Re: any experiences with executing parallel NAMD in a NAMD simulation

From: Peter Freddolino (
Date: Mon Feb 09 2009 - 22:13:43 CST

Hi Yinglong,
when you say that you have a certain performance expectation for the
embedded part, what are you basing that expectation on? What kind of
benchmarking have you done? Are you taking into the account the fact
that a minimization step will be slower than a normal MD step?


Yinglong Miao wrote:
> Dear Peter,
> Thanks for your reply!
> Peter Freddolino wrote:
>> Hi Yinglong,
>> how long is your embedded run, relative to your overall simulation? Is
>> it on the same system? Do you end up running on the same nodes? Have you
>> verified that you're running on as many processors as you think you are?
> I have been running cycles for my overall simulation. In each cycle,
> the embedded run is basically energy-minimization of the system of the
> overall simulation excluding water and ions. It accounts for about 1/5
> of the computation time with the speed expected. I have double checked
> the output: the same nodes are used for the embedded run and the
> overall simulation.
>> What you're doing is quite unusual, and depending on the exact
>> relationship between your two systems there is probably a better way to
>> handle it. Especially if the embedded runs are small relative to the
>> full run, please keep in mind that namd has a high startup cost. If your
>> embedded run is on a system whose topology doesn't change (and only
>> needs coordinates once in awhile) you will probably be better off
>> starting two separate namd jobs on disjoint sets of nodes and having
>> them communicate with sockets (as is done in the replica exchange
>> scripts distributed with namd). This gets around both the startup costs
>> and other potential problems with having two copies of namd running (if
>> your system is large, for example, you're putting a lot of stress on the
>> head node in terms of memory).
> As mentioned above, the system input to the embedded run is basically
> that for the overall simulation excluding host medium, and they are
> different. The systems are pretty large, about half a million atoms
> for the core structure and much more for the entire system. I have
> been thinking of writing batch scripts to invoke NAMD sequentially,
> but that will take a lot of efforts to rewrite my NAMD configuration
> scripts to set up the running cycles. It would be great if the
> technical issues can be solved to have embedded run executed at a
> reasonable speed.
> Thanks,
> Yinglong
>> Best,
>> Peter
>> Yinglong Miao wrote:
>>> Dear NAMD developers/users,
>>> I have been trying to embed a parallel NAMD run in a bigger NAMD
>>> simulation; that is by calling "exec mpirun -np $nprocessors
>>> -machinefile $machinelist namd2 ${str}.conf" in a NAMD configuration
>>> script to run a different structure and generate proper output for the
>>> big simulation. The program runs fine except that the embedded part is
>>> executed much more slowly than expected (~1/5 of the speed) and
>>> sometimes such error messages pop up: "Max retransmit retries reached
>>> (829) for message". I thought it's because the message passing is
>>> slowed down and the MPI environment is messed up upon NAMD exit for
>>> the embedded run. Is there anybody have experiences with this? How to
>>> run the embedded part with normal speed? Any suggestions will be
>>> greatly appreciated.
>>> Thanks!
>>> --
>>> Yinglong Miao
>>> Ph.D. Candidate
>>> Center for Cell and Virus Theory
>>> Chemistry Department, Indiana University
>>> 800 E Kirkwood Ave Room C203A, Bloomington, IN 47405
>>> Tel: 1-812-856-0981
> --
> Yinglong Miao
> Ph.D. Candidate
> Center for Cell and Virus Theory
> Department of Chemistry, Indiana University
> Address: 800 E Kirkwood Ave Room C203A, Bloomington, IN 47405
> Phone: 1-812-856-0981 (office) 1-812-272-8196 (cell)

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