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

Mon Mar 12 18:42:44 CET 2018

On 3/12/18 1:40 PM, Viveca Lindahl wrote:
> Hi Justin,
>
> I'm using semi-isotropic pressure coupling and the periodicity is along z. I
> should say that I'm also adaptively biasing a base pair to open, which is
> triggering the fluctuations.
>
> I guess you mean using only OpenMP? I have not tried that no, thanks for
> the suggestion. Now I changed to Berendsen coupling which avoids the
> problem (at least the fatal errors).

Yes, the problem is coming from either DD bookkeeping or actual 
instability. Trying with only OpenMP parallelization and therefore no 
domains will sort out whether it's physical or just a software problem. 
There's a lot going on if you've got periodic molecules, NPT, and a 
biasing potential, all with DD. Probably something no one has ever 
tested in GROMACS.

-Justin

> --
> Viveca
>
>
> On Mon, Mar 12, 2018 at 3:46 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>> 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>
>>>>
>>>> --
>>>> Gromacs Users mailing list
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>>>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>
>> ==================================================
>>
>>
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>> Gromacs Users mailing list
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-- 
==================================================

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

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==================================================