Product specifications
Table Of Contents
- Table of Contents
- 1 Introduction
- 2 Feature Overview
- 3 Step-by-Step Cluster Setup and MPI Usage Checklists
- 4 InfiniPath Cluster Setup and Administration
- Introduction
- Installed Layout
- Memory Footprint
- BIOS Settings
- InfiniPath and OpenFabrics Driver Overview
- OpenFabrics Drivers and Services Configuration and Startup
- Other Configuration: Changing the MTU Size
- Managing the InfiniPath Driver
- More Information on Configuring and Loading Drivers
- Performance Settings and Management Tips
- Host Environment Setup for MPI
- Checking Cluster and Software Status
- 5 Using QLogic MPI
- Introduction
- Getting Started with MPI
- QLogic MPI Details
- Use Wrapper Scripts for Compiling and Linking
- Configuring MPI Programs for QLogic MPI
- To Use Another Compiler
- Process Allocation
- mpihosts File Details
- Using mpirun
- Console I/O in MPI Programs
- Environment for Node Programs
- Environment Variables
- Running Multiple Versions of InfiniPath or MPI
- Job Blocking in Case of Temporary InfiniBand Link Failures
- Performance Tuning
- MPD
- QLogic MPI and Hybrid MPI/OpenMP Applications
- Debugging MPI Programs
- QLogic MPI Limitations
- 6 Using Other MPIs
- A mpirun Options Summary
- B Benchmark Programs
- C Integration with a Batch Queuing System
- D Troubleshooting
- Using LEDs to Check the State of the Adapter
- BIOS Settings
- Kernel and Initialization Issues
- OpenFabrics and InfiniPath Issues
- Stop OpenSM Before Stopping/Restarting InfiniPath
- Manual Shutdown or Restart May Hang if NFS in Use
- Load and Configure IPoIB Before Loading SDP
- Set $IBPATH for OpenFabrics Scripts
- ifconfig Does Not Display Hardware Address Properly on RHEL4
- SDP Module Not Loading
- ibsrpdm Command Hangs when Two Host Channel Adapters are Installed but Only Unit 1 is Connected to the Switch
- Outdated ipath_ether Configuration Setup Generates Error
- System Administration Troubleshooting
- Performance Issues
- QLogic MPI Troubleshooting
- Mixed Releases of MPI RPMs
- Missing mpirun Executable
- Resolving Hostname with Multi-Homed Head Node
- Cross-Compilation Issues
- Compiler/Linker Mismatch
- Compiler Cannot Find Include, Module, or Library Files
- Problem with Shell Special Characters and Wrapper Scripts
- Run Time Errors with Different MPI Implementations
- Process Limitation with ssh
- Number of Processes Exceeds ulimit for Number of Open Files
- Using MPI.mod Files
- Extending MPI Modules
- Lock Enough Memory on Nodes When Using a Batch Queuing System
- Error Creating Shared Memory Object
- gdb Gets SIG32 Signal Under mpirun -debug with the PSM Receive Progress Thread Enabled
- General Error Messages
- Error Messages Generated by mpirun
- MPI Stats
- E Write Combining
- F Useful Programs and Files
- G Recommended Reading
- Glossary
- Index
4–InfiniPath Cluster Setup and Administration
Host Environment Setup for MPI
IB6054601-00 H 4-25
A
Host Environment Setup for MPI
After the InfiniPath software and the GNU (GCC) compilers have been installed on
all the nodes, the host environment can be set up for running MPI programs.
Configuring for ssh
Running MPI programs with the command mpirun on an InfiniPath cluster
depends, by default, on secure shell ssh to launch node programs on the nodes.
In QLogic MPI, mpirun uses the secure shell command
ssh to start instances of
the given MPI program on the remote compute nodes without the need for
interactive password entry on every node.
To use ssh, you must have generated Rivest, Shamir, Adleman (RSA) or Digital
Signal Algorithm (DSA) keys, public and private. The public keys must be
distributed and stored on all the compute nodes so that connections to the remote
machines can be established without supplying a password.
You or your administrator must set up the ssh keys and associated files on the
cluster. There are two methods for setting up ssh on your cluster. The first
method, the shosts.equiv mechanism, is typically set up by the cluster
administrator. The second method, using ssh-agent, is more easily
accomplished by an individual user.
Configuring ssh and sshd Using shosts.equiv
This section describes how the cluster administrator can set up ssh and sshd
through the shosts.equiv mechanism. This method is recommended, provided
that your cluster is behind a firewall and accessible only to trusted users.
“Configuring for ssh Using ssh-agent” on page 4-27 shows how an individual user
can accomplish the same thing using ssh-agent.
NOTE:
rsh can be used instead of ssh. To use rsh, set the environment
variable MPI_SHELL=rsh. See “Environment Variables” on page 5-18
for information on setting environment variables. Also see “Shell
Options” on page A-6 for information on setting shell options in mpirun.
rsh has a limit on the number of concurrent connections it can have,
typically 255, which may limit its use on larger clusters.