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

[Viveca Lindahl]

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.

--
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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