AMBER Archive (2009)

Subject: Re: [AMBER] AMBER is running silently

From: Kefa Lu (kefa.lu_at_gmail.com)
Date: Mon Aug 17 2009 - 20:25:14 CDT

Thanks a lot! Ross. I tried some of your suggestions, but looks it
doesn't help a lot.

Ross Walker wrote:
> Hi Kefa,
>
> At what point does it cease producing output? Do you get anything at all or
> just a completely blank mdout file?
>
It cease after it read in the .mdin file. There is something output in
the .mdout. The last several lines I got in .mdout file is following,

--------------------------------------------------------------------------------
   3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------

                                                                                

 begin time read from input coords = 0.000 ps

 Number of triangulated 3-point waters found: 16002

After this, it would never print any more things until the Q time runs out.

> Also if you kill the job in the queue do you ultimately get any mdout file,
> I.e. was it just buffering it. What about the queue system Job output and
> error files? Do these have anything?
>
>
When I kill the job in the queue. There won't be anything in the mdout
file. And in the job output and error files, nothing but standard output
just like the program was running normally.

> A few things to try.
>
> 1) If you use sander vs pmemd is the behavior the same? You should probably
> use PMEMD here, you will get much better performance.
>
>
I didn't try pmemd yet. I'll try that.

> 2) Hot starting a membrane system at 310k is VERY dicey!. You should
> probably do some careful heating at constant volume first.
>
I'm trying to run such constant volume simulation run, but got similar
problem here. It ceased. My .mdin file is following,

molecular dynamics run
 &cntrl
    imin=0,irest=0,ntx=1,
    cut=10.0,scee=1.2,
    tempi=0.0,temp0=310.0,
    ntt=3,gamma_ln=1.0,
    ntp=0,pres0=1.0,taup=5.0,
    vlimit=25.0,
    ntb=1,ntc=2,ntf=2,
    nstlim=10000,
    iwrap=1,
    ntwe=100,ntwx=100,ntpr=100,
    ntr=1,
 &end
GRP1
1.0
ATOM 1 13613
END
END

> 3) Set nstlim=100 and ntwx=100 and ntpr=100 and run it - do you get any
> output?
>
>
OK. I'll try this.
> 4) You are running periodic boundaries are you certain your inpcrd file has
> box information in it? Sander and PMEMD can hang if they expect box info but
> do not find it.
>
>
Yes, I have box information in the inpcrd file.

> 5) Have you run this in serial on your desktop - just to see if you get any
> output - does it work here?
>
>
I'll try this.

> 6) Are you certain you aren't just running into a bad node? Clusters can be
> notoriously unreliable and often queuing systems do not help by keep
> assigning you the same batch of nodes containing the bad node. You can
> eliminate this possibility by confirming you can run in serial and/or
> interactively to see if you get output.
>
>
I'm pretty sure there is no bad node.

> 7) Cut of 12 is pretty large. You can probably reduce this to 9.0 or even
> maybe 8.0 and save yourself 50% or more in computation cost.
>

I just reduced cutoff to 10.0. But looks it doesn't help.
> 8) Are you using too many processors? Performance in parallel only increases
> to a point (hardware, problem, compiler blah blah blah specific) and then it
> falls off massively. Thus if you ask for too many cpus you can end up
> running much much slower than even serial. You should benchmark you run, say
> 1000 steps or so on different cpu counts to see how the performance varies
> and choose the optimal performance vs computational cost tradeoff that you
> are prepared to stomach.
>
>
I'm just running on 8 processors. The system size is 94,000 atoms totally.

> All the best
> Ross
>
>
>> -----Original Message-----
>> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
>> Behalf Of Kefa Lu
>> Sent: Monday, August 17, 2009 4:10 PM
>> To: AMBER Mailing List
>> Subject: Re: [AMBER] AMBER is running silently
>>
>> My .mdin file is simply as following,
>>
>> &cntrl
>> imin=0,irest=0,ntx=1,
>> cut=12.0,scee=1.2,
>> tempi=310.0,temp0=310.0,
>> ntt=3,gamma_ln=1.0,
>> ntp=2,pres0=1.0,taup=5.0,
>> vlimit=25.0,
>> ntb=2,ntc=2,ntf=2,
>> nstlim=1000000,
>> iwrap=1,
>> ntwe=100,ntwx=1000,ntpr=100,
>> &end
>>
>> Really appreciate for any suggestions.
>>
>> Kefa
>>
>>
>> Bill Ross wrote:
>>
>>
>>> It would help to send your mdin.
>>>
>>> Bill
>>>
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>
>
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