From: Joel Moniz (jram802_at_yahoo.co.uk)
Date: Tue Jul 08 2014 - 22:17:19 CDT
Thank you very much, Mr. Geist.
On Monday, 7 July 2014, 13:20, Norman Geist <norman.geist_at_uni-greifswald.de> wrote:
Von:owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von Joel
Gesendet: Montag, 7. Juli 2014 08:42
Betreff: namd-l: Regarding NAMD and MD simulations
I'm using NAMD for benchmarking a GPU cluster, and I don't have
any experience with molecular dynamic simulations.I had a few doubts regarding
NAMD, as well as regarding molecular dynamics:
Not the best base to carry out benchmarks, as it relies also on
understanding what the code is doing.
1. Regarding the Linux-x86_64 and the Linux-x86_64-TCP versions, I
have noticed better performance of the former, UDP version when compared to the
TCP version on a Gigabit Ethernet network with 4 nodes on it. Is
Of course, as TCP has time consuming safety protocols which UDP
have not. The required integrity checks are implemented in the charm++.
Please notice that Gigabit is mostly insufficient for a GPU
2. Is there anyway that I could specify which GPU devices I want
to use on each individual node when using the ibverbs-CUDA-smp distribution,
like I can specify the number of CPUs per node with the ++cpus parameter in the
nodelist file? Right now, I can only specify one +devices parameter, which
seems to affect all the nodes, and a +devices next to each node of the nodelist
seems to have no effect.
No. You need to hack the code to do that. I’ve done it so
I could provide you a patch. Which means you have to recompile.
3. What does the stepspercycle parameter represent? I read
that this represents the number of timesteps in a cycle, and each cycle
represents the number of timesteps between pairlist generations and atom
reassignments, but what exactly are pairlist generations and atom
The periodic simulation cell is departed into patches (box
slices) to depart the work (parallelization). As the atoms move, they may
change the patches. But, the patches are build with parameters that do allow to
not update these patches every simulation step, only every stepspercycle. So it
is not expected that a atom changes the patch within 20 timesteps or get into
the interaction cutoff distance to an atom which is not considered by the
4. Would the stmv example be representative of a typical MD
simulation run (for example, in terms of number of particles)? Where
could I find other example simulations?
Its quite large. Another example for small to medium sized is “apoa1”.
5. Would the performance of a simulation vary significantly across
simulations (provided parameters like numsteps, timestep, stepspercycle, etc.,
as well as the number of particles, remains constant)?
No, if same compute power is used.
6. What are the most frequently used values (or ranges) for
numsteps, timestep and stepspercycle (though I realise that this would
definitely depend on the application)?
None of them should be changed for benchmarks but you may want
Command line switches to namd2:
In namd script:
Fullelectfrequency 4; #in any case
Twoawayx yes; #if it brings speed
Twoawayy yes; #if twoawayx brought speed and this brings speed
I'm extremely sorry if these doubts are a little too basic, but I
have not been able to find any information regarding these doubts, and have no
experience in molecular dynamics.
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