[mvapich-discuss] Diagnosing Slow MVAPICH2 Startup
Thompson, Matt (GSFC-610.1)[SCIENCE SYSTEMS AND APPLICATIONS INC]
matthew.thompson at nasa.gov
Fri Jan 15 14:10:29 EST 2016
Hari,
Our admins installed a new MVAPICH2 with that disabling. I also modified
my ziatest scripts since I think some of them did not correctly use -export.
I re-ran my tests and MVAPICH2 didn't change much. Here's results at 16
nodes:
Without --disable-rdma-cm:
MV2 2.2b: 8897.59
MV2 2.2b + DISABLE_AFFINITY: 7227.84
MV2 2.2b + HOMOGENEOUS: 7557
With --disable-rdma-cm:
MV2 2.2b: 8393.73
MV2 2.2b + DISABLE_AFFINITY: 7403.94
MV2 2.2b + HOMOGENEOUS: 7224.22
So. Hmm.
On 01/14/2016 01:09 PM, Hari Subramoni wrote:
> Hello Matt,
>
> Can you please do the following two things and let us know what numbers
> you get with MVAPICH2?
>
> 1. Re-configure MVAPICH2 after disabling RDMA_CM
> - Give "--disable-rdma-cm" when you configure MVAPICH2
> 2. Set the environment variable MV2_HOMOGENEOUS_CLUSTER=1
>
> Thx,
> Hari.
>
> On Wed, Jan 13, 2016 at 3:20 PM, Hari Subramoni <subramoni.1 at osu.edu
> <mailto:subramoni.1 at osu.edu>> wrote:
>
> Hello Matt,
>
> Thanks for providing the information. We're taking a look at this
> issue. We will update you with our findings soon.
>
> Thx,
> Hari.
>
> On Wed, Jan 13, 2016 at 10:41 AM, Thompson, Matt
> (GSFC-610.1)[SCIENCE SYSTEMS AND APPLICATIONS INC]
> <matthew.thompson at nasa.gov <mailto:matthew.thompson at nasa.gov>> wrote:
>
> DK,
>
> Also, for your edification, our admins said they compiled
> MVAPICH2 2.2b as:
>
> ./configure --with-cma --with-limic2 --disable-wrapper-rpath
> --with-device=ch3:mrail --with-rdma=gen2 CC=icc CXX=icpc
> F77=ifort FC=ifort CFLAGS="-fpic -m64" CXXFLAGS="-fpic -m64"
> FFLAGS="-m64 -fpic" FCFLAGS="-m64 -fpic" --enable-f77
> --enable-fc --enable-cxx --enable-romio --enable-threads=default
> --with-hwloc -disable-multi-aliases -enable-xrc=yes -enable-hybrid
>
> Matt
>
> On 01/12/2016 10:03 AM, Panda, Dhabaleswar wrote:
>
> Hi Matt,
>
> Thanks for your note. We will take a look at the ZiaTest to
> see what could be going-on here. At a first glance,
> you should not run MVAPICH2 with MV2_USE_SHMEM_COLL=0?
> There are many optimized collectives which are disabled by
> making this parameter=0. Have you run the test without
> setting this parameter=0? Just use the
> default version with affinity=0.
>
> Thanks,
>
> DK
>
>
> ________________________________________
> From: mvapich-discuss-bounces at cse.ohio-state.edu
> <mailto:mvapich-discuss-bounces at cse.ohio-state.edu> on
> behalf of Thompson, Matt (GSFC-610.1)[SCIENCE SYSTEMS AND
> APPLICATIONS INC] [matthew.thompson at nasa.gov
> <mailto:matthew.thompson at nasa.gov>]
> Sent: Tuesday, January 12, 2016 9:26 AM
> To: mvapich-discuss at cse.ohio-state.edu
> <mailto:mvapich-discuss at cse.ohio-state.edu>
> Subject: [mvapich-discuss] Diagnosing Slow MVAPICH2 Startup
>
> MVAPICH2 Gurus,
>
> (NOTE: I am resending this. The last one appeared as garbage
> for some
> reason.)
>
> Every so often on a cluster here at NASA Goddard I like to
> see how
> different MPI stacks size up in startup time. The test I use
> (rightly or
> wrongly) is a slightly old, multi-MPI-version-aware version
> of ziatest
> (like that seen here
> https://www.nersc.gov/users/computational-systems/cori/nersc-8-procurement/trinity-nersc-8-rfp/nersc-8-trinity-benchmarks/ziatest/
> but mine doesn't have the 100MB bit).
>
> Using it, I run a series of tests (timings averages over 10
> runs) on
> 28-core Haswell nodes from 8 to 256 nodes. If we look at,
> for example,
> 16 nodes, MVAPICH2 is about 4x slower:
>
> Intel MPI 5.1.2.150 <http://5.1.2.150>: 2009.29 +/- 218.23 µs
> SGI MPT 2.12: 1337.88 +/- 99.62 µs
> Open MPI 1.10.0: 1937.89 +/- 163.66 µs
>
> MVAPICH2 2.1rc1: 8575.81 +/- 862.41 us
> MVAPICH2 2.2b_aa: 7998.25 +/- 116.06 us
> MVAPICH2 2.2b_bb: 8175.28 +/- 608.01 us
> MVAPICH2 2.2b_cc: 8422.5 +/- 928.19 us
>
> For the MVAPICH2 tests, I use mpirun_rsh as the launcher. The
> "subscripts" are: aa is no environment set, bb is
> MV2_ENABLE_AFFINITY=0
> (there was a warning so I tried its advice), and cc is
> MV2_ENABLE_AFFINITY=0 plus MV2_USE_SHMEM_COLL=0 based on
> maybe trying
> this:
> http://mailman.cse.ohio-state.edu/pipermail/mvapich-discuss/2015-October/005733.html.
>
> As you can see, MVAPICH2 seems to be a slow starter, and it
> stays that
> way at the high end too, though not as bad at 256 nodes[1]:
>
> Intel MPI 5.1.2.150 <http://5.1.2.150>: 2841.19 +/- 566.81 us
> SGI MPT 2.12: 10961.4 +/- 1070.88 us
> Open MPI 1.10.0: 8959.72 +/- 244.46 us
>
> MVAPICH2 2.1rc1: 16099 +/- 1035.97 us
> MVAPICH2 2.2b_aa: 16570.7 +/- 2089.64 us
> MVAPICH2 2.2b_bb: 16197.3 +/- 1414.67 us
> MVAPICH2 2.2b_cc: 16358 +/- 1123.69 us
>
> Now the cluster I'm running is SLURM 14-based (I think) so I
> can't yet
> have the admins try out the PMIx patch I see on your
> download page (as
> it seems to be SLURM 15 versioned). I'd imagine that could
> possibly
> help, right?
>
> Still, I'm thinking it could be something as basic as a need
> to build
> differently or perhaps a needed environment variable?
>
> Matt
>
> [1] Note, not sure why Intel MPI is doing so well. I'm
> thinking my test
> and Intel MPI might be magically missing some interaction
> the others are
> seeing.
>
> --
> Matt Thompson, SSAI, Sr Scientific Programmer/Analyst
> NASA GSFC, Global Modeling and Assimilation Office
> Code 610.1, 8800 Greenbelt Rd, Greenbelt, MD 20771
> Phone: 301-614-6712 <tel:301-614-6712> Fax:
> 301-614-6246 <tel:301-614-6246>
> http://science.gsfc.nasa.gov/sed/bio/matthew.thompson
> _______________________________________________
> mvapich-discuss mailing list
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> <mailto:mvapich-discuss at cse.ohio-state.edu>
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>
>
>
> --
> Matt Thompson, SSAI, Sr Scientific Programmer/Analyst
> NASA GSFC, Global Modeling and Assimilation Office
> Code 610.1, 8800 Greenbelt Rd, Greenbelt, MD 20771
> Phone: 301-614-6712 <tel:301-614-6712> Fax:
> 301-614-6246 <tel:301-614-6246>
> http://science.gsfc.nasa.gov/sed/bio/matthew.thompson
> _______________________________________________
> mvapich-discuss mailing list
> mvapich-discuss at cse.ohio-state.edu
> <mailto:mvapich-discuss at cse.ohio-state.edu>
> http://mailman.cse.ohio-state.edu/mailman/listinfo/mvapich-discuss
>
>
>
--
Matt Thompson, SSAI, Sr Scientific Programmer/Analyst
NASA GSFC, Global Modeling and Assimilation Office
Code 610.1, 8800 Greenbelt Rd, Greenbelt, MD 20771
Phone: 301-614-6712 Fax: 301-614-6246
http://science.gsfc.nasa.gov/sed/bio/matthew.thompson
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