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- Outdated ipath_ether Configuration Setup Generates Error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
D–Troubleshooting
QLogic MPI Troubleshooting
D-24 IB6054601-00 H
S
The following message displays after installation:
$ mpirun -m ~/tmp/sm -np 2 -mpi_latency 1000 1000000
node-00:1.ipath_update_tid_err: failed: Cannot allocate memory
mpi_latency:
/fs2/scratch/infinipath-build-1.3/mpi-1.3/mpich/psm/src
mq_ips.c:691:
mq_ipath_sendcts: Assertion ‘rc == 0’ failed. MPIRUN: Node program
unexpectedly quit. Exiting.
You can check the ulimit -l on all the nodes by running ipath_checkout. A
warning similar to this displays if ulimit -l
is less than 4096:
!!!ERROR!!! Lockable memory less than 4096KB on x nodes
To fix this error, install the infinipath RPM on the node, and reboot it to ensure
that /etc/initscript is run.
Alternately, you can create your own /etc/initscript and set the ulimit
there.
Error Creating Shared Memory Object
QLogic MPI (and PSM) use Linux’s shared memory mapped files to share
memory within a node. When an MPI job is started, a shared memory file is
created on each node for all MPI ranks sharing memory on that one node. During
job execution, the shared memory file remains in /dev/shm. At program exit, the
file is removed automatically by the operating system when the QLogic MPI
(InfiniPath) library properly exits. Also, as an additional backup in the sequence of
commands invoked by mpirun during every MPI job launch, the file is explicitly
removed at program termination.
However, under circumstances such as hard and explicit program termination (i.e.
kill -9 on the mpirun process PID), QLogic MPI cannot guarantee that the
/dev/shm file is properly removed. As many stale files accumulate on each node,
an error message like the following can appear at startup:
node023:6.Error creating shared memory object in shm_open(/dev/shm
may have stale shm files that need to be removed):
If this occurs, administrators should clean up all stale files by running this
command (as a root user):
# rm -rf /dev/shm/psm_shm.*
You can also selectively identify stale files by using a combination of the fuser,
ps, and rm commands (all files start with the psm_shm prefix). Once identified,
you can issue rm commands on the stale files that you own.