AMBER Archive (2008)

Subject: Re: AMBER: Non bond list error

From: Wang,Ying (wangying_at_ufl.edu)
Date: Thu Oct 23 2008 - 16:58:06 CDT

Thanks a lot!!!

On Thu Oct 23 16:44:29 EDT 2008, Robert Duke <rduke_at_email.unc.edu>
wrote:

> Actually, I noticed I said "you overflowed the counter", and then
> show that
> you didn't... (oh, oops). So it is memory corruption. What I
> don't
> understand is why you are not dying with some sort of "out of
> memory" error
> from sander, associated with asking for more memory than is
> available. For
> pmemd, anywhere I allocate dynamic memory, I check for a success
> return
> code, so the way you should experience running out of memory
> there is to get
> an explicit error message. Because sander has a preallocated
> memory pool
> strategy, I suspect that other things are possible... Bottom
> line on all
> this - I think it is a good idea to not run more than roughly
> 100,000 atoms
> on a single processor, especially for sander. And if you run it
> on 4
> processors but they all share the same limited physical memory,
> you may also
> hit trouble. I attached a graphic on pmemd memory requirements -
> a jpg so
> it should be widely viewable. My rule of thumb for pmemd is that
> 4
> processors, each with 1 GB of actual physical memory, can handle
> up to 1
> million atoms with the default 8 angstrom cutoff. Sander will
> take more.
> There are also buffer space considerations in an mpi application
> (within mpi
> itself, not in the app), that further muddy the waters, but
> following this
> guideline you should be safe.
> Regards - Bob
>
> ----- Original Message ----- From: "Robert Duke"
> <rduke_at_email.unc.edu>
> To: <amber_at_scripps.edu>
> Sent: Thursday, October 23, 2008 4:14 PM
> Subject: Re: AMBER: Non bond list error
>
>
>> 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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>>
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> 

--
Wang,Ying

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