[gmx-users] LINCS warnings and number of cpus

[Matthew Zwier]

Ciao,

I've seen this behavior (something running fine on one core but
failing on multiple cores, or certain multiples of cores) frequently.
It's almost always due to an unstable system.  Have your user try
equilibrating longer, or minimize with flexible water before trying
equilibration.  You can search the GROMACS web site for the phrase
"blowing up" for more information.

Cheers,
Matt Z.

On Mon, Jan 16, 2012 at 8:37 AM, Marani Alessandro <a.marani at cineca.it> wrote:
> Dear users,
> I would like to ask your help about understanding a problem i'm not able to
> recognize by myself.
> Basically, a user of our sistem (IBM SP6, power6 architecture) is trying to
> run a simulation of a very simple sistem, a polymer chain in a lot of water
> molecules. While the simulation works perfectly in serial on her local pc,
> when she tries to run it in SP6 using 2 cpus in parallel, the simulation
> doesn't even start due of these errors:
>
> starting mdrun 'PVA head29tail in water'
> 2500000 steps,   5000.0 ps.
>
> Step 0, time 0 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 83427404711319.468750, max 431899260485632.000000 (between atoms 59 and
> 60)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>      37     38   89.6    0.1530 124222742528.0000      0.1530
>      38     41   89.1    0.1530 104382357504.0000      0.1530
>
> Step 0, time 0 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 56829711484907.867188, max 212898492186624.000000 (between atoms 3 and
> 4)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>      61     62   89.0    0.1530 1380386603008.0000      0.1530
>      58     61   87.6    0.1530 669758914560.0000      0.1530
>      58     59   89.2    0.1430 1994809540608.0000      0.1430
>      59     60   90.0    0.1000 43189926887424.0000      0.1000
>      57     58   88.3    0.1530 1126801342464.0000      0.1530
>      54     57   85.9    0.1530 198269452288.0000      0.1530
>      54     55   89.6    0.1430 1261346488320.0000      0.1430
>      38     39   89.6    0.1430 156364750848.0000      0.1430
>      39     40   90.0    0.1000 3183089549312.0000      0.1000
>      [...]
>      18     21   89.9    0.1530 215265542144.0000      0.1530
>      18     19   90.0    0.1430 872386920448.0000      0.1430
>      19     20   90.0    0.1000 6085561286656.0000      0.1000
>      95     96   90.0    0.1000 5006930477056.0000      0.1000
>      97     98   89.7    0.1530 215830478848.0000      0.1530
>      98    101   90.5    0.1530 232671739904.0000      0.1530
>      98     99   90.0    0.1430 746076962816.0000      0.1430
>      99    100   90.0    0.1000 6068662435840.0000      0.1000
> step 0: Water molecule starting at atom 6014 can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> step 0: Water molecule starting at atom 7355 can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
> Wrote pdb files with previous and current coordinates
> Wrote pdb files with previous and current coordinates
> step 0
> Warning: 1-4 interaction between 37 and 40 at distance 3039839053625.364
> which is larger than the 1-4 table size 2.200 nm
> These are ignored for the rest of the simulation
> This usually means your system is exploding,
> if not, you should increase table-extension in your mdp file
> or with user tables increase the table size
> Warning: 1-4 interaction between 61 and 64 at distance 15924520737123.646
> which is larger than the 1-4 table size 2.200 nm
> These are ignored for the rest of the simulation
> This usually means your system is exploding,
> if not, you should increase table-extension in your mdp file
> or with user tables increase the table size
> ERROR: 0031-250  task 0: Segmentation fault
> ERROR: 0031-250  task 1: Segmentation fault
>
> The same errors occur when trying the simulation up to 4 cpus, but (and
> that's the strange thing), everything works fine with 6+ cpus (actually,
> there are some numbers giving an incompatibility error, like "There is no
> domain decomposition for 7 nodes that is compatible with the given box and a
> minimum cell size of 0.95625 nm", but for example 6 or 8 cpus give a
> successful run).
>
> Can anyone understand what is the reason of this strange behaviour?
> Thanks,
> Marani Alessandro (HPC User support, CINECA - Italy)
>
> --
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