CN112015440A - Installation method, device, equipment and readable medium of molecular dynamics software - Google Patents
Installation method, device, equipment and readable medium of molecular dynamics software Download PDFInfo
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Abstract
The invention discloses a method for installing molecular dynamics software, which comprises the following steps: detecting a hardware architecture of a super computing cluster and recording hardware information, and detecting a software environment of the computing cluster and recording software information; acquiring user demand information, judging whether to depend on an MPI parallel mode or not and whether to need a third-party math library or not according to the demand information, and selecting molecular dynamics software according to a judgment result; and installing the selected molecular dynamics software based on the hardware information and the software information. The invention also discloses an installation device, computer equipment and a readable storage medium of the molecular dynamics software. The invention helps users to cross the professional barriers of computer hardware and software, simplifies the installation and compilation of molecular dynamics software, saves the deployment time of the software in a cluster to the maximum extent, and improves the working efficiency of implementers.
Description
Technical Field
The invention relates to the technical field of computers, in particular to a method, a device, equipment and a readable medium for installing molecular dynamics software.
Background
From the viewpoint of computational simulation, research methods in the field of material science can be divided into: macroscopically, based on statistical molecular dynamics and monte carlo simulations, and microscopically, based on the density functional theory of first principles calculations. The former is based on classical newton mechanics, while the latter is based on quantum mechanics. The density functional theory is generally considered to have higher calculation precision and accuracy, but because the calculation core is an eigenvalue problem for solving energy, the actual calculation amount is increased by O (N3) to the third power with the scale N of a simulation system. Meanwhile, due to the limitation of algorithm expansibility, even if E-level super-calculation with strong calculation power is adopted, it is still very difficult to simulate an example with the scale of tens of thousands of atomic systems by completely utilizing a density functional theory. When faced with practical problems, many microscopic systems, such as viruses, typically contain tens of thousands of atoms, and the arrangement of these atoms is completely non-periodic. This situation cannot be handled effectively at all using the density functional theory, and molecular dynamics is an effective way to handle such very large scale computing systems.
In recent years, more and more computational simulation software using molecular dynamics as core algorithms, such as NAMD, CP2K, LAMMPS, gromecs, CPMD, etc., have appeared on the market. These software have their own unique algorithms, parallel architecture, and applicable force fields. Typically, computational simulators will choose the appropriate molecular dynamics software depending on the problem being addressed. However, since these software are developed by different subject groups, they have completely different modes in terms of installation, compilation, and actual use. For example, most software can utilize an MPI parallel mode to realize cross-node calculation, NAMD software develops a chramam + + parallel framework, and LAMMPS can use a KOKKOS framework to perform calculation; the computing performance of open source software such as CP2K or LAMMPS depends heavily on third party math libraries, which often integrate the latest solving algorithm and have much higher efficiency than the traditional LAPACK or BLAS. CP2K is more dependent on 7 open-source third party math libraries. In contrast, the gromac software is relatively closed, and the core algorithm and performance security of the gromac software are completed by internal codes; for another example, gromac can only use cmake language in the bottom layer compiling stage, CP2K uses make language, and LAMMPS is compatible with both.
Based on the above analysis, it can be known that the deployment of these distinctive molecular dynamics software is simultaneously implemented on a supercomputing cluster, and it is very difficult and time consuming even for a professional cluster administrator to consider that it exerts the maximum computational performance on the platform. The cluster administrator needs to start from a cluster bottom layer framework and know all factors such as a software parallel mode, third-party mathematic library installation and compilation, software dependency relationship and the like, so that installation and deployment of multiple molecular dynamics software can be realized.
Disclosure of Invention
In view of this, an object of the embodiments of the present invention is to provide a method, an apparatus, a device, and a readable medium for installing molecular dynamics software, so as to implement one-key deployment of multiple molecular dynamics software on different supercomputing clusters based on an x _86 architecture, where the deployment process includes automatically selecting a compiler, a parallel mode, compiling a third-party math library, and implementing correct interface linking between the math library and the molecular dynamics software; and performing micro-architecture level application optimization according to a hardware bottom architecture of the supercomputing cluster. The method helps users to cross professional barriers of computer hardware and software, simplifies the installation and compilation of the molecular dynamics software, saves the deployment time of the software in a cluster to the maximum extent, and improves the working efficiency of implementers.
Based on the above purpose, an aspect of the embodiments of the present invention provides a method for installing molecular dynamics software, including the following steps: detecting a hardware architecture of a super computing cluster and recording hardware information, and detecting a software environment of the computing cluster and recording software information; acquiring user demand information, judging whether to depend on an MPI parallel mode or not and whether to need a third-party math library or not according to the demand information, and selecting molecular dynamics software according to a judgment result; and installing the selected molecular dynamics software based on the hardware information and the software information.
In some embodiments, detecting the supercomputing cluster hardware architecture and recording hardware information comprises: searching the CPU processor type and version of the super computing cluster through an lscpu instruction, and consulting a system log to determine the number of CPU computing nodes; searching GPU equipment configured by the cluster through an nvidia-smi tool, and recording the number of GPU display cards and the computing capacity of the display cards; and searching the network interconnection type among the CPU nodes through an MPI tool, and recording the version of the network interconnection type.
In some embodiments, detecting a computing cluster software environment and recording software information includes: searching the installed compiler type, version and installation path through keywords; searching the version and the installation path of the MPI parallel software through keywords; and searching the configuration information of the basic linear algebra library through keywords, and if the necessary third-party math library is lacked, downloading the lacked necessary third-party math library according to the address provided by the tool kit.
In some embodiments, determining whether to rely on the MPI parallel mode and whether to require a third party math library based on the demand information, and selecting the molecular dynamics software based on the determination comprises: if the MPI parallel mode is not relied on and a third-party mathematic library is not needed, NAMD software is installed; if the MPI parallel mode is relied on and a third-party mathematic library is not needed, installing GROMACS software; if the MPI parallel mode is relied on and a third party math library is required, the CP2K software is installed.
In some embodiments, installing the selected molecular dynamics software based on hardware information, software information comprises: judging the number of CPU nodes, whether GPU acceleration equipment and network types are contained, and whether a Multi-copy algorithm is loaded based on hardware information; and downloading and installing NAMD software of a corresponding version according to the judgment result.
In some embodiments, installing the selected molecular dynamics software based on hardware information, software information comprises: judging whether the version of the compiler is lower than the preset version or not based on the software information, if so, downloading and installing the compiler of the preset version; detecting whether GPU equipment exists or not based on the hardware information, and if yes, closing the GPU; selecting a parallel mode, configuring a math library, downloading and installing GROMACS software.
In some embodiments, installing the selected molecular dynamics software based on hardware information, software information comprises: judging whether the version of the compiler is lower than the preset version or not based on the software information, if so, downloading and installing the compiler of the preset version; a compiler is selected and a third party math library path is added to the environment variables and the CP2K software is downloaded and installed.
In another aspect of the embodiments of the present invention, there is also provided an apparatus for installing molecular dynamics software, including: the detection module is configured for detecting the supercomputing cluster hardware architecture and recording hardware information, and detecting a computing cluster software environment and recording software information; the judging module is configured for acquiring user demand information, judging whether to depend on an MPI parallel mode or not and whether to need a third-party math library or not according to the demand information, and selecting molecular dynamics software according to a judgment result; and an installation module configured to install the selected molecular dynamics software based on the hardware information and the software information.
In another aspect of the embodiments of the present invention, there is also provided a computer device, including: at least one processor; and a memory storing computer instructions executable on the processor, the instructions when executed by the processor implementing the steps of the method.
In a further aspect of the embodiments of the present invention, a computer-readable storage medium is also provided, in which a computer program for implementing the above method steps is stored when the computer program is executed by a processor.
The invention has the following beneficial technical effects: the method comprises the following steps of realizing one-key deployment of a plurality of molecular dynamics software on different supercomputing clusters based on an x-86 architecture, wherein the deployment process comprises the steps of automatically selecting a compiler, performing a parallel mode, compiling a third-party mathematic library and realizing correct interface linkage of the mathematic library and the molecular dynamics software; and performing micro-architecture level application optimization according to a hardware bottom architecture of the supercomputing cluster. The method helps users to cross professional barriers of computer hardware and software, simplifies the installation and compilation of the molecular dynamics software, saves the deployment time of the software in a cluster to the maximum extent, and improves the working efficiency of implementers.
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In order to more clearly illustrate the embodiments of the present invention or the technical solutions in the prior art, the drawings used in the description of the embodiments or the prior art will be briefly described below, and it is obvious that the drawings in the following description are only some embodiments of the present invention, and it is obvious for those skilled in the art that other embodiments can be obtained by using the drawings without creative efforts.
FIG. 1 is a schematic diagram of an embodiment of a method for installing molecular dynamics software provided by the present invention;
FIG. 2 is a schematic diagram of an embodiment of a molecular dynamics software installation apparatus provided by the present invention;
FIG. 3 is a schematic diagram of an embodiment of a computer device provided by the present invention;
FIG. 4 is a schematic diagram of an embodiment of a computer-readable storage medium provided by the present invention.
Detailed Description
In order to make the objects, technical solutions and advantages of the present invention more apparent, the following embodiments of the present invention are described in further detail with reference to the accompanying drawings.
It should be noted that all expressions using "first" and "second" in the embodiments of the present invention are used for distinguishing two entities with the same name but different names or different parameters, and it should be noted that "first" and "second" are merely for convenience of description and should not be construed as limitations of the embodiments of the present invention, and they are not described in any more detail in the following embodiments.
In view of the above objects, a first aspect of embodiments of the present invention proposes embodiments of a method for installing molecular dynamics software. Fig. 1 is a schematic diagram illustrating an embodiment of a method for installing molecular dynamics software according to the present invention. As shown in fig. 1, the embodiment of the present invention includes the following steps:
s01, detecting a supercomputing cluster hardware architecture and recording hardware information, and detecting a computing cluster software environment and recording software information;
s02, acquiring user demand information, judging whether the MPI parallel mode is relied on or not and whether a third-party math library is needed or not according to the demand information, and selecting molecular dynamics software according to a judgment result; and
and S03, installing the selected molecular dynamics software based on the hardware information and the software information.
In this embodiment, the deployment process includes automatically selecting a compiler, a parallel mode, compiling a third-party math library, and implementing correct interface linking of the math library and the molecular dynamics software; and performing micro-architecture level application optimization according to a hardware bottom architecture of the supercomputing cluster. The method fully considers the difference and the same points of software and hardware environments possibly faced by different software in the installation and compiling processes, and divides the factors into modules to realize the adaptation of the deployment software and the cluster platform software and hardware environments; the dependency relationship and compatibility between the configuration of a compiler, a parallel environment and a third-party math library and deployment software are fully considered; and automatically adding an optimizable compiler option according to the hardware architecture in the software deployment process to complete micro-architecture optimization. The method helps a user to retrieve and calculate the hardware architecture model of the cluster, configure the related software compiling environment, automatically install the matched mathematical library and the MPI parallel environment according to the type of the compiler, and optimize the software in the compiler level. The intelligent tool greatly saves the deployment time of software on different computer clusters and the learning time cost of the software and the hardware of the computer for users.
In some embodiments of the invention, detecting the supercomputing cluster hardware architecture and recording hardware information comprises: searching the CPU processor type and version of the super computing cluster through an lscpu instruction, and consulting a system log to determine the number of CPU computing nodes; searching GPU equipment configured by the cluster through an nvidia-smi tool, and recording the number of GPU display cards and the computing capacity of the display cards; and searching the network interconnection type among the CPU nodes through an MPI tool, and recording the version of the network interconnection type.
In the embodiment, firstly, the type and the version of a CPU processor of the super computing cluster are automatically searched by using an 'lscpu' instruction, and the number of CPU computing nodes is determined by referring to a system log; meanwhile, searching GPU equipment configured by the cluster by using an nvidia-smi tool, wherein the GPU equipment comprises the number of GPU display cards and the computing capacity of each display card; then, the MPI tool is used for searching the network interconnection type among the CPU nodes, recording the version of the network interconnection type, and feeding back the detection information to the user.
In some embodiments of the invention, detecting a computing cluster software environment and recording software information comprises: searching the installed compiler type, version and installation path through keywords; searching the version and the installation path of the MPI parallel software through keywords; and searching the configuration information of the basic linear algebra library through keywords, and if the necessary third-party math library is lacked, downloading the lacked necessary third-party math library according to the address provided by the tool kit.
In this embodiment, under a system directory, a keyword is used to automatically search the installed compiler type, version (fortran \ C + +) and installation path thereof of the current supercomputing cluster; for the GNU compiler, the keyword is gcc/g + +/gforran; for the intel compiler, the keywords are icc/icpc/ifort; for a parallel compiler, the keywords are mpicc, mpiport, mpicxx; meanwhile, continuously searching MPI parallel software by using the keywords, and recording the version and the installation path of the MPI parallel software; the keyword is set as mpirun; searching the configuration conditions of a basic linear algebra library by using keywords, wherein the configuration conditions comprise LAPACK, BLAS and SCALAPACK libraries; the keywords are libelack, libplas and libscalapack; and feeding back the detection information to the user.
In this embodiment, in the user environment, whether the following third-party math library is configured in the search cluster by using the keywords is determined: FFTW, ELPA, PLUMED, LIBXC, LIBINT, PEXSI, LIBXSMM, and recording the version and installation path thereof; the keywords are in sequence as follows: libfftw3, libelpa, libplus, libxc, libint, libpexsi, libxsmm; if the necessary third-party math library is lacked, software is automatically downloaded according to the address provided in the tool kit, and the detected information is fed back to the user.
In some embodiments of the present invention, determining whether to rely on the MPI parallel mode and whether to require a third party math library based on the requirement information, and selecting the molecular dynamics software based on the determination result includes: if the MPI parallel mode is not relied on and a third-party mathematic library is not needed, NAMD software is installed; if the MPI parallel mode is relied on and a third-party mathematic library is not needed, installing GROMACS software; if the MPI parallel mode is relied on and a third party math library is required, the CP2K software is installed.
In this embodiment, the user may select one or more software to install and input the corresponding numeric code using the keyboard for feedback to the back end. If the system detects that no selection signal has been introduced for a long time, all molecular dynamics software is installed by default.
In some embodiments of the invention, installing selected molecular dynamics software based on hardware information, software information comprises: judging the number of CPU nodes, whether GPU acceleration equipment and network types are contained, and whether a Multi-copy algorithm is loaded based on hardware information; and downloading and installing NAMD software of a corresponding version according to the judgment result.
In this embodiment, the following is selected according to the number of CPU nodes configured by the cluster, the type of network communication between nodes, and the algorithm based on the hardware information: if only one CPU computing node is contained, a single-node installation mode is started by default; and judging whether the hardware information contains GPU acceleration equipment or not, and automatically downloading and installing a Linux-x 86-64-multistorey-CUDA version if the hardware information contains the GPU acceleration equipment.
In this embodiment, the following is selected according to the number of CPU nodes configured by the cluster, the type of network communication between nodes, and the algorithm based on the hardware information: if only one CPU computing node is contained, a single-node installation mode is started by default; and judging whether the GPU acceleration equipment is contained in the hardware information or not, and automatically downloading and installing the Linux-x 86-64-multicore version if the GPU acceleration equipment is not contained in the hardware information.
In this embodiment, the following is selected according to the number of CPU nodes configured by the cluster, the type of network communication between nodes, and the algorithm based on the hardware information: if the node is a multi-CPU node, firstly, judging whether the GPU acceleration equipment is contained in the hardware information in the main node, and if so, automatically downloading and installing a Linux-x 86-64-multistorey-CUDA version; if not, the Linux-x86_ 64-multicast version is automatically downloaded and installed. Then, the network is subdivided into an Eth mode and an Ib mode according to the network type: if the nodes are Ethernet, the user selects whether to load a Multi-copy algorithm, if so, the Linux-x 86-64-netlrts-smp-CUDA version is automatically downloaded and installed; if not, automatically downloading and installing the Linux-x86_64-netlrts-CUDA version.
In this embodiment, the following is selected according to the number of CPU nodes configured by the cluster, the type of network communication between nodes, and the algorithm based on the hardware information: if the node is a multi-CPU node, firstly, judging whether the GPU acceleration equipment is contained in the hardware information in the main node, and if so, automatically downloading and installing a Linux-x 86-64-multistorey-CUDA version; if not, the Linux-x86_ 64-multicast version is automatically downloaded and installed. Then, the network is subdivided into an Eth mode and an Ib mode according to the network type: if the nodes are InfiniBand networks, the user selects whether to load a Multi-copy algorithm, and if so, automatically downloads and installs a Linux-x 86-64-verbs-smp-CUDA version; if not, automatically downloading and installing the Linux-x86_64-verbs-CUDA version.
In some embodiments of the invention, installing selected molecular dynamics software based on hardware information, software information comprises: judging whether the version of the compiler is lower than the preset version or not based on the software information, if so, downloading and installing the compiler of the preset version; detecting whether GPU equipment exists or not based on the hardware information, and if yes, closing the GPU; selecting a parallel mode, configuring a math library, downloading and installing GROMACS software.
In this embodiment, it is first determined whether the GCC compiler version is appropriate based on the software information: if the GCC version is below 5.1, a high version of GCC-9.2.0 is automatically downloaded and installed. The reason for using this version is that, through practical tests, it is a stable version that enables all software to run normally; detecting whether GPU equipment exists or not according to the hardware information, and if yes, closing the GPU option related to the software; specifying an appropriate C/C + + compiler; selecting a parallel mode consistent with the type of a compiler, namely a pure process MPI or a process and thread mixed mode MPI + OMP; configuring an FFTW mathematical library consistent with a parallel mode, libfftw3.so or libfftw3_ reads.so; and adding an instruction set and compiler optimization options according to the CPU model fed back from the hardware information. If the architecture is the architecture behind the intel purley platform, an AVX512 instruction set is automatically added; and after all the processes are finished, completing cmake configuration, starting GROMACS installation, and finally obtaining an executable program gmax _ mpi.
In some embodiments of the invention, installing selected molecular dynamics software based on hardware information, software information comprises: judging whether the version of the compiler is lower than the preset version or not based on the software information, if so, downloading and installing the compiler of the preset version; a compiler is selected and a third party math library path is added to the environment variables and the CP2K software is downloaded and installed.
In this embodiment, the GCC compiler version is detected based on the software information. If the GCC version is lower than 5.1, downloading and installing a high-version GCC-9.2.0 and configuring a corresponding path to an environment variable; selecting an available compiler, Intel or GNU, and sequentially installing all downloaded third-party software including FFTW, ELPA, PLUMED, LIBXC, LIBITT, PEXSI and LIBXSMM; adding installation paths of dynamic link libraries of all third-party libraries to environment variables; configuring an installation file makefile of CP2K software according to all the steps; configuring micro-architecture optimization options according to the compiler type; CP2K installation is started, resulting in executable program cp2k.
It should be particularly noted that, the steps in the embodiments of the installation method of molecular dynamics software described above can be mutually intersected, replaced, added, and deleted, so that the installation method of molecular dynamics software by these reasonable permutation and combination transformations shall also fall within the scope of the present invention, and shall not limit the scope of the present invention to the embodiments.
In view of the above object, according to a second aspect of the embodiments of the present invention, an apparatus for installing molecular dynamics software is provided. Fig. 2 is a schematic diagram of an embodiment of the installation apparatus of the molecular dynamics software provided by the present invention. As shown in fig. 2, the embodiment of the present invention includes the following modules: the detection module S11 is configured to detect the supercomputing cluster hardware architecture and record hardware information, and detect a computing cluster software environment and record software information; the judging module S12 is configured to acquire user demand information, judge whether to depend on the MPI parallel mode and whether to need a third-party math library according to the demand information, and select molecular dynamics software according to the judgment result; and an installation module S13 configured to install the selected molecular dynamics software based on the hardware information and the software information.
In view of the above object, a third aspect of the embodiments of the present invention provides a computer device. Fig. 3 is a schematic diagram of an embodiment of a computer device provided by the present invention. As shown in fig. 3, an embodiment of the present invention includes the following means: at least one processor S21; and a memory S22, the memory S22 storing computer instructions S23 executable on the processor, the instructions when executed by the processor implementing the steps of the above method.
The invention also provides a computer readable storage medium. FIG. 4 is a schematic diagram illustrating an embodiment of a computer-readable storage medium provided by the present invention. As shown in fig. 4, the computer readable storage medium stores S31 a computer program that, when executed by a processor, performs the method as described above S32.
Finally, it should be noted that, as one of ordinary skill in the art can appreciate that all or part of the processes of the methods of the above embodiments can be implemented by a computer program to instruct related hardware, and the program of the installation method of the molecular dynamics software can be stored in a computer readable storage medium, and when executed, can include the processes of the embodiments of the methods as described above. The storage medium of the program may be a magnetic disk, an optical disk, a Read Only Memory (ROM), a Random Access Memory (RAM), or the like. The embodiments of the computer program may achieve the same or similar effects as any of the above-described method embodiments.
Furthermore, the methods disclosed according to embodiments of the present invention may also be implemented as a computer program executed by a processor, which may be stored in a computer-readable storage medium. Which when executed by a processor performs the above-described functions defined in the methods disclosed in embodiments of the invention.
Further, the above method steps and system elements may also be implemented using a controller and a computer readable storage medium for storing a computer program for causing the controller to implement the functions of the above steps or elements.
Those of skill would further appreciate that the various illustrative logical blocks, modules, circuits, and algorithm steps described in connection with the disclosure herein may be implemented as electronic hardware, computer software, or combinations of both. To clearly illustrate this interchangeability of hardware and software, various illustrative components, blocks, modules, circuits, and steps have been described above generally in terms of their functionality. Whether such functionality is implemented as software or hardware depends upon the particular application and design constraints imposed on the overall system. Skilled artisans may implement the described functionality in varying ways for each particular application, but such implementation decisions should not be interpreted as causing a departure from the scope of the disclosed embodiments of the present invention.
In one or more exemplary designs, the functions may be implemented in hardware, software, firmware, or any combination thereof. If implemented in software, the functions may be stored on or transmitted over as one or more instructions or code on a computer-readable medium. Computer-readable media includes both computer storage media and communication media including any medium that facilitates transfer of a computer program from one place to another. A storage media may be any available media that can be accessed by a general purpose or special purpose computer. By way of example, and not limitation, such computer-readable media can comprise RAM, ROM, EEPROM, CD-ROM or other optical disk storage, magnetic disk storage or other magnetic storage devices, or any other medium that can be used to carry or store desired program code in the form of instructions or data structures and that can be accessed by a general-purpose or special-purpose computer, or a general-purpose or special-purpose processor. Also, any connection is properly termed a computer-readable medium. For example, if the software is transmitted from a website, server, or other remote source using a coaxial cable, fiber optic cable, twisted pair, Digital Subscriber Line (DSL), or wireless technologies such as infrared, radio, and microwave, then the coaxial cable, fiber optic cable, twisted pair, DSL, or wireless technologies such as infrared, radio, and microwave are included in the definition of medium. Disk and disc, as used herein, includes Compact Disc (CD), laser disc, optical disc, Digital Versatile Disc (DVD), floppy disk, blu-ray disc where disks usually reproduce data magnetically, while discs reproduce data optically with lasers. Combinations of the above should also be included within the scope of computer-readable media.
The foregoing is an exemplary embodiment of the present disclosure, but it should be noted that various changes and modifications could be made herein without departing from the scope of the present disclosure as defined by the appended claims. The functions, steps and/or actions of the method claims in accordance with the disclosed embodiments described herein need not be performed in any particular order. Furthermore, although elements of the disclosed embodiments of the invention may be described or claimed in the singular, the plural is contemplated unless limitation to the singular is explicitly stated.
It should be understood that, as used herein, the singular forms "a", "an" and "the" are intended to include the plural forms as well, unless the context clearly supports the exception. It should also be understood that "and/or" as used herein is meant to include any and all possible combinations of one or more of the associated listed items.
The numbers of the embodiments disclosed in the embodiments of the present invention are merely for description, and do not represent the merits of the embodiments.
It will be understood by those skilled in the art that all or part of the steps for implementing the above embodiments may be implemented by hardware, or may be implemented by a program instructing relevant hardware, and the program may be stored in a computer-readable storage medium, and the above-mentioned storage medium may be a read-only memory, a magnetic disk or an optical disk, etc.
Those of ordinary skill in the art will understand that: the discussion of any embodiment above is meant to be exemplary only, and is not intended to intimate that the scope of the disclosure, including the claims, of embodiments of the invention is limited to these examples; within the idea of an embodiment of the invention, also technical features in the above embodiment or in different embodiments may be combined and there are many other variations of the different aspects of the embodiments of the invention as described above, which are not provided in detail for the sake of brevity. Therefore, any omissions, modifications, substitutions, improvements, and the like that may be made without departing from the spirit and principles of the embodiments of the present invention are intended to be included within the scope of the embodiments of the present invention.
Claims (10)
1. A method for installing molecular dynamics software is characterized by comprising the following steps:
detecting a hardware architecture of a super computing cluster and recording hardware information, and detecting a software environment of the computing cluster and recording software information;
acquiring user demand information, judging whether to depend on an MPI parallel mode or not and whether to need a third-party math library or not according to the demand information, and selecting molecular dynamics software according to the judgment result; and
and installing the selected molecular dynamics software based on the hardware information and the software information.
2. The method of molecular dynamics software installation according to claim 1, wherein detecting supercomputing cluster hardware architecture and recording hardware information comprises:
searching the CPU processor type and version of the super computing cluster through an lscpu instruction, and consulting a system log to determine the number of CPU computing nodes;
searching GPU equipment configured by the cluster through an nvidia-smi tool, and recording the number of GPU display cards and the computing capacity of the display cards;
and searching the network interconnection type among the CPU nodes through an MPI tool, and recording the version of the network interconnection type.
3. The method of molecular dynamics software installation according to claim 1, wherein detecting a computing cluster software environment and recording software information comprises:
searching the installed compiler type, version and installation path through keywords;
searching the version and the installation path of the MPI parallel software through keywords;
and searching configuration information of the basic linear algebra library through keywords, if the necessary third-party math library is lacked, downloading the lacked necessary third-party math library according to an address provided by the toolkit.
4. The method of claim 1, wherein determining whether to rely on the MPI parallel mode and whether a third party math library is required based on the requirement information, and selecting the molecular dynamics software based on the determination comprises:
if the MPI parallel mode is not relied on and a third-party mathematic library is not needed, NAMD software is installed;
if the MPI parallel mode is relied on and a third-party mathematic library is not needed, installing GROMACS software;
if the MPI parallel mode is relied on and a third party math library is required, the CP2K software is installed.
5. The method of installing molecular dynamics software according to claim 1, wherein installing the selected molecular dynamics software based on the hardware information and software information comprises:
judging the number of CPU nodes, whether GPU acceleration equipment is contained or not, the network type and whether a Multi-copy algorithm is loaded or not based on the hardware information;
and downloading and installing NAMD software of a corresponding version according to the judgment result.
6. The method of installing molecular dynamics software according to claim 1, wherein installing the selected molecular dynamics software based on the hardware information and software information comprises:
judging whether the version of the compiler is lower than a preset version or not based on the software information, if so, downloading and installing the compiler with the preset version;
detecting whether GPU equipment exists or not based on the hardware information, and if yes, closing the GPU;
selecting a parallel mode, configuring a math library, downloading and installing GROMACS software.
7. The method of installing molecular dynamics software according to claim 1, wherein installing the selected molecular dynamics software based on the hardware information and software information comprises:
judging whether the version of the compiler is lower than a preset version or not based on the software information, if so, downloading and installing the compiler with the preset version;
a compiler is selected and a third party math library path is added to the environment variables and the CP2K software is downloaded and installed.
8. An apparatus for installing molecular dynamics software, comprising:
the detection module is configured for detecting the supercomputing cluster hardware architecture and recording hardware information, and detecting a computing cluster software environment and recording software information;
the judging module is configured for acquiring user demand information, judging whether to depend on an MPI parallel mode or not and whether to need a third-party math library or not according to the demand information, and selecting molecular dynamics software according to the judgment result; and
an installation module configured to install the selected molecular dynamics software based on the hardware information and the software information.
9. A computer device, comprising:
at least one processor; and
a memory storing computer instructions executable on the processor, the instructions when executed by the processor implementing the steps of any of the methods 1-7.
10. A computer-readable storage medium, in which a computer program is stored which, when being executed by a processor, carries out the steps of the method according to any one of claims 1 to 7.
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| WO2022062647A1 (en) * | 2020-09-25 | 2022-03-31 | 苏州浪潮智能科技有限公司 | Method and apparatus for installing molecular dynamics software, and device and readable medium |
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