Error running HOOMD script

[abhijeet kapoor]

Hello all,

I am trying to simulate a system of 605 particles connected by harmonic bonds (total of 2419 bonds), but getting following error at the start of simulation:

***Error! out of memory before /libhoomd/data_structures/GPUArray.h:455

Traceback (most recent call last):
  File "simu_script", line 41, in <module>
    run(10e6)
  File "/usr/local/lib/hoomd/python-module/hoomd_script/__init__.py", line 199, in run
    globals.system.run(int(tsteps), callback_period, callback, limit_hours, int(limit_multiple));
RuntimeError: CUDA Error


I ran the same simulation on a smaller system of about 170 particles (720 harmonic bonds between them) successfully.
I tried tuning the hoomd performacnce by running the command tune.find_optimal_block_sizes() but that didn`t solve the problem. Please let me know how to resolve this issue. Please find attached the error and neighbourlist exclusion statistic output that I am getting after running the simulation script..

Thanks a lot,
Abhijeet

------------------------------------------------------------------------------------------------
OUTPUT:
simu_script:037  |  all=group.all()
simu_script:039  |  integrate.mode_standard(dt=0.005)
simu_script:040  |  integrate.bdnvt(group=all, T=1.0)
simu_script:041  |  run(10e6)
-- Neighborlist exclusion statistics:
Max. number of exclusions: 13
Particles with 2 exclusions: 4
Particles with 3 exclusions: 6
Particles with 4 exclusions: 29
Particles with 5 exclusions: 34
Particles with 6 exclusions: 89
Particles with 7 exclusions: 74
Particles with 8 exclusions: 119
Particles with 9 exclusions: 97
Particles with 10 exclusions: 76
Particles with 11 exclusions: 42
Particles with 12 exclusions: 28
Particles with 13 exclusions: 7
** starting run **
Notice: cell list overflow, allocating 240 slots per cell
Notice: neighbor list overflow, allocating 64 slots per particle
Notice: cell list overflow, allocating 248 slots per cell
Notice: neighbor list overflow, allocating 72 slots per particle
Notice: neighbor list overflow, allocating 80 slots per particle

***Error! out of memory before /libhoomd/data_structures/GPUArray.h:455

Traceback (most recent call last):
  File "simu_script", line 41, in <module>
    run(10e6)
  File "/usr/local/lib/hoomd/python-module/hoomd_script/__init__.py", line 199, in run
    globals.system.run(int(tsteps), callback_period, callback, limit_hours, int(limit_multiple));
RuntimeError: CUDA Error



 

--

[Carolyn Phillips]

You ran out of memory on your card.

See ***Error! out of memory before /libhoomd/data_structures/GPUArray.h:455

I think you have too many bonds. There used to be a limit on the number of bonds or exclusions you can have. I am trying to find where that is documented now. There may not be limits any more, but you still may have exceeded what your card can actually hold.

What are you running on?

-Carolyn

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[Joshua A. Anderson]

On Nov 8, 2010, at 6:51 PM, Carolyn Phillips wrote:

> You ran out of memory on your card.
>
> See ***Error! out of memory before /libhoomd/data_structures/GPUArray.h:455
>
> I think you have too many bonds. There used to be a limit on the number of bonds or exclusions you can have. I am trying to find where that is documented now. There may not be limits any more, but you still may have exceeded what your card can actually hold.

The limit is now only the amount of memory available on the card.
13 exclusions * 605 particles = not very much memory in the exclusion list.

>> Notice: cell list overflow, allocating 248 slots per cell
>> Notice: neighbor list overflow, allocating 72 slots per particle
>> Notice: neighbor list overflow, allocating 80 slots per particle
>>
>> ***Error! out of memory before /libhoomd/data_structures/GPUArray.h:455

248 slots * 16 bytes per slot * unknown number of cells = a HUGE amount of memory.

Decrease your box dimensions and try again. Your system is also apparently extremely dense to have 248 particles in each cell.

--------
Joshua A. Anderson, Ph.D.

[abhijeet kapoor]

Thanks!
Reducing the box dimensions worked.

-Abhijeet
 

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[Carolyn Phillips]

Cool.  Sounds like a nifty simulation!