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Subject: Re: [OMPI devel] Open-MPI build of NAMD launched from srun over 20% slowed than with mpirun
From: Christopher Samuel (samuel_at_[hidden])
Date: 2013-09-06 02:15:52


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On 06/09/13 14:14, Christopher Samuel wrote:

> However, modifying the test program confirms that variable is getting
> propagated as expected with both mpirun and srun for 1.6.5 and the 1.7
> snapshot. :-(

Investigating further by setting:

export OMPI_MCA_orte_report_bindings=1
export SLURM_CPU_BIND=core
export SLURM_CPU_BIND_VERBOSE=verbose

reveals that only OMPI 1.6.5 with mpirun reports bindings being set
(see below). We cannot understand why Slurm doesn't *appear* to be
setting bindings as we have the correct settings according to the
documentation.

Whilst it may explain the difference between 1.6.5 mpirun and srun
it doesn't to explain why the 1.7 snapshot is so much better as you'd
expect them to be hurt in the same way.

======================OPENMPI 1.6.5======================
======================mpirun======================
[barcoo003:03633] System has detected external process binding to cores 0001
[barcoo003:03633] MCW rank 0 bound to socket 0[core 0]: [B]
[barcoo004:04504] MCW rank 1 bound to socket 0[core 0]: [B]
Hello, World, I am 0 of 2 on host barcoo003 from app number 0 universe size 2 universe envar 2
Hello, World, I am 1 of 2 on host barcoo004 from app number 0 universe size 2 universe envar 2
======================srun======================
Hello, World, I am 0 of 2 on host barcoo003 from app number 1 universe size 2 universe envar NULL
Hello, World, I am 1 of 2 on host barcoo004 from app number 1 universe size 2 universe envar NULL
=========================================================
======================OPENMPI 1.7.3======================
DANGER: YOU ARE LOADING A TEST VERSION OF OPENMPI. THIS MAY BE BAD.
======================mpirun======================
Hello, World, I am 0 of 2 on host barcoo003 from app number 0 universe size 2 universe envar 2
Hello, World, I am 1 of 2 on host barcoo004 from app number 0 universe size 2 universe envar 2
======================srun======================
Hello, World, I am 0 of 2 on host barcoo003 from app number 0 universe size 2 universe envar NULL
Hello, World, I am 1 of 2 on host barcoo004 from app number 0 universe size 2 universe envar NULL
=========================================================

- --
 Christopher Samuel Senior Systems Administrator
 VLSCI - Victorian Life Sciences Computation Initiative
 Email: samuel_at_[hidden] Phone: +61 (0)3 903 55545
 http://www.vlsci.org.au/ http://twitter.com/vlsci

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