AMBER Archive (2008)

Subject: Re: AMBER: Non bond list error

From: Robert Duke (rduke_at_email.unc.edu)
Date: Thu Oct 23 2008 - 15:14:13 CDT

As Ross will tell you too:
1) Don't increase cut to 12, leave it at the default (of 8)
2) Run this on at least 4 processors using the MPI version of pmemd or
sander (I know you are using sander here; pmemd requires less memory). Even
higher processor counts will reduce your risk of memory overflow further.
Your pairlist went negative because you incremented it past a 31 bit digit;
with the commonly used integer format on computers these days
(twos-complement), this results in a negative number (and is clearly an
error condition). Is this memory usage reasonable for the size problem you
have? Well, that cutoff plus skin will produce about 552 pairs per atom.
If you had 1,000,000 atoms (and you are close), that would be 552,000,000
pairs. Not enough to overflow the list counter. BUT that is 552,000,000
pairs * 4 bytes per integer, means 2 GB in the nonbonded list alone. Most
machines, you are pushing it to get much over 1.5 GB for the application (I
have not looked recently, so that is off the top of my head). With true 32
bit executables, you are out of address space; with the newer 64 bit chips,
you have bits to specify more than 2 GB of addresses, but you may not have
enough actual memory. And remember that the pairlist is only part of your
memory consumption. No resource is infinite on a computer...
Regards - Bob Duke
----- Original Message -----
From: "Wang,Ying" <wangying_at_ufl.edu>
To: <amber_at_scripps.edu>
Sent: Thursday, October 23, 2008 3:26 PM
Subject: RE: AMBER: Non bond list error

> Hi, Ross,
>
> Thanks a lot!
>
> My input file is as below:
> 50ps MD with res
> &cntrl
> imin = 0,
> irest = 0,
> ntx = 1,
> ntb = 1,
> cut = 12,
> ntr = 1,
> ntc = 2,
> ntf = 2,
> tempi = 0.0,
> temp0 = 300.0,
> ntt = 3,
> gamma_ln = 2.0,
> nstlim = 50000, dt = 0.001
> ntpr = 1000, ntwx = 1000, ntwr = 1000
> nmropt=1
> /
> &wt TYPE='TEMP0', istep1=0, istep2=50000,
> value1=0.1, value2=300.0, /
> &wt TYPE='END' /
> Keep system fixed with weak restraints
> 20.0
> RES 1 5076
> END
> END
>
> and the NPT is as below:
>
> NPT: 50ps MD
> &cntrl
> imin = 0, irest = 1, ntx = 7,
> ntb = 2, pres0 = 1.0, ntp = 1,
> taup = 2.0,
> cut = 12, ntr = 1,
> ntc = 2, ntf = 2,
> tempi = 300.0, temp0 = 300.0,
> ntt = 3, gamma_ln = 2.0,
> nstlim = 50000, dt = 0.001,
> ntpr = 1000, ntwx = 1000, ntwr = 1000
> /
> Keep fixed with weak restraints
> 20.0
> RES 217 954
> END
> Keep fixed with weak restraints
> 20.0
> RES 1909 2646
> END
> Keep fixed with weak restraints
> 20.0
> RES 3601 4338
> END
> res also
> 5.0
> RES 955 1692
> END
> res also
> 5.0
> RES 2647 3384
> END
> res also
> 5.0
> RES 4339 5076
> END
> END
>
>
>
> Thanks again!!!!!!!!!!!!!!!
>
>
>
> On Thu Oct 23 14:38:09 EDT 2008, Ross Walker <ross_at_rosswalker.co.uk>
> wrote:
>
>> Hi Wang,
>>
>> 800K atoms is pretty large and while sander / pmemd should support this
>> size
>> (I think 999,999 is the limit right now due to file formatting) you may
>> run
>> into problems that haven't been seen before.
>>
>> It's not obvious what is going wrong in your case but the numbers don't
>> make
>> any sense (a negative capacity!) which suggests either memory corruption
>> through an array overflow or the number of pairs is larger than a signed
>> integer and is overflowing. Even at 800K atoms you shouldn't have this
>> many
>> pairs though. Can you post your input file so we can take a look? I
>> suspect
>> you have cut set too high or perhaps are not running PME etc.
>>
>> All the best
>> Ross
>>
>>> -----Original Message-----
>>> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
>>> Of Wang,Ying
>>> Sent: Thursday, October 23, 2008 10:20 AM
>>> To: amber_at_scripps.edu
>>> Subject: AMBER: Non bond list error
>>>
>>> Hi, Dear AMBERs,
>>>
>>> I meet a problem when I run a simulation of a system consist of
>>> 799889 atoms.
>>>
>>> * NB pairs 451 0 exceeds capacity (
>>> -28510921) 7
>>> SIZE OF NONBOND LIST = -28510921
>>> SANDER BOMB in subroutine nonbond_list
>>> Non bond list overflow!
>>> check MAXPR in locmem.f
>>>
>>> Could anyone tell me what's happen?
>>>
>>> Thanks a lot!
>>>
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>>
>
>
>
> --
> Wang,Ying
>
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