CN105511882A - Realizing method and device for tasks of CPMD (car-parrinello molecular dynamics) - Google Patents
Realizing method and device for tasks of CPMD (car-parrinello molecular dynamics) Download PDFInfo
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- CN105511882A CN105511882A CN201510921059.9A CN201510921059A CN105511882A CN 105511882 A CN105511882 A CN 105511882A CN 201510921059 A CN201510921059 A CN 201510921059A CN 105511882 A CN105511882 A CN 105511882A
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- G—PHYSICS
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- G16C—COMPUTATIONAL CHEMISTRY; CHEMOINFORMATICS; COMPUTATIONAL MATERIALS SCIENCE
- G16C20/00—Chemoinformatics, i.e. ICT specially adapted for the handling of physicochemical or structural data of chemical particles, elements, compounds or mixtures
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- G06F9/44—Arrangements for executing specific programs
- G06F9/448—Execution paradigms, e.g. implementations of programming paradigms
- G06F9/4482—Procedural
Abstract
The invention discloses a realizing method and device for computation tasks of CPMD (car-parrinello molecular dynamics). The realizing method comprises steps as follows: acquiring a computation command input by a user; analyzing the computation command, and determining a computation type and a computation parameter contained in the computation command; substituting the computation parameter into a pre-allocated computation command statement corresponding to the computation type, and executing the computation command statement. By the aid of the technical scheme, the realizing process of the computation tasks of the CPMD does not require a command line, the computation tasks can be completed only through simple operation based on a graphical interface, accordingly, the operation difficulty is greatly reduced, the executing efficiency is improved, and the error probability is reduced.
Description
Technical field
The present invention relates to scientific algorithm field, and especially, relate to task implementation method and the device of a kind of CPMD.
Background technology
CPMD (Car-ParrinelloMolecularDynamics) is the quantum chemistry calculation program of a HF Ab initio (abinitio), and this program utilizes plane wave, pseudopotential method to calculate the kinetic property of molecule by density functional theory (DensityFunctionalTheory).
In traditional HPCC environment, user will run CPMD calculation procedure to be needed to use remote character terminal to perform sequence of operations under command line environment usually, generally has following flow process:
Get out the executable file of CPMD calculation procedure, input file, data file etc.These files need the overall situation being placed on cluster to share in storage usually, and user generally uses the instruments such as FTP, SFTP to upload these files to cluster, and in most of the cases, user also needs to carry out edit-modify with the text edit tool to input file etc.
Determine the process number running calculative CPMD example needs, and run on which node, these information are passed to the process initiation device of MPI by the mode of command line parameter, as mpirun, mpiexec etc.By the process initiation device startup optimization CPMD calculation procedure of MPI.
After program has been run, check result of calculation, or use the instruments such as FTP, SFTP to download destination file to user local terminal, then by analysis software result.
It is more than the main flow directly running CPMD calculation procedure; under actual conditions; user submits parallel computation task on HPCC; need the unified interface using job scheduling software to provide; user also needs to write a job scheduling script more usually; in script, apply for computational resource, submit parallel computation task to by this script, come Processing tasks queuing, Resources allocation, initiation concurrent program by job scheduling software.
Be described above in traditional HPCC environment, user runs the basic procedure of CPMD calculation procedure, and these flow processs need usually under remote character terminal, is realized by the mode of order line.For the vast domestic consumer of non-bone ash level, operation easier is large, and execution efficiency is low, and error probability is large.
The drawback of tradition executive mode is mainly manifested in:
Use difficulty very large.Want to submit a CPMD calculation task to smoothly, user often needs to be familiar with very much a lot of and that its specialty background is irrelevant a lot of knowledge and instrument, use of such as (SuSE) Linux OS basic operation, Shell script, conventional text editing and character handling implement, the calling of MPI environment, job scheduling software etc., the learning curve of these knowledge or instrument is very steep, and skilled grasp usually needs the time spending the several years.Such trace utilization cost is very huge concerning vast domestic consumer.
Execution efficiency is low.Want to submit a CPMD calculation task to smoothly, need to perform multiple flow process, need to use some professional tools, need to perform complicated loaded down with trivial details operation in command line environment, thus cause the submission of parallel computation task to be wasted time and energy, execution efficiency is low.
For most of domestic consumer, perform complicated loaded down with trivial details operation in command line environment, occur that the probability of human operational error is very large.Particularly for the unfamiliar user of operating process, all easily encounter problems at the links performed.
In addition, for the keeper of HPCC, to the capable terminal of domestic consumer's open command, also there is the risk of security.The maloperation of user may the stable operation of influential system, and hacker also likely avails oneself of the opportunity to get in.
In the prior art, the parallel computation task of oneself is provided to carry out instruction submission by graphical interface of submitting to although there are some business software for calculation, but be all for individual software, there is no universality, and, also need special client software to coordinate, cannot realize or exist problem in various degree with the combination of job scheduling software.
Need to be realized by the mode of order line under remote character terminal when running CPMD calculation procedure for user in correlation technique, operation easier is large, and execution efficiency is low, the problem that error probability is large, not yet proposes effective solution at present.
Summary of the invention
Need to be realized by the mode of order line under remote character terminal when running CPMD calculation procedure for user in correlation technique, operation easier is large, execution efficiency is low, the problem that error probability is large, the present invention proposes task implementation method and the device of a kind of CPMD, user can be made without the need to the mode by order line, only input computations by shirtsleeve operation, just can realize whole calculating process.
Technical scheme of the present invention is achieved in that
According to an aspect of the present invention, provide the task implementation method of a kind of CPMD, this implementation method comprises:
Obtain the computations of user's input;
Computations is resolved, determines the calculating parameter that comprises in the type that calculates and computations;
Judge that whether the computations that user inputs is legal, when the result judged is no, forbid performing calculation command statement and pointing out;
Calculating parameter is updated in the pre-configured calculation command statement corresponding with compute type, and performs this calculation command statement.
In addition, this implementation method comprises further: the whether legal condition that judges computations that user inputs comprises the scope of calculating parameter in the form of computations and/or computations.
In addition, before being updated to by calculating parameter in the pre-configured calculation command statement corresponding with compute type, implementation method comprises further:
Obtain the resource request instruction of user's input, resolve resource request instruction, obtain resource parameters, wherein, resource parameters is for representing user's requested resource amount;
Resource parameters is updated to pre-configured computational resource scheduling statement, and performs this computational resource scheduling statement.
In addition, before resource parameters is updated to pre-configured computational resource scheduling statement by execution, implementation method comprises further:
Judge that whether the resource request instruction that user inputs is legal, and when judged result is no, forbid performing computational resource scheduling statement and pointing out;
Wherein, whether legal condition comprises form and/or user's requested resource amount of computational resource request instruction to judge resource request instruction that user inputs.
Wherein, computational resource comprise following one of at least:
The store path of computing node, CPU check figure, calculating duration, result of calculation.
In addition, the computations obtaining user's input comprises:
By providing graphical interfaces in advance, obtaining the calculating parameter that inputs in the parameters input frame of user in graphical interfaces and/or obtain according to the store path inputted in the path input frame of user in graphical interfaces the file that comprises calculating parameter and determine the input parameter in this file.
Wherein, graphical interfaces comprises web interface.
According to a further aspect in the invention, provide the task implement device of a kind of CPMD, this implement device comprises:
First acquisition module, for obtaining the computations of user's input;
Parsing module, for resolving computations, determines the calculating parameter that comprises in the type that calculates and computations;
Judge module, judges that whether the computations that user inputs is legal, when the result judged is no, forbids performing calculation command statement and pointing out;
First execution module, for being updated to pre-configured and compute classes by calculating parameter; In the calculation command statement that type is corresponding, and perform this calculation command statement.
In addition, this implement device comprises further, and the whether legal condition that judges computations that user inputs comprises the scope of calculating parameter in the form of computations and/or computations.
In addition, this implement device comprises further:
Second acquisition module, before calculating parameter being updated in the pre-configured calculation command statement corresponding with compute type, obtain the resource request instruction of user's input, resource request instruction is resolved, obtain resource parameters, wherein, resource parameters is for representing user's requested resource amount;
Second execution module, for resource parameters being updated to pre-configured computational resource scheduling statement, and performs this computational resource scheduling statement.
The present invention is by resolving the calculating parameter and compute type that obtain the computations from user's input, and calculating parameter is updated to the pre-configured calculation command statement corresponding with this compute type, and perform this calculation command statement, user can be made only need to input simple computations, without the need to carrying out complicated order line operation, just can complete calculating, reducing the difficulty that user uses CPMD calculation procedure, improve execution efficiency, reduce error probability.
Accompanying drawing explanation
In order to be illustrated more clearly in the embodiment of the present invention or technical scheme of the prior art, be briefly described to the accompanying drawing used required in embodiment below, apparently, accompanying drawing in the following describes is only some embodiments of the present invention, for those of ordinary skill in the art, under the prerequisite not paying creative work, other accompanying drawing can also be obtained according to these accompanying drawings.
Fig. 1 is the implementation method process flow diagram of the calculation task of CPMD according to the embodiment of the present invention;
Fig. 2 is the implement device block diagram of the calculation task of CPMD according to the embodiment of the present invention.
Embodiment
Below in conjunction with the accompanying drawing in the embodiment of the present invention, be clearly and completely described the technical scheme in the embodiment of the present invention, obviously, described embodiment is only the present invention's part embodiment, instead of whole embodiments.Based on the embodiment in the present invention, the every other embodiment that those of ordinary skill in the art obtain, all belongs to the scope of protection of the invention.
According to embodiments of the invention, provide the implementation method of the calculation task of a kind of CPMD.
As shown in Figure 1, this implementation method comprises:
Step S101, obtains the computations of user's input;
Step S103, resolves computations, determines the calculating parameter that comprises in the type that calculates and computations;
Step S105, judges that whether the computations that user inputs is legal, when the result judged is no, forbids performing calculation command statement and pointing out;
Step S107, is updated to calculating parameter in the pre-configured calculation command statement corresponding with compute type, and performs this calculation command statement.
In addition, this implementation method comprises further:
The whether legal condition that judges computations that user inputs comprises the scope of calculating parameter in the form of computations and/or computations.
In addition, before performing the statement substituting into calculating parameter, this implementation method comprises further:
Obtain the resource request instruction of user's input, resolve resource request instruction, obtain resource parameters, wherein, resource parameters is for representing user's requested resource amount;
Resource parameters is updated to pre-configured computational resource scheduling statement, and performs this computational resource scheduling statement.
In addition, before execution computational resource scheduling statement, this implementation method comprises further:
Judge that whether the resource request instruction that user inputs is legal, and when judged result is no, forbid performing computational resource scheduling statement and pointing out;
Wherein, the whether legal condition that judges resource request instruction that user inputs comprise following one of at least:
The form of computational resource request instruction, user's requested resource amount.
Wherein, computational resource comprise following one of at least:
The store path of computing node, CPU check figure, calculating duration, result of calculation.
In addition, the computations obtaining user's input comprises:
By providing graphical interfaces in advance, obtaining the calculating parameter that inputs in the parameters input frame of user in graphical interfaces and/or obtain according to the store path inputted in the path input frame of user in graphical interfaces the file that comprises calculating parameter and determine the input parameter in this file.
Wherein, graphical interfaces comprises web interface.
According to embodiments of the invention, additionally provide the implement device of the calculation task of a kind of CPMD.
As shown in Figure 2, this implement device comprises:
First acquisition module 21, for obtaining the computations of user's input;
Parsing module 22, for resolving computations, determines the calculating parameter that comprises in the type that calculates and computations;
Judge module 23, judges that whether the computations that user inputs is legal, when the result judged is no, forbids performing calculation command statement and pointing out;
First execution module 24, for being updated to by calculating parameter in the pre-configured calculation command statement corresponding with compute type, and performs this calculation command statement.
In addition, this implement device comprises further:
The whether legal condition that judges computations that user inputs comprises the scope of calculating parameter in the form of computations and/or computations.
In addition, this implement device comprises further:
Second acquisition module (not shown), for before performing the statement substituting into calculating parameter, obtains the resource request instruction of user's input, resource request instruction is resolved, obtain resource parameters, wherein, resource parameters is for representing user's requested resource amount;
Second execution module (not shown), for resource parameters being updated to pre-configured computational resource scheduling statement, and performs this computational resource scheduling statement.
Such as, in one embodiment, according to technical scheme of the present invention, carried out web encapsulation for CPMD calculation procedure, and write corresponding software interface and realize concrete function.
By encapsulation, the job invocation flow process of CPMD calculation procedure is hidden in bottom, be supplied to the web interface of user's simple, intuitive, user only needs to perform shirtsleeve operation in web interface, such as: input calculates desired parameters, seletion calculation type, resource required for input calculates, the store path of seletion calculation result, etc., the implementation method of the CPMD calculation task that embodiments of the invention provide and device, calculating parameter and the compute type of above-mentioned user input can be obtained, and the calculating parameter acquired is updated to the pre-configured calculation command statement corresponding with this compute type, perform this calculation command statement and return result of calculation, and, user can check result of calculation according to the store path of the result of calculation of oneself application.
And, the implementation method of the CPMD calculation task provided according to embodiments of the invention and device, validity judgement can also be carried out to the computations of user's input, if the calculation command statement identification that the computations form of user's input can not be preconfigured, then refusal performs this statement, and send prompting message, thus avoid user error operation or the malicious attack to software.
In addition, apply in the process of computational resource user, the quantity of the computational resource for application and/or resource type is only needed to input in corresponding text box, or select in corresponding drop-down menu, the implementation method of the CPMD calculation task provided in the embodiment of the present invention can obtain the resource request content of user's input, resource in server is dispatched, be supplied to user, simultaneously, if the total resources that the computational resource quantity that user applies for can provide at present beyond server, then refuse the application of user, and send prompting message.
The web method for packing provided by above-described embodiment, just can realize data file preparation, computational resource application, calculation task is submitted to, result of calculation such as to check at the entire work flow, without the need to the mode by order line, greatly reduces the use threshold of user, improve service efficiency, reduce error probability.
In the present embodiment, carry out web encapsulation for CPMD calculation procedure, for user brings brand-new use-pattern, effect is mainly reflected in:
1. greatly reduce and use difficulty.User no longer needs skillfully to grasp the knowledge irrelevant with its specialty background and the instrument such as (SuSE) Linux OS basic operation, Shell script, conventional text editing and character handling implement, the calling of MPI environment, job scheduling software, just easily can complete the work such as preparation, execution of CPMD calculation task, greatly reduce use threshold.
2. greatly improve service efficiency.The order line operation Hide All of very complicated, at bottom, performs at bottom automatic batch, can save a large amount of manual operation time, improve service efficiency.
3. improve the success ratio of job invocation.According to the web method for packing that embodiment provides, the parameter can submitted in web interface user and data carry out the validity checking of different latitude.Such as, check whether the computational resource of user's application exceedes its authority, whether the parameter of user's input is legal, and whether the input file form of user is correct, if the mistake of judging, can provide corresponding prompting in web interface.The success ratio of parallel task submission greatly can be improved by these validity checkings.
4. easily realize sophisticated functions.Some complicated or Premium Features when MPI concurrent program runs, the selection of such as computational grid, start cpu process binding etc., if need to specify complicated parameter by command line mode, complex operation, use difficulty comparatively large, after carrying out web encapsulation, user only needs just can realize these functions by some Option Boxs in web interface.
5. improve the safety in utilization of HPCC.After the operation of the job invocation of domestic consumer is encapsulated in web interface, what user performed is all enclosed operation, avoids influential system to a great extent and stablizes or user's illegal operation of safety.
In sum, by means of technique scheme of the present invention, by obtaining the computations inputted in the parameters input frame of user in graphical interfaces, and/or resource bid instruction, and be updated to corresponding command statement by resolving the parameter information obtained from instruction, and perform this command statement, the implementation procedure of the calculation task of CPMD can be made without the need to passing through order line, greatly reduce operation easier, improve execution efficiency, reduce error probability, and, by the validity judgement to user's input information, the safe and stable operation of CPMD calculation procedure can be ensured well.
The foregoing is only preferred embodiment of the present invention, not in order to limit the present invention, within the spirit and principles in the present invention all, any amendment done, equivalent replacement, improvement etc., all should be included within protection scope of the present invention.
Claims (10)
1. for a task implementation method of CPMD, it is characterized in that, comprising:
Obtain the computations of user's input;
Described computations is resolved, determines the calculating parameter that comprises in the type that calculates and described computations;
Judge that whether the computations that described user inputs is legal, wherein, when the result of described judgement is no, forbid performing calculation command statement and pointing out;
Described calculating parameter is updated in the pre-configured calculation command statement corresponding with described compute type, and performs this calculation command statement.
2. task implementation method according to claim 1, is characterized in that, the whether legal condition that judges computations that described user inputs comprises the scope of calculating parameter in the form of described computations and/or described computations.
3. task implementation method according to claim 1, is characterized in that, before being updated to by described calculating parameter in the pre-configured calculation command statement corresponding with described compute type, described implementation method comprises further:
Obtain the resource request instruction of user's input, resolve described resource request instruction, obtain resource parameters, wherein, described resource parameters is for representing user's requested resource amount;
Described resource parameters is updated to pre-configured computational resource scheduling statement, and performs this computational resource scheduling statement.
4. task implementation method according to claim 3, is characterized in that, before described resource parameters is updated to pre-configured computational resource scheduling statement by execution, described implementation method comprises further:
Judge that whether the resource request instruction that described user inputs is legal, and when described judged result is no, forbid performing computational resource scheduling statement and pointing out;
Wherein, whether legal condition comprises form and/or user's requested resource amount of described computational resource request instruction to judge resource request instruction that described user inputs.
5. task implementation method according to claim 3, is characterized in that, described computational resource comprise following one of at least:
The store path of computing node, CPU check figure, calculating duration, result of calculation.
6. task implementation method as claimed in any of claims 1 to 5, is characterized in that, the computations obtaining user's input comprises:
By providing graphical interfaces in advance, obtaining the calculating parameter that inputs in the parameters input frame of user in described graphical interfaces and/or obtain according to the store path inputted in the path input frame of user in described graphical interfaces the file that comprises calculating parameter and determine the input parameter in this file.
7. task implementation method as claimed in any of claims 1 to 5, is characterized in that, described graphical interfaces comprises web interface.
8. a task implement device of CPMD, is characterized in that, comprising:
First acquisition module, for obtaining the computations of user's input;
Parsing module, for resolving described computations, determines the calculating parameter that comprises in the type that calculates and described computations;
Judge module, judges that whether the computations that described user inputs is legal, when the result of described judgement is no, forbids performing calculation command statement and pointing out;
First execution module, pre-configured with described compute classes for described calculating parameter is updated to; In the calculation command statement that type is corresponding, and perform this calculation command statement.
9. task implement device according to claim 8, is characterized in that, comprise further: the whether legal condition that judges computations that described user inputs comprises the scope of calculating parameter in the form of described computations and/or described computations.
10. task implement device according to claim 8, is characterized in that, comprise further:
Second acquisition module, before described calculating parameter being updated in the pre-configured calculation command statement corresponding with described compute type, obtain the resource request instruction of user's input, described resource request instruction is resolved, obtain resource parameters, wherein, described resource parameters is for representing user's requested resource amount;
Second execution module, for described resource parameters being updated to pre-configured computational resource scheduling statement, and performs this computational resource scheduling statement.
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| CN103530091A (en) * | 2013-10-29 | 2014-01-22 | 曙光信息产业(北京)有限公司 | Method and device for implementing task of calculating CPMD (car-Parrinello molecular dynamics simulations) |
| CN103530131A (en) * | 2013-10-28 | 2014-01-22 | 曙光信息产业(北京)有限公司 | Method and device for implementing Gaussian calculating task |
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| US20080005490A1 (en) * | 2006-05-31 | 2008-01-03 | Shinjiro Shiraki | Storage control apparatus and method for controlling number of commands executed in storage control apparatus |
| CN103294485A (en) * | 2013-06-27 | 2013-09-11 | 曙光信息产业(北京)有限公司 | Web service packaging method and Web service packaging system both used for ABINIT parallel computing system |
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Application publication date: 20160420 |