Hi,
thanks a lot for your quick answers, and I see my error, it is
"--bind-to none" instead of "--bind-to-none".
However, I need to be able to run "mpirun -np 2" without any binding
argument and get a "--bind-to none" behaviour. I don't know if I can
export an environment variable to do that, and I don't mind to
re-compile with some flag I missed or to alter the code.
Any suggestion?
Albert
On 23/05/14 14:32, Ralph Castain wrote:
Note that the lama mapper described in those slides may not work as it hasn't
been maintained in a while. However, you can use the map-by and bind-to options
to do the same things.
If you want to disable binding, you can do so by adding "--bind-to none" to the cmd line,
or via the MCA param "hwloc_base_binding_policy=none"
If you want to bind your process to multiple cores (say one per thread), then you can use "--map-by
core:pe=N". Many hybrid users prefer to bind to a socket, with one process for each socket - that can be
done with "--map-by socket --bind-to socket". This keeps all the threads in the same NUMA domain.
If you aren't sure that each socket is its own NUMA domain, you can alternatively "--map-by numa
--bind-to numa" - that'll keep you in your own NUMA domain regardless of whether that's at the socket
level or elsewhere.
I'm working on adding a full description of the mapping/binding system to our
web site.
HTH
Ralph
On May 23, 2014, at 6:22 AM, Brock Palen <bro...@umich.edu> wrote:
Albert,
Actually doing affinity correctly for hybrid got easier in OpenMPI 1.7 and
newer, In the past you had to make a lot of assumptions, stride by node etc,
Now you can define a layout:
http://blogs.cisco.com/performance/eurompi13-cisco-slides-open-mpi-process-affinity-user-interface/
Brock Palen
www.umich.edu/~brockp
CAEN Advanced Computing
XSEDE Campus Champion
bro...@umich.edu
(734)936-1985
On May 23, 2014, at 9:19 AM, Albert Solernou <albert.soler...@oerc.ox.ac.uk>
wrote:
Hi,
after compiling and installing OpenMPI 1.8.1, I find that OpenMPI is pinning
processes onto cores. Although this may be
desirable on some cases, it is a complete disaster when runnning hybrid
OpenMP-MPI applications. Therefore, I want to disable this behaviour, but don't
know how.
I configured OpenMPI with:
./configure \
--prefix=$OPENMPI_HOME \
--with-psm \
--with-tm=/system/software/arcus/lib/PBS/11.3.0.121723 \
--enable-mpirun-prefix-by-default \
--enable-mpi-thread-multiple
and:
ompi_info | grep paffinity
does not report anything. However,
mpirun -np 2 --report-bindings ./wrk
reports bindings:
[login3:04574] MCW rank 1 bound to socket 0[core 1[hwt 0-1]]:
[../BB/../../../../../..][../../../../../../../..]
[login3:04574] MCW rank 0 bound to socket 0[core 0[hwt 0-1]]:
[BB/../../../../../../..][../../../../../../../..]
but they cannot be disabled as:
mpirun -np 2 --bind-to-none ./wrk
returns:
mpirun: Error: unknown option "--bind-to-none"
Any idea on what went wrong?
Best,
Albert
--
---------------------------------
Dr. Albert Solernou
Research Associate
Oxford Supercomputing Centre,
University of Oxford
Tel: +44 (0)1865 610631
---------------------------------
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Dr. Albert Solernou
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University of Oxford
Tel: +44 (0)1865 610631
---------------------------------
