From: Yinglong Miao (ylmiao.indiana_at_gmail.com)
Date: Mon Feb 09 2009 - 22:26:37 CST
Dear Peter,
I compared the embedded run to a standalone energy minimization of the
same structure with the same number of processors. It's more than 10
times slower when checking the NAMD output benchmarking results. I did
notice energy minimization is slower than MD, normally 1/3 of the speed
for my system.
Thanks,
Yinglong
Peter Freddolino wrote:
> 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?
>
> Peter
>
> 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)
>>
>
>
-- 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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