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Subject: Re: [OMPI devel] RFC: Force Slurm to use PMI-1 unless PMI-2 is specifically requested
From: Joshua Ladd (jladd.mlnx_at_[hidden])
Date: 2014-05-07 10:39:24


Just saw this thread, and I second Chris' observations: at scale we are
seeing huge gains in jobstart performance with PMI2 over PMI1. We
*CANNOT*loose this functionality. For competitive reasons, I cannot
provide exact
numbers, but let's say the difference is in the ballpark of a full
order-of-magnitude on 20K ranks versus PMI1. PMI1 is completely
unacceptable/unusable at scale. Certainly PMI2 still has scaling issues,
but there is no contest between PMI1 and PMI2. We (MLNX) are actively
working to resolve some of the scalability issues in PMI2.

Josh

Joshua S. Ladd
Staff Engineer, HPC Software
Mellanox Technologies

Email: joshual_at_[hidden]

On Wed, May 7, 2014 at 4:00 AM, Ralph Castain <rhc_at_[hidden]> wrote:

> Interesting - how many nodes were involved? As I said, the bad scaling
> becomes more evident at a fairly high node count.
>
> On May 7, 2014, at 12:07 AM, Christopher Samuel <samuel_at_[hidden]>
> wrote:
>
> > -----BEGIN PGP SIGNED MESSAGE-----
> > Hash: SHA1
> >
> > Hiya Ralph,
> >
> > On 07/05/14 14:49, Ralph Castain wrote:
> >
> >> I should have looked closer to see the numbers you posted, Chris -
> >> those include time for MPI wireup. So what you are seeing is that
> >> mpirun is much more efficient at exchanging the MPI endpoint info
> >> than PMI. I suspect that PMI2 is not much better as the primary
> >> reason for the difference is that mpriun sends blobs, while PMI
> >> requires that everything be encoded into strings and sent in little
> >> pieces.
> >>
> >> Hence, mpirun can exchange the endpoint info (the dreaded "modex"
> >> operation) much faster, and MPI_Init completes faster. Rest of the
> >> computation should be the same, so long compute apps will see the
> >> difference narrow considerably.
> >
> > Unfortunately it looks like I had an enthusiastic cleanup at some point
> > and so I cannot find the out files from those runs at the moment, but
> > I did find some comparisons from around that time.
> >
> > This first pair are comparing running NAMD with OMPI 1.7.3a1r29103
> > run with mpirun and srun successively from inside the same Slurm job.
> >
> > mpirun namd2 macpf.conf
> > srun --mpi=pmi2 namd2 macpf.conf
> >
> > Firstly the mpirun output (grep'ing the interesting bits):
> >
> > Charm++> Running on MPI version: 2.1
> > Info: Benchmark time: 512 CPUs 0.0959179 s/step 0.555081 days/ns 1055.19
> MB memory
> > Info: Benchmark time: 512 CPUs 0.0929002 s/step 0.537617 days/ns 1055.19
> MB memory
> > Info: Benchmark time: 512 CPUs 0.0727373 s/step 0.420933 days/ns 1055.19
> MB memory
> > Info: Benchmark time: 512 CPUs 0.0779532 s/step 0.451118 days/ns 1055.19
> MB memory
> > Info: Benchmark time: 512 CPUs 0.0785246 s/step 0.454425 days/ns 1055.19
> MB memory
> > WallClock: 1403.388550 CPUTime: 1403.388550 Memory: 1119.085938 MB
> >
> > Now the srun output:
> >
> > Charm++> Running on MPI version: 2.1
> > Info: Benchmark time: 512 CPUs 0.0906865 s/step 0.524806 days/ns 1036.75
> MB memory
> > Info: Benchmark time: 512 CPUs 0.0874809 s/step 0.506255 days/ns 1036.75
> MB memory
> > Info: Benchmark time: 512 CPUs 0.0746328 s/step 0.431903 days/ns 1036.75
> MB memory
> > Info: Benchmark time: 512 CPUs 0.0726161 s/step 0.420232 days/ns 1036.75
> MB memory
> > Info: Benchmark time: 512 CPUs 0.0710574 s/step 0.411212 days/ns 1036.75
> MB memory
> > WallClock: 1230.784424 CPUTime: 1230.784424 Memory: 1100.648438 MB
> >
> >
> > The next two pairs are first launched using mpirun from 1.6.x and then
> with srun
> > from 1.7.3a1r29103. Again each pair inside the same Slurm job with the
> same inputs.
> >
> > First pair mpirun:
> >
> > Charm++> Running on MPI version: 2.1
> > Info: Benchmark time: 64 CPUs 0.410424 s/step 2.37514 days/ns 909.57 MB
> memory
> > Info: Benchmark time: 64 CPUs 0.392106 s/step 2.26913 days/ns 909.57 MB
> memory
> > Info: Benchmark time: 64 CPUs 0.313136 s/step 1.81213 days/ns 909.57 MB
> memory
> > Info: Benchmark time: 64 CPUs 0.316792 s/step 1.83329 days/ns 909.57 MB
> memory
> > Info: Benchmark time: 64 CPUs 0.313867 s/step 1.81636 days/ns 909.57 MB
> memory
> > WallClock: 8341.524414 CPUTime: 8341.524414 Memory: 975.015625 MB
> >
> > First pair srun:
> >
> > Charm++> Running on MPI version: 2.1
> > Info: Benchmark time: 64 CPUs 0.341967 s/step 1.97897 days/ns 903.883 MB
> memory
> > Info: Benchmark time: 64 CPUs 0.339644 s/step 1.96553 days/ns 903.883 MB
> memory
> > Info: Benchmark time: 64 CPUs 0.284424 s/step 1.64597 days/ns 903.883 MB
> memory
> > Info: Benchmark time: 64 CPUs 0.28115 s/step 1.62702 days/ns 903.883 MB
> memory
> > Info: Benchmark time: 64 CPUs 0.279536 s/step 1.61769 days/ns 903.883 MB
> memory
> > WallClock: 7476.643555 CPUTime: 7476.643555 Memory: 968.867188 MB
> >
> >
> > Second pair mpirun:
> >
> > Charm++> Running on MPI version: 2.1
> > Info: Benchmark time: 64 CPUs 0.366327 s/step 2.11995 days/ns 939.527 MB
> memory
> > Info: Benchmark time: 64 CPUs 0.359805 s/step 2.0822 days/ns 939.527 MB
> memory
> > Info: Benchmark time: 64 CPUs 0.292342 s/step 1.69179 days/ns 939.527 MB
> memory
> > Info: Benchmark time: 64 CPUs 0.293499 s/step 1.69849 days/ns 939.527 MB
> memory
> > Info: Benchmark time: 64 CPUs 0.292355 s/step 1.69187 days/ns 939.527 MB
> memory
> > WallClock: 7842.831543 CPUTime: 7842.831543 Memory: 1004.050781 MB
> >
> > Second pair srun:
> >
> > Charm++> Running on MPI version: 2.1
> > Info: Benchmark time: 64 CPUs 0.347864 s/step 2.0131 days/ns 904.91 MB
> memory
> > Info: Benchmark time: 64 CPUs 0.346367 s/step 2.00444 days/ns 904.91 MB
> memory
> > Info: Benchmark time: 64 CPUs 0.29007 s/step 1.67865 days/ns 904.91 MB
> memory
> > Info: Benchmark time: 64 CPUs 0.279447 s/step 1.61717 days/ns 904.91 MB
> memory
> > Info: Benchmark time: 64 CPUs 0.280824 s/step 1.62514 days/ns 904.91 MB
> memory
> > WallClock: 7522.677246 CPUTime: 7522.677246 Memory: 969.433594 MB
> >
> >
> > So to me it looks like (for NAMD on our system at least) that
> > PMI2 does seem to give better scalability.
> >
> > All the best!
> > Chris
> > - --
> > 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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> > iEYEARECAAYFAlNp28UACgkQO2KABBYQAh8hagCfewbbxUR6grg5R40GrwjtIZV0
> > 1KYAn2uX0yKLdOEbkHARKouzwFilaTTD
> > =A/Yw
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