[gmx-users] LINCS warnings and number of cpus

[Marani Alessandro]

Thank for you answer. Meanwhile, our user told us that she found the 
ideal configuration for running her simulations; nevertheless, i linked 
her this discussion in case she can find some interesting suggestion.

Cheers,
Alessandro

Il 16/01/2012 16.05, Matthew Zwier ha scritto:
> 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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