[gmx-users] Help with interpreting message for fatal error

[Justin Lemkul]

On 3/12/18 10:42 AM, Viveca Lindahl wrote:
> Hi Gregory,
>
> In the sense that I see it happening repeatedly yes :) But I can't
> reproduce it very predictably.
>
> After seeing that (for my small system) I get very large box vector
> fluctuations using Parrinello-Rahman, my current assumption is that there
> are some stability assumptions made by mdrun internally that are being
> violated.
> I would still be interested in understanding what actually goes wrong
> though.

Periodic molecules are usually used in CNT systems or similar, and the 
typical advice is to not apply pressure coupling along the long axis. I 
suspect interactions get lost when the box fluctuates and the domain 
topology does not get updated correctly. Does it work correctly with OpenMP?

-Justin

> --
> Viveca
>
>
> On Mon, Mar 12, 2018 at 4:49 PM, Gregory Poon <gpoon at gsu.edu> wrote:
>
>> Since there hasn't been any response to your question yet, may I ask: is
>> it reproducible?
>>
>> Gregory
>>
>>
>> On 3/11/2018 7:30 AM, Viveca Lindahl wrote:
>>
>>> Hi,
>>>
>>> I'm running a simulation of a periodic DNA molecule. After some time I
>>> get,
>>> sometimes the following error message:
>>>
>>> ---------------
>>>
>>> A list of missing interactions:
>>>            Proper Dih. of   3917 missing      1
>>>
>>> Molecule type 'DNA_chain_A'
>>> the first 10 missing interactions, except for exclusions:
>>>            Proper Dih. atoms  414  417  418  421 global   414   417   418
>>> 421
>>>
>>> -------------------------------------------------------
>>> Program:     gmx mdrun, version 2018.1-dev-20180306-33093601f
>>> Source file: src/gromacs/domdec/domdec_topology.cpp (line 436)
>>> MPI rank:    0 (out of 32)
>>>
>>> Fatal error:
>>> 1 of the 10381 bonded interactions could not be calculated because some
>>> atoms
>>> involved moved further apart than the multi-body cut-off distance (0.5465
>>> nm)
>>> or the two-body cut-off distance (1.093 nm), see option -rdd, for pairs
>>> and
>>> tabulated bonds also see option -ddcheck
>>>
>>> For more information and tips for troubleshooting, please check the
>>> GROMACS
>>> website at https://na01.safelinks.protection.outlook.com/?url=http%3A%
>>> 2F%2Fwww.gromacs.org%2FDocumentation%2FErrors&data=02%7C01%
>>> 7Cgpoon%40gsu.edu%7C18eac9ccdd4b479d86c708d5875cbb61%7C515ad
>>> 73d8d5e4169895c9789dc742a70%7C0%7C0%7C636563754716997653&
>>> sdata=wUdEASAxNIPHNAmQwBO8EO0Ec8EI%2FVdjY7f7i9R0IYc%3D&reserved=0
>>> -------------------------------------------------------
>>> Rank 0 [Sun Mar 11 13:37:32 2018] [c0-0c1s3n0] application called
>>> MPI_Abort(MPI_COMM_WORLD, 1) - process 0
>>> _pmiu_daemon(SIGCHLD): [NID 00076] [c0-0c1s3n0] [Sun Mar 11 13:37:32 2018]
>>> PE RANK 0 exit signal Aborted
>>> [NID 00076] 2018-03-11 13:37:32 Apid 12709959: initiated application
>>> termination
>>> Application 12709959 exit codes: 134
>>> Application 12709959 resources: utime ~1083s, stime ~16s, Rss ~21376,
>>> inblocks ~34261, outblocks ~55016
>>> ---> Reached end of run script.
>>>
>>>
>>> How should I... proceed here? Is my system set up poorly, is it a bug in
>>> mdrun? Suggestions appreciated.
>>>
>>> --
>>> Viveca
>>>
>> --
>>
>> *Gregory M. K. Poon, PhD, RPh*
>> Associate Professor
>> Departments of Chemistry and Nutrition | Georgia State University
>> NSC 414/415/416 | 50 Decatur St. SE, Atlanta, GA 30302
>> P.O. Box 3965 | Atlanta, GA 30303
>> Ph (404) 413-5491 | gpoon at gsu.edu <mailto:gpoon at gsu.edu>
>>
>> --
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>>
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
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jalemkul at vt.edu | (540) 231-3129
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