From: Andrew Pearson (andrew.j.pearson_at_gmail.com)
Date: Mon Feb 25 2013 - 06:28:05 CST
Hi Norman
Thanks for the response. I didn't phrase my question well - I know I'm
experiencing scaling problems, and I'm trying to determine whether
precompiled namd binaries are known to cause problems. I ask this since
many people seem to say that you should compile namd yourself to save
headaches.
Your explanation about charm++ displaying information about the number of
cores makes sense. I'll bet that's what's happening.
My scaling problem is that for a given system (27 patches, 50000 atoms) I
get perfect speedup until nprocs = 12 and then the speedup line goes almost
flat. This occurs for runs performed on a single 16 core node.
Andrew
On Monday, February 25, 2013, Norman Geist wrote:
> Hi Andrew,****
>
> ** **
>
> its a bad idea to ask someone else if you have scaling problems. You
> should know if you have or not. The information from the outfile just comes
> from the charm++ startup and is simply a information about the underlying
> hardware. It doesnt mean it uses smp. It just tells you its a
> multiprocessor/multicore node. Watch the output carefully and you will see
> IMHO that it uses the right number of cpus (for example the Benchmark
> lines). So what kind of scaling problems you have? Dont you get the
> expected speedup?****
>
> ** **
>
> Norman Geist.****
>
> ** **
>
> *Von:* owner-namd-l_at_ks.uiuc.edu <javascript:_e({}, 'cvml',
> 'owner-namd-l_at_ks.uiuc.edu');> [mailto:owner-namd-l_at_ks.uiuc.edu<javascript:_e({}, 'cvml', 'owner-namd-l_at_ks.uiuc.edu');>]
> *Im Auftrag von *Andrew Pearson
> *Gesendet:* Freitag, 22. Februar 2013 19:30
> *An:* namd-l_at_ks.uiuc.edu <javascript:_e({}, 'cvml',
> 'namd-l_at_ks.uiuc.edu');>
> *Betreff:* namd-l: Always 24-way SMP?****
>
> ** **
>
> I'm investigating scaling problems with NAMD. I'm running precompiled
> linux-64-tcp binaries on a linux cluster with 12-core nodes using "charmrun
> +p $NPROCS ++mpiexec".
>
> I know scaling problems have been covered, but I can't find the answer to
> my specific question. No matter how many cores I use or how many nodes
> they are spread over, at the top of stdout charm++ always reports "Running
> on # unique compute nodes (24-way SMP)". It gets # correct, but it's
> always 24-way SMP. Is this supposed to be this way? If so, why?****
>
> Everyone seems to say that you should recompile NAMD with your own MPI
> library, but I don't seem to have problems running NAMD jobs to completion
> with charmrun + OpenMPI built with intel (except for the scaling). Could
> using the precompiled binaries result in scaling problems?
>
> Thank you.****
>
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