[mvapich-discuss] Diagnosing Slow MVAPICH2 Startup

[Thompson, Matt (GSFC-610.1)[SCIENCE SYSTEMS AND APPLICATIONS INC]]

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 on behalf of Thompson, Matt (GSFC-610.1)[SCIENCE SYSTEMS AND APPLICATIONS INC] [matthew.thompson at nasa.gov]
> Sent: Tuesday, January 12, 2016 9:26 AM
> To: 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: 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:  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                 Fax: 301-614-6246
> http://science.gsfc.nasa.gov/sed/bio/matthew.thompson
> _______________________________________________
> mvapich-discuss mailing list
> 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                 Fax: 301-614-6246
http://science.gsfc.nasa.gov/sed/bio/matthew.thompson