[gmx-users] Re: LINCS warnings and number of cpus

[Dr. Vitaly V. Chaban]

>
> 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)


Hmm... Try "mdrun -pd %NUMPROC"


-- 
Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ. Rochester, Rochester, New York 14627-0216
THE UNITED STATES OF AMERICA