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- Outdated ipath_ether Configuration Setup Generates Error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
IB6054601-00 H C-1
C Integration with a Batch
Queuing System
Most cluster systems use some kind of batch queuing system as an orderly way to
provide users with access to the resources they need to meet their job’s
performance requirements. One task of the cluster administrator is to allow users
to submit MPI jobs through these batch queuing systems. Two methods are
described in this document:
Use mpiexec within the Portable Batch System (PBS) environment.
Invoke a script, similar to mpirun, within the SLURM context to submit MPI
jobs. A sample is provided in “Using SLURM for Batch Queuing” on
page C-2.
Using mpiexec with PBS
mpiexec can be used as a replacement for mpirun within a PBS cluster
environment. The PBS software performs job scheduling.
For PBS-based batch systems, QLogic MPI processes can be spawned using the
mpiexec utility distributed and maintained by the Ohio Supercomputer Center
(OSC).
Starting with mpiexec version 0.84, MPI applications compiled and linked with
QLogic MPI can use mpiexec and PBS’s Task Manager (TM) interface to spawn
and correctly terminate parallel jobs.
To download the latest version of mpiexec, go to:
http://www.osc.edu/~pw/mpiexec/
To build mpiexec for QLogic MPI and install it in /usr/local, type:
$ tar zxvf mpiexec-0.84.tgz
$ cd mpiexec-0.84
$ ./configure --enable-default-comm=mpich-psm && gmake all install