Re: Fwd: About wall clock time

From: Chitrak Gupta (chgupta_at_mix.wvu.edu)
Date: Mon Oct 16 2017 - 08:48:38 CDT

Hi Rik,

Any specific reason why you are looking at the wall clock time and not the
benchmark times in your log file? From what I understand, benchmark times
are more accurate than the wall clock time.

Chitrak.

On Mon, Oct 16, 2017 at 9:18 AM, Renfro, Michael <Renfro_at_tntech.edu> wrote:

> Two things I’ve found influenced benchmarking:
>
> - model size: smaller models don’t provide enough compute work before
> needing to communicate back across cores and nodes
> - network interconnect: on a modern Xeon system, gigabit Ethernet is a
> bottleneck, at least on large models (possibly all models)
>
> I benchmarked a relatively similar system starting in July (Dell 730 and
> 6320, Infiniband, K80 GPUs in the 730 nodes). Results are at [1]. If I
> wasn’t using a ibverbs-smp build of NAMD, and was using the regular tcp
> version, 2 nodes gave slower run times than 1. 20k atom models topped out
> at around 5 28-core nodes, and 3M atom models kept getting better run
> times, even out to 34 28-core nodes.
>
> A 73k system certainly should show a consistent speedup across your 6
> nodes, though. And a CUDA-enabled build showed a 3-5x speedup compared to a
> non-CUDA run on our tests, so 1-2 of your GPU nodes could run as fast as
> all your non-GPU nodes combined.
>
> So check your NAMD build features for ibverbs, and maybe verify your
> Infiniband is working correctly — I used [2] for checking Infiniband, even
> though I’m not using Debian on my cluster.
>
> [1] https://its.tntech.edu/display/MON/HPC+Sample+Job%3A+NAMD
> [2] https://pkg-ofed.alioth.debian.org/howto/infiniband-howto.html
>
> --
> Mike Renfro / HPC Systems Administrator, Information Technology Services
> 931 372-3601 / Tennessee Tech University
>
> > On Oct 16, 2017, at 1:20 AM, Rik Chakraborty <
> rik.chakraborty01_at_gmail.com> wrote:
> >
> > Dear NAMD experts,
> >
> > Recently, we have installed a new cluster and the configurations are
> following below,
> >
> > 1. Master node with storage node- DELL PowerEdge R730xd Server
> > 2. CPU only node- DELL PowerEdge R430 Server (6 nos.)
> > 3. GPU node- DELL PowerEdge R730 Server (3 nos.)
> > 4. 18 ports Infiniband Switch- Mellanox SX6015
> > 5. 24 ports Gigabit Ethernet switch- D-link make
> >
> > We have run a NAMD job using this cluster to check *the efiiciency in
> time with increasing number of CPU node. Each CPU node has 24 processor.
> The details of the given system and the outcomes are listed below,
> >
> > 1. No. of atoms used: 73310
> > 2. Total simulation time: 1ns
> > 3. Time step: 2fs
> >
> > No. of nodes
> >
> > Wall Clock Time (s)
> >
> > 1
> >
> > 27568.892578
> >
> > 2
> >
> > 28083.976562
> >
> > 3
> >
> > 30725.347656
> >
> > 4
> >
> > 33117.160156
> >
> > 5
> >
> > 35750.988281
> >
> > 6
> >
> > 39922.492188
> >
> >
> > As we can see, wall clock time is increased with the increase of no. of
> CPU nodes which is not expected.
> >
> > So, this is my kind request to check this out and let me know about the
> problem.
> >
> > Thanking you,
> >
> > Rik Chakraborty
> > Junior Research Fellow (Project)
> > Dept. of Biological Sciences
> > Indian Institute of Science Education and Research, Kolkata
> > Mohanpur, Dist. Nadia
> > Pin 721246
> > West Bengal, India
> >
> >
> >
> >
>
>
>

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