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Open MPI
| Open MPI is an Message Passing Interface (MPI) library project combining technologies and resources from several other projects (FT-MPI, LA-MPI, LAM/MPI, and PACX-MPI). |
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Examples
Simple example
This example shows the basic steps when using Open MPI.
Load the necessary module
Compile your application using the MPI wrapper compilers mpicc, mpic++ or mpif90:
The wrapper compiler will pass any other option to the underlying base compiler (e.g. GNU, Intel, PGI). To figure out Open MPI's default options passed to the base compiler is by using
and it's variants -showme:compile, -showme:link and the like.
Now you can allocate compute nodes via the Batch_system and run your application with
Specifying the number of processes per node
Open MPI divides resources in something called 'slots'. By specifying ppn:X to the batch system, the number of slots per node is specified.
So for a simple MPI job with 8 process per node (=1 process per core) ppn:8 is best choice, as in above example. Details can be specified on mpirun command line. PBS setup is adjusted for ppn:8, please do not use other values.
If you want to use less processes per node e.g. because you are restricted by memory requirements, or you have a hybrid parallel application using MPI and OpenMP, MPI would always put the first 8 processes on the first node, second 8 on second and so on. To avoid this, you can use the -npernode option.
This would start 2 processes per node. Like this, you can use a larger number of nodes with a smaller number of processes, or you can e.g. start threads out of the processes.
Process pinning
Open MPI allows the pinning of processes via the '--bind-to-*' options.
Binding processes to CPU cores is done with
Binding processes to a socket is done with
The actuall binding policy of Open MPI can be displayed with
Thread pinning
For pinning of hybrid MPI/OpenMP, use the following wrapper script
#!/bin/bash
export KMP_AFFINITY=verbose,scatter # Intel specific environment variable
export OMP_NUM_THREADS=4
RANK=${OMPI_COMM_WORLD_RANK:=$PMI_RANK}
if [ $(expr $RANK % 2) = 0 ]
then
export GOMP_CPU_AFFINITY=0-3
numactl --preferred=0 --cpunodebind=0 $@
else
export GOMP_CPU_AFFINITY=4-7
numactl --preferred=1 --cpunodebind=1 $@
fi
Run your application with the following command
Valgrind Debugging
You may easily debug Your application with the memory-error detector valgrind.
This will detect errors such as usage of uninitialized memory, buffer over-runs, double-free's, lost memory (leaks).
To run with Open MPI, just pass it just before specifying the application:
This will show up many false positives from Open MPI itselve -- e.g. memory communicated via TCP/IP
with known uninitialized memory, buffer copied from the kernel to the InfiniBand Verbs library.
Valgrind offers suppressing these false positives. Open MPI provides a suppression-file installed
in the default location:
Common Problems
InfiniBand retry count
I get an error message about timeouts, what can I do?
-
If your parallel programs sometimes crash with an error message like this:
--------------------------------------------------------------------------
The InfiniBand retry count between two MPI processes has been
exceeded. "Retry count" is defined in the InfiniBand spec 1.2
(section 12.7.38):
The total number of times that the sender wishes the receiver to
retry timeout, packet sequence, etc. errors before posting a
completion error.
This error typically means that there is something awry within the
InfiniBand fabric itself. You should note the hosts on which this
error has occurred; it has been observed that rebooting or removing a
particular host from the job can sometimes resolve this issue.
Two MCA parameters can be used to control Open MPI's behavior with
respect to the retry count:
* btl_openib_ib_retry_count - The number of times the sender will
attempt to retry (defaulted to 7, the maximum value).
* btl_openib_ib_timeout - The local ACK timeout parameter (defaulted
to 10). The actual timeout value used is calculated as:
4.096 microseconds * (2^btl_openib_ib_timeout)
See the InfiniBand spec 1.2 (section 12.7.34) for more details.
--------------------------------------------------------------------------
This means that the mpi messages can't pass through our infiniband switches before the btl_openib_ib_timeout is over. How often this occurs depends also on the traffic on the network. We have adjusted the parameters such that it should normally work, but if you have compiled your own OpenMPI, maybe also as part of another program package, you might not have adjusted this value correctly. However, you can specify it when calling mpirun:
mpirun -mca btl_openib_ib_timeout 20 -np ... your-program ...
you can check the preconfigured parameters of the module currently loaded by:
ompi_info --param btl openib
where you can grep for the above mentioned parameters.