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

Mon Mar 12 18:40:11 CET 2018

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).

--
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
>>>
>>> * Please search the archive at http://www.gromacs.org/Support
>>> /Mailing_Lists/GMX-Users_List before posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-request at gromacs.org.
>>>
>>>
> --
> ==================================================
>
> 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
>
> ==================================================
>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>