AU2021105451A4 - Collaborative Computing System and Method in Different Places for Marine Medicinal Bio-resources - Google Patents
Collaborative Computing System and Method in Different Places for Marine Medicinal Bio-resources Download PDFInfo
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- AU2021105451A4 AU2021105451A4 AU2021105451A AU2021105451A AU2021105451A4 AU 2021105451 A4 AU2021105451 A4 AU 2021105451A4 AU 2021105451 A AU2021105451 A AU 2021105451A AU 2021105451 A AU2021105451 A AU 2021105451A AU 2021105451 A4 AU2021105451 A4 AU 2021105451A4
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- 238000000034 method Methods 0.000 title claims abstract description 16
- 238000004891 communication Methods 0.000 claims description 18
- 238000013461 design Methods 0.000 claims description 6
- 238000004364 calculation method Methods 0.000 claims description 5
- 230000008569 process Effects 0.000 claims description 4
- 102000004169 proteins and genes Human genes 0.000 claims description 4
- 108090000623 proteins and genes Proteins 0.000 claims description 4
- 238000003041 virtual screening Methods 0.000 claims description 3
- 238000009510 drug design Methods 0.000 abstract description 12
- 238000012362 drug development process Methods 0.000 abstract description 5
- 238000009509 drug development Methods 0.000 description 6
- 239000003814 drug Substances 0.000 description 5
- 229940079593 drug Drugs 0.000 description 5
- 238000005192 partition Methods 0.000 description 5
- 238000011161 development Methods 0.000 description 4
- 238000010586 diagram Methods 0.000 description 2
- 230000000694 effects Effects 0.000 description 2
- 238000004422 calculation algorithm Methods 0.000 description 1
- 239000000470 constituent Substances 0.000 description 1
- 238000001647 drug administration Methods 0.000 description 1
- 238000005516 engineering process Methods 0.000 description 1
- 230000003993 interaction Effects 0.000 description 1
- 230000002452 interceptive effect Effects 0.000 description 1
- 238000012986 modification Methods 0.000 description 1
- 230000004048 modification Effects 0.000 description 1
- 238000000329 molecular dynamics simulation Methods 0.000 description 1
- 238000000324 molecular mechanic Methods 0.000 description 1
- 238000000302 molecular modelling Methods 0.000 description 1
- 229920001184 polypeptide Polymers 0.000 description 1
- 102000004196 processed proteins & peptides Human genes 0.000 description 1
- 108090000765 processed proteins & peptides Proteins 0.000 description 1
- 238000012216 screening Methods 0.000 description 1
- 238000004088 simulation Methods 0.000 description 1
- 150000003384 small molecules Chemical class 0.000 description 1
- 239000000126 substance Substances 0.000 description 1
- 230000008093 supporting effect Effects 0.000 description 1
- 230000001960 triggered effect Effects 0.000 description 1
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- G—PHYSICS
- G06—COMPUTING; CALCULATING OR COUNTING
- G06F—ELECTRIC DIGITAL DATA PROCESSING
- G06F9/00—Arrangements for program control, e.g. control units
- G06F9/06—Arrangements for program control, e.g. control units using stored programs, i.e. using an internal store of processing equipment to receive or retain programs
- G06F9/46—Multiprogramming arrangements
- G06F9/50—Allocation of resources, e.g. of the central processing unit [CPU]
- G06F9/5061—Partitioning or combining of resources
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- G—PHYSICS
- G06—COMPUTING; CALCULATING OR COUNTING
- G06N—COMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
- G06N5/00—Computing arrangements using knowledge-based models
- G06N5/04—Inference or reasoning models
- G06N5/043—Distributed expert systems; Blackboards
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- Engineering & Computer Science (AREA)
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- Physics & Mathematics (AREA)
- General Engineering & Computer Science (AREA)
- General Physics & Mathematics (AREA)
- Medical Treatment And Welfare Office Work (AREA)
Abstract
The present invention discloses a collaborative computing system and method in different
places for marine medicinal bio-resources. The system comprises a resource database, a
collaborative computing and managing platform in different places, and a plurality of
computing nodes, wherein the computing nodes comprise local computing nodes and
computing nodes in different places; the resource database is used for storing data of the marine
medicinal bio-resources; the collaborative computing and managing platform in different
places is used for receiving computing task request of the local computing nodes and
scheduling, and receiving computing task results of the computing nodes in different places;
and the computing nodes are used for computing the data in the resource database. In a drug
design and development process of the marine medicinal bio-resources, local and different
place computing resources are sufficiently utilized to strength collaborative computing ability
in different places, thereby realizing low-time-delay exchange of large-scale data information
and low-cost use of computing ability.
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Description
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Collaborative Computing System and Method in Different Places for Marine
Medicinal Bio-resources
The present invention relates to the field of high-performance computing, and in
particular, to a collaborative computing system and method in different places for
marine medicinal bio-resources.
Drug development is a process with high cost and lower efficiency. Generally, it
averagely takes three to five years, and even ten years or more to successfully develop
a drug, which great input in fund. Only a few developed drugs can accomplish the
clinical trials, and can pass through the final examination of the management
department for drug administration. As one of the core technologies for innovative
drug study at present, a computer-assisted drug design can greatly improve drug
development efficiency, and reduces the drug development cost.
As one of most important application fields of the computer-assisted drug design,
high-performance computing is mainly applied to the drug design, a drug
development and utilization high-performance computer and study on interaction
between biomacromolecules (proteins, DNA and RNA) and related active molecules
(chemical small molecules, polypeptides and the like; and the used method mainly
include molecular modeling, molecular mechanics, molecular dynamics simulation
and the like. At present, the successful drug design and drug development directly
depends on high-performance computing ability as methods such as molecular
simulation and molecular screening need a great number of computing resources. At
present, computing in drug design and development processes mainly depends on
computing resources of a place at which development work is carried out, which may cause great pressure on the computing resources, delay on development work and certain loss.
Therefore, it is desirable to develop a collaborative computing system in
different places for marine medicinal bio-resources, which can strength collaborative
computing ability in different places in an interactive mode, realizes low-time-delay
exchange of large-scale data information and low-cost use of computing ability,
achieves era-flops-level computing effect, and brings high-performance computing
supporting effect of a super-computing center into play better.
The objective of the present invention is to provide a collaborative computing
system and method in different places for marine medicinal bio-resources, to solve the
problems in the prior art. In a drug design and development process of the marine
medicinal bio-resources, local and different-place computing resources are
sufficiently utilized to strength collaborative computing ability in different places,
thereby realizing low-time-delay exchange of large-scale data information and
low-cost use of computing ability.
To achieve the objective, the present invention provides the following scheme: a
collaborative computing system in different places for marine medicinal bio-resources
includes a resource database, a collaborative computing and managing platform in
different places, and a plurality of computing nodes, where the computing nodes
include local computing nodes and computing nodes in different places;
the resource database is used for storing data of the marine medicinal
bio-resources;
the collaborative computing and managing platform in different places is used
for receiving computing task request of the local computing nodes and scheduling, and receiving computing task results of the computing nodes in different places; and the computing nodes are used for computing the data in the resource database.
Preferably, the resource database includes a virtual screening database, a protein
database and a molecule database.
Preferably, the collaborative computing and managing platform in different
places includes a safety module, a task scheduling module, a data exchange storage
module and a communication module, where the safety module is connected to the
task scheduling module, the data exchange storge module is connected to the
computing node module through the communication module, and the task scheduling
module is connected to the computing nodes in different places through the
communication module.
Preferably, each of the computing nodes include a task request module, a task
receiving module, a computing ability estimation module, a search module, a
computing module, a data encryption module and a communication unit, where the
task request module is connected to the computing ability estimation module, the task
receiving module is connected to the computing module, the computing module is
connected to the search module, the data encryption module is separately connected to
the computing module and the task request module, the search module is connected to
the resource database through the communication unit, and the computing module is
connected to the data exchange storage module through the communication unit.
Preferably, the local computing nodes and the computing nodes in different
places are set with same task processing program.
A collaborative computing method in different places for marine medicinal
bio-resources is further provided, including the following steps:
Si, obtaining a computing task, estimating the quantity of the local computing
resources and the different-place computing resources needed for the computing task,
and generating a different-place collaborative design request based on the quantity of
the different-place computing resources;
S2, registering the collaborative computing and managing platform in different
places, sending the different-place collaborative design request to the collaborative
computing and managing platform in different places, and generating a different-place
collaborative computing task;
S3, encrypting and distributing the collaborative computing task;
S4, receiving the different-place collaborative computing task, searching and
calling data based on the different-place collaborative computing task, performing the
different-place collaborative computing task, and encrypting and feeding performed
results of the different-place collaborative computing task, where the data are
resources needed for the different-place collaborative computing task; and
S5, integrating the local task performed results and the performed results of the
different-place collaborative computing task to accomplish the computing task.
Preferably, S2 includes:
S2.1, registering the collaborative computing and managing platform in different
places, and inputting authentication information and performing user authentication;
S2.2, issuing the different-place collaborative computing result based on the
results of the user authentication; and
S2.3, selecting the different-place collaborative computing resources based on
the different-place collaborative computing request to generate the different-place
collaborative computing task.
Preferably, in the S4 process of performing the different-place collaborative computing task, a dynamic space sharing method is adopted for computing resource scheduling.
The present invention discloses the following technical effects:
According to the collaborative computing system and method in different places
for marine medicinal bio-resources provided by the present invention, efficient
reasonable configuration of the local computing resources and the different-place
computing resources is realized by adopting the resource database, the collaborative
computing and managing platform in different places and a plurality of computing
nodes, calling the data in the resource database, and scheduling the computing
resources of the computing nodes in different places through the collaborative
computing and managing platform. In such a manner, the local and different-place
computing resources are sufficiently utilized to strength different-place collaborative
computing ability in the drug design and development processes utilizing the marine
medical bio-resources, thereby realizing low-time-delay of the large-scale data
information and low-cost use of computing ability, and reducing computing cost in
the drug design and development processes.
In order to explain the technical solutions in the embodiments of the present
invention or the prior art clearer, the drawings used in the embodiments will be briefly
introduced below. Obviously, the drawings in the following description are some
embodiments of the present invention. For a person of ordinary skill in the art, other
drawings can be obtained based on these drawings without paying creative labor.
FIG. 1 is a constituent schematic diagram of a collaborative computing system in
different places for marine medicinal bio-resources in an embodiment of the present
invention; and
FIG. 2 is a schematic diagram showing a process of a collaborative computing
method in different places for marine medicinal bio-resources in an embodiment of
the present invention.
The technical solutions in the embodiments of the present invention will be
described clearly and completely in combination with the drawings in the
embodiments of the present invention. Obviously, the described embodiments are part
of, but not all of, the embodiments of the present invention. Based on the
embodiments in the present invention, all other embodiments obtained by a person of
ordinary skill in the art without creative efforts shall fall within the protection scope
of the present invention.
In order to make the above-mentioned objectives, features and advantages of the
present invention more obvious and understandable, the specific embodiments of the
present invention will be described in detail below with reference to the
accompanying drawings.
As shown in FIG. 1, the present invention provides a collaborative computing
system in different places for marine medicinal bio-resources. The system includes a
resource database, a collaborative computing and managing platform in different
places and a plurality of computing nodes, where the computing nodes include local
computing nodes and computing nodes in different places. The local computing nodes
and the computing nodes in different places in the system are set in different regions
or cities, and include a plurality of computing nodes in different places. When the
computing resources of the local computing nodes cannot meet the needs, the
plurality of the computing nodes in different places may be used for collaborative
computing simultaneously. The resource database is used for storing the data of the marine medical bio-resources, namely providing data needed for drug design and development utilizing the marine medical bio-resources. The resource database at least includes a virtual screening database, a protein database and a molecule database, the resource database being connected to all of the computing nodes. The collaborative computing and managing platform in different places is connected to the computing nodes, and is used for receiving computing task request of local computing nodes, sending the computing task request content of the local computing nodes and receiving computing task results of the computing nodes in different places. The computing nodes are used for computing the data in the resource database.
Specifically, the collaborative computing and managing platform in different
places includes a safety module, a task scheduling module, a data exchange storage
module and a communication module, where the safety module is connected to the
task scheduling module for performing authentication on a user who registers in the
collaborative computing and managing platform in different places. The data
exchange storage module is connected to the computing node module through the
communication module for storing the collaborative computing request performing
results when the collaborative computing request of the local computing nodes
reaches the computing nodes in different places at the same time. The task scheduling
module is connected to the computing nodes in different places through the
communication module. The task scheduling module generates a different-place
collaborative computing task from the collaborative computing request content of the
local computing nodes, schedules and distributes according to the computing
resources of the different-place computing nodes, encrypts the specific collaborative
computing task and sends the encrypted collaborative computing task to a target
computing node in different places.
Each of the computing nodes includes a task request module, a task receiving
module, a computing ability estimation module, a search module, a computing
module, a data encryption module and a communication unit, where the task request
module is connected to the computing ability estimation module for estimating the
self-computing ability when the local computing nodes or the computing nodes in
different places perform respective tasks; when the computing ability of the local
computing nodes is insufficient, the task request module puts forward the
collaborative computing needs for being sent to the collaborative computing and
managing platform in different places. The computing nodes in different places send
free computing resources thereof to the collaborative computing and managing
platform in different places as reference for scheduling and computing resources. The
task request module is further connected to the data encryption module. The
different-place collaborative computing request must be encrypted before being issued,
so that the safety of the content is guaranteed. The task receiving module is connected
to the computing module, the computing module is connected to the search module
for searching the data needed for searching the task according to the received
collaborative computing task, and transmitting the data to the computing module to
perform the collaborative computing task. The data encryption module is separately
connected to the computing module, the search module is connected to the resource
database through the communication unit, and the computing module is connected to
the data exchange storage module through the communication unit for sending the
results of the different-place collaborative computing task to the collaborative
computing and managing platform in different places.
According to a further optimized scheme, the same task processing program is
installed on the local computing nodes and the computing nodes in different places to guarantee that the data calculated through the local computing nodes and the computing nodes in different places have the same format.
As shown in FIG. 2, the present invention further provides a collaborative
computing method in different places for marine medicinal bio-resources, including
the following steps:
S100, obtaining a computing task for drug design and development through the
marine medical bio-resources, estimating the quantity of the local computing
resources and the different-place computing resources needed for the computing task,
and generating a different-place collaborative design request based on the quantity of
the different-place computing resources; and
S200, registering the collaborative computing and managing platform in different
places, sending the different-place collaborative design request to the collaborative
computing and managing platform in different places, and generating a different-place
collaborative computing task.
User authentication is performed by registering the collaborative computing and
managing platform in different places and inputting authentication information. If the
authentication is successful, issue the different-place collaborative computing request,
otherwise, exist the collaborative computing and managing platform in different
places.
The different-place collaborative computing task is generated by checking a
computing resource distribution condition of the computing nodes in different places
according to the different-place collaborative computing request, and selecting a
target different-place collaborative computing node.
S300, encrypting the different-place collaborative computing task and issuing the
encrypted task to the target different-place collaborative computing node.
S400, receiving the different-place collaborative computing task, searching and
calling data based on the different-place collaborative computing task, performing the
different-place collaborative computing task, and encrypting and feeding performed
results of the different-place collaborative computing task.
When the target different-place computing node performs the different-place
collaborative computing task, the computing resources need to be reasonably
scheduled; and a dynamic space sharing method is adopted for distributing free
processors to operation that can effectively utilize them. The embodiment may be
realized through the processors, and the scheduling program is used for distributing
one group of the processors from a pond to unscheduled operation. When the
processors distributed to the operation accomplish the distributing operation, the
processors immediately return into the pond to waist for being distributed to another
operation.
The scheduling program is triggered and started under three conditions: firstly,
the operation starts; secondly, the operation ends; and thirdly, a (greater than or equal
to 0 and smaller than or equal to P) processors are in the processor pond, where a is
an adjustable parameter, and P is a total number of the processors in the system. While
called, an algorithm will distribute one group of processors, where the sizes of target
partitions of the group of the processors are equal to the smallest one in the maximum
parallelism of the operation, and the maximum parallelism of the operation being
given when the operation reaches.
The sizes of the sub partitions are computed as the following formula (1):
The sizes of the partitions
P (quantity of queue-up operations +1)+(.5xquanaity of operations in execution)
The scheduling program enters a processor selecting stage for selecting proper processors for the operation. The processor selecting stage is based on the following principle: (1) if possible, the processors in the same cluster are preferably selected; and (2) The proximity of the cluster needs to be considered while the processors are selected.
The scheduling program determines a specific task number distributed to each
processor Pi in the target partitions as shown in formula (2):
The quantity of tasks
=ff(pi) x maximum parallelism of the operation (2) ff (system)
ff is a fitting factor of each Pi in the system, defined as shown in formula (3):
ffCPU speed x MPL maximum parallelism default value (3) lowest processor speed in system
Finally, the task distributed to the processor Pi is combined to the size of the
target partition distributed to the operation. If three tasks are distributed for Pi, the
operation is supposed to have extensibility, and the tasks are combined into a large
task.
(3) operation queue-up management is performed:
The operation enters a waist queue when the resources are insufficient, the
operation queue-up strategy of the system integrates a FCFS strategy based on
proportion with a short operation prior SJF strategy. And various distribution strategy
of reservation and backfilling, preemptive, exclusive, self-adaptive and the like are
used under a complex condition, so that the multiple strategies are combined for use.
In such a manner, the integral resource collaboration and utilization ability of the
collaborative computing operation scheduling system in different places are
improved.
S500, integrating the local task performed results and performed results of
different-place collaborative computing task to accomplish the computing task for drug design and development utilizing the marine medical bio-resources.
The embodiments described above are only intended to describe the preferred
embodiments of the present invention, and are not intended to limit the scope of the
present invention, and various modifications and improvements made to the technical
solutions of the present invention by a person skilled in the art without departing from
the spirit of the invention are intended to fall within the scope as defined by the claims
of the present invention.
Claims (8)
1. A collaborative computing system in different places for marine medicinal
bio-resources, comprising a resource database, a collaborative computing and
managing platform in different places, and a plurality of computing nodes, wherein
the computing nodes comprise local computing nodes and computing nodes in
different places;
the resource database is used for storing data of the marine medicinal
bio-resources;
the collaborative computing and managing platform in different places is used
for receiving computing task request of the local computing nodes and scheduling,
receiving computing task results of the computing nodes in different places, and
sending the computing task results to the local computing nodes;
and the computing nodes are used for computing the data in the resource
database.
2. The collaborative computing system in different places for marine medicinal
bio-resources according to claim 1, wherein the resource database comprise a virtual
screening database, a protein database and a molecule database.
3. The collaborative computing system in different places for marine medicinal
bio-resources according to claim 1, wherein the collaborative computing and
managing platform in different places comprises a safety module, a task scheduling
module, a data exchange storage module and a communication module; the safety
module is connected to the task scheduling module, the data exchange storage module
is connected to the computing node module through the communication module, and
the task scheduling module is connected to the computing nodes in different places
through the communication module.
4. The collaborative computing system in different places for marine medicinal
bio-resources according to claim 3, wherein each of the computing nodes comprises a
task request module, a task receiving module, a computing ability estimation module,
a search module, a computing module, a data encryption module and a
communication unit; the task request module is connected to the computing ability
estimation module, the task receiving module is connected to the computing module,
the computing module is connected to the search module, the data encryption module
is separately connected to the computing module and the task request module, the
search module is connected to the resource database through the communication unit,
and the computing module is connected to the data exchange storage module through
the communication unit.
5. The collaborative computing system in different places for marine medicinal
bio-resources according to claim 1, wherein the local computing nodes and the
computing nodes in different places are set with same task processing program.
6. A collaborative computing method in different places for marine medicinal
bio-resources utilizing the collaborative computing system in different places for
marine medicinal bio-resources according to any one of claims 1 to 5, comprising the
following steps:
SI, obtaining a computing task, estimating the quantity of the local computing
resources and the different-place computing resources needed for the computing task,
and generating a different-place collaborative design request based on the quantity of
the different-place computing resources;
S2, registering the collaborative computing and managing platform in different
places, sending the different-place collaborative design request to the collaborative
computing and managing platform in different places, and generating a different-place collaborative computing task;
S3, encrypting and distributing the collaborative computing task;
S4, receiving the different-place collaborative computing task, searching and
calling data based on the different-place collaborative computing task, performing the
different-place collaborative computing task, and encrypting and feeding performed
results of the different-place collaborative computing task, where the data are
resources needed for the different-place collaborative computing task; and
S5, integrating the local task performed results and the performed results of the
different-place collaborative computing task to accomplish the computing task.
7. The collaborative computing method in different places for marine medicinal
bio-resources according to claim 6, wherein S2 comprises:
S2.1, registering the collaborative computing and managing platform in different
places, and inputting authentication information and performing user authentication;
S2.2, issuing the different-place collaborative computing result based on the
results of the user authentication; and
S2.3, selecting the different-place collaborative computing resources based on
the different-place collaborative computing request to generate the different-place
collaborative computing task.
8. The collaborative computing method in different places for marine medicinal
bio-resources according to claim 6, wherein in the S4 process of performing the
different-place collaborative computing task, a dynamic space sharing method is
adopted for computing resource scheduling.
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| Application Number | Priority Date | Filing Date | Title |
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| AU2021105451A AU2021105451A4 (en) | 2021-08-13 | 2021-08-13 | Collaborative Computing System and Method in Different Places for Marine Medicinal Bio-resources |
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| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| AU2021105451A AU2021105451A4 (en) | 2021-08-13 | 2021-08-13 | Collaborative Computing System and Method in Different Places for Marine Medicinal Bio-resources |
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| Publication Number | Publication Date |
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| AU2021105451A4 true AU2021105451A4 (en) | 2021-10-14 |
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| AU2021105451A Ceased AU2021105451A4 (en) | 2021-08-13 | 2021-08-13 | Collaborative Computing System and Method in Different Places for Marine Medicinal Bio-resources |
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2021
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