
High Performance Linux Clusters with OSCAR, Rocks, OpenMosix, and MPI
Description
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Content
- Intro
- Table of Contents
- Preface
- Audience
- Organization
- Conventions
- How to Contact Us
- Using Code Examples
- Acknowledgments
- Part I
- Cluster Architecture
- Modern Computing and the Role of Clusters
- Uniprocessor Computers
- Multiple Processors
- Centralized multiprocessors
- Multicomputers
- Cluster structure
- Types of Clusters
- Distributed Computing and Clusters
- Limitations
- Amdahl's Law
- My Biases
- Cluster Planning
- Design Steps
- Determining Your Cluster's Mission
- What Is Your User Base?
- How Heavily Will the Cluster Be Used?
- What Kinds of Software Will You Run on the Cluster?
- How Much Control Do You Need?
- Will This Be a Dedicated or Shared Cluster?
- What Resources Do You Have?
- How Will Cluster Access Be Managed?
- What Is the Extent of Your Cluster?
- What Security Concerns Do You Have?
- Architecture and Cluster Software
- System Software
- Programming Software
- Control and Management
- Cluster Kits
- CD-ROM-Based Clusters
- BCCD
- Benchmarks
- Cluster Hardware
- Design Decisions
- Node Hardware
- CPUs and motherboards
- Memory and disks
- Monitors, keyboards, and mice
- Adapters, power supplies, and cases
- Cluster Head and Servers
- Cluster Network
- Environment
- Cluster Layout
- Power and Air Conditioning
- Power
- HVAC
- Physical Security
- Linux for Clusters
- Installing Linux
- Selecting a Distribution
- Downloading Linux
- What to Install?
- Configuring Services
- DHCP
- NFS
- Running NFS
- Automount
- Other Cluster File System
- SSH
- Using SSH
- Other Services and Configuration Tasks
- Apache
- Network Time Protocol (NTP)
- Virtual Network Computing (VNC)
- Multicasting
- Hosts file and name services
- Cluster Security
- Part II
- openMosix
- What Is openMosix?
- How openMosix Works
- Selecting an Installation Approach
- Installing a Precompiled Kernel
- Downloading
- Installing
- Configuration Changes
- Using openMosix
- User Tools
- mps and mtop
- migrate
- mosctl
- mosmon
- mosrun
- setpe
- openMosixView
- Testing openMosix
- Recompiling the Kernel
- Is openMosix Right for You?
- OSCAR
- Why OSCAR?
- What's in OSCAR
- Installing OSCAR
- Prerequisites
- Network Configuration
- Loading Software on Your Server
- A Basic OSCAR Installation
- Step 0: Downloading additional packages
- Step 1: Package selection
- Step 2: Configuring packages
- Step 3: Installing server software
- Step 4: Building a client image
- Step 5: Defining clients
- Step 6: Setting up the network
- Step 7: Completing the setup
- Step 8: Testing
- Custom Installations
- Changes OSCAR Makes
- Making Changes
- Security and OSCAR
- pfilter
- SSH and OPIUM
- Using switcher
- Using LAM/MPI with OSCAR
- Rocks
- Installing Rocks
- Prerequisites
- Downloading Rocks
- Installing the Frontend
- Install Compute Nodes
- Customizing the Frontend
- User management with 411
- X Window System
- Customizing Compute Nodes
- Adding packages
- Changing disk partitions
- Other changes
- Managing Rocks
- Using MPICH with Rocks
- Part III
- Cloning Systems
- Configuring Systems
- Distributing Files
- Pushing files with rsync
- Automating Installations
- Kickstart
- Configuration file
- Using Kickstart
- g4u
- SystemImager
- Image server setup
- Golden client setup
- Retrieving the image
- Cloning the systems
- Other tasks
- Notes for OSCAR and Rocks Users
- Programming Software
- Programming Languages
- Selecting a Library
- LAM/MPI
- Installing LAM/MPI
- User Configuration
- Using LAM/MPI
- Testing the Installation
- MPICH
- Installing
- User Configuration
- Using MPICH
- Testing the Installation
- MPE
- Other Programming Software
- Debuggers
- HDF5
- SPRNG
- Notes for OSCAR Users
- Adding MPE
- Notes for Rocks Users
- Management Software
- C3
- Installing C3
- Using C3 Commands
- cexec
- cget
- ckill
- cpush
- crm
- cshutdown
- clist, cname, and cnum
- Further examples and comments
- Ganglia
- Installing and Using Ganglia
- RRDTool
- Apache and PHP
- Ganglia monitor core
- Web frontend
- Notes for OSCAR and Rocks Users
- Scheduling Software
- OpenPBS
- Architecture
- Installing OpenPBS
- Configuring PBS
- Managing PBS
- Using PBS
- PBS's GUI
- Maui Scheduler
- Notes for OSCAR and Rocks Users
- Parallel Filesystems
- PVFS
- Installing PVFS on the Head Node
- Configuring the Metadata Server
- I/O Server Setup
- Client Setup
- Running PVFS
- Troubleshooting
- Using PVFS
- Notes for OSCAR and Rocks Users
- Part IV
- Getting Started with MPI
- MPI
- Core MPI
- MPI_Init
- MPI_Finalize
- MPI_Comm_size
- MPI_Comm_rank
- MPI_Get_processor_name
- A Simple Problem
- Background
- Single-Processor Program
- An MPI Solution
- A C Solution
- Transferring Data
- MPI_Send
- MPI_Recv
- MPI Using FORTRAN
- MPI Using C++
- I/O with MPI
- Broadcast Communications
- Broadcast Functions
- MPI_Bcast
- MPI_Reduce
- Additional MPI Features
- More on Point-to-Point Communication
- Non-Blocking Communication
- MPI_Isend and MPI_Irecv
- MPI_Wait
- MPI_Test
- MPI_Iprobe
- MPI_Cancel
- MPI_Sendrecv and MPI_Sendrecv_replace
- More on Collective Communication
- Gather and Scatter
- MPI_Gather
- MPI_Scatter
- Managing Communicators
- Communicator Commands
- MPI_Comm_group
- MPI_Group_incl and MPI_Group_excl
- MPI_Comm_create
- MPI_Comm_free and MPI_Group_free
- MPI_Comm_split
- Packaging Data
- User-Defined Types
- MPI_Type_struct
- MPI_Type_commit
- Packing Data
- MPI_Pack
- MPI_Unpack
- Designing Parallel Programs
- Overview
- Problem Decomposition
- Decomposition Strategies
- Data decomposition
- Control decomposition
- Mapping Tasks to Processors
- Communication Overhead
- Load Balancing
- Other Considerations
- Parallel I/O
- MPI-IO Functions
- MPI_File_open
- MPI_File_seek
- MPI_File_read
- MPI_File_close
- Random Numbers
- Debugging Parallel Programs
- Debugging and Parallel Programs
- Avoiding Problems
- Programming Tools
- Rereading Code
- Tracing with printf
- Symbolic Debuggers
- gdb
- ddd
- Using gdb and ddd with MPI
- Notes for OSCAR and Rocks Users
- Profiling Parallel Programs
- Why Profile?
- Writing and Optimizing Code
- Timing Complete Programs
- Timing C Code Segments
- Manual Timing with MPI
- MPI Functions
- MPI_Wtime
- MPI_Wtick
- MPI_Barrier
- PMPI
- Profilers
- gprof
- gcov
- Profiling Parallel Programs with gprof and gcov
- MPE
- Using MPE
- Customized MPE Logging
- Notes for OSCAR and Rocks Users
- Part V
- References
- Books
- URLs
- General Cluster Information
- Linux
- Cluster Software
- Grid Computing and Tools
- Cloning and Management Software
- Filesystems
- Parallel Benchmarks
- Programming Software
- Scheduling Software
- System Software and Utilities
- Index
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