CN102945298A - Neighbor particle pair searching method, molecular dynamics calculation method and many-core processing system - Google Patents
Neighbor particle pair searching method, molecular dynamics calculation method and many-core processing system Download PDFInfo
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Abstract
The invention provides a neighbor particle pair searching method, and a many-core processing system suitable for doing the molecular dynamics calculation. The neighbor particle pair searching method comprises the following steps: taking every particle as the main particle to establish the neighbor particle pair for each particle, wherein the neighbor particle of each main particle is determined in the rest particles within the calculation domain where the main particle is arranged so as to establish the neighbor particle information of all the particles in the calculation domain in all the calculation domains. The invention further provides a molecular dynamics calculation method using the neighbor particle pair searching method, and the many-core processing system of the molecular dynamics calculation method. The neighbor particle searching method makes distinction targeting at different domains where the particles are, so that different calculation methods can be adopted according to the domains where the neighbor particles are arranged. Therefore, the processing capacities of sub-cores of the many-core processing system can be developed fully.
Description
Technical field
The present invention relates to data processing field, particularly towards neighbours' particle of many-core processor search, Molecular Dynamics Calculation method and the crowd that uses the method are examined disposal system.
Background technology
In recent years multinuclear design becomes the trend of high-performance development and the focus of academic research gradually.Polycaryon processor can be divided into isomorphism polycaryon processor and heterogeneous multi-nucleus processor according to integration mode.
The isomorphism polycaryon processor is the integrated processor core of a plurality of isomorphisms in a chip, and all processor cores all move complete operating system, towards identical operating load.Therefore, its design of program based on the isomorphism processor realizes relatively simple.This class processor is introduced to the market comprehensively at present.
Heterogeneous multi-nucleus processor is compared with the isomorphism polycaryon processor on structural design has diverse characteristic.The integrated processor core of a plurality of isomeries in the chip of heterogeneous multi-nucleus processor, comprise: the processor core that a few functions is complete is referred to as primary processor nuclear and (claims again main nuclear, such as the PPE among the Cell, Sync Node among the Godson), mainly finish the intensive operation of control; And the core of a large amount of function limitations, we are referred to as mainly to finish data-intensive operation from processor core (claim again from nuclear, such as the SPE among the Cell, the Tile Node among the Godson).
In general, a main nuclear and a plurality of from nuclear group of nuclear formation, a plurality of nuclear groups consist of a complete chip.Because the logic of complete process device nuclear is complicated, be subjected to the processor core less (being generally dozens of) that the restriction isomorphism polycaryon processor of production technology can be integrated, and heterogeneous multi-nucleus processor is because from examining the processor core numerous (more than 64) that logic function simply can be integrated, so claim also that usually heterogeneous multi-nucleus processor is many-core processor (many-core processor).
Molecular dynamics simulation is the important applied field of high-performance calculation, GROMACS is a powerful molecular dynamics simulation software of increasing income, its research range can comprise glass and liquid crystal, arrive polymkeric substance, crystal and biomolecule solution, it has great advantage aspect newtonian motion of a large amount of molecular systems of simulation, owing to carried out a large amount of algorithm optimizations, this software calculated performance can reach 3 to 10 times of similar software, but still can't satisfy the growing computation requirement of molecular dynamics simulation.
When GROMACS transplanted to many-core processor, operating on the main nuclear that the control in the process is intensive carried out, and operating in from nuclear of computation-intensive carried out, thereby gives full play to from the supercomputing performance of nuclear the acceleration in the implementation process.Yet, when utilizing prior art that GROMACS is transplanted to many-core processor, have the problems such as the low and data write conflict of parallel efficiency.
Summary of the invention
For the problems referred to above, the invention provides a kind of neighbours' particle towards many-core processor to searching method and Molecular Dynamics Calculation method, and the crowd who uses said method examine disposal system, so that the acceleration computing in the many-core processor system implementation process, further shorten program runtime, and solved the problem of write conflict.
For addressing the above problem, the embodiment of the invention provides a kind of neighbours' particle to searching method, and the crowd who is applicable to be configured to carry out Molecular Dynamics Calculation examines disposal system; The method comprises:
Set up respectively neighbours' particle pair of each particle as main particle with each particle; Wherein, for each main particle, all determine the neighbour of this main particle in all the other particles in its zoning of living in;
Thereby in each zoning, set up neighbours' particle of all particles in this zoning to information.
Alternatively, described neighbours' particle also comprises searching method: described neighbours' particle to information in record main particle and neighbour interaction calculation of force mode.
Alternatively, described neighbours' particle also comprises searching method, for each main particle, further determines the neighbour of this main particle in the particle on its border, zoning of living in.
Alternatively, described neighbours' particle also comprises searching method, described neighbours' particle to information in the main particle of record and neighbour interaction calculation of force mode.
Alternatively, described neighbours' particle also comprises searching method, the first account form; The second account form.
Alternatively, described neighbours' particle also comprises searching method, records neighbours' particle of all particles in described each zoning to information with tabular form.
The embodiment of the invention also provides a kind of Molecular Dynamics Calculation method, is applicable to many nuclear disposal systems; The method comprises:
Set up respectively neighbours' particle pair of each particle as main particle with each particle; Wherein, for each main particle, all determine the neighbour of this main particle in all the other particles in its zoning of living in;
To information, calculate the stressed of each main particle based on neighbours' particle of all particles in this zoning of setting up in each zoning.
Alternatively, the described neighbours' of foundation particle also comprises the main particle of record and neighbour interaction calculation of force mode to information.
Alternatively, described Molecular Dynamics Calculation method also comprises, records neighbours' particle of all particles in described each zoning to information with tabular form.
Alternatively, described Molecular Dynamics Calculation method adopts the first account form to calculate the stressed of each main particle, and described the first account form does not adopt Newton third law.
Alternatively, described neighbours' particle of setting up each particle as main particle with each particle respectively is to also comprising:
For each main particle, further in the particle on its border, zoning of living in, determine the neighbour of this main particle.
Alternatively, described Molecular Dynamics Calculation method also comprises, records neighbours' particle of all particles in described each zoning to information with tabular form.
Alternatively, described Molecular Dynamics Calculation method is each main particle of border, zoning particle for neighbour, adopts the second account form to calculate the stressed of this each main particle, and described the second account form adopts Newton third law.
The embodiment of the invention also provides a kind of many nuclear disposal systems, is applicable to Molecular Dynamics Calculation, comprises primary processor nuclear and a plurality of from processor core:
This crowd examines disposal system and comprises that neighbours' particle is to search module and computing module; Wherein, described neighbours' particle is applicable to respectively to set up as main particle with each particle neighbours' particle pair of each particle to search module; Wherein, for each main particle, all determine the neighbour of this main particle in all the other particles in its zoning of living in;
Neighbours' particle of all particles calculates the stressed of each main particle to information in this zoning that described computing module is set up in each zoning search module based on neighbours' particle.
Alternatively, for each main particle, described neighbours' particle further is applicable to determine the neighbour of this main particle in the particle on its border, zoning of living in to search module.
Alternatively, described neighbours' particle to search module further be applicable to described neighbours' particle to information in record main particle and neighbour interaction calculation of force mode.
Alternatively, described many nuclear disposal systems comprise that also neighbor list sets up module, are applicable to neighbours' particle with all particles in described each zoning of tabular form record to information.
Alternatively, described many nuclear disposal systems also comprise the neighbor list analysis module, for the neighbours' particle pair that is in the zoning, adopt the first account form to calculate the stressed of each right main particle of this neighbours' particle, described the first account form does not adopt Newton third law.
Alternatively, described many nuclear disposal systems also comprise the neighbor list analysis module, are neighbours' particle pair of border, zoning particle for neighbour, adopt the second account form to calculate the stressed of each right main particle of this neighbours' particle, described the second account form adopts Newton third law.
Compared with prior art, embodiments of the invention have the following advantages:
1, the present invention with all the other all particles in the main particle zoning of living in as the neighbour hunting zone, determine the neighbour of this main particle, the prior art of comparing, enlarged the hunting zone of neighbour, thereby can in each zoning, set up neighbours' particle of all particles in this zoning to information, the neighbours' particle that generate to repeat pair, thus Newton third law can be used, eliminate from internuclear write conflict.
2, the present invention further with the particle on border, main particle zoning of living in as the neighbour hunting zone, improved the neighbor seaching method that prior art is not distinguished neighbour zone of living in (intra-zone or zone boundary), thereby be conducive to adopt different account forms according to the residing zone of neighbour.
3, the present invention in searching the zoning and all neighbours' particles on border, zoning to after, further set up neighbor list based on the different hunting zones of neighbour, adopt different non-one-tenth bonding force account forms based on this neighbor list, specifically comprise again:
A. for the neighbours' particle pair that is in the zoning, do not adopt Newton third law to calculate interaction force between this neighbours' particle centering master's particle and the neighbour, therefore do not need to upgrade the stressed of from the processor core neighbour, avoided the write conflict from processor core.
B. be neighbours' particle pair of border, zoning particle for neighbour, adopt Newton third law to calculate the stressed of each right main particle of this neighbours' particle, thereby guarantee the stressed correct of border, zoning particle, simultaneously, owing to only upgrade from examining the stressed of upper neighbour, and then by the unified renewal that adds up of main nuclear, so also avoided the write conflict from processor core.
4, the right searching method of neighbours' particle of the present invention, so that the Force Calculation of the most of particle in the counting system can not used Newton third law, can give full play to from the processing power of nuclear walking abreast from nuclear that many karyonides are united, realized the in-process speed-up computation of many nuclear disposal systems.
Description of drawings
Fig. 1 shows one group of neighbor list synoptic diagram setting up according to prior art;
The one group of neighbor list synoptic diagram that provides according to one embodiment of the invention is provided Fig. 2;
A kind of neighbours' particle that Fig. 3 first embodiment of the invention provides is to the schematic flow sheet of searching method;
Fig. 4 is that another kind of neighbours' particle of providing of first embodiment of the invention is to the schematic flow sheet of searching method;
Fig. 5 is that another neighbours' particle of providing of first embodiment of the invention is to the schematic flow sheet of searching method;
Fig. 6 is a kind of Molecular Dynamics Calculation method flow synoptic diagram that the second embodiment of the present invention provides;
Fig. 7 is the another kind of Molecular Dynamics Calculation method flow synoptic diagram that the second embodiment of the present invention provides;
Fig. 8 is the another kind of Molecular Dynamics Calculation method flow synoptic diagram that the second embodiment of the present invention provides; And
Fig. 9 is a kind of many block diagrams of examining disposal systems that the embodiment of the invention provides.
Embodiment
The inventor finds according to each module proportion grading working time of program that the GROMACS program provides, during the conducting molecule dynamics calculation, neighbor seaching and calculation of force module account for the nearly more than 90% of one process program total operation time, and the calculation of force module is divided into into that bonding force calculates and non-ly become bonding force calculating (PME), wherein be calculated as the master with non-one-tenth bonding force again, and non-one-tenth bonding force computing module and neighbor seaching module link the tightst.When GROMACS is transplanted to many-core processor, non-one-tenth bonding force computing module needs the stressing conditions of all particles in the counting system, be to calculate the most intensive part in the GROMACS program, thereby at first consider the distribution of force of a plurality of particles is carried out parallel computation to a plurality of from nuclear.
For the ease of understanding the parallel computation of a plurality of particles, below will illustrate neighbours' particle to and neighbor list.For example, if i particle and j particle are a pair of neighbours (certainly, j particle and i particle also are a pair of neighbours), then neighbours' particle is in (i, j), and the i particle is main particle, and the j particle is neighbour, can calculate to obtain j particle that the i particle is subject to the power of i particle; Neighbours' particle is in (j, i), and the j particle is main particle, and the i particle is neighbour, can calculate to obtain i particle that the j particle is subject to the power of j particle; And neighbours' particle is called as neighbours' particle pair of repetition to (j, i) to (i, j) and neighbours' particle.
Fig. 1 shows one group of neighbor list synoptic diagram setting up according to prior art.With reference to figure 1, this neighbor list comprises three hurdle contents, is respectively: neighbor list title, neighbours' particle are to (between main particle and the neighbour) acting force type between type and particle.
In the neighbor list of prior art, neighbours' particle that can not duplicate pair, that is, neighbours' particle only occurs once (j, i) (i, j) or neighbours' particle, for example, only occurs neighbours' particle in the neighbor list to (i, j).Therefore, can calculate neighbours' particle to (i, j) the j particle that the i particle is subject in is to the power of i particle, and then, the i particle that neighbours' particle is subject to j particle in (j, i) need to utilize Newton third law to the power of j particle, the j particle that i particle in (i, j) is subject to by neighbours' particle obtains the power of i particle.Therefore, to searching method, need to utilize that Newton third law is parallel carries out non-one-tenth bonding force and calculate based on neighbours' particle of prior art.
Yet, non-one-tenth bonding force computing module since the application of Newton third law directly and guild cause parallel efficiency low and have a problem of data write conflict.Specifically comprise:
1, according to the neighbor list of above-mentioned foundation, if the k particle is the neighbour of i particle and j particle simultaneously, and the Force Calculation of i particle and j particle is to be distributed in different carrying out from nuclear, then, when these are different when adopting Newton third law to upgrade simultaneously k particle stressed from nuclear, can cause the write conflict of k particle stress data.
If 2 solve the problem of above-mentioned write conflict, do not adopt Newton third law by revising neighbor list, the neighbours' particle that then duplicates in the neighbor list pair, i.e. (i, j) and (j, i).Because the mode that concurrent program adopts the zoning to decompose will cause the stressed problem of losing of particle on border, zoning.
For above-mentioned purpose of the present invention, feature and advantage can be become apparent more, below in conjunction with accompanying drawing the specific embodiment of the present invention is described in detail.Set forth in the following description a lot of details so that fully understand the present invention, implement but the present invention can also adopt other to be different from alternate manner described here, so the present invention has not been subjected to the restriction of following public specific embodiment.
The first embodiment:
With reference to figure 3, be to solve the data write conflict problem between above slave nucleus, the embodiment of the invention provides a kind of neighbours' particle to searching method, and the crowd who is applicable to be configured to carry out Molecular Dynamics Calculation examines disposal system.
As one embodiment of the present of invention, this neighbours' particle comprises searching method:
Set up respectively neighbours' particle pair of each particle as main particle with each particle; Wherein, for each main particle, all determine the neighbour of this main particle in all the other particles in its zoning of living in;
Thereby in each zoning, set up neighbours' particle of all particles in this zoning to information.
As one embodiment of the present of invention, describedly set up neighbours' particle pair of each particle with each particle as main particle, all particles that refers in each zoning is the hunting zone of main particle; For each main particle, all determine the neighbour of this main particle in all the other particles in its zoning of living in, refer to, except main particle, with the neighbour hunting zone of all the other all particles in this main particle zoning of living in as this main particle, the prior art of comparing has enlarged the hunting zone, and neighbours' particle of foundation is to neighbours' particle of comprising repetition in the information pair.
For example, if comprise in the zoning of n particle one, i particle and j particle are a pair of neighbours, then above-mentioned neighbours' particle according to the present invention is to searching method, when searching for take the i particle as main particle, then all the other n-1 particle except the i particle is searched the neighbour of i particle as the hunting zone in this zoning, can obtain neighbours' particle to (i, j); When searching for take the j particle as main particle, then all the other n-1 particle except the j particle is searched the neighbour of i particle as the hunting zone in this zoning, can obtain neighbours' particle to (j, i), thereby neighbours' particle of setting up comprises neighbours' particle pair of repetition to information, namely comprise neighbours' particle to (i, j) and neighbours' particle to (j, i).
With reference to figure 4, Fig. 4 is that another kind of neighbours' particle of providing of first embodiment of the invention is to the schematic flow sheet of searching method.Further, in each zoning, set up neighbours' particle to information after, described neighbours' particle also comprises searching method: described neighbours' particle to information in record main particle and neighbour interaction calculation of force mode; Record neighbours' particle of all particles in described each zoning to information with tabular form.About setting up the detailed introduction of neighbor list, this paper will be described in detail in a second embodiment.
Neighbours' particle of the prior art of comparing is to searching method, owing to only search neighbours' particle to (i, j), can only calculate this neighbours' particle to (i, j) stressing conditions of i particle in, therefore neighbours' particle need to adopt Newton third law to obtain easy like this causing from internuclear data write conflict to the stressing conditions of j in (j, i).
In the embodiment of the invention, utilize neighbours' particle of said method foundation to information, this neighbours' particle is to neighbours' particle of comprising repetition in the information pair, namely search neighbours' particle to (i, j) and neighbours' particle to (j, i), therefore described account form can not adopt Newton third law, just can obtain the interaction force between main particle and the neighbour, avoided like this since adopt that Newton third law causes from the concurrent write collision problem between the nuclear.
For the one process program, above-mentioned neighbours' particle can be set up neighbours' particle of all particles in each zoning to information to searching method, yet, for the multi-process program, be in the stressed of border, zoning particle if still adopt above-mentioned neighbours' particle may lose the searcher rule.
Particularly, in the one process program, each particle all is in the zoning, therefore adopts said method can set up neighbours' particle of all particles in this zoning to information; For the multi-process program, owing to adopt the mode of Region Decomposition to form a plurality of zonings, except being in the particle in the zoning, also comprise the particle that is in the border, zoning, therefore, adopt above-mentioned neighbours' particle can only search for the neighbours that are in particle in the zoning to searching method, can't search the neighbours that are in border, zoning particle, be in the stressed of border, zoning particle thereby may lose.
For example, if i particle and j particle are a pair of neighbours, the i particle is the particle that is in the zoning, the j particle is to be in the borderline particle in zoning, then adopts said method of the present invention can only search the neighbour j of i particle, namely finds (i, j) this neighbours' particle pair, and can't search (j, i) this neighbours' particle pair, then Loss will occur to the power of j particle in the i particle that is subject to of j particle.
Based on the problems referred to above, the embodiment of the invention further provides a kind of neighbours' particle to searching method, finishes for the first time search---and namely finish the neighbours' particle zoning in to after searching for, also comprise, search is searched for for the particle that is in the border, zoning for the second time.Those skilled in the art will be appreciated that the above-mentioned first time, for the second time search are to distinguish different neighbours' particle search zones, and should not become the restriction of the sequencing of neighbor seaching.
With reference to figure 5, Fig. 5 is that another neighbours' particle of providing of first embodiment of the invention is to the schematic flow sheet of searching method.
As one embodiment of the present of invention, this neighbours' particle further comprises searching method: neighbours' particle pair of setting up respectively each particle with each particle as main particle; For each main particle, further in the particle on its border, zoning of living in, determine the neighbour of this main particle.
As one embodiment of the present of invention, all particles in each zoning is the hunting zone of main particle, the hunting zone take the particle on border, zoning as neighbour.As one embodiment of the present of invention, when search comprised the particle on border, zoning, the particle that is in the border, zoning all was the form appearance with neighbour.
For example, neighbours' particle of multi-process program to searching method in, if i particle and j particle are a pair of neighbours, wherein the i particle is in the zoning, and the j particle is in the border of this zoning, and then above-mentioned neighbours' particle according to the present invention is to searching method, search for take the i particle as main particle, then search the neighbour of i particle take the particle on this border, zoning as the hunting zone, can obtain neighbours' particle to (i, j).
Further, finish for the second time search, set up neighbours' particle to information after, described neighbours' particle also comprises searching method: described neighbours' particle to information in the main particle of record and neighbour interaction calculation of force mode; Record neighbours' particle of all particles in described each zoning to information with tabular form.
Because neighbours' particle of search is in the information for the second time, the particle that is in the border, zoning only occurs with the form of neighbour, therefore, in the embodiment of the invention, utilize neighbours' particle that searching method for the second time sets up to information, need to adopt Newton third law to obtain to be in the stressing conditions of the particle on border, zoning.
For example, find neighbours' particle to (i, j) by for the second time search, wherein the i particle is in the zoning, and the j particle is in the border of this zoning; And the j particle can not occur with the form of main particle as the particle that is in the border of zoning, that is to say by for the second time search, can't obtain neighbours' particle to (j, i).Therefore, can calculate by non-one-tenth bonding force and obtain this neighbours' particle to the stressing conditions of i particle in (i, j), and neighbours' particle can obtain by adopting Newton third law the stressing conditions of j particle in (j, i).
To sum up, the present invention with all the other all particles in the main particle zoning of living in as the neighbour hunting zone, determine the neighbour of this main particle, the prior art of comparing, enlarged the hunting zone of neighbour, thus the neighbours' particle that can in each zoning, set up all particles in this zoning to information, the neighbours' particle that generate to repeat pair, thereby can use Newton third law, eliminate from internuclear write conflict.
Secondly, the present invention further with the particle on border, main particle zoning of living in as the neighbour hunting zone, improved the neighbor seaching method that prior art is not distinguished neighbour zone of living in (intra-zone or zone boundary), thereby be conducive to adopt different account forms according to the residing zone of neighbour.
The second embodiment:
The embodiment of the invention further provides a kind of and uses above-mentioned neighbours' particle to the Molecular Dynamics Calculation method of searching method.With reference to figure 6, Fig. 6 is a kind of Molecular Dynamics Calculation method flow synoptic diagram that the second embodiment of the present invention provides.
As one embodiment of the present of invention, this Molecular Dynamics Calculation method is applicable to many nuclear disposal systems; The method comprises:
Set up respectively neighbours' particle pair of each particle as main particle with each particle; Wherein, for each main particle, all determine the neighbour of this main particle in all the other particles in its zoning of living in;
To information, calculate the stressed of each main particle based on neighbours' particle of all particles in this zoning of setting up in each zoning.
Molecular Dynamics Calculation method of the present invention is at first carried out neighbours' particle to search, obtains neighbours' particle of all particles in the zoning to information, then, to information, calculates the stressed of each main particle based on neighbours' particle of this acquisition.
Further, adopt the first account form to calculate the stressed of each main particle, described the first account form does not adopt Newton third law.
As one embodiment of the present of invention, describedly set up neighbours' particle pair of each particle with each particle as main particle, all particles that refers in each zoning is the hunting zone of main particle; For each main particle, all determine the neighbour of this main particle in all the other particles in its zoning of living in, refer to, except main particle, with the neighbour hunting zone of all the other all particles in this main particle zoning of living in as this main particle, the prior art of comparing has enlarged the hunting zone, and neighbours' particle of foundation is to neighbours' particle of comprising repetition in the information pair.
Further, described neighbours' particle to information in record main particle and neighbour interaction calculation of force mode, and, with neighbours' particle of all particles in described each zoning of tabular form record to information.
With reference to figure 2, the one group of neighbor list synoptic diagram that provides according to the inventive method is provided Fig. 2.The Fig. 1 that compares, Fig. 2 has increased by the 4th hurdle content, and has increased the expansion neighbor list that several rows are masked as SW.
With reference to figure 2, this neighbor list comprises four hurdle contents, be respectively: neighbor list title, neighbours' particle are to (between main particle and the neighbour) acting force type between type, particle, and Calculation of the force mode, in embodiments of the present invention, described Calculation of the force mode comprises the first account form; The second account form is specifically selected " whether using Newton third law " according to the zone of living in of neighbour.
As one embodiment of the present of invention, neighbor list title one hurdle among the figure, there is the neighbour among these neighbours of representative of SW sign to be in the border, zoning after the title, and all is in the zoning without main particle and neighbour among these neighbours of representative of SW sign after the title; Neighbours' particle is to type one hurdle, and wherein enlistATOM represents that main particle and neighbour are non-water particle, and enlistWATER represents that main particle is hydrone, and neighbour is non-water particle, and enlistWATERWATER represents that main particle, neighbour are hydrone; Interparticle force type one hurdle, vdw represents Van der Waals force, coul represents the Coulomb force.
The neighbours' particle that searches based on said method pair all is in the scope of zoning, the neighbor list of therefore based on this neighbours' particle information being set up, the just neighbor list of front ten row (namely not having SW indicates) as shown in Figure 2.This neighbours' particle is to neighbours' particle of comprising repetition in the information pair, namely search neighbours' particle to (i, j) and neighbours' particle to (j, i), therefore described account form can not adopt Newton third law, just can obtain stressed to (i, j) middle i particle of neighbours' particle, and stressed to j particle in (j, i) of neighbours' particle.
Therefore, neighbor list corresponding to front ten row, " whether use Newton third law " on Fig. 2 the 4th hurdle, what record is "No" information, namely for neighbours' particle of in the zoning, searching for pair, do not adopt Newton third law to calculate non-one-tenth bonding force, avoided like this because the concurrent write collision problem that adopts Newton third law to cause.
Described in aforementioned the first embodiment, if only search is in the neighbours of particle in the zoning, for the multi-process program, then can't search the neighbours that are in border, zoning particle, the phenomenon that causes the stressing conditions of border particle to be lost.
Based on the problems referred to above, neighbor seaching process of the present invention is divided into twice carries out, and not only comprises for the first time search---and namely in the zoning, carry out neighbours' particle to search, also comprise for the second time search.Those skilled in the art will be appreciated that the above-mentioned first time, for the second time search are to distinguish different neighbours' particle search zones, and should not become the restriction of the sequencing of neighbor seaching.
With reference to figure 7, Fig. 7 is the another kind of Molecular Dynamics Calculation method flow synoptic diagram that the second embodiment of the present invention provides.
As one embodiment of the present of invention, the method comprises: neighbours' particle pair of setting up respectively each particle with each particle as main particle; For each main particle, further in the particle on its border, zoning of living in, determine the neighbour of this main particle.
Further, to information, calculate the stressed of each main particle based on neighbours' particle of all particles; Be each main particle of border, zoning particle for neighbour, adopt the second account form to calculate the stressed of this each main particle, described the second account form adopts Newton third law.
As one embodiment of the present of invention, all particles in each zoning is the hunting zone of main particle, the hunting zone take the particle on border, zoning as neighbour.As one embodiment of the present of invention, when search comprised the particle on border, zoning, the particle that is in the border, zoning all was the form appearance with neighbour.
The neighbours' particle that searches based on said method pair, its neighbour is the particle that is in the border, zoning, the neighbor list of therefore based on this neighbours' particle information being set up, just as shown in Figure 2 after the expansion neighbor list (namely having the SW sign) of ten row.
Therefore, expansion neighbor list corresponding to rear ten row, " whether use Newton third law " on Fig. 2 the 4th hurdle, what record is "Yes" information, it namely is each main particle of border, zoning particle for neighbour, need to adopt Newton third law to calculate non-one-tenth bonding force, can correctly obtain like this stressing conditions of border, zoning particle.
Need to prove; form and content in the one group of neighbor list that provides among Fig. 2; be in order to be illustrated more clearly in the Molecular Dynamics Calculation method of the embodiment of the invention, those skilled in the art will be appreciated that this neighbor list should not become limiting the scope of the invention.
With reference to figure 8, Fig. 8 is the another kind of Molecular Dynamics Calculation method flow synoptic diagram that the second embodiment of the present invention provides.
As one embodiment of the present of invention, the method comprises: neighbours' particle pair of setting up respectively each particle with each particle as main particle; Wherein, for each main particle, all determine the neighbour of this main particle in all the other particles in its zoning of living in; For each main particle, further in the particle on its border, zoning of living in, determine the neighbour of this main particle; Neighbours' particle of all particles of setting up based on each zoning calculates the stressed of each main particle to information; Be in each main particle in the zoning for neighbour, adopt the first account form to calculate the stressed of each main particle, described the first account form does not adopt Newton third law; Be each main particle of border, zoning particle for neighbour, adopt the second account form to calculate the stressed of this each main particle, described the second account form adopts Newton third law.
Generally speaking, based on neighbours' particle of the present invention to being in twice search of zones of different: the neighbours' particle in the zoning is to for the first time search, and neighbours' particle on border, zoning is to for the second time search, the neighbor list that the present invention sets up also correspondingly comprises two parts, do not use Newton third law (front ten row) when namely calculating for the neighbor list that the first time, search was set up, and use Newton third law (rear ten row) when the neighbor list of setting up calculates for searching for for the second time.
The neighbor seaching method that the prior art of comparing is not distinguished neighbour zone of living in (intra-zone or zone boundary), the present invention is according to neighbour zone of living in different (intra-zone or zone boundary), adopt the neighbor seaching method of distinguishing, thereby be conducive to adopt different account forms according to the residing zone of neighbour, like this, solved the write conflict problem, and the Force Calculation of the most of particle in the whole counting system is not used Newton third law, so that can give full play to from the computation capability of nuclear.
The 3rd embodiment:
The embodiment of the invention also provides a kind of many nuclear disposal systems, is applicable to carry out the described neighbours' particle of above-described embodiment to searching method and Molecular Dynamics Calculation.
With reference to figure 9, Fig. 9 is a kind of many block diagrams of examining disposal systems that the embodiment of the invention provides.
As one embodiment of the present of invention, this crowd examines disposal system 10 and comprises primary processor nuclear (main nuclear) and a plurality of from processor core (from nuclear), and this crowd examines disposal system and comprises that neighbours' particle is to search module 101 and computing module 104; Wherein, described neighbours' particle is applicable to respectively to set up as main particle with each particle neighbours' particle pair of each particle to search module 101; Wherein, for each main particle, all determine the neighbour of this main particle in all the other particles in its zoning of living in; Neighbours' particle of all particles calculates the stressed of each main particle to information in this zoning that described computing module 104 is set up in each zoning search module based on neighbours' particle.
Wherein, described computing module 104 calculates the stressed non-one-tenth bonding force that calculates each main particle of neighbours' particle centering that refers to of each main particle.
The main nuclear of described many nuclear disposal systems and usually have separately independently storage space from examining, each from nuclear have that relative capacity is less, access speed local storage (not shown) faster.
In the embodiment of the invention, neighbours' particle utilizes neighbours' particle of said method foundation to information to search module 101, this neighbours' particle is to neighbours' particle of comprising repetition in the information pair, namely search neighbours' particle to (i, j) and neighbours' particle to (j, i), therefore described account form can not adopt Newton third law, just can obtain the interaction force between main particle and the neighbour, avoid like this because the concurrent write collision problem that adopts Newton third law to cause.
For the one process program, neighbours' particle utilizes above-mentioned neighbours' particle can set up neighbours' particle of all particles in each zoning to information to searching method to search module 101, yet, for the multi-process program, be in the stressed of border, zoning particle if still adopt above-mentioned neighbours' particle may lose the searcher rule.
Therefore, neighbours' particle of the present invention is divided into twice to search module 101 with the neighbor seaching process to carry out, and not only comprises for the first time search---and namely in the zoning, carry out neighbours' particle to search, also comprise for the second time search.Those skilled in the art will be appreciated that the above-mentioned first time, for the second time search are to distinguish different neighbours' particle search zones, and should not become the restriction of the sequencing of neighbor seaching.
According to one embodiment of present invention, for each main particle, described neighbours' particle further is applicable to determine the neighbour of this main particle in the particle on its border, zoning of living in to search module 101; Described neighbours' particle to search module further be applicable to described neighbours' particle to information in record main particle and neighbour interaction calculation of force mode.
Because neighbours' particle of search is in the information for the second time, the particle that is in the border, zoning only occurs with the form of neighbour, therefore, in the embodiment of the invention, utilize neighbours' particle that for the second time search sets up to information, need to adopt Newton third law to obtain to be in the stressing conditions of the particle on border, zoning.
Described many nuclear disposal systems 10 comprise that also neighbor list sets up module 102, are applicable to neighbours' particle with all particles in described each zoning of tabular form record to information.
Generally speaking, neighbours' particle is in zones of different to search module 101 based on neighbours' particle and carries out twice search, comprises respectively: the neighbours' particle in the zoning is to for the first time search, and neighbours' particle on border, zoning is to for the second time search.The neighbor list that the present invention sets up also correspondingly comprises two parts, when calculating, do not use the neighbor list of namely setting up for for the first time search Newton third law (front ten row), and use Newton third law (rear ten row) when calculating for the neighbor list that for the second time search is set up, specifically please refer to Fig. 2.
As one embodiment of the present of invention, the neighbours' particle that search module 101 is searched when neighbours' particle when reaching some (this quantity can by user's self-defining) is unifiedly put into neighbor list by the put_in_list function.Yet, examine in the disposal system the crowd, because that the circulation of electric charge group splits is a plurality of from the nuclear parallel processing, if a plurality ofly call simultaneously the write conflict that the put_in_list function may cause the neighbor list data from nuclear.
Therefore, in embodiments of the present invention, described neighbours' particle to search module 101 neighbours' particle of setting up each particle to after, first the neighbor seaching outcome record is got off, the unified mode of being write neighbor list by main nuclear, that is to say that described neighbor list is set up module 102 and controlled by main nuclear.
Do like this two benefits: at first avoid calling simultaneously the write conflict problem that the put_in_list function causes by each from nuclear; Secondly, by the order of main nuclear control write operation, can keep neighbor list information consistent with original program, be beneficial to the verification of correctness of concurrent program.
In addition, according to one embodiment of present invention, described many nuclear disposal systems 10 also comprise neighbor list analysis module 103, for the neighbours' particle pair that is in the zoning, adopt the first account form to calculate the stressed of each right main particle of this neighbours' particle, described the first account form does not adopt Newton third law; Be neighbours' particle pair of border, zoning particle for neighbour, adopt the second account form to calculate the stressed of each right main particle of this neighbours' particle, described the second account form adopts Newton third law.
Owing to also comprise the particle that is in the border, zoning in the neighbor list, in order to keep the unitarity of neighbor seaching on program realizes, the embodiment of the invention further increases a bool parameter in the put_in_list function, this parameter is in order to indicate whether neighbour is the situation of border particle.
Described many nuclear disposal systems can also comprise update module 105, are applicable to upgrade the stressed of each main particle after computing module 104 calculates each main particle stressed.Because the first account form does not adopt Newton third law, therefore only need to calculate and upgrade the stressed of main particle this neighbours' particle centering, and can not occur respectively from internuclear owing to utilize Newton third law to upgrade simultaneously the stressed write conflict problem that causes of certain particle.In this case, this update module 105 is by controlling from nuclear.
For the expansion neighbor list that adopts Newton third law, only need to be from the local storage of nuclear, upgrade this from examining the stressed of upper neighbour, and by unified cumulative renewal of main nuclear, so also can avoid from internuclear data write conflict problem.In this case, this update module 105 is controlled by main nuclear.
For example, if certain k particle that is in the border, zoning is respectively two particles, the neighbour of i particle and j particle for example, this i particle and j particle are in different processing from nuclear, so when utilizing Newton third law to upgrade simultaneously k particle stressed, also be to upgrade difference from examining the stressed of upper k particle, upgrade by main nuclear is cumulative more afterwards.
About the detailed introduction of neighbours' particle to search module 101 and computing module 104, can be further with reference to neighbours' particle of the first embodiment to searching method, and the Molecular Dynamics Calculation method of the second embodiment does not repeat them here.
For further specifying the beneficial effect of the embodiment of the invention, the inventor provides following test data of experiment and analysis:
The concurrent testing environment is that 64 many-core processors from examining are arranged, and the serial test environment is Intel E5430, because test environment is different from Intel E5430 frequency, it is umber of beats unit as a comparison that test data is chosen clock periodicity, shown in the following page table I of result.
Table I: test data
By upper table data as seen, because the present invention has adopted neighbours' particle to substep search (for the first time with for the second time search), the method of non-one-tenth bonding force classified calculating has caused the significantly increase of calculated amount, but under the many-core processor environment, given full play to from the high-speed computational capability of nuclear, neighbours' particle is 1.3 to the speed-up ratio of search module, non-one-tenth bonding force computing module nb_kernel312 speed-up ratio the most consuming time has reached 14.59, in addition, the overall speed-up ratio of non-one-tenth bonding force module according to the time scale weighting reaches 8.83, under the different parallel scales, the complete routine speed-up ratio is between 3-4 times, limited by search time, all there is certain optimization space in these data.
Therefore, further specify based on above-mentioned test data, use neighbours' particle of the present invention the crowd of searching method and Molecular Dynamics Calculation method is examined disposal system, can give full play to from the parallel processing capability of nuclear, shorten program runtime.
The above only is preferred embodiment of the present invention, is not the present invention is done any pro forma restriction.Any those of ordinary skill in the art, do not breaking away from the technical solution of the present invention scope situation, all can utilize method and the technology contents of above-mentioned announcement that technical solution of the present invention is made many possible changes and modification, or be revised as the equivalent embodiment of equivalent variations.Therefore, every content that does not break away from technical solution of the present invention according to any simple modification, equivalent variations and the modification that technical spirit of the present invention is done above embodiment, all still belongs in the scope of technical solution of the present invention protection.
Claims (19)
1. neighbours' particle is to searching method, and the crowd who is applicable to be configured to carry out Molecular Dynamics Calculation examines disposal system; It is characterized in that the method comprises:
Set up respectively neighbours' particle pair of each particle as main particle with each particle; Wherein, for each main particle, all determine the neighbour of this main particle in all the other particles in its zoning of living in;
Thereby in each zoning, set up neighbours' particle of all particles in this zoning to information.
2. neighbours' particle as claimed in claim 1 is characterized in that searching method, also comprises: described neighbours' particle to information in record main particle and neighbour interaction calculation of force mode.
3. neighbours' particle as claimed in claim 1 is characterized in that searching method, also comprises, for each main particle, further determines the neighbour of this main particle in the particle on its border, zoning of living in.
4. neighbours' particle as claimed in claim 3 is characterized in that searching method, also comprise, described neighbours' particle to information in record main particle and neighbour interaction calculation of force mode.
5. neighbours' particle as claimed in claim 4 is characterized in that searching method, also comprises the first account form; The second account form.
Such as each described neighbours' particle of claim 1 to 5 to searching method, it is characterized in that, also comprise, with neighbours' particle of all particles in described each zoning of tabular form record to information.
7. a Molecular Dynamics Calculation method is applicable to many nuclear disposal systems; It is characterized in that the method comprises:
Set up respectively neighbours' particle pair of each particle as main particle with each particle; Wherein, for each main particle, all determine the neighbour of this main particle in all the other particles in its zoning of living in;
To information, calculate the stressed of each main particle based on neighbours' particle of all particles in this zoning of setting up in each zoning.
8. Molecular Dynamics Calculation method as claimed in claim 7 is characterized in that, the described neighbours' of foundation particle also comprises the main particle of record and neighbour interaction calculation of force mode to information.
9. Molecular Dynamics Calculation method as claimed in claim 8 is characterized in that, also comprises, records neighbours' particle of all particles in described each zoning to information with tabular form.
10. Molecular Dynamics Calculation method as claimed in claim 7 is characterized in that, adopts the first account form to calculate the stressed of each main particle, and described the first account form does not adopt Newton third law.
11. Molecular Dynamics Calculation method as claimed in claim 7 is characterized in that, described neighbours' particle of setting up each particle as main particle with each particle respectively is to also comprising:
For each main particle, further in the particle on its border, zoning of living in, determine the neighbour of this main particle.
12. Molecular Dynamics Calculation method as claimed in claim 11 is characterized in that, also comprises, records neighbours' particle of all particles in described each zoning to information with tabular form.
13. Molecular Dynamics Calculation method as claimed in claim 11, it is characterized in that, be each main particle of border, zoning particle for neighbour, adopt the second account form to calculate the stressed of this each main particle, described the second account form adopts Newton third law.
14. many nuclear disposal systems are applicable to Molecular Dynamics Calculation, comprise primary processor nuclear and a plurality of from processor core, it is characterized in that:
This crowd examines disposal system and comprises that neighbours' particle is to search module and computing module; Wherein, described neighbours' particle is applicable to respectively to set up as main particle with each particle neighbours' particle pair of each particle to search module; Wherein, for each main particle, all determine the neighbour of this main particle in all the other particles in its zoning of living in;
Neighbours' particle of all particles calculates the stressed of each main particle to information in this zoning that described computing module is set up in each zoning search module based on neighbours' particle.
15. many nuclear disposal systems as claimed in claim 14 is characterized in that: for each main particle, described neighbours' particle further is applicable to determine the neighbour of this main particle in the particle on its border, zoning of living in to search module.
16. many nuclear disposal systems as claimed in claim 15 is characterized in that: described neighbours' particle to search module further be applicable to described neighbours' particle to information in the main particle of record and neighbour interaction calculation of force mode.
17. such as each described many nuclear disposal systems of claim 14 to 16, it is characterized in that: comprise that also neighbor list sets up module, be applicable to neighbours' particle with all particles in described each zoning of tabular form record to information.
18. many nuclear disposal systems as claimed in claim 17, it is characterized in that: also comprise the neighbor list analysis module, for the neighbours' particle pair that is in the zoning, adopt the first account form to calculate the stressed of each right main particle of this neighbours' particle, described the first account form does not adopt Newton third law.
19. many nuclear disposal systems as claimed in claim 17, it is characterized in that: also comprise the neighbor list analysis module, be neighbours' particle pair of border, zoning particle for neighbour, adopt the second account form to calculate the stressed of each right main particle of this neighbours' particle, described the second account form adopts Newton third law.
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| CN111429974B (en) * | 2020-03-24 | 2023-05-05 | 山东大学 | Molecular dynamics simulation short-range force parallel optimization method on super computer platform |
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