gmx::internal Namespace Reference

Description

Internal GROMACS namespace.

This namespace is used to contain some implementation-specific functions and classes. These are not meant for direct user access, but typically reside in public headers because of implementation reasons.

Namespaces
	anonymous_namespace{selection.cpp}

Classes
class	AnalysisDataHandleImpl
	Private implementation class for AnalysisDataHandle. More...
class	AnalysisDataStorageImpl
	Private implementation class for AnalysisDataStorage. More...
class	AnalysisDataStorageFrameData
	Internal representation for a single stored frame. More...
class	BasicAverageHistogramModule
	Implements average histogram module that averages per-frame histograms. More...
class	BasicHistogramImpl
	Base class for private implementation classes for histogram modules. More...
class	EnumIndexStoreInterface
	Interface for handling storage of the enum indexes. More...
class	EnumIndexStore
	Type-specific implementation for EnumIndexStoreInterface. More...
class	OptionsImpl
	Private implementation class for Options. More...
class	SelectionData
	Internal data for a single selection. More...
class	IExceptionInfo
	Base class for ExceptionInfo. More...

Typedefs
typedef std::unique_ptr < AnalysisDataStorageFrame >	AnalysisDataFrameBuilderPointer
	Smart pointer type for managing a storage frame builder.
typedef std::vector < std::exception_ptr >	NestedExceptionList
	Internal container type for storing a list of nested exceptions.
typedef std::unique_ptr < IExceptionInfo >	ExceptionInfoPointer
	Smart pointer to manage IExceptionInfo ownership.

Functions
AbstractOptionStorage *	createEnumOptionStorage (const AbstractOption &option, const char *const *enumValues, int count, int defaultValue, int defaultValueIfSet, EnumIndexStoreInterface *store)
	Helper to create EnumOptionStorage instances. More...
static void *	alignedMallocGeneric (std::size_t bytes, std::size_t alignment)
	Allocate aligned memory in a fully portable way. More...
static void	alignedFreeGeneric (void *p)
	Free aligned memory. More...
void *	alignedMalloc (std::size_t bytes)
	Allocate aligned memory. More...
void	alignedFree (void *p)
	Free aligned memory. More...
template<typename T >
static void	ignoreValueHelper (const T &)
	Helper for ignoring values in macros. More...
void	current_function_helper ()
	Helper for defining GMX_CURRENT_FUNCTION.
void	printFatalErrorHeader (FILE *fp, const char *title, const char *func, const char *file, int line)
	Formats a common header for fatal error messages. More...
void	printFatalErrorMessageLine (FILE *fp, const char *text, int indent)
	Formats a line of fatal error message text. More...
void	printFatalErrorFooter (FILE *fp)
	Formats a common footer for fatal error messages. More...
void	assertHandler (const char *condition, const char *msg, const char *func, const char *file, int line)
	Called when an assert fails. More...

Function Documentation

void gmx::internal::alignedFree

(

void *

p

)

Free aligned memory.

Parameters

p	Memory pointer previously returned from gmx::internal::alignedMalloc()

Note

This routine should only be called with pointers obtained from gmx::internal::alignedMalloc(), and absolutely not any pointers obtained the system malloc().

static void gmx::internal::alignedFreeGeneric ( void *  p )

static

Free aligned memory.

Parameters

p	Memory pointer previously returned from gmx::internal::alignedFreePortable().

Since this routine relies on the original pointer being stored just before the memory area p points to, bad things will happen if you call this routine with a pointer obtained any other way, or if you call the system free() with a pointer obtained from std::alignedMalloc().

Note

This is an internal routine that should only be called from gmx::alignedFree().

void * gmx::internal::alignedMalloc

(

std::size_t

bytes

)

Allocate aligned memory.

Parameters

bytes

Amount of memory (bytes) to allocate. It is valid to ask for 0 bytes, which will return a non-null pointer that is properly aligned and padded (but that you should not use).

Returns

Valid pointer if the allocation worked, otherwise nullptr.

The memory will always be aligned to 128 bytes, which is our estimate of the longest cache lines on architectures currently in use. It will also be padded by the same amount at the end of the area, to help avoid false cache sharing.

Note

Memory allocated with this routine must be released with gmx::internal::alignedFree(), and absolutely not the system free().

static void* gmx::internal::alignedMallocGeneric ( std::size_t  bytes, std::size_t  alignment  )

static

Allocate aligned memory in a fully portable way.

Parameters

bytes	Amount of memory (bytes) to allocate. The routine will return nullptr if the allocation fails. However, note that asking for zero bytes will return a pointer that is non-null and properly aligned (but obviously you cannot use it, since you promised not to access data beyond the 0 bytes you asked for).
alignment	Alignment specification in bytes, must be a power of 2.

Returns

Nonzero pointer if the allocation worked, otherwise nullptr. This routine should only be called from alignedMalloc(), which also does the checking for valid values. This particular function is used for platforms where we have no control of the alignment of memory returned by the system. Instead, we increase the amount of memory requested internally such that we both can create a pointer inside this memory that fulfills the memory alignment requested, and that we have room to store the original pointer just before this area.

Note

This is an internal routine that should only be called from gmx::alignedMalloc(). Just like system-provided routines, it provides memory that is aligned - but not padded.