[gmx-users] version 3.3 - Range checking error

[David van der Spoel]

Joanne Hanna wrote:

>Hello
>
>What I did was to use the files that were the output from a posres md 500ps run in v 3.2.1 (posres on protein, truc oct box spc water) and do grompp_d with v 3.3 and then mdrun_d with v3.3
>  
>
Please compare the single and double precision tpr files using gmxcheck. 
In addition try to reproduce the problem by using the single precision 
tpr file with mdrun_d. If the tpr files are different there may be a 
problem with grompp, if they are identical there may be a problem with 
mdrun_d. Either way it is necessary to find out what is going on. If you 
can pinpoint the problem please submit a bugzilla.

>The hardware and os details are:
>
>Altix
>node type: 1 x 1.6 GHz Itanium2 56-way SMP
>interconnect: SGI NUMAlink4
>OS: RedHat Enterprise Linux AS 3.0 / SGI ProPack
>
>All code was compiled with:
>intel-cc-9/9.0.026
>intel-fc-9/9.0.028
>using lmpi
>and enable threads for fftw
>
>I compiled fftw v 3 with the flags below, as there were no default flags for the intel compilers:
>export CFLAGS="-ftz -O3 -tpp2 -no-gcc"
>export FFLAGS="-ftz -O3 -tpp2"
>
>The only messages i got during during gromacs v3.3 compilation that i was unsure about are:
>
>checking dynamic linker characteristics... ifort: Command line warning: ignoring option '-p'; no argument required
>ifort: Command line error: no files specified; for help type "ifort -help"
>
>mknb_innerloop.c(362): warning #188: enumerated type mixed with another type
>                         mknb_func.coul=coulsave;
>                                       ^
>mknb_innerloop.c(363): warning #188: enumerated type mixed with another type
>                         mknb_func.vdw=vdwsave;
>                                      ^
>Hope this is what you were asking
>
>Jo
>
>
>
>Joanne Hanna
>Department of Chemistry
>University of Warwick
>Coventry
>CV4 7AL
>
>J.F.Hanna at warwick.ac.uk
>  
>
>>>>spoel at xray.bmc.uu.se 11/25/05 10:02 AM >>>
>>>>        
>>>>
>Joanne Hanna wrote:
>
>  
>
>>Hello
>>
>>I have recently tried to re run a simualtion with gromacs v3.3 in double precision that I have managed to run in v3.2.1 single prescision and v3.3 single precision. This simulations is failing with the following error:
>> 
>>
>>    
>>
>Is this run with the same tpr file that works in single precision?
>
>What kind of hardware do you run on?
>
>  
>
>>*******************************************************
>>
>>          Step           Time         Lambda
>>        104000      208.00000        0.00000
>>
>>  Energies (kJ/mol)
>>      G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
>>   8.43377e+03    3.79108e+03    2.53005e+03    3.13091e+02    5.79138e+04
>>       LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
>>   1.38869e+05   -1.05323e+06   -1.68330e+05   -1.00971e+06    1.91922e+05
>>  Total Energy    Temperature Pressure (bar)
>>  -8.17790e+05    3.11754e+02    4.49698e+01
>>
>>-------------------------------------------------------
>>Program mdrun_d, VERSION 3.3
>>Source code file: nsgrid.c, line: 226
>>
>>Range checking error:
>>Explanation: During neighborsearching, we assign each particle to a grid
>>based on its coordinates. If your system contains collisions or parameter
>>errors that give particles very high velocities you might end up with some
>>coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
>>put these on a grid, so this is usually where we detect those errors.
>>Make sure your system is properly energy-minimized and that the potential
>>energy seems reasonable before trying again.
>>
>>Variable ci has value 5926. It should have been within [ 0 .. 5760 ]
>>Please report this to the mailing list (gmx-users at gromacs.org)
>>-------------------------------------------------------
>>
>>"Clickety Clickety Click" (System Manager From Hell)
>>
>>*******************************************************
>>
>>Could anyone please explain to me what I have done wrong? Should I have re-do the entire process with the double preision? i.e. from starting structure, solvate minimise, md with posres on protein to equilib water and then run my simualtion?
>>
>>Many thanks
>>Jo
>>
>>Joanne Hanna
>>Department of Chemistry
>>University of Warwick
>>Coventry
>>CV4 7AL
>>
>>J.F.Hanna at warwick.ac.uk
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>> 
>>
>>    
>>
>
>
>  
>


-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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