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GridSearchPair Struct Reference

linked list of atom index pairs generated by the vmd_gridsearch1 and vmd_gridsearch2 XXX on 64-bit machines the next pointers are as large as the atom index data in each node, so half of the memory is wasted in pointer chasing. Calling malloc/free once per pair when building the linked list is a severe multithreading scalability bottleneck due to OS-level mutex locks in malloc/free and/or the kernel VM. On Linux, it is also problematic due to the threaded version of malloc allocating huge blocks and fragmenting memory tremendously. This implementation should not be used for any threaded code. More...

#include <SpatialSearch.h>

List of all members.

Public Attributes
int	ind1
int	ind2
GridSearchPair *	next

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Detailed Description

linked list of atom index pairs generated by the vmd_gridsearch1 and vmd_gridsearch2 XXX on 64-bit machines the next pointers are as large as the atom index data in each node, so half of the memory is wasted in pointer chasing. Calling malloc/free once per pair when building the linked list is a severe multithreading scalability bottleneck due to OS-level mutex locks in malloc/free and/or the kernel VM. On Linux, it is also problematic due to the threaded version of malloc allocating huge blocks and fragmenting memory tremendously. This implementation should not be used for any threaded code.

Definition at line 37 of file SpatialSearch.h.

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Member Data Documentation

int GridSearchPair::ind1

Definition at line 38 of file SpatialSearch.h. Referenced by add_link, VolMapCreateDistance::compute_frame, contacts, measure_clustsize, measure_hbonds, measure_pointset_overlap, measure_sasa, measure_sasa_thread, and vmd_measure_contacts.

int GridSearchPair::ind2

Definition at line 38 of file SpatialSearch.h. Referenced by add_link, VolMapCreateDistance::compute_frame, contacts, measure_clustsize, measure_hbonds, measure_pointset_overlap, measure_sasa, measure_sasa_thread, and vmd_measure_contacts.

GridSearchPair* GridSearchPair::next

Definition at line 39 of file SpatialSearch.h. Referenced by add_link, VolMapCreateDistance::compute_frame, contacts, measure_clustsize, measure_hbonds, measure_pointset_overlap, measure_sasa, measure_sasa_thread, vmd_gridsearch1, vmd_gridsearch2, vmd_gridsearch3, and vmd_measure_contacts.

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The documentation for this struct was generated from the following file:

• SpatialSearch.h

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