include(gmxCFlags)
gmx_c_flags()
-# This variable should be used for additional compiler flags which are not
-# generated in gmxCFlags nor are SIMD or MPI related.
+# These variables should be used for CMake-style lists (ie. separated
+# by semicolons) of additional compiler flags which are not generated
+# in gmxCFlags nor are SIMD or MPI related.
#
# TODO These variables should be consolidated into
# EXTRA_COMPILER_FLAGS so that we we don't perpetrate bugs where
# things that work in C compilation (e.g. merging from old branches)
-# also work for C++ compilation.
+# might not also work for C++ compilation.
set(EXTRA_C_FLAGS "")
set(EXTRA_CXX_FLAGS "")
# Our own GROMACS tests
########################################################################
-add_definitions( -DHAVE_CONFIG_H )
include_directories(BEFORE ${CMAKE_SOURCE_DIR}/src)
-# TODO required at high level because both libgromacs and progs/mdrun
-# require it, both for thread-MPI and its atomics and mutexes.
-include_directories(BEFORE SYSTEM ${CMAKE_SOURCE_DIR}/src/external/thread_mpi/include)
# Required for config.h, maybe should only be set in src/CMakeLists.txt
include_directories(BEFORE ${CMAKE_BINARY_DIR}/src)
# # # # # # # # # # NO MORE TESTS AFTER THIS LINE! # # # # # # # # # # #
# these are set after everything else
if (NOT GMX_SKIP_DEFAULT_CFLAGS)
- set(CMAKE_C_FLAGS "${SIMD_C_FLAGS} ${MPI_COMPILE_FLAGS} ${EXTRA_C_FLAGS} ${CMAKE_C_FLAGS}")
- set(CMAKE_CXX_FLAGS "${SIMD_CXX_FLAGS} ${MPI_COMPILE_FLAGS} ${EXTRA_CXX_FLAGS} ${CMAKE_CXX_FLAGS}")
set(CMAKE_EXE_LINKER_FLAGS "${FFT_LINKER_FLAGS} ${MPI_LINKER_FLAGS} ${CMAKE_EXE_LINKER_FLAGS}")
set(CMAKE_SHARED_LINKER_FLAGS "${FFT_LINKER_FLAGS} ${MPI_LINKER_FLAGS} ${CMAKE_SHARED_LINKER_FLAGS}")
else()
message("Recommended flags which are not added because GMX_SKIP_DEFAULT_CFLAGS=yes:")
- message("CMAKE_C_FLAGS: ${SIMD_C_FLAGS} ${MPI_COMPILE_FLAGS} ${EXTRA_C_FLAGS} ${GMXC_CFLAGS}")
- message("CMAKE_C_FLAGS_RELEASE: ${GMXC_CFLAGS_RELEASE}")
- message("CMAKE_C_FLAGS_DEBUG: ${GMXC_CFLAGS_DEBUG}")
- message("CMAKE_CXX_FLAGS: ${SIMD_CXX_FLAGS} ${MPI_COMPILE_FLAGS} ${EXTRA_CXX_FLAGS} ${GMXC_CXXFLAGS}")
- message("CMAKE_CXX_FLAGS_RELEASE: ${GMXC_CXXFLAGS_RELEASE}")
- message("CMAKE_CXX_FLAGS_DEBUG: ${GMXC_CXXFLAGS_DEBUG}")
+ message("CMAKE_C_FLAGS: ${SIMD_C_FLAGS};${MPI_COMPILE_FLAGS};${EXTRA_C_FLAGS};${GMXC_CFLAGS}")
+ foreach(build_type ${build_types_with_explicit_flags})
+ message("CMAKE_C_FLAGS_${build_type}: ${GMXC_CFLAGS_${build_type}}")
+ endforeach()
+ message("CMAKE_CXX_FLAGS: ${SIMD_CXX_FLAGS};${MPI_COMPILE_FLAGS};${EXTRA_CXX_FLAGS};${GMXC_CXXFLAGS}")
+ foreach(build_type ${build_types_with_explicit_flags})
+ message("CMAKE_CXX_FLAGS_${build_type}: ${GMXC_CXXFLAGS_${build_type}}")
+ endforeach()
message("CMAKE_EXE_LINKER_FLAGS: ${FFT_LINKER_FLAGS} ${MPI_LINKER_FLAGS}")
message("CMAKE_SHARED_LINKER_FLAGS: ${FFT_LINKER_FLAGS} ${MPI_LINKER_FLAGS}")
endif()
CHECK_C_COMPILER_FLAG("${FLAGS}" ${VARIABLE})
ENDIF()
IF (${VARIABLE})
- SET (${CFLAGSVAR} "${FLAGS} ${${CFLAGSVAR}}")
+ list(APPEND ${CFLAGSVAR} "${FLAGS}")
ENDIF ()
ENDMACRO(GMX_TEST_CFLAG VARIABLE FLAGS CFLAGSVAR)
CHECK_CXX_COMPILER_FLAG("${FLAGS}" ${VARIABLE})
ENDIF()
IF (${VARIABLE})
- SET (${CXXFLAGSVAR} "${FLAGS} ${${CXXFLAGSVAR}}")
+ list(APPEND ${CXXFLAGSVAR} "${FLAGS}")
ENDIF ()
ENDMACRO(GMX_TEST_CXXFLAG VARIABLE FLAGS CXXFLAGSVAR)
# inconvenient in CMake to pass more than one list, and such a
# list is only used here.
foreach(build_type RELWITHDEBINFO RELWITHASSERT MINSIZEREL PROFILE)
- set(GMXC_${language}FLAGS_${build_type} "${GMXC_${language}FLAGS_RELEASE} ${GMXC_${language}FLAGS_${build_type}}")
+ set(GMXC_${language}FLAGS_${build_type} "${GMXC_${language}FLAGS_RELEASE}" "${GMXC_${language}FLAGS_${build_type}}")
endforeach()
# Copy the flags that are only used by the real Release build
# type. Used for, e.g., -Wno-array-bounds in Release to work around
# while using RelWithAssert (ie. without that suppression) in Jenkins.
#
# TODO check the behaviour of more recent gcc on the improved code
- set(GMXC_${language}FLAGS_RELEASE "${GMXC_${language}FLAGS_RELEASE} ${GMXC_${language}FLAGS_RELEASE_ONLY}")
-
- # Modify the real CMake variables for compiler flags for all
- # builds and language types, and also those common to all
- # build types.
- foreach(build_type "" ${build_types_with_explicit_flags})
- if("${build_type}" STREQUAL "")
- set(punctuation "") # for general compiler flags (e.g.) CMAKE_CXX_FLAGS
- else()
- set(punctuation "_") # for build-type-specific compiler flags (e.g.) CMAKE_CXX_FLAGS_RELEASE
- endif()
+ set(GMXC_${language}FLAGS_RELEASE "${GMXC_${language}FLAGS_RELEASE}" "${GMXC_${language}FLAGS_RELEASE_ONLY}")
+ endforeach()
+endfunction()
- # Append to the variables for the given build type for
- # each language, in the parent scope. We add our new variables at the end, so
- # compiler-specific choices are more likely to override default CMake choices.
- # This is for instance useful for RelWithDebInfo builds, where we want to use the full
- # set of our optimization flags detected in this file, rather than having -O2 override them.
- set(CMAKE_${language}_FLAGS${punctuation}${build_type}
- "${CMAKE_${language}_FLAGS${punctuation}${build_type}} ${GMXC_${language}FLAGS${punctuation}${build_type}}"
- PARENT_SCOPE)
+# Add compiler flags expected for all GROMACS build configurations,
+# and those expected for the current CMake build type (e.g. Release)
+# to TARGET.
+#
+# Most targets (ie. libraries, executables) need compiler flags that
+# are characteristic of the build configuration. This function
+# provides a central point for adding such flags. This approach is
+# more flexible than e.g. setting CMAKE_CXX_FLAGS globally, because
+# that setting will apply globally, which means it applies also to
+# "external" code that the build of GROMACS might also build.
+function(gmx_target_compile_options TARGET)
+ if (NOT GMX_SKIP_DEFAULT_CFLAGS)
+ target_compile_options(${TARGET}
+ PRIVATE
+ $<$<COMPILE_LANGUAGE:C>:${SIMD_C_FLAGS};${MPI_COMPILE_FLAGS};${EXTRA_C_FLAGS};${GMXC_CFLAGS}>
+ $<$<COMPILE_LANGUAGE:CXX>:${SIMD_CXX_FLAGS};${MPI_COMPILE_FLAGS};${EXTRA_CXX_FLAGS};${GMXC_CXXFLAGS}>
+ )
+ foreach(build_type ${build_types_with_explicit_flags})
+ target_compile_options(${TARGET}
+ BEFORE PRIVATE
+ $<$<AND:$<COMPILE_LANGUAGE:C>,$<CONFIG:${build_type}>>:${GMXC_CFLAGS_${build_type}}>
+ $<$<AND:$<COMPILE_LANGUAGE:CXX>,$<CONFIG:${build_type}>>:${GMXC_CXXFLAGS_${build_type}}>
+ )
endforeach()
- endforeach()
+ endif()
endfunction()
+# Add the WARNING_FLAG to the compile options for TARGET if the
+# compiler supports that flag. VARNAME is used to cache the result of
+# the check whether the compiler supports that flag, as multiple
+# targets may use the same suppression.
+#
+# This is generally used to suppress warnings judged not worth fixing
+# in code external to, or generated by, GROMACS.
function(gmx_target_warning_suppression TARGET WARNING_FLAG VARNAME)
check_cxx_compiler_flag(${WARNING_FLAG} ${VARNAME})
if(${VARNAME})
GMX_TEST_CFLAG(CFLAGS_PRAGMA "-Wno-unknown-pragmas" GMXC_CFLAGS)
endif()
if (GMX_COMPILER_WARNINGS)
- GMX_TEST_CFLAG(CFLAGS_WARN "-Wall -Wno-unused -Wunused-value -Wunused-parameter" GMXC_CFLAGS)
- GMX_TEST_CFLAG(CFLAGS_WARN_EXTRA "-Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith" GMXC_CFLAGS)
+ GMX_TEST_CFLAG(CFLAGS_WARN "-Wall;-Wno-unused;-Wunused-value;-Wunused-parameter" GMXC_CFLAGS)
+ GMX_TEST_CFLAG(CFLAGS_WARN_EXTRA "-Wextra;-Wno-missing-field-initializers;-Wno-sign-compare;-Wpointer-arith" GMXC_CFLAGS)
GMX_TEST_CFLAG(CFLAGS_WARN_UNDEF "-Wundef" GMXC_CFLAGS)
GMX_TEST_CFLAG(CFLAGS_WARN_REL "-Wno-array-bounds" GMXC_CFLAGS_RELEASE_ONLY)
if(CYGWIN)
GMX_TEST_CXXFLAG(CXXFLAGS_WARN "-Wall" GMXC_CXXFLAGS)
# Problematic with CUDA
# GMX_TEST_CXXFLAG(CXXFLAGS_WARN_EFFCXX "-Wnon-virtual-dtor" GMXC_CXXFLAGS)
- GMX_TEST_CXXFLAG(CXXFLAGS_WARN_EXTRA "-Wextra -Wno-missing-field-initializers -Wpointer-arith -Wmissing-declarations" GMXC_CXXFLAGS)
+ GMX_TEST_CXXFLAG(CXXFLAGS_WARN_EXTRA "-Wextra;-Wno-missing-field-initializers;-Wpointer-arith;-Wmissing-declarations" GMXC_CXXFLAGS)
# CUDA versions prior to 7.5 come with a header (math_functions.h) which uses the _MSC_VER macro
# unconditionally, so we don't use -Wundef for earlier CUDA versions.
if(NOT(GMX_GPU AND CUDA_VERSION VERSION_LESS "7.5"))
#3280: declaration hides member ".."
#11074: Inlining inhibited by limit max-size(/max-total-size)
#11076: To get full report use -opt-report=3 -opt-report-phase ipo (shown for previous remark)
- GMX_TEST_CFLAG(CFLAGS_WARN "-w3 -wd177 -wd411 -wd593 -wd981 -wd1418 -wd1419 -wd1572 -wd1599 -wd2259 -wd2415 -wd2547 -wd2557 -wd3280 -wd11074 -wd11076" GMXC_CFLAGS)
+ GMX_TEST_CFLAG(CFLAGS_WARN "-w3;-wd177;-wd411;-wd593;-wd981;-wd1418;-wd1419;-wd1572;-wd1599;-wd2259;-wd2415;-wd2547;-wd2557;-wd3280;-wd11074;-wd11076" GMXC_CFLAGS)
endif()
GMX_TEST_CFLAG(CFLAGS_STDGNU "-std=gnu99" GMXC_CFLAGS)
- GMX_TEST_CFLAG(CFLAGS_OPT "-ip -funroll-all-loops -alias-const -ansi-alias -no-prec-div -fimf-domain-exclusion=14 -qoverride-limits" GMXC_CFLAGS_RELEASE)
+ GMX_TEST_CFLAG(CFLAGS_OPT "-ip;-funroll-all-loops;-alias-const;-ansi-alias;-no-prec-div;-fimf-domain-exclusion=14;-qoverride-limits" GMXC_CFLAGS_RELEASE)
GMX_TEST_CFLAG(CFLAGS_DEBUG "-O0" GMXC_CFLAGS_DEBUG) #icc defaults to -O2 even with -g
- GMX_TEST_CFLAG(CFLAGS_FP_RELASSERT "-fp-model except -fp-model precise" GMXC_CFLAGS_RELWITHASSERT)
+ # The "except" fp-model requires something other than the
+ # default "fast" model, so we test and use it with
+ # "precise".
+ GMX_TEST_CFLAG(CFLAGS_FP_MODEL_RELASSERT "-fp-model=except;-fp-model=precise" GMXC_CFLAGS_RELWITHASSERT)
else()
if(NOT GMX_OPENMP)
GMX_TEST_CFLAG(CFLAGS_PRAGMA "/wd3180" GMXC_CFLAGS)
#only on Windows
#161: unrecognized pragma
#1786 function was declared deprecated (is issued for stdlib function such as strncpy which have a _s version)
-GMX_TEST_CFLAG(CFLAGS_WARN "/W3 /wd161 /wd177 /wd411 /wd593 /wd981 /wd1418 /wd1419 /wd1572 /wd1599 /wd1786 /wd2259 /wd2415 /wd2547 /wd2557 /wd3280" GMXC_CFLAGS)
+GMX_TEST_CFLAG(CFLAGS_WARN "/W3;/wd161;/wd177;/wd411;/wd593;/wd981;/wd1418;/wd1419;/wd1572;/wd1599;/wd1786;/wd2259;/wd2415;/wd2547;/wd2557;/wd3280" GMXC_CFLAGS)
endif()
GMX_TEST_CFLAG(CFLAGS_OPT "/Qip" GMXC_CFLAGS_RELEASE)
endif()
# 444: destructor for base class ".." is not virtual
# 869: was never referenced (false positives)
#2282: unrecognized GCC pragma
- GMX_TEST_CXXFLAG(CXXFLAGS_WARN "-w3 -wd177 -wd304 -wd383 -wd411 -wd444 -wd869 -wd981 -wd1418 -wd1572 -wd1599 -wd2259 -wd2547 -wd3280 -wd11074 -wd11076 -wd2282" GMXC_CXXFLAGS)
+ GMX_TEST_CXXFLAG(CXXFLAGS_WARN "-w3;-wd177;-wd304;-wd383;-wd411;-wd444;-wd869;-wd981;-wd1418;-wd1572;-wd1599;-wd2259;-wd2547;-wd3280;-wd11074;-wd11076;-wd2282" GMXC_CXXFLAGS)
endif()
- GMX_TEST_CXXFLAG(CXXFLAGS_OPT "-ip -funroll-all-loops -alias-const -ansi-alias -no-prec-div -fimf-domain-exclusion=14 -qoverride-limits" GMXC_CXXFLAGS_RELEASE)
+ GMX_TEST_CXXFLAG(CXXFLAGS_OPT "-ip;-funroll-all-loops;-alias-const;-ansi-alias;-no-prec-div;-fimf-domain-exclusion=14;-qoverride-limits" GMXC_CXXFLAGS_RELEASE)
GMX_TEST_CXXFLAG(CXXFLAGS_DEBUG "-O0" GMXC_CXXFLAGS_DEBUG)
- GMX_TEST_CXXFLAG(CXXFLAGS_FP_RELASSERT "-fp-model except -fp-model precise" GMXC_CXXFLAGS_RELWITHASSERT)
+ # The "except" fp-model requires something other than the
+ # default "fast" model, so we test and use it with
+ # "precise".
+ GMX_TEST_CXXFLAG(CXXFLAGS_FP_MODEL_RELASSERT "-fp-model=except;-fp-model=precise" GMXC_CXXFLAGS_RELWITHASSERT)
else()
if(NOT GMX_OPENMP)
GMX_TEST_CXXFLAG(CXXFLAGS_PRAGMA "/wd3180" GMXC_CFLAGS)
if (GMX_COMPILER_WARNINGS)
#161: unrecognized pragma
#809: exception specification for virtual function X is incompatible with that of overridden function
- GMX_TEST_CXXFLAG(CXXFLAGS_WARN "/W3 /wd161 /wd177 /wd304 /wd383 /wd411 /wd444 /wd809 /wd869 /wd981 /wd1418 /wd1572 /wd1599 /wd1786 /wd2259 /wd2547 /wd3280 /wd11074 /wd11076 /wd2282" GMXC_CXXFLAGS)
+ GMX_TEST_CXXFLAG(CXXFLAGS_WARN "/W3;/wd161;/wd177;/wd304;/wd383;/wd411;/wd444;/wd809;/wd869;/wd981;/wd1418;/wd1572;/wd1599;/wd1786;/wd2259;/wd2547;/wd3280;/wd11074;/wd11076;/wd2282" GMXC_CXXFLAGS)
endif()
GMX_TEST_CXXFLAG(CXXFLAGS_OPT "/Qip" GMXC_CXXFLAGS_RELEASE)
endif()
GMX_TEST_CFLAG(CFLAGS_PRAGMA "-Wno-unknown-pragmas" GMXC_CFLAGS)
endif()
if (GMX_COMPILER_WARNINGS)
- GMX_TEST_CFLAG(CFLAGS_WARN "-Wall -Wno-unused -Wunused-value" GMXC_CFLAGS)
+ GMX_TEST_CFLAG(CFLAGS_WARN "-Wall;-Wno-unused;-Wunused-value" GMXC_CFLAGS)
endif()
- GMX_TEST_CFLAG(CFLAGS_OPT "-OPT:Ofast -fno-math-errno -ffast-math"
+ GMX_TEST_CFLAG(CFLAGS_OPT "-OPT:Ofast;-fno-math-errno;-ffast-math"
GMXC_CFLAGS_RELEASE)
GMX_TEST_CFLAG(CFLAGS_LANG "-std=gnu99" GMXC_CFLAGS)
endif()
GMX_TEST_CXXFLAG(CXXFLAGS_PRAGMA "-Wno-unknown-pragmas" GMXC_CXXFLAGS)
endif()
if (GMX_COMPILER_WARNINGS)
- GMX_TEST_CXXFLAG(CXXFLAGS_WARN "-Wall -Wno-unused -Wunused-value" GMXC_CXXFLAGS)
+ GMX_TEST_CXXFLAG(CXXFLAGS_WARN "-Wall;-Wno-unused;-Wunused-value" GMXC_CXXFLAGS)
endif()
- GMX_TEST_CXXFLAG(CXXFLAGS_OPT "-OPT:Ofast -fno-math-errno -ffast-math"
+ GMX_TEST_CXXFLAG(CXXFLAGS_OPT "-OPT:Ofast;-fno-math-errno;-ffast-math"
GMXC_CXXFLAGS_RELEASE)
endif()
# 1500-010: (W) about correct PBC-related use of maximum array indices of DIM-sized C arrays
# 1500-030: (I) Additional optimization may be attained by recompiling and specifying MAXMEM option with a value greater than 8192.
if (CMAKE_C_COMPILER_ID MATCHES "XL")
- GMX_TEST_CFLAG(CFLAGS_ARCH "-qarch=auto -qtune=auto" GMXC_CFLAGS)
+ GMX_TEST_CFLAG(CFLAGS_ARCH "-qarch=auto;-qtune=auto" GMXC_CFLAGS)
GMX_TEST_CFLAG(CFLAGS_OPT "-O3" GMXC_CFLAGS_RELEASE)
GMX_TEST_CFLAG(CFLAGS_LANG "-qlanglvl=extc99" GMXC_CFLAGS)
- GMX_TEST_CFLAG(CFLAGS_LANG "-qsuppress=1500-036 -qsuppress=1500-010 -qsuppress=1500-030" GMXC_CFLAGS)
+ GMX_TEST_CFLAG(CFLAGS_LANG "-qsuppress=1500-036;-qsuppress=1500-010;-qsuppress=1500-030" GMXC_CFLAGS)
endif()
if (CMAKE_CXX_COMPILER_ID MATCHES "XL")
- GMX_TEST_CXXFLAG(CXXFLAGS_ARCH "-qarch=auto -qtune=auto" GMXC_CXXFLAGS)
+ GMX_TEST_CXXFLAG(CXXFLAGS_ARCH "-qarch=auto;-qtune=auto" GMXC_CXXFLAGS)
GMX_TEST_CXXFLAG(CXXFLAGS_OPT "-O3" GMXC_CXXFLAGS_RELEASE)
- GMX_TEST_CXXFLAG(CXXFLAGS_LANG "-qsuppress=1500-036 -qsuppress=1500-010 -qsuppress=1500-030" GMXC_CXXFLAGS)
+ GMX_TEST_CXXFLAG(CXXFLAGS_LANG "-qsuppress=1500-036;-qsuppress=1500-010;-qsuppress=1500-030" GMXC_CXXFLAGS)
endif()
# msvc
# forcing value to bool
# "this" in initializer list
# deprecated (posix, secure) functions
- # truncation (double -> float)
- # conversion from 'double' to 'real', possible loss of data
+ # C4305: truncation (double -> float)
+ # C4244: conversion from 'double' to 'real', possible loss of data
# unreferenced local variable (only C)
- # conversion from 'size_t' to 'int', possible loss of data
+ # C4267: conversion from 'size_t' to 'int', possible loss of data
# conversion from 'const char*' to 'void*', different 'const' qualifiers (only C)
# unknown pragma (4068)
if(NOT CMAKE_CONFIGURATION_TYPES)
- GMX_TEST_CFLAG(CFLAGS_WARN "/wd4800 /wd4355 /wd4996 /wd4305 /wd4244 /wd4101 /wd4267 /wd4090 /wd4068" GMXC_CFLAGS)
- GMX_TEST_CXXFLAG(CXXFLAGS_WARN "/wd4800 /wd4355 /wd4996 /wd4305 /wd4244 /wd4267 /wd4068" GMXC_CXXFLAGS)
+ GMX_TEST_CFLAG(CFLAGS_WARN "/wd4800;/wd4355;/wd4996;/wd4305;/wd4244;/wd4101;/wd4267;/wd4090;/wd4068" GMXC_CFLAGS)
+ GMX_TEST_CXXFLAG(CXXFLAGS_WARN "/wd4800;/wd4355;/wd4996;/wd4305;/wd4244;/wd4267;/wd4068" GMXC_CXXFLAGS)
else() # MSVC projects only use the C++ flags
- GMX_TEST_CXXFLAG(CXXFLAGS_WARN "/wd4800 /wd4355 /wd4996 /wd4305 /wd4244 /wd4101 /wd4267 /wd4090 /wd4068" GMXC_CXXFLAGS)
+ GMX_TEST_CXXFLAG(CXXFLAGS_WARN "/wd4800;/wd4355;/wd4996;/wd4305;/wd4244;/wd4101;/wd4267;/wd4090;/wd4068" GMXC_CXXFLAGS)
endif()
endif()
GMX_TEST_CFLAG(CFLAGS_PRAGMA "-Wno-unknown-pragmas" GMXC_CFLAGS)
endif()
if (GMX_COMPILER_WARNINGS)
- GMX_TEST_CFLAG(CFLAGS_WARN "-Wall -Wno-unused -Wunused-value -Wunused-parameter" GMXC_CFLAGS)
+ GMX_TEST_CFLAG(CFLAGS_WARN "-Wall;-Wno-unused;-Wunused-value;-Wunused-parameter" GMXC_CFLAGS)
GMX_TEST_CFLAG(CFLAGS_WARN_EXTRA "-Wpointer-arith" GMXC_CFLAGS_EXTRA)
endif()
endif()
if (CMAKE_CXX_COMPILER_ID MATCHES "Clang")
- if(NOT GMX_OPENMP)
- GMX_TEST_CXXFLAG(CXXFLAGS_PRAGMA "-Wno-unknown-pragmas" GMXC_CXXFLAGS)
- endif()
if (GMX_COMPILER_WARNINGS)
+ # If used, -Wall should precede other options that silence warnings it enables
+ GMX_TEST_CXXFLAG(CXXFLAGS_WARN "-Wall" GMXC_CXXFLAGS)
if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS "6.0") #LLVM BUG #21629
GMX_TEST_CXXFLAG(CXXFLAGS_WARN_NO_BRACES "-Wno-missing-braces" GMXC_CXXFLAGS)
endif()
- GMX_TEST_CXXFLAG(CXXFLAGS_WARN "-Wall" GMXC_CXXFLAGS)
- GMX_TEST_CXXFLAG(CXXFLAGS_WARN_EXTRA "-Wextra -Wno-missing-field-initializers -Wpointer-arith -Wmissing-prototypes" GMXC_CXXFLAGS)
+ GMX_TEST_CXXFLAG(CXXFLAGS_WARN_EXTRA "-Wextra;-Wno-missing-field-initializers;-Wpointer-arith;-Wmissing-prototypes" GMXC_CXXFLAGS)
GMX_TEST_CXXFLAG(CXXFLAGS_DEPRECATED "-Wdeprecated" GMXC_CXXFLAGS)
endif()
+ if(NOT GMX_OPENMP)
+ GMX_TEST_CXXFLAG(CXXFLAGS_PRAGMA "-Wno-unknown-pragmas" GMXC_CXXFLAGS)
+ endif()
endif()
# Fujitsu compilers on PrimeHPC/Sparc64
if(${CMAKE_C_COMPILER_ID} MATCHES Fujitsu OR
(${CMAKE_C_COMPILER_ID} MATCHES unknown AND ${CMAKE_C_COMPILER} MATCHES ^fcc))
- GMX_TEST_CFLAG(CFLAG_GNUCOMPAT "-Xg -w" GMXC_CFLAGS)
- GMX_TEST_CFLAG(CFLAG_OPT "-Kfast,reduction,swp,simd=2,uxsimd,fsimple -x100" GMXC_CFLAGS)
+ GMX_TEST_CFLAG(CFLAG_GNUCOMPAT "-Xg;-w" GMXC_CFLAGS)
+ GMX_TEST_CFLAG(CFLAG_OPT "-Kfast,reduction,swp,simd=2,uxsimd,fsimple;-x100" GMXC_CFLAGS)
endif()
if(${CMAKE_CXX_COMPILER_ID} MATCHES Fujitsu OR
(${CMAKE_CXX_COMPILER_ID} MATCHES unknown AND ${CMAKE_CXX_COMPILER} MATCHES ^FCC))
- GMX_TEST_CXXFLAG(CXXFLAG_GNUCOMPAT "-Xg -w" GMXC_CXXFLAGS)
- GMX_TEST_CXXFLAG(CXXFLAG_OPT "-Kfast,reduction,swp,simd=2,uxsimd,fsimple -x100" GMXC_CXXFLAGS)
+ GMX_TEST_CXXFLAG(CXXFLAG_GNUCOMPAT "-Xg;-w" GMXC_CXXFLAGS)
+ GMX_TEST_CXXFLAG(CXXFLAG_OPT "-Kfast,reduction,swp,simd=2,uxsimd,fsimple;-x100" GMXC_CXXFLAGS)
endif()
# now actually set the flags:
endif()
# Some versions of icc require this in order that mkl.h can be
# found at compile time.
- set(EXTRA_C_FLAGS "${EXTRA_C_FLAGS} ${FFT_LINKER_FLAGS}")
- set(EXTRA_CXX_FLAGS "${EXTRA_CXX_FLAGS} ${FFT_LINKER_FLAGS}")
+ list(APPEND EXTRA_C_FLAGS ${FFT_LINKER_FLAGS})
+ list(APPEND EXTRA_CXX_FLAGS ${FFT_LINKER_FLAGS})
set(MKL_ERROR_MESSAGE "Make sure you have configured your compiler so that ${FFT_LINKER_FLAGS} will work.")
else()
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2012,2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+# Copyright (c) 2012,2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
gmx_give_fatal_error_when_simd_support_not_found("SSE2" "disable SIMD support (slow)" "${SUGGEST_BINUTILS_UPDATE}")
endif()
- set(SIMD_C_FLAGS "${SIMD_SSE2_C_FLAGS}")
- set(SIMD_CXX_FLAGS "${SIMD_SSE2_CXX_FLAGS}")
+ # If multiple flags are neeed, make them into a list
+ string(REPLACE " " ";" SIMD_C_FLAGS ${SIMD_SSE2_C_FLAGS})
+ string(REPLACE " " ";" SIMD_CXX_FLAGS ${SIMD_SSE2_CXX_FLAGS})
set(GMX_SIMD_X86_${GMX_SIMD_ACTIVE} 1)
set(SIMD_STATUS_MESSAGE "Enabling SSE2 SIMD instructions using CXX flags: ${SIMD_SSE2_CXX_FLAGS}")
gmx_give_fatal_error_when_simd_support_not_found("SSE4.1" "choose SSE2 SIMD (slower)" "${SUGGEST_BINUTILS_UPDATE}")
endif()
- set(SIMD_C_FLAGS "${SIMD_SSE4_1_C_FLAGS}")
- set(SIMD_CXX_FLAGS "${SIMD_SSE4_1_CXX_FLAGS}")
+ # If multiple flags are neeed, make them into a list
+ string(REPLACE " " ";" SIMD_C_FLAGS ${SIMD_SSE4_1_C_FLAGS})
+ string(REPLACE " " ";" SIMD_CXX_FLAGS ${SIMD_SSE4_1_CXX_FLAGS})
set(GMX_SIMD_X86_SSE4_1 1)
set(SIMD_STATUS_MESSAGE "Enabling SSE4.1 SIMD instructions using CXX flags: ${SIMD_SSE4_1_CXX_FLAGS}")
gmx_give_fatal_error_when_simd_support_not_found("128-bit AVX with FMA support" "choose SSE4.1 SIMD (slower)" "${SUGGEST_BINUTILS_UPDATE}")
endif()
- set(SIMD_C_FLAGS "${SIMD_AVX_128_FMA_C_FLAGS}")
- set(SIMD_CXX_FLAGS "${SIMD_AVX_128_FMA_CXX_FLAGS}")
+ # If multiple flags are neeed, make them into a list
+ string(REPLACE " " ";" SIMD_C_FLAGS ${SIMD_AVX_128_FMA_C_FLAGS})
+ string(REPLACE " " ";" SIMD_CXX_FLAGS ${SIMD_AVX_128_FMA_CXX_FLAGS})
set(GMX_SIMD_X86_${GMX_SIMD_ACTIVE} 1)
set(SIMD_STATUS_MESSAGE "Enabling 128-bit AMD FMA SIMD instructions using CXX flags: ${SIMD_AVX_128_FMA_CXX_FLAGS}")
gmx_give_fatal_error_when_simd_support_not_found("AVX" "choose SSE4.1 SIMD (slower)" "${SUGGEST_BINUTILS_UPDATE}")
endif()
- set(SIMD_C_FLAGS "${SIMD_AVX_C_FLAGS}")
- set(SIMD_CXX_FLAGS "${SIMD_AVX_CXX_FLAGS}")
+ # If multiple flags are neeed, make them into a list
+ string(REPLACE " " ";" SIMD_C_FLAGS ${SIMD_AVX_C_FLAGS})
+ string(REPLACE " " ";" SIMD_CXX_FLAGS ${SIMD_AVX_CXX_FLAGS})
set(GMX_SIMD_X86_${GMX_SIMD_ACTIVE} 1)
set(SIMD_STATUS_MESSAGE "Enabling 256-bit AVX SIMD instructions using CXX flags: ${SIMD_AVX_CXX_FLAGS}")
gmx_give_fatal_error_when_simd_support_not_found("AVX2" "choose AVX SIMD (slower)" "${SUGGEST_BINUTILS_UPDATE}")
endif()
- set(SIMD_C_FLAGS "${SIMD_AVX2_C_FLAGS}")
- set(SIMD_CXX_FLAGS "${SIMD_AVX2_CXX_FLAGS}")
+ # If multiple flags are neeed, make them into a list
+ string(REPLACE " " ";" SIMD_C_FLAGS ${SIMD_AVX2_C_FLAGS})
+ string(REPLACE " " ";" SIMD_CXX_FLAGS ${SIMD_AVX2_CXX_FLAGS})
set(GMX_SIMD_X86_${GMX_SIMD_ACTIVE} 1)
if(GMX_SIMD_ACTIVE STREQUAL "AVX2_128")
gmx_give_fatal_error_when_simd_support_not_found("AVX 512F" "choose a lower level of SIMD (slower)" "${SUGGEST_BINUTILS_UPDATE}")
endif()
- set(SIMD_C_FLAGS "${SIMD_AVX_512_C_FLAGS}")
- set(SIMD_CXX_FLAGS "${SIMD_AVX_512_CXX_FLAGS}")
+ # If multiple flags are neeed, make them into a list
+ string(REPLACE " " ";" SIMD_C_FLAGS ${SIMD_AVX_512_C_FLAGS})
+ string(REPLACE " " ";" SIMD_CXX_FLAGS ${SIMD_AVX_512_CXX_FLAGS})
set(GMX_SIMD_X86_${GMX_SIMD_ACTIVE} 1)
set(SIMD_STATUS_MESSAGE "Enabling 512-bit AVX-512 SIMD instructions using CXX flags: ${SIMD_AVX_512_CXX_FLAGS}")
gmx_give_fatal_error_when_simd_support_not_found("AVX 512ER" "choose a lower level of SIMD (slower)" "${SUGGEST_BINUTILS_UPDATE}")
endif()
- set(SIMD_C_FLAGS "${SIMD_AVX_512_KNL_C_FLAGS}")
- set(SIMD_CXX_FLAGS "${SIMD_AVX_512_KNL_CXX_FLAGS}")
+ # If multiple flags are neeed, make them into a list
+ string(REPLACE " " ";" SIMD_C_FLAGS ${SIMD_AVX_512_KNL_C_FLAGS})
+ string(REPLACE " " ";" SIMD_CXX_FLAGS ${SIMD_AVX_512_KNL_CXX_FLAGS})
set(GMX_SIMD_X86_${GMX_SIMD_ACTIVE} 1)
set(SIMD_STATUS_MESSAGE "Enabling 512-bit AVX-512-KNL SIMD instructions using CXX flags: ${SIMD_AVX_512_KNL_CXX_FLAGS}")
gmx_give_fatal_error_when_simd_support_not_found("ARM NEON" "disable SIMD support (slower)" "${SUGGEST_BINUTILS_UPDATE}")
endif()
- set(SIMD_C_FLAGS "${SIMD_ARM_NEON_C_FLAGS}")
- set(SIMD_CXX_FLAGS "${SIMD_ARM_NEON_CXX_FLAGS}")
+ # If multiple flags are neeed, make them into a list
+ string(REPLACE " " ";" SIMD_C_FLAGS ${SIMD_ARM_NEON_C_FLAGS})
+ string(REPLACE " " ";" SIMD_CXX_FLAGS ${SIMD_ARM_NEON_CXX_FLAGS})
set(GMX_SIMD_${GMX_SIMD_ACTIVE} 1)
set(SIMD_STATUS_MESSAGE "Enabling 32-bit ARM NEON SIMD instructions using CXX flags: ${SIMD_ARM_NEON_CXX_FLAGS}")
gmx_give_fatal_error_when_simd_support_not_found("ARM (AArch64) NEON Advanced SIMD" "particularly gcc version 4.9 or later, or disable SIMD support (slower)" "${SUGGEST_BINUTILS_UPDATE}")
endif()
- set(SIMD_C_FLAGS "${SIMD_ARM_NEON_ASIMD_C_FLAGS}")
- set(SIMD_CXX_FLAGS "${SIMD_ARM_NEON_ASIMD_CXX_FLAGS}")
+ # If multiple flags are neeed, make them into a list
+ string(REPLACE " " ";" SIMD_C_FLAGS ${SIMD_ARM_NEON_ASIMD_C_FLAGS})
+ string(REPLACE " " ";" SIMD_CXX_FLAGS ${SIMD_ARM_NEON_ASIMD_CXX_FLAGS})
set(GMX_SIMD_${GMX_SIMD_ACTIVE} 1)
set(SIMD_STATUS_MESSAGE "Enabling ARM (AArch64) NEON Advanced SIMD instructions using CXX flags: ${SIMD_ARM_NEON_ASIMD_CXX_FLAGS}")
gmx_give_fatal_error_when_simd_support_not_found("IBM VMX" "disable SIMD support (slower)" "${SUGGEST_BINUTILS_UPDATE}")
endif()
- set(SIMD_C_FLAGS "${SIMD_IBM_VMX_C_FLAGS}")
- set(SIMD_CXX_FLAGS "${SIMD_IBM_VMX_CXX_FLAGS}")
+ # If multiple flags are neeed, make them into a list
+ string(REPLACE " " ";" SIMD_C_FLAGS ${SIMD_IBM_VMX_C_FLAGS})
+ string(REPLACE " " ";" SIMD_CXX_FLAGS ${SIMD_IBM_VMX_CXX_FLAGS})
set(GMX_SIMD_${GMX_SIMD_ACTIVE} 1)
set(SIMD_STATUS_MESSAGE "Enabling IBM VMX SIMD instructions using CXX flags: ${SIMD_IBM_VMX_CXX_FLAGS}")
gmx_give_fatal_error_when_simd_support_not_found("IBM VSX" "disable SIMD support (slower)" "${SUGGEST_BINUTILS_UPDATE}")
endif()
- set(SIMD_C_FLAGS "${SIMD_IBM_VSX_C_FLAGS}")
- set(SIMD_CXX_FLAGS "${SIMD_IBM_VSX_CXX_FLAGS}")
+ # If multiple flags are neeed, make them into a list
+ string(REPLACE " " ";" SIMD_C_FLAGS ${SIMD_IBM_VSX_C_FLAGS})
+ string(REPLACE " " ";" SIMD_CXX_FLAGS ${SIMD_IBM_VSX_CXX_FLAGS})
set(GMX_SIMD_${GMX_SIMD_ACTIVE} 1)
set(SIMD_STATUS_MESSAGE "Enabling IBM VSX SIMD instructions using CXX flags: ${SIMD_IBM_VSX_CXX_FLAGS}")
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2016, by the GROMACS development team, led by
+# Copyright (c) 2016,2019, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
include(${BUNDLED_TNG_LOCATION}/BuildTNG.cmake)
add_tng_io_library(tng_io OBJECT ${_zlib_arg})
add_library(tng_io::tng_io ALIAS tng_io)
+ gmx_target_compile_options(tng_io_obj)
target_link_libraries(libgromacs PRIVATE $<BUILD_INTERFACE:tng_io::tng_io>)
endif()
endif()
# the research papers on the package. Check out http://www.gromacs.org.
add_executable(template template.cpp)
+if (WIN32)
+ gmx_target_warning_suppression(template /wd4244 HAS_NO_MSVC_LOSSY_CONVERSION_DOUBLE_TO_REAL)
+ gmx_target_warning_suppression(template /wd4267 HAS_NO_MSVC_LOSSY_CONVERSION_SIZE_T_TO_INT)
+endif()
target_link_libraries(template libgromacs ${GMX_EXE_LINKER_FLAGS})
set(DOCUMENTATION_HTTP_URL_BASE
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2011,2012,2013,2014,2015,2019, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
AnalysisTemplate::initAnalysis(const TrajectoryAnalysisSettings &settings,
const TopologyInformation & /*top*/)
{
- nb_.setCutoff(cutoff_);
+ nb_.setCutoff(static_cast<real>(cutoff_));
data_.setColumnCount(0, sel_.size());
if(GMX_USE_CUDA)
if(NOT GMX_CLANG_CUDA)
GMX_SET_CUDA_NVCC_FLAGS()
+ # Source files generated by NVCC can include gmxmpi.h, and so
+ # need access to thread-MPI.
+ set(CUDA_INCLUDE_DIRS ${PROJECT_SOURCE_DIR}/src/external/thread_mpi/include)
endif()
get_cuda_compiler_info(CUDA_COMPILER_INFO CUDA_COMPILER_FLAGS)
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2018, by the GROMACS development team, led by
+# Copyright (c) 2018,2019, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
system.cpp
version.cpp
workflow.cpp)
+gmx_target_compile_options(gmxapi)
+target_compile_definitions(gmxapi PRIVATE HAVE_CONFIG_H)
+target_include_directories(gmxapi SYSTEM BEFORE PRIVATE ${PROJECT_SOURCE_DIR}/src/external/thread_mpi/include)
# Define public interface. Make sure targets linking against `gmxapi` in the build
# system don't accidentally have the implementation headers (this directory))
list(APPEND GMOCK_COMPILE_DEFINITIONS "GTEST_HAS_PTHREAD=0")
set(GTEST_IS_THREADSAFE 0)
endif()
+if (WIN32)
+ list(APPEND GMOCK_COMPILE_DEFINITIONS _SILENCE_TR1_NAMESPACE_DEPRECATION_WARNING)
+endif()
set(GMOCK_DIR ${CMAKE_CURRENT_SOURCE_DIR}/googlemock)
set(GTEST_DIR ${CMAKE_CURRENT_SOURCE_DIR}/googletest)
add_library(gmock STATIC ${UNITTEST_TARGET_OPTIONS} ${GMOCK_SOURCES} ${GTEST_SOURCES})
set_property(TARGET gmock APPEND PROPERTY COMPILE_DEFINITIONS
- "_GNU_SOURCE=1;${GMOCK_COMPILE_DEFINITIONS};GTEST_CAN_STREAM_RESULTS=0")
+ "_GNU_SOURCE=1;${GMOCK_COMPILE_DEFINITIONS};GTEST_CAN_STREAM_RESULTS=0")
set_property(TARGET gmock APPEND PROPERTY COMPILE_FLAGS "${GMOCK_COMPILE_FLAGS}")
set(GMOCK_LIBRARIES gmock ${PTHREADS_LIBRARIES} PARENT_SCOPE)
add_subdirectory(topology)
add_subdirectory(trajectory)
add_subdirectory(utility)
-add_subdirectory(fileio)
add_subdirectory(swap)
add_subdirectory(essentialdynamics)
add_subdirectory(pulling)
add_subdirectory(statistics)
add_subdirectory(analysisdata)
add_subdirectory(coordinateio)
- add_subdirectory(selection)
add_subdirectory(trajectoryanalysis)
add_subdirectory(energyanalysis)
add_subdirectory(tools)
#target_link_libraries(gmx ${GMX_EXTRA_LIBRARIES} ${THREAD_MPI_LIB})
tmpi_get_source_list(THREAD_MPI_SOURCES ${PROJECT_SOURCE_DIR}/src/external/thread_mpi/src)
add_library(thread_mpi OBJECT ${THREAD_MPI_SOURCES})
+target_compile_definitions(thread_mpi PRIVATE HAVE_CONFIG_H)
+gmx_target_compile_options(thread_mpi)
+if (WIN32)
+ gmx_target_warning_suppression(thread_mpi /wd4996 HAS_NO_MSVC_UNSAFE_FUNCTION)
+endif()
list(APPEND libgromacs_object_library_dependencies thread_mpi)
configure_file(version.h.cmakein version.h)
# This code is here instead of utility/CMakeLists.txt, because CMake
# custom commands and source file properties can only be set in the directory
# that contains the target that uses them.
-# TODO: Generate a header instead that can be included from baseversion.c.
+# TODO: Generate a header instead that can be included from baseversion.cpp.
# That probably simplifies things somewhat.
set(GENERATED_VERSION_FILE utility/baseversion-gen.cpp)
gmx_configure_version_file(
add_library(libgromacs ${LIBGROMACS_SOURCES})
endif()
+add_subdirectory(fileio)
+if (NOT GMX_BUILD_MDRUN_ONLY)
+ add_subdirectory(selection)
+endif()
+
# Handle the object libraries that contain the source file
# dependencies that need special handling because they are generated
# or external code.
# Add the sources from the object libraries to the main library.
target_sources(libgromacs PRIVATE $<TARGET_OBJECTS:${object_library}>)
endforeach()
+gmx_target_compile_options(libgromacs)
+target_compile_definitions(libgromacs PRIVATE HAVE_CONFIG_H)
+target_include_directories(libgromacs SYSTEM BEFORE PRIVATE ${PROJECT_SOURCE_DIR}/src/external/thread_mpi/include)
if (GMX_USE_OPENCL)
option(GMX_EXTERNAL_CLFFT "True if an external clFFT is required to be used" FALSE)
//! Returns the number of columns included in this set.
int columnCount() const
{
- return values().size();
+ return ssize(values());
}
//! Returns zero-based index of the last column included in this set (inclusive).
int lastColumn() const
*/
int pointSetCount() const
{
- return pointSets_.size();
+ return ssize(pointSets_);
}
/*! \brief
* Returns point set reference for a given point set.
corner[d] -= corner[ZZ]*box[ZZ][d]/box[ZZ][ZZ];
}
/* Apply the triclinic couplings */
- assert(ddbox->npbcdim <= DIM);
- for (i = YY; i < ddbox->npbcdim; i++)
+ for (i = YY; i < ddbox->npbcdim && i < DIM; i++)
{
for (j = XX; j < i; j++)
{
spline->n = n;
}
+// At run time, the values of order used and asserted upon mean that
+// indexing out of bounds does not occur. However compilers don't
+// always understand that, so we suppress this warning for this code
+// region.
+#pragma GCC diagnostic push
+#pragma GCC diagnostic ignored "-Warray-bounds"
+
/* Macro to force loop unrolling by fixing order.
* This gives a significant performance gain.
*/
}
}
+#pragma GCC diagnostic pop
+
/* This has to be a macro to enable full compiler optimization with xlC (and probably others too) */
#define DO_BSPLINE(order) \
for (ithx = 0; (ithx < (order)); ithx++) \
file(GLOB FILEIO_SOURCES *.cpp)
+target_sources(libgromacs PRIVATE ${FILEIO_SOURCES})
+
if(GMX_USE_PLUGINS)
add_library(vmddlopen OBJECT ${CMAKE_SOURCE_DIR}/src/external/vmd_molfile/vmddlopen.cpp)
+ gmx_target_compile_options(vmddlopen)
if (WIN32)
gmx_target_warning_suppression(vmddlopen /wd4996 HAS_NO_MSVC_UNSAFE_FUNCTION)
endif()
set(libgromacs_object_library_dependencies ${libgromacs_object_library_dependencies} PARENT_SCOPE)
endif()
-set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${FILEIO_SOURCES} PARENT_SCOPE)
-
gmx_install_headers(
confio.h
enxio.h
${LINEARALGEBRA_SOURCES} ${BLAS_SOURCES} ${LAPACK_SOURCES})
add_library(linearalgebra OBJECT ${LINEARALGEBRA_SOURCES})
+gmx_target_compile_options(linearalgebra)
+target_compile_definitions(linearalgebra PRIVATE HAVE_CONFIG_H)
# The linearalgebra code is all considered external, and we will
# not keep it free of warnings. Any compiler suppressions required
# should be added here.
posA *= pbc->box[m][m];
posB *= pbc->box[m][m];
assert(npbcdim <= DIM);
- for (d = m+1; d < npbcdim; d++)
+ for (d = m+1; d < npbcdim && d < DIM; d++)
{
posA += pos0A[d]*pbc->box[d][m];
posB += pos0B[d]*pbc->box[d][m];
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016,2018, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2018,2019, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
static inline real series_sinhx(real x)
{
real x2 = x*x;
- return (1 + (x2/6.0)*(1 + (x2/20.0)*(1 + (x2/42.0)*(1 + (x2/72.0)*(1 + (x2/110.0))))));
+ return (1 + (x2/6.0_real)*(1 + (x2/20.0_real)*(1 + (x2/42.0_real)*(1 + (x2/72.0_real)*(1 + (x2/110.0_real))))));
}
/*! \brief Inverse error function, double precision.
static inline void copy_dvec_to_rvec(const dvec a, rvec b)
{
- b[XX] = a[XX];
- b[YY] = a[YY];
- b[ZZ] = a[ZZ];
+ b[XX] = static_cast<real>(a[XX]);
+ b[YY] = static_cast<real>(a[YY]);
+ b[ZZ] = static_cast<real>(a[ZZ]);
}
static inline void copy_rvecn(const rvec *a, rvec *b, int startn, int endn)
ipab = ipa*ipb;
if (ipab > 0)
{
- cosval = ip*gmx::invsqrt(ipab); /* 7 */
+ cosval = static_cast<real>(ip*gmx::invsqrt(ipab)); /* 7 */
}
else
{
file(GLOB SCANNER_SOURCES scanner.cpp parser.cpp)
list(REMOVE_ITEM SELECTION_SOURCES ${SCANNER_SOURCES})
# Add the non-generated sources to libgromacs, so that they have only the normal warning suppressions
-set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${SELECTION_SOURCES} PARENT_SCOPE)
+target_sources(libgromacs PRIVATE ${SELECTION_SOURCES})
add_library(scanner OBJECT ${SCANNER_SOURCES})
+gmx_target_compile_options(scanner)
+target_compile_definitions(scanner PRIVATE HAVE_CONFIG_H)
# Compilers give lots of warnings on these generated files. These
# are awkward to suppress inline, so we do it in the compilation
# command (after testing that the compiler supports the
else()
gmx_target_warning_suppression(scanner -Wno-unused HAS_NO_UNUSED)
gmx_target_warning_suppression(scanner -Wno-unused-parameter HAS_NO_UNUSED_PARAMETER)
- gmx_target_warning_suppression(scanner -Wno-missing-declarartions HAS_NO_MISSING_DECLARATIONS)
+ gmx_target_warning_suppression(scanner -Wno-missing-declarations HAS_NO_MISSING_DECLARATIONS)
gmx_target_warning_suppression(scanner -wd1419 HAS_DECL_IN_SOURCE)
endif()
list(APPEND libgromacs_object_library_dependencies scanner)
* Initializes positions from a vector of position vectors.
*/
AnalysisNeighborhoodPositions(const std::vector<RVec> &x)
- : count_(x.size()), index_(-1), x_(as_rvec_array(x.data())),
+ : count_(ssize(x)), index_(-1), x_(as_rvec_array(x.data())),
exclusionIds_(nullptr), indices_(nullptr)
{
}
AnalysisNeighborhoodPositions &
indexed(ArrayRef<const int> indices)
{
- count_ = indices.size();
+ count_ = ssize(indices);
indices_ = indices.data();
return *this;
}
/*! \brief Returns the number of blocks */
int numBlocks() const
{
- return index_.size() - 1;
+ return static_cast<int>(index_.size() - 1);
}
/*! \brief Returns the size of the block with index \p blockIndex */
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2018,2019, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
GMX_ASSERT(iparams.size() == functype.size(), "Parameters and function types go together");
- return functype.size();
+ return gmx::ssize(functype);
}
/* TODO: Consider merging functype and iparams, either by storing
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2018,2019, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/* Returns the total number of elements in iatoms */
int size() const
{
- return iatoms.size();
+ return gmx::ssize(iatoms);
}
/* List of interactions, see explanation further down */
*
* \param[in] group Integer value for the group type.
*/
- int numberOfGroupNumbers(SimulationAtomGroupType group) const { return groupNumbers[group].size(); }
+ int numberOfGroupNumbers(SimulationAtomGroupType group) const { return gmx::ssize(groupNumbers[group]); }
};
/*! \brief
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2018,2019, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*
* This factor leads to 4 realloc calls to double the array size.
*/
-constexpr float OVER_ALLOC_FAC = 1.19;
+constexpr float OVER_ALLOC_FAC = 1.19F;
/*! \brief
* Turns over allocation for variable size atoms/cg/top arrays on or off,
file(GLOB MDRUN_SOURCES mdrun/*.cpp)
# make an "object library" that we can re-use for multiple targets
add_library(mdrun_objlib OBJECT ${MDRUN_SOURCES})
+gmx_target_compile_options(mdrun_objlib)
+target_compile_definitions(mdrun_objlib PRIVATE HAVE_CONFIG_H)
+target_include_directories(mdrun_objlib SYSTEM BEFORE PRIVATE ${PROJECT_SOURCE_DIR}/src/external/thread_mpi/include)
if(GMX_FAHCORE)
# The lack of a real source file here alongside the object library
target_link_libraries(fahcore PRIVATE ${GMX_COMMON_LIBRARIES})
elseif(GMX_BUILD_MDRUN_ONLY)
add_executable(mdrun $<TARGET_OBJECTS:mdrun_objlib> mdrun_main.cpp)
+ gmx_target_compile_options(mdrun)
+ target_compile_definitions(mdrun PRIVATE HAVE_CONFIG_H)
target_link_libraries(mdrun libgromacs
${GMX_COMMON_LIBRARIES}
${GMX_EXE_LINKER_FLAGS})
file(GLOB VIEW_SOURCES view/view.cpp)
endif()
add_library(view_objlib OBJECT ${VIEW_SOURCES})
+ gmx_target_compile_options(view_objlib)
+ target_compile_definitions(view_objlib PRIVATE HAVE_CONFIG_H)
add_executable(gmx
${GMX_MAIN_SOURCES}
$<TARGET_OBJECTS:mdrun_objlib>
$<TARGET_OBJECTS:view_objlib>)
+ gmx_target_compile_options(gmx)
+ target_compile_definitions(gmx PRIVATE HAVE_CONFIG_H)
target_link_libraries(gmx libgromacs
${GMX_COMMON_LIBRARIES}
${GMX_EXE_LINKER_FLAGS})
trajectorycomparison.cpp
trajectoryreader.cpp
)
+gmx_target_compile_options(mdrun_test_objlib)
+target_compile_definitions(mdrun_test_objlib PRIVATE HAVE_CONFIG_H)
+target_include_directories(mdrun_test_objlib SYSTEM BEFORE PRIVATE ${PROJECT_SOURCE_DIR}/src/external/thread_mpi/include)
set(testname "MdrunTests")
set(exename "mdrun-test")
endif()
add_library(testutils STATIC ${UNITTEST_TARGET_OPTIONS} ${TESTUTILS_SOURCES})
+gmx_target_compile_options(testutils)
+target_compile_definitions(testutils PRIVATE HAVE_CONFIG_H)
+target_include_directories(testutils SYSTEM BEFORE PRIVATE ${PROJECT_SOURCE_DIR}/src/external/thread_mpi/include)
set(TESTUTILS_LIBS testutils)
set_property(TARGET testutils APPEND PROPERTY COMPILE_DEFINITIONS "${GMOCK_COMPILE_DEFINITIONS}")
set_property(TARGET testutils APPEND PROPERTY COMPILE_FLAGS "${GMOCK_COMPILE_FLAGS}")
function (gmx_add_unit_test_object_library NAME)
if (GMX_BUILD_UNITTESTS AND BUILD_TESTING)
- include_directories(BEFORE SYSTEM ${GMOCK_INCLUDE_DIRS})
add_library(${NAME} OBJECT ${UNITTEST_TARGET_OPTIONS} ${ARGN})
- set_property(TARGET ${NAME} APPEND PROPERTY COMPILE_DEFINITIONS "${GMOCK_COMPILE_DEFINITIONS}")
- set_property(TARGET ${NAME} APPEND PROPERTY COMPILE_FLAGS "${GMOCK_COMPILE_FLAGS}")
+ gmx_target_compile_options(${NAME})
+ target_compile_options(${NAME} PRIVATE "${GMOCK_COMPILE_FLAGS}")
+ target_compile_definitions(${NAME} PRIVATE HAVE_CONFIG_H "${GMOCK_COMPILE_DEFINITIONS}")
+ target_include_directories(${NAME} SYSTEM BEFORE PRIVATE ${PROJECT_SOURCE_DIR}/src/external/thread_mpi/include ${GMOCK_INCLUDE_DIRS})
endif()
endfunction ()
include_directories(BEFORE SYSTEM ${GMOCK_INCLUDE_DIRS})
add_executable(${EXENAME} ${UNITTEST_TARGET_OPTIONS}
${_source_files} ${TESTUTILS_DIR}/unittest_main.cpp)
- target_link_libraries(${EXENAME}
- ${TESTUTILS_LIBS} libgromacs ${GMOCK_LIBRARIES}
- ${GMX_COMMON_LIBRARIES} ${GMX_EXE_LINKER_FLAGS})
- set_property(TARGET ${EXENAME}
- APPEND PROPERTY COMPILE_FLAGS "${GMOCK_COMPILE_FLAGS}")
- set_property(TARGET ${EXENAME}
- APPEND PROPERTY COMPILE_DEFINITIONS "${GMOCK_COMPILE_DEFINITIONS}")
- set_property(TARGET ${EXENAME}
- APPEND PROPERTY COMPILE_DEFINITIONS "${EXTRA_COMPILE_DEFINITIONS}")
-
+ gmx_target_compile_options(${EXENAME})
+ target_compile_options(${EXENAME} PRIVATE "${GMOCK_COMPILE_FLAGS}")
+ target_compile_definitions(${EXENAME} PRIVATE HAVE_CONFIG_H "${GMOCK_COMPILE_DEFINITIONS}" "${EXTRA_COMPILE_DEFINITIONS}")
+ target_include_directories(${EXENAME} SYSTEM BEFORE PRIVATE ${PROJECT_SOURCE_DIR}/src/external/thread_mpi/include)
# Permit GROMACS code to include externally developed headers,
# such as the functionality from the nonstd project that we
# use for gmx::compat::optional. These are included as system
# headers so that no warnings are issued from them.
target_include_directories(${EXENAME} SYSTEM PRIVATE ${PROJECT_SOURCE_DIR}/src/external)
+ target_link_libraries(${EXENAME}
+ ${TESTUTILS_LIBS} libgromacs ${GMOCK_LIBRARIES}
+ ${GMX_COMMON_LIBRARIES} ${GMX_EXE_LINKER_FLAGS})
+
if(GMX_CLANG_TIDY)
set_target_properties(${EXENAME} PROPERTIES CXX_CLANG_TIDY
"${CLANG_TIDY_EXE};-warnings-as-errors=*;-header-filter=.*")
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff