Unit 2 HPCcontent
Unit 2 HPCcontent
• Peer-to-peer systems: The peer-to-peer techniques contain nodes that are equal
participants in data sharing. The nodes communicate with each other as needed
to share resources. This is done with the help of a network. All the tasks are
equally separated between all the nodes.
• Three-tier: Three-tier system uses a separate layer and server for each function
of a program. In this data of the client is stored in the middle tier rather than
sorted into the client system or on their server through which development can
be done easily. It includes an Application Layer, Data Layer, and Presentation
Layer. This is mostly used in web or online applications.
• N-tier: N-tier is also called a multitier distributed system. The N-tier system can
contain any number of functions in the network. N-tier systems contain similar
structures to three-tier architecture. When interoperability sends the request to
another application to perform a task or to provide a service. N-tier is commonly
used in web applications and data systems.
3. Hybrids
Synchronous Computation/Communication
Advantages:
Use Cases:
Comparison
• Complexity: Synchronous systems are often simpler to design and reason about
due to their deterministic behavior, while asynchronous systems require careful
consideration of concurrency and potential race conditions.
• Fault Tolerance: Asynchronous systems are often more resilient to failures and
network partitions, as they can continue operating independently even if some
components fail or become unreachable.
Hybrid Approaches
In practice, many distributed systems employ hybrid approaches that combine elements
of both synchronous and asynchronous computation and communication. For example,
systems may use asynchronous messaging for communication between loosely coupled
components while coordinating certain tasks synchronously when necessary.
CO4 Utilize appropriate models and frameworks for specific workloads in parallel
and distributed computing environments
PCC is a concurrency control mechanism that assumes conflicts are likely to occur and
takes a pessimistic approach by acquiring locks on resources upfront to prevent
conflicts. It ensures that transactions acquire exclusive access to resources, preventing
other transactions from modifying or accessing them until the locks are released.
1. Two-Phase Locking (2PL) — Acquires locks on data resources upfront and releases
them at the end of the transaction. Example: In a shared database, when a user wants to
update a specific row of data, 2PL ensures that other users cannot access or modify the
same row until the lock is released, preventing conflicts. Learn more about 2PL here.
2. Strict Two-Phase Locking (Strict 2PL) — A variant of 2PL where all locks
acquired during a transaction are held until the transaction is committed or rolled back.
Example: In a distributed database, a transaction locks all the necessary resources (e.g.,
tables, rows) at the beginning and holds the locks until the transaction is completed,
ensuring no other transactions can access or modify the locked resources.
Here are key concepts and techniques involved in achieving fault tolerance in
distributed systems:
1. Redundancy
Replication: Storing copies of data or services on multiple nodes. If one node fails, the
system can retrieve data or services from another node.
Backup: Regularly creating copies of data that can be restored in case of failure.
2. Consensus Algorithms
Components of OpenMPI
MPI Libraries: Core libraries that provide the MPI standard functions.
Resource Managers: Integrates with job schedulers and resource managers like Slurm,
PBS, and Torque.
These are typically built using commodity hardware and open-source software. They
are cost-effective solutions for parallel computing and are often used in academic and
research environments.
Load Balancing Clusters
Also known as failover clusters, these ensure that services remain available even when
one or more nodes fail. They are crucial for critical applications that require continuous
uptime.
Grid Computing Clusters
Grid computing involves loosely coupled clusters that work together on a common task
but are geographically dispersed. They leverage resources from multiple administrative
domains.
HPC Clusters
Definition of Clusters
A cluster in computing is a group of interconnected computers that work together as a
single system. These computers, often referred to as nodes, collaborate to perform tasks,
share resources, and provide redundancy. Clusters are used to enhance performance,
increase availability, and ensure scalability and fault tolerance.
Taxonomy of Clusters
Clusters can be categorized based on various criteria such as their purpose, architecture,
and management. Here is a detailed taxonomy of clusters:
Based on Purpose
1. High Performance Computing (HPC) Clusters
• Designed for computationally intensive tasks.
• Used in scientific research, simulations, and complex calculations.
• Examples: NASA's Pleiades, DOE's Summit.
2. High Availability (HA) Clusters
• Ensure continuous operation by providing failover capabilities.
• Critical for applications that require minimal downtime.
• Examples: Financial services, e-commerce platforms.
3. Load Balancing Clusters
• Distribute workloads across multiple nodes to optimize resource use and
avoid overload.
• Common in web services and databases.
• Examples: Web servers, application servers.
4. Grid Computing Clusters
• Combine resources from multiple locations to work on a common task.
• Often geographically distributed and managed by different organizations.
• Examples: SETI@home, CERN's LHC Computing Grid.
5. Storage Clusters
• Focus on providing scalable and reliable data storage.
• Ensure data redundancy and quick access.
• Examples: Amazon S3, Google File System.
Based on Architecture
1. Homogeneous Clusters
• All nodes have similar or identical hardware and software configurations.
• Easier to manage and maintain.
• Examples: Beowulf clusters.
2. Heterogeneous Clusters
• Nodes have different hardware and software configurations.
• Flexible and can utilize a variety of resources.
• Examples: Computational grids.
Based on Management
1. Centralized Management
• Managed by a single entity or organization.
• Simplifies administration and resource allocation.
• Examples: Corporate data centers, university research clusters.
2. Decentralized Management
• Managed by multiple entities.
• Often found in grid computing and volunteer computing projects.
• Examples: BOINC projects, federated cloud services.
Based on Deployment
1. On-Premises Clusters
• Physically located and managed within an organization's own facilities.
• Provides control over hardware and security.
• Examples: Private data centers, university labs.
2. Cloud-Based Clusters
• Deployed and managed in the cloud.
• Offers flexibility, scalability, and often cost savings.
• Examples: AWS EC2 clusters, Google Cloud Kubernetes Engine.
3. Hybrid Clusters
• Combine on-premises and cloud-based resources.
• Allow for bursting into the cloud during peak demand.
• Examples: Enterprises with both local and cloud resources.
Examples of Cluster Implementations
1. Beowulf Clusters
• Built using commodity hardware and open-source software.
• Example: A university research cluster using Linux and inexpensive PCs.
2. Apache Hadoop Clusters
• Designed for big data processing.
• Uses HDFS for distributed storage and MapReduce for distributed
processing.
• Example: Data analytics platforms used by large enterprises.
3. Kubernetes Clusters
• Orchestrate containerized applications.
• Provide automated deployment, scaling, and management.
• Example: Cloud-native applications running on Google Kubernetes
Engine (GKE).
4. OpenMPI Clusters
• Facilitate communication in parallel computing environments.
• Example: Scientific simulations using MPI for message passing.
5. SLURM (Simple Linux Utility for Resource Management) Clusters
• Job scheduling and workload management.
• Example: Managing job queues and resources in an HPC environment.
CO4 Utilize appropriate models and frameworks for specific workloads in parallel
and distributed computing environments
Cluster Components
Advantages of Cluster Computing :
1. High Performance :
The systems offer better and enhanced performance than that of mainframe computer
networks.
2. Easy to manage :
Cluster Computing is manageable and easy to implement.
3. Scalable :
Resources can be added to the clusters accordingly.
4. Expandability :
Computer clusters can be expanded easily by adding additional computers to the
network. Cluster computing is capable of combining several additional resources or
the networks to the existing computer system.
5. Availability :
The other nodes will be active when one node gets failed and will function as a proxy
for the failed node. This makes sure for enhanced availability.
6. Flexibility :
It can be upgraded to the superior specification or additional nodes can be added.
Disadvantages of Cluster Computing :
1. High cost :
It is not so much cost-effective due to its high hardware and its design.
2. Problem in finding fault :
It is difficult to find which component has a fault.
3. More space is needed :
Infrastructure may increase as more servers are needed to manage and monitor.
Applications of Cluster Computing :
• Various complex computational problems can be solved.
• It can be used in the applications of aerodynamics, astrophysics and in data
mining.
• Weather forecasting.
• Image Rendering.
• Various e-commerce applications.
• Earthquake Simulation.
• Petroleum reservoir simulation.
CO4 Utilize appropriate models and frameworks for specific workloads in parallel
and distributed computing environments
Design Decisions
Designing a cluster system involves several critical decisions that can significantly
impact the system's performance, scalability, reliability, and cost. These decisions cover
a wide range of aspects, from hardware selection to software configuration and network
design. Here are some key design decisions to consider when building a cluster system:
1. Purpose and Use Case
• Define Objectives: Clearly define the primary goals of the cluster, such as high
performance computing (HPC), high availability (HA), load balancing, or big
data processing.
• Workload Characteristics: Understand the types of workloads the cluster will
handle (e.g., computational tasks, data-intensive applications) to tailor the design
accordingly.
2. Node Hardware Configuration
• Node Specifications: Choose the CPU, memory, storage, and network
capabilities of each node based on the anticipated workload requirements.
• Homogeneous vs. Heterogeneous: Decide whether to use homogeneous nodes
(identical hardware) for simplicity and predictability, or heterogeneous nodes
(varied hardware) for flexibility and potentially better resource utilization.
• Scalability: Ensure the hardware is scalable to allow for future expansion
without significant redesign.
3. Network Architecture
• Network Topology: Select an appropriate network topology (e.g., star, mesh,
tree) based on performance, fault tolerance, and cost considerations.
• Interconnect Technology: Choose high-speed interconnects like InfiniBand,
Ethernet, or specialized HPC networks to minimize latency and maximize
throughput.
• Redundancy and Failover: Design the network with redundancy to handle
failures gracefully and maintain connectivity.
4. Storage Solutions
• Storage Type: Decide between local storage, shared storage, or a combination.
Local storage is faster for node-specific data, while shared storage is essential
for data that needs to be accessible across the cluster.
• Distributed File Systems: Implement distributed file systems (e.g., HDFS,
GlusterFS, Ceph) to ensure data redundancy, scalability, and availability.
• Data Management: Plan for efficient data distribution, replication, and access
patterns to minimize bottlenecks and ensure data integrity.
5. Software Stack
• Operating System: Select an operating system that is optimized for cluster
environments, typically a variant of Linux.
• Middleware: Choose middleware that supports resource management, job
scheduling, and communication (e.g., Slurm, Torque, OpenMPI).
• Application Frameworks: Incorporate application frameworks suited for the
workload, such as Apache Hadoop or Spark for big data, or TensorFlow for
machine learning.
6. Resource Management and Scheduling
• Scheduler: Implement a job scheduler (e.g., Slurm, Kubernetes) to manage job
queues, allocate resources, and optimize workload distribution.
• Resource Allocation: Develop policies for resource allocation, prioritizing tasks
based on urgency, resource requirements, and user priorities.
7. Fault Tolerance and High Availability
• Redundancy: Design the system with redundant components (e.g., power
supplies, network paths) to ensure high availability.
• Failover Mechanisms: Implement failover mechanisms to automatically handle
node or component failures without significant disruption.
• Monitoring and Alerts: Set up monitoring tools (e.g., Nagios, Prometheus) to
continuously track the health of the cluster and alert administrators to potential
issues.
8. Security
• Access Control: Implement robust authentication and authorization mechanisms
to ensure that only authorized users can access the cluster.
• Data Security: Use encryption for data in transit and at rest to protect sensitive
information.
• Network Security: Employ firewalls, VPNs, and other network security
measures to protect against unauthorized access and attacks.
9. Scalability and Flexibility
• Modular Design: Design the cluster to be modular, allowing for easy addition
or removal of nodes without significant reconfiguration.
• Elasticity: Consider using cloud-based resources or hybrid cloud approaches to
dynamically scale the cluster based on workload demands.
10. Cost Considerations
• Initial Investment: Balance the cost of high-performance hardware and network
components with the budget constraints.
• Operational Costs: Factor in the ongoing costs of power, cooling, maintenance,
and administration.
• Total Cost of Ownership (TCO): Evaluate the long-term costs and benefits,
including potential savings from increased efficiency and productivity.
11. Performance Optimization
• Load Balancing: Implement load balancing strategies to ensure even
distribution of workloads and avoid bottlenecks.
• Performance Tuning: Continuously monitor and tune the system for optimal
performance, adjusting configurations as needed based on real-world usage
patterns.
Example Scenario: Designing an HPC Cluster
1. Define Objectives
• Goal: Perform large-scale scientific simulations.
• Workloads: CPU-intensive with occasional GPU acceleration.
2. Node Hardware Configuration
• Compute Nodes: High-end CPUs, 128GB RAM, SSDs for local storage,
optional GPUs.
• Head Node: High-performance CPU, 256GB RAM, large SSD.
3. Network Architecture
• Topology: Fat-tree topology for low-latency, high-bandwidth
communication.
• Interconnect: InfiniBand for inter-node communication, Ethernet for
management traffic.
4. Storage Solutions
• Local Storage: SSDs on compute nodes for scratch space.
• Shared Storage: Lustre file system for large data sets and project files.
5. Software Stack
• OS: CentOS or Ubuntu.
• Middleware: Slurm for resource management and scheduling, OpenMPI
for inter-process communication.
• Application Frameworks: Libraries and tools for scientific computing
(e.g., MATLAB, TensorFlow).
6. Resource Management and Scheduling
• Scheduler: Slurm configured with fair-share scheduling and job
prioritization.
• Resource Allocation: Policies for CPU/GPU time, memory usage based
on project and user priorities.
7. Fault Tolerance and High Availability
• Redundancy: Dual power supplies, redundant network paths.
• Failover: Hot-swappable components, automatic failover configurations.
• Monitoring: Nagios for health checks, alerting system administrators of
issues.
8. Security
• Access Control: LDAP integration for user management, role-based
access controls.
• Data Security: SSL/TLS for data in transit, encryption for sensitive data.
• Network Security: Firewalls, VPN for remote access.
9. Scalability and Flexibility
• Modular Design: Easy addition of new compute nodes.
• Elasticity: Hybrid cloud setup with AWS for peak load handling.
10. Cost Considerations
• Initial Investment: High upfront cost for hardware and infrastructure.
• Operational Costs: Budgeting for power, cooling, maintenance.
• TCO: Evaluated over 5 years, considering hardware lifecycle and performance
gains.
11. Performance Optimization
• Load Balancing: Slurm configuration for even workload distribution.
• Performance Tuning: Regular benchmarking and tuning based on usage patterns.
CO4 Utilize appropriate models and frameworks for specific workloads in parallel
and distributed computing environments