <parameter.h>
#include <stats.h>
#include <timing.h>
#ifdef __SIMD_KERNEL__
#include <simd.h>
#endif
double computeForceLJFullNeigh(
Parameter* param, Atom* atom, Neighbor* neighbor, Stats* stats)
{
int nLocal = atom->Nlocal;
int* neighs;
#ifndef EXPLICIT_TYPES
MD_FLOAT cutforcesq = param->cutforce * param->cutforce;
MD_FLOAT sigma6 = param->sigma6;
MD_FLOAT epsilon = param->epsilon;
#endif
const MD_FLOAT num1 = 1.0;
const MD_FLOAT num48 = 48.0;
const MD_FLOAT num05 = 0.5;
for (int i = 0; i < nLocal; i++) {
atom_fx(i) = 0.0;
atom_fy(i) = 0.0;
atom_fz(i) = 0.0;
}
double timeStart = getTimeStamp();
#pragma omp parallel
{
LIKWID_MARKER_START("force");
#pragma omp for schedule(runtime)
for (int i = 0; i < nLocal; i++) {
neighs = &neighbor->neighbors[i * neighbor->maxneighs];
int numneighs = neighbor->numneigh[i];
MD_FLOAT xtmp = atom_x(i);
MD_FLOAT ytmp = atom_y(i);
MD_FLOAT ztmp = atom_z(i);
MD_FLOAT fix = 0;
MD_FLOAT fiy = 0;
MD_FLOAT fiz = 0;
#ifdef EXPLICIT_TYPES
const int type_i = atom->type[i];
#endif
for (int k = 0; k < numneighs; k++) {
int j = neighs[k];
MD_FLOAT delx = xtmp - atom_x(j);
MD_FLOAT dely = ytmp - atom_y(j);
MD_FLOAT delz = ztmp - atom_z(j);
MD_FLOAT rsq = delx * delx + dely * dely + delz * delz;
#ifdef EXPLICIT_TYPES
const int type_j = atom->type[j];
const int type_ij = type_i * atom->ntypes + type_j;
const MD_FLOAT cutforcesq = atom->cutforcesq[type_ij];
const MD_FLOAT sigma6 = atom->sigma6[type_ij];
const MD_FLOAT epsilon = atom->epsilon[type_ij];
#endif
if (rsq < cutforcesq) {
MD_FLOAT sr2 = num1 / rsq;
MD_FLOAT sr6 = sr2 * sr2 * sr2 * sigma6;
MD_FLOAT force = num48 * sr6 * (sr6 - num05) * sr2 * epsilon;
fix += delx * force;
fiy += dely * force;
fiz += delz * force;
#ifdef USE_REFERENCE_VERSION
addStat(stats->atoms_within_cutoff, 1);
} else {
addStat(stats->atoms_outside_cutoff, 1);
#endif
}
}
atom_fx(i) += fix;
atom_fy(i) += fiy;
atom_fz(i) += fiz;
#ifdef USE_REFERENCE_VERSION
if (numneighs % VECTOR_WIDTH > 0) {
addStat(stats->atoms_outside_cutoff,
VECTOR_WIDTH - (numneighs % VECTOR_WIDTH));
}
#endif
addStat(stats->total_force_neighs, numneighs);
addStat(stats->total_force_iters,
(numneighs + VECTOR_WIDTH - 1) / VECTOR_WIDTH);
}
LIKWID_MARKER_STOP("force");
}
double timeStop = getTimeStamp();
return timeStop - timeStart;
}
double computeForceLJHalfNeigh(
Parameter* param, Atom* atom, Neighbor* neighbor, Stats* stats)
{
int nlocal = atom->Nlocal;
int* neighs;
#ifndef EXPLICIT_TYPES
MD_FLOAT cutforcesq = param->cutforce * param->cutforce;
MD_FLOAT sigma6 = param->sigma6;
MD_FLOAT epsilon = param->epsilon;
#endif
const MD_FLOAT num1 = 1.0;
const MD_FLOAT num48 = 48.0;
const MD_FLOAT num05 = 0.5;
for (int i = 0; i < nlocal; i++) {
atom_fx(i) = 0.0;
atom_fy(i) = 0.0;
atom_fz(i) = 0.0;
}
double timeStart = getTimeStamp();
#pragma omp parallel
{
LIKWID_MARKER_START("forceLJ-halfneigh");
#pragma omp for schedule(runtime)
for (int i = 0; i < nlocal; i++) {
neighs = &neighbor->neighbors[i * neighbor->maxneighs];
int numneighs = neighbor->numneigh[i];
MD_FLOAT xtmp = atom_x(i);
MD_FLOAT ytmp = atom_y(i);
MD_FLOAT ztmp = atom_z(i);
MD_FLOAT fix = 0;
MD_FLOAT fiy = 0;
MD_FLOAT fiz = 0;
#ifdef EXPLICIT_TYPES
const int type_i = atom->type[i];
#endif
// Pragma required to vectorize the inner loop
#ifdef ENABLE_OMP_SIMD
#pragma omp simd reduction(+ : fix, fiy, fiz)
#endif
for (int k = 0; k < numneighs; k++) {
int j = neighs[k];
MD_FLOAT delx = xtmp - atom_x(j);
MD_FLOAT dely = ytmp - atom_y(j);
MD_FLOAT delz = ztmp - atom_z(j);
MD_FLOAT rsq = delx * delx + dely * dely + delz * delz;
#ifdef EXPLICIT_TYPES
const int type_j = atom->type[j];
const int type_ij = type_i * atom->ntypes + type_j;
const MD_FLOAT cutforcesq = atom->cutforcesq[type_ij];
const MD_FLOAT sigma6 = atom->sigma6[type_ij];
const MD_FLOAT epsilon = atom->epsilon[type_ij];
#endif
if (rsq < cutforcesq) {
MD_FLOAT sr2 = num1 / rsq;
MD_FLOAT sr6 = sr2 * sr2 * sr2 * sigma6;
MD_FLOAT force = num48 * sr6 * (sr6 - num05) * sr2 * epsilon;
fix += delx * force;
fiy += dely * force;
fiz += delz * force;
// We do not need to update forces for ghost atoms
if (j < nlocal) {
atom_fx(j) -= delx * force;
atom_fy(j) -= dely * force;
atom_fz(j) -= delz * force;
}
}
}
atom_fx(i) += fix;
atom_fy(i) += fiy;
atom_fz(i) += fiz;
addStat(stats->total_force_neighs, numneighs);
addStat(stats->total_force_iters,
(numneighs + VECTOR_WIDTH - 1) / VECTOR_WIDTH);
}
LIKWID_MARKER_STOP("forceLJ-halfneigh");
}
double timeStop = getTimeStamp();
return timeStop - timeStart;
}
double computeForceLJFullNeigh_simd(
Parameter* param, Atom* atom, Neighbor* neighbor, Stats* stats)
{
int Nlocal = atom->Nlocal;
int* neighs;
MD_FLOAT cutforcesq = param->cutforce * param->cutforce;
MD_FLOAT sigma6 = param->sigma6;
MD_FLOAT epsilon = param->epsilon;
for (int i = 0; i < Nlocal; i++) {
atom_fx(i) = 0.0;
atom_fy(i) = 0.0;
atom_fz(i) = 0.0;
}
double S = getTimeStamp();
#ifndef __SIMD_KERNEL__
fprintf(stderr, "Error: SIMD kernel not implemented for specified instruction set!");
exit(-1);
#else
MD_SIMD_FLOAT cutforcesq_vec = simd_broadcast(cutforcesq);
MD_SIMD_FLOAT sigma6_vec = simd_broadcast(sigma6);
MD_SIMD_FLOAT eps_vec = simd_broadcast(epsilon);
MD_SIMD_FLOAT c48_vec = simd_broadcast(48.0);
MD_SIMD_FLOAT c05_vec = simd_broadcast(0.5);
#pragma omp parallel
{
LIKWID_MARKER_START("force");
#pragma omp for schedule(runtime)
for (int i = 0; i < Nlocal; i++) {
neighs = &neighbor->neighbors[i * neighbor->maxneighs];
int numneighs = neighbor->numneigh[i];
MD_SIMD_INT numneighs_vec = simd_int_broadcast(numneighs);
MD_SIMD_FLOAT xtmp = simd_broadcast(atom_x(i));
MD_SIMD_FLOAT ytmp = simd_broadcast(atom_y(i));
MD_SIMD_FLOAT ztmp = simd_broadcast(atom_z(i));
MD_SIMD_FLOAT fix = simd_zero();
MD_SIMD_FLOAT fiy = simd_zero();
MD_SIMD_FLOAT fiz = simd_zero();
for (int k = 0; k < numneighs; k += VECTOR_WIDTH) {
// If the last iteration of this loop is separated from the rest, this
// mask can be set only there
MD_SIMD_MASK mask_numneighs = simd_mask_int_cond_lt(
simd_int_add(simd_int_broadcast(k), simd_int_seq()),
numneighs_vec);
MD_SIMD_INT j = simd_int_mask_load(&neighs[k], mask_numneighs);
#ifdef AOS
MD_SIMD_INT j3 = simd_int_add(simd_int_add(j, j), j); // j * 3
MD_SIMD_FLOAT delx = xtmp -
simd_gather(j3, &(atom->x[0]), sizeof(MD_FLOAT));
MD_SIMD_FLOAT dely = ytmp -
simd_gather(j3, &(atom->x[1]), sizeof(MD_FLOAT));
MD_SIMD_FLOAT delz = ztmp -
simd_gather(j3, &(atom->x[2]), sizeof(MD_FLOAT));
#else
MD_SIMD_FLOAT delx = xtmp - simd_gather(j, atom->x, sizeof(MD_FLOAT));
MD_SIMD_FLOAT dely = ytmp - simd_gather(j, atom->y, sizeof(MD_FLOAT));
MD_SIMD_FLOAT delz = ztmp - simd_gather(j, atom->z, sizeof(MD_FLOAT));
#endif
MD_SIMD_FLOAT rsq = simd_fma(delx,
delx,
simd_fma(dely, dely, simd_mul(delz, delz)));
MD_SIMD_MASK cutoff_mask = simd_mask_and(mask_numneighs,
simd_mask_cond_lt(rsq, cutforcesq_vec));
MD_SIMD_FLOAT sr2 = simd_reciprocal(rsq);
MD_SIMD_FLOAT sr6 = simd_mul(sr2,
simd_mul(sr2, simd_mul(sr2, sigma6_vec)));
MD_SIMD_FLOAT force = simd_mul(c48_vec,
simd_mul(sr6,
simd_mul(simd_sub(sr6, c05_vec), simd_mul(sr2, eps_vec))));
fix = simd_masked_add(fix, simd_mul(delx, force), cutoff_mask);
fiy = simd_masked_add(fiy, simd_mul(dely, force), cutoff_mask);
fiz = simd_masked_add(fiz, simd_mul(delz, force), cutoff_mask);
}
atom_fx(i) += simd_h_reduce_sum(fix);
atom_fy(i) += simd_h_reduce_sum(fiy);
atom_fz(i) += simd_h_reduce_sum(fiz);
}
LIKWID_MARKER_STOP("force");
}
#endif
double E = getTimeStamp();
return E - S;
}

2
lammps/includes/atom.h → verletlist/includes/atom.h
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@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.

2
lammps/includes/integrate.h → verletlist/includes/integrate.h
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@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.

2
lammps/includes/neighbor.h → verletlist/includes/neighbor.h
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@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.

4
lammps/includes/pbc.h → verletlist/includes/pbc.h
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@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.
@ -11,7 +11,7 @@
#ifndef __PBC_H_
#define __PBC_H_
extern void initPbc();
extern void initPbc(Atom*);
extern void updatePbc_cpu(Atom*, Parameter*, bool);
extern void updateAtomsPbc_cpu(Atom*, Parameter*);
extern void setupPbc(Atom*, Parameter*);

2
lammps/includes/stats.h → verletlist/includes/stats.h
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@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.

2
lammps/includes/tracing.h → verletlist/includes/tracing.h
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@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.

2
lammps/includes/vtk.h → verletlist/includes/vtk.h
View File

@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.

2
lammps/main-stub.c → verletlist/main-stub.c
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@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.

254
lammps/main.c → verletlist/main.c
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@ -1,18 +1,16 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.
*/
#include <stdlib.h>
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <unistd.h>
#include <limits.h>
#include <math.h>
#include <float.h>
#include <omp.h>
// #include <omp.h>
#include <likwid-marker.h>
#include <allocate.h>
@ -20,20 +18,19 @@
#include <device.h>
#include <eam.h>
#include <integrate.h>
#include <thermo.h>
#include <timing.h>
#include <neighbor.h>
#include <parameter.h>
#include <pbc.h>
#include <stats.h>
#include <thermo.h>
#include <timers.h>
#include <timing.h>
#include <util.h>
#include <vtk.h>
#define HLINE "----------------------------------------------------------------------------\n"
#define HLINE "------------------------------------------------------------------\n"
extern double computeForceLJFullNeigh_plain_c(Parameter*, Atom*, Neighbor*, Stats*);
extern double computeForceLJFullNeigh_simd(Parameter*, Atom*, Neighbor*, Stats*);
extern double computeForceLJHalfNeigh(Parameter*, Atom*, Neighbor*, Stats*);
extern double computeForceEam(Eam*, Parameter*, Atom*, Neighbor*, Stats*);
extern double computeForceDemFullNeigh(Parameter*, Atom*, Neighbor*, Stats*);
@ -42,20 +39,23 @@ extern double computeForceDemFullNeigh(Parameter*, Atom*, Neighbor*, Stats*);
extern double computeForceLJFullNeigh_cuda(Parameter*, Atom*, Neighbor*);
#endif
double setup(Parameter *param, Eam *eam, Atom *atom, Neighbor *neighbor, Stats *stats) {
if(param->force_field == FF_EAM) { initEam(eam, param); }
double S, E;
double setup(Parameter* param, Eam* eam, Atom* atom, Neighbor* neighbor, Stats* stats)
{
if (param->force_field == FF_EAM) {
initEam(eam, param);
}
double timeStart, timeStop;
param->lattice = pow((4.0 / param->rho), (1.0 / 3.0));
param->xprd = param->nx * param->lattice;
param->yprd = param->ny * param->lattice;
param->zprd = param->nz * param->lattice;
param->xprd = param->nx * param->lattice;
param->yprd = param->ny * param->lattice;
param->zprd = param->nz * param->lattice;
S = getTimeStamp();
timeStart = getTimeStamp();
initAtom(atom);
initPbc(atom);
initStats(stats);
initNeighbor(neighbor, param);
if(param->input_file == NULL) {
if (param->input_file == NULL) {
createAtom(atom, param);
} else {
readAtom(atom, param);
@ -63,49 +63,59 @@ double setup(Parameter *param, Eam *eam, Atom *atom, Neighbor *neighbor, Stats *
setupNeighbor(param);
setupThermo(param, atom->Natoms);
if(param->input_file == NULL) { adjustThermo(param, atom); }
#ifdef SORT_ATOMS
if (param->input_file == NULL) {
adjustThermo(param, atom);
}
#ifdef SORT_ATOMS
atom->Nghost = 0;
sortAtom(atom);
#endif
#endif
setupPbc(atom, param);
initDevice(atom, neighbor);
updatePbc(atom, param, true);
buildNeighbor(atom, neighbor);
E = getTimeStamp();
return E-S;
timeStop = getTimeStamp();
return timeStop - timeStart;
}
double reneighbour(Parameter *param, Atom *atom, Neighbor *neighbor) {
double S, E;
S = getTimeStamp();
double reneighbour(Parameter* param, Atom* atom, Neighbor* neighbor)
{
double timeStart, timeStop;
timeStart = getTimeStamp();
LIKWID_MARKER_START("reneighbour");
updateAtomsPbc(atom, param);
#ifdef SORT_ATOMS
#ifdef SORT_ATOMS
atom->Nghost = 0;
sortAtom(atom);
#endif
#endif
setupPbc(atom, param);
updatePbc(atom, param, true);
buildNeighbor(atom, neighbor);
LIKWID_MARKER_STOP("reneighbour");
E = getTimeStamp();
return E-S;
timeStop = getTimeStamp();
return timeStop - timeStart;
}
void printAtomState(Atom *atom) {
printf("Atom counts: Natoms=%d Nlocal=%d Nghost=%d Nmax=%d\n", atom->Natoms, atom->Nlocal, atom->Nghost, atom->Nmax);
void printAtomState(Atom* atom)
{
printf("Atom counts: Natoms=%d Nlocal=%d Nghost=%d Nmax=%d\n",
atom->Natoms,
atom->Nlocal,
atom->Nghost,
atom->Nmax);
// int nall = atom->Nlocal + atom->Nghost;
// for (int i=0; i<nall; i++) {
// printf("%d %f %f %f\n", i, atom->x[i], atom->y[i], atom->z[i]);
// }
}
double computeForce(Eam *eam, Parameter *param, Atom *atom, Neighbor *neighbor, Stats *stats) {
if(param->force_field == FF_EAM) {
double computeForce(
Eam* eam, Parameter* param, Atom* atom, Neighbor* neighbor, Stats* stats)
{
if (param->force_field == FF_EAM) {
return computeForceEam(eam, param, atom, neighbor, stats);
} else if(param->force_field == FF_DEM) {
if(param->half_neigh) {
} else if (param->force_field == FF_DEM) {
if (param->half_neigh) {
fprintf(stderr, "Error: DEM cannot use half neighbor-lists!\n");
return 0.0;
} else {
@ -113,29 +123,38 @@ double computeForce(Eam *eam, Parameter *param, Atom *atom, Neighbor *neighbor,
}
}
if(param->half_neigh) {
if (param->half_neigh) {
return computeForceLJHalfNeigh(param, atom, neighbor, stats);
}
#ifdef CUDA_TARGET
#ifdef CUDA_TARGET
return computeForceLJFullNeigh(param, atom, neighbor);
#else
#else
return computeForceLJFullNeigh(param, atom, neighbor, stats);
#endif
#endif
}
void writeInput(Parameter *param, Atom *atom) {
FILE *fpin = fopen("input.in", "w");
void writeInput(Parameter* param, Atom* atom)
{
FILE* fpin = fopen("input.in", "w");
fprintf(fpin, "0,%f,0,%f,0,%f\n", param->xprd, param->yprd, param->zprd);
for(int i = 0; i < atom->Nlocal; i++) {
fprintf(fpin, "1,%f,%f,%f,%f,%f,%f\n", atom_x(i), atom_y(i), atom_z(i), atom_vx(i), atom_vy(i), atom_vz(i));
for (int i = 0; i < atom->Nlocal; i++) {
fprintf(fpin,
"1,%f,%f,%f,%f,%f,%f\n",
atom_x(i),
atom_y(i),
atom_z(i),
atom_vx(i),
atom_vy(i),
atom_vz(i));
}
fclose(fpin);
}
int main(int argc, char** argv) {
int main(int argc, char** argv)
{
double timer[NUMTIMER];
Eam eam;
Atom atom;
@ -147,81 +166,87 @@ int main(int argc, char** argv) {
#pragma omp parallel
{
LIKWID_MARKER_REGISTER("force");
//LIKWID_MARKER_REGISTER("reneighbour");
//LIKWID_MARKER_REGISTER("pbc");
// LIKWID_MARKER_REGISTER("reneighbour");
// LIKWID_MARKER_REGISTER("pbc");
}
initParameter(&param);
for(int i = 0; i < argc; i++) {
if((strcmp(argv[i], "-p") == 0) || strcmp(argv[i], "--params") == 0) {
for (int i = 0; i < argc; i++) {
if ((strcmp(argv[i], "-p") == 0) || strcmp(argv[i], "--params") == 0) {
readParameter(&param, argv[++i]);
continue;
}
if((strcmp(argv[i], "-f") == 0)) {
if((param.force_field = str2ff(argv[++i])) < 0) {
if ((strcmp(argv[i], "-f") == 0)) {
if ((param.force_field = str2ff(argv[++i])) < 0) {
fprintf(stderr, "Invalid force field!\n");
exit(-1);
}
continue;
}
if((strcmp(argv[i], "-i") == 0)) {
if ((strcmp(argv[i], "-i") == 0)) {
param.input_file = strdup(argv[++i]);
continue;
}
if((strcmp(argv[i], "-e") == 0)) {
if ((strcmp(argv[i], "-e") == 0)) {
param.eam_file = strdup(argv[++i]);
continue;
}
if((strcmp(argv[i], "-n") == 0) || (strcmp(argv[i], "--nsteps") == 0)) {
if ((strcmp(argv[i], "-n") == 0) || (strcmp(argv[i], "--nsteps") == 0)) {
param.ntimes = atoi(argv[++i]);
continue;
}
if((strcmp(argv[i], "-nx") == 0)) {
if ((strcmp(argv[i], "-nx") == 0)) {
param.nx = atoi(argv[++i]);
continue;
}
if((strcmp(argv[i], "-ny") == 0)) {
if ((strcmp(argv[i], "-ny") == 0)) {
param.ny = atoi(argv[++i]);
continue;
}
if((strcmp(argv[i], "-nz") == 0)) {
if ((strcmp(argv[i], "-nz") == 0)) {
param.nz = atoi(argv[++i]);
continue;
}
if((strcmp(argv[i], "-half") == 0)) {
if ((strcmp(argv[i], "-half") == 0)) {
param.half_neigh = atoi(argv[++i]);
continue;
}
if((strcmp(argv[i], "-r") == 0) || (strcmp(argv[i], "--radius") == 0)) {
if ((strcmp(argv[i], "-r") == 0) || (strcmp(argv[i], "--radius") == 0)) {
param.cutforce = atof(argv[++i]);
continue;
}
if((strcmp(argv[i], "-s") == 0) || (strcmp(argv[i], "--skin") == 0)) {
if ((strcmp(argv[i], "-s") == 0) || (strcmp(argv[i], "--skin") == 0)) {
param.skin = atof(argv[++i]);
continue;
}
if((strcmp(argv[i], "--freq") == 0)) {
if ((strcmp(argv[i], "--freq") == 0)) {
param.proc_freq = atof(argv[++i]);
continue;
}
if((strcmp(argv[i], "--vtk") == 0)) {
if ((strcmp(argv[i], "--vtk") == 0)) {
param.vtk_file = strdup(argv[++i]);
continue;
}
if((strcmp(argv[i], "-w") == 0)) {
if ((strcmp(argv[i], "-w") == 0)) {
param.write_atom_file = strdup(argv[++i]);
continue;
}
if((strcmp(argv[i], "-h") == 0) || (strcmp(argv[i], "--help") == 0)) {
if ((strcmp(argv[i], "-h") == 0) || (strcmp(argv[i], "--help") == 0)) {
printf("MD Bench: A minimalistic re-implementation of miniMD\n");
printf(HLINE);
printf("-p / --params <string>: file to read parameters from (can be specified more than once)\n");
printf("-f <string>: force field (lj, eam or dem), default lj\n");
printf("-i <string>: input file with atom positions (dump)\n");
printf("-p / --params <string>: file to read parameters from (can be "
"specified more than once)\n");
printf("-f <string>: force field (lj, eam or dem), "
"default lj\n");
printf("-i <string>: input file with atom positions "
"(dump)\n");
printf("-e <string>: input file for EAM\n");
printf("-n / --nsteps <int>: set number of timesteps for simulation\n");
printf("-nx/-ny/-nz <int>: set linear dimension of systembox in x/y/z direction\n");
printf("-half <int>: use half (1) or full (0) neighbor lists\n");
printf("-n / --nsteps <int>: set number of timesteps for "
"simulation\n");
printf("-nx/-ny/-nz <int>: set linear dimension of systembox in "
"x/y/z direction\n");
printf("-half <int>: use half (1) or full (0) neighbor "
"lists\n");
printf("-r / --radius <real>: set cutoff radius\n");
printf("-s / --skin <real>: set skin (verlet buffer)\n");
printf("-w <file>: write input atoms to file\n");
@ -239,48 +264,48 @@ int main(int argc, char** argv) {
printf("step\ttemp\t\tpressure\n");
computeThermo(0, &param, &atom);
#if defined(MEM_TRACER) || defined(INDEX_TRACER)
#if defined(MEM_TRACER) || defined(INDEX_TRACER)
traceAddresses(&param, &atom, &neighbor, n + 1);
#endif
#endif
if(param.write_atom_file != NULL) {
if (param.write_atom_file != NULL) {
writeAtom(&atom, &param);
}
//writeInput(&param, &atom);
// writeInput(&param, &atom);
timer[FORCE] = computeForce(&eam, &param, &atom, &neighbor, &stats);
timer[NEIGH] = 0.0;
timer[TOTAL] = getTimeStamp();
if(param.vtk_file != NULL) {
if (param.vtk_file != NULL) {
write_atoms_to_vtk_file(param.vtk_file, &atom, 0);
}
for(int n = 0; n < param.ntimes; n++) {
for (int n = 0; n < param.ntimes; n++) {
bool reneigh = (n + 1) % param.reneigh_every == 0;
initialIntegrate(reneigh, &param, &atom);
if((n + 1) % param.reneigh_every) {
if ((n + 1) % param.reneigh_every) {
updatePbc(&atom, &param, false);
} else {
timer[NEIGH] += reneighbour(&param, &atom, &neighbor);
}
#if defined(MEM_TRACER) || defined(INDEX_TRACER)
#if defined(MEM_TRACER) || defined(INDEX_TRACER)
traceAddresses(&param, &atom, &neighbor, n + 1);
#endif
#endif
timer[FORCE] += computeForce(&eam, &param, &atom, &neighbor, &stats);
finalIntegrate(reneigh, &param, &atom);
if(!((n + 1) % param.nstat) && (n+1) < param.ntimes) {
#ifdef CUDA_TARGET
if (!((n + 1) % param.nstat) && (n + 1) < param.ntimes) {
#ifdef CUDA_TARGET
memcpyFromGPU(atom.x, atom.d_atom.x, atom.Nmax * sizeof(MD_FLOAT) * 3);
#endif
#endif
computeThermo(n + 1, &param, &atom);
}
if(param.vtk_file != NULL) {
if (param.vtk_file != NULL) {
write_atoms_to_vtk_file(param.vtk_file, &atom, n + 1);
}
}
@ -289,36 +314,49 @@ int main(int argc, char** argv) {
computeThermo(-1, &param, &atom);
printf(HLINE);
printf("System: %d atoms %d ghost atoms, Steps: %d\n", atom.Natoms, atom.Nghost, param.ntimes);
printf("System: %d atoms %d ghost atoms, Steps: %d\n",
atom.Natoms,
atom.Nghost,
param.ntimes);
printf("TOTAL %.2fs FORCE %.2fs NEIGH %.2fs REST %.2fs\n",
timer[TOTAL], timer[FORCE], timer[NEIGH], timer[TOTAL]-timer[FORCE]-timer[NEIGH]);
timer[TOTAL],
timer[FORCE],
timer[NEIGH],
timer[TOTAL] - timer[FORCE] - timer[NEIGH]);
printf(HLINE);
int nthreads = 0;
int chunkSize = 0;
omp_sched_t schedKind;
char schedType[10];
#pragma omp parallel
#pragma omp master
{
omp_get_schedule(&schedKind, &chunkSize);
switch (schedKind)
{
case omp_sched_static: strcpy(schedType, "static"); break;
case omp_sched_dynamic: strcpy(schedType, "dynamic"); break;
case omp_sched_guided: strcpy(schedType, "guided"); break;
case omp_sched_auto: strcpy(schedType, "auto"); break;
}
nthreads = omp_get_max_threads();
}
printf("Num threads: %d\n", nthreads);
printf("Schedule: (%s,%d)\n", schedType, chunkSize);
// int nthreads = 0;
// int chunkSize = 0;
// omp_sched_t schedKind;
// char schedType[10];
// #pragma omp parallel
// #pragma omp master
// {
// omp_get_schedule(&schedKind, &chunkSize);
//
// switch (schedKind) {
// case omp_sched_static:
// strcpy(schedType, "static");
// break;
// case omp_sched_dynamic:
// strcpy(schedType, "dynamic");
// break;
// case omp_sched_guided:
// strcpy(schedType, "guided");
// break;
// case omp_sched_auto:
// strcpy(schedType, "auto");
// break;
// }
//
// nthreads = omp_get_max_threads();
// }
//
// printf("Num threads: %d\n", nthreads);
// printf("Schedule: (%s,%d)\n", schedType, chunkSize);
printf("Performance: %.2f million atom updates per second\n",
1e-6 * (double) atom.Natoms * param.ntimes / timer[TOTAL]);
1e-6 * (double)atom.Natoms * param.ntimes / timer[TOTAL]);
#ifdef COMPUTE_STATS
displayStatistics(&atom, &param, &stats, timer);
#endif

2
lammps/neighbor.c → verletlist/neighbor.c
View File

@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.

234
verletlist/pbc.c Normal file
View File

@ -0,0 +1,234 @@
/*
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.
*/
#include <stdbool.h>
#include <stdio.h>
#include <stdlib.h>
//---
#include <allocate.h>
#include <atom.h>
#include <pbc.h>
#define DELTA 20000
int nmaxGhost;
int *PBCx, *PBCy, *PBCz;
static void growPbc(Atom*);
/* exported subroutines */
void initPbc(Atom* atom)
{
nmaxGhost = 0;
atom->border_map = NULL;
PBCx = NULL;
PBCy = NULL;
PBCz = NULL;
}
/* update coordinates of ghost atoms */
/* uses mapping created in setupPbc */
void updatePbc_cpu(Atom* atom, Parameter* param, bool doReneighbor)
{
int* borderMap = atom->border_map;
int nlocal = atom->Nlocal;
MD_FLOAT xprd = param->xprd;
MD_FLOAT yprd = param->yprd;
MD_FLOAT zprd = param->zprd;
for (int i = 0; i < atom->Nghost; i++) {
atom_x(nlocal + i) = atom_x(borderMap[i]) + PBCx[i] * xprd;
atom_y(nlocal + i) = atom_y(borderMap[i]) + PBCy[i] * yprd;
atom_z(nlocal + i) = atom_z(borderMap[i]) + PBCz[i] * zprd;
}
}
/* relocate atoms that have left domain according
* to periodic boundary conditions */
void updateAtomsPbc_cpu(Atom* atom, Parameter* param)
{
MD_FLOAT xprd = param->xprd;
MD_FLOAT yprd = param->yprd;
MD_FLOAT zprd = param->zprd;
for (int i = 0; i < atom->Nlocal; i++) {
if (atom_x(i) < 0.0) {
atom_x(i) += xprd;
} else if (atom_x(i) >= xprd) {
atom_x(i) -= xprd;
}
if (atom_y(i) < 0.0) {
atom_y(i) += yprd;
} else if (atom_y(i) >= yprd) {
atom_y(i) -= yprd;
}
if (atom_z(i) < 0.0) {
atom_z(i) += zprd;
} else if (atom_z(i) >= zprd) {
atom_z(i) -= zprd;
}
}
}
/* setup periodic boundary conditions by
* defining ghost atoms around domain
* only creates mapping and coordinate corrections
* that are then enforced in updatePbc */
#define ADDGHOST(dx, dy, dz) \
Nghost++; \
border_map[Nghost] = i; \
PBCx[Nghost] = dx; \
PBCy[Nghost] = dy; \
PBCz[Nghost] = dz; \
atom->type[atom->Nlocal + Nghost] = atom->type[i]
void setupPbc(Atom* atom, Parameter* param)
{
int* border_map = atom->border_map;
MD_FLOAT xprd = param->xprd;
MD_FLOAT yprd = param->yprd;
MD_FLOAT zprd = param->zprd;
MD_FLOAT cutneigh = param->cutneigh;
int Nghost = -1;
for (int i = 0; i < atom->Nlocal; i++) {
if (atom->Nlocal + Nghost + 7 >= atom->Nmax) {
growAtom(atom);
}
if (Nghost + 7 >= nmaxGhost) {
growPbc(atom);
border_map = atom->border_map;
}
MD_FLOAT x = atom_x(i);
MD_FLOAT y = atom_y(i);
MD_FLOAT z = atom_z(i);
/* Setup ghost atoms */
/* 6 planes */
if (param->pbc_x != 0) {
if (x < cutneigh) {
ADDGHOST(+1, 0, 0);
}
if (x >= (xprd - cutneigh)) {
ADDGHOST(-1, 0, 0);
}
}
if (param->pbc_y != 0) {
if (y < cutneigh) {
ADDGHOST(0, +1, 0);
}
if (y >= (yprd - cutneigh)) {
ADDGHOST(0, -1, 0);
}
}
if (param->pbc_z != 0) {
if (z < cutneigh) {
ADDGHOST(0, 0, +1);
}
if (z >= (zprd - cutneigh)) {
ADDGHOST(0, 0, -1);
}
}
/* 8 corners */
if (param->pbc_x != 0 && param->pbc_y != 0 && param->pbc_z != 0) {
if (x < cutneigh && y < cutneigh && z < cutneigh) {
ADDGHOST(+1, +1, +1);
}
if (x < cutneigh && y >= (yprd - cutneigh) && z < cutneigh) {
ADDGHOST(+1, -1, +1);
}
if (x < cutneigh && y < cutneigh && z >= (zprd - cutneigh)) {
ADDGHOST(+1, +1, -1);
}
if (x < cutneigh && y >= (yprd - cutneigh) && z >= (zprd - cutneigh)) {
ADDGHOST(+1, -1, -1);
}
if (x >= (xprd - cutneigh) && y < cutneigh && z < cutneigh) {
ADDGHOST(-1, +1, +1);
}
if (x >= (xprd - cutneigh) && y >= (yprd - cutneigh) && z < cutneigh) {
ADDGHOST(-1, -1, +1);
}
if (x >= (xprd - cutneigh) && y < cutneigh && z >= (zprd - cutneigh)) {
ADDGHOST(-1, +1, -1);
}
if (x >= (xprd - cutneigh) && y >= (yprd - cutneigh) &&
z >= (zprd - cutneigh)) {
ADDGHOST(-1, -1, -1);
}
}
/* 12 edges */
if (param->pbc_x != 0 && param->pbc_z != 0) {
if (x < cutneigh && z < cutneigh) {
ADDGHOST(+1, 0, +1);
}
if (x < cutneigh && z >= (zprd - cutneigh)) {
ADDGHOST(+1, 0, -1);
}
if (x >= (xprd - cutneigh) && z < cutneigh) {
ADDGHOST(-1, 0, +1);
}
if (x >= (xprd - cutneigh) && z >= (zprd - cutneigh)) {
ADDGHOST(-1, 0, -1);
}
}
if (param->pbc_y != 0 && param->pbc_z != 0) {
if (y < cutneigh && z < cutneigh) {
ADDGHOST(0, +1, +1);
}
if (y < cutneigh && z >= (zprd - cutneigh)) {
ADDGHOST(0, +1, -1);
}
if (y >= (yprd - cutneigh) && z < cutneigh) {
ADDGHOST(0, -1, +1);
}
if (y >= (yprd - cutneigh) && z >= (zprd - cutneigh)) {
ADDGHOST(0, -1, -1);
}
}
if (param->pbc_x != 0 && param->pbc_y != 0) {
if (y < cutneigh && x < cutneigh) {
ADDGHOST(+1, +1, 0);
}
if (y < cutneigh && x >= (xprd - cutneigh)) {
ADDGHOST(-1, +1, 0);
}
if (y >= (yprd - cutneigh) && x < cutneigh) {
ADDGHOST(+1, -1, 0);
}
if (y >= (yprd - cutneigh) && x >= (xprd - cutneigh)) {
ADDGHOST(-1, -1, 0);
}
}
}
// increase by one to make it the ghost atom count
atom->Nghost = Nghost + 1;
}
/* internal subroutines */
void growPbc(Atom* atom)
{
int nold = nmaxGhost;
nmaxGhost += DELTA;
atom->border_map = (int*)reallocate(atom->border_map,
ALIGNMENT,
nmaxGhost * sizeof(int),
nold * sizeof(int));
PBCx = (int*)reallocate(PBCx, ALIGNMENT, nmaxGhost * sizeof(int), nold * sizeof(int));
PBCy = (int*)reallocate(PBCy, ALIGNMENT, nmaxGhost * sizeof(int), nold * sizeof(int));
PBCz = (int*)reallocate(PBCz, ALIGNMENT, nmaxGhost * sizeof(int), nold * sizeof(int));
}

2
lammps/stats.c → verletlist/stats.c
View File

@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.

2
lammps/tracing.c → verletlist/tracing.c
View File

@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.

2
lammps/vtk.c → verletlist/vtk.c
View File

@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.