[gmx-users] version 3.3 - Range checking error
Joanne Hanna
J.F.Hanna at warwick.ac.uk
Sun Nov 27 21:20:41 CET 2005
Hi
The output from the single precision tpr with mdrun_d in gmx 3.3 is as follows;
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 5785. It should have been within [ 0 .. 5760 ]
Please report this to the mailing list (gmx-users at gromacs.org)
-------------------------------------------------------
"Don't Follow Me Home" (Throwing Muses)
-------------------------------------------------------
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 5785. It should have been within [ 0 .. 5760 ]
Please report this to the mailing list (gmx-users at gromacs.org)
-------------------------------------------------------
"Don't Follow Me Home" (Throwing Muses)
Error on node 2, will try to stop all the nodes
Halting parallel program mdrun_d on CPU 2 out of 4
-------------------------------------------------------
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 5785. It should have been within [ 0 .. 5760 ]
Please report this to the mailing list (gmx-users at gromacs.org)
-------------------------------------------------------
"Don't Follow Me Home" (Throwing Muses)
Error on node 3, will try to stop all the nodes
Halting parallel program mdrun_d on CPU 3 out of 4
Error on node 1, will try to stop all the nodes
Halting parallel program mdrun_d on CPU 1 out of 4
gcq#84: "Don't Follow Me Home" (Throwing Muses)
MPI: On host skua.csc.warwick.ac.uk, Program /users/msrcbk/gromacs33/bin/mdrun_d , Rank 2, Process 2072 called MPI_Abort(<communicator>, -1)
MPI: --------stack traceback-------
gcq#84: "Don't Follow Me Home" (Throwing Muses)
gcq#84: "Don't Follow Me Home" (Throwing Muses)
sh: line 1: idb: command not found
MPI: -----stack traceback ends-----
MPI: MPI_COMM_WORLD rank 2 has terminated without calling MPI_Finalize()
MPI: aborting job
********************
this message was given in my pbs output file after 115ps of simulation.
Does this help pinpont the problem?
Thanks
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 10:39 AM >>>
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
>>_______________________________________________
>>gmx-users mailing list
>>gmx-users at gromacs.org
>>http://www.gromacs.org/mailman/listinfo/gmx-users
>>Please don't post (un)subscribe requests to the list. Use the
>>www interface or send it to gmx-users-request at gromacs.org.
>>
>>
>>
>>
>
>
>
>
--
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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