[gmx-users] Gromacs-GPU with an Nvidia GeForce GTX 580 error?

[Matt Larson]

Szilárd,

 Thanks- gromacs 4.5.5 is working with my NVidia card with the "force
option".  I found one weirdness - if I check the card temperature
(using NVIDIA's configuration tool in X11) it seems like this messes
up the MR and all the trajectories after that point have no atoms in
VMD.  So, that's probably not a good thing.

This is something of a big question:
 I tried running a simulation using intrinsic solvation, amber99 or
amber99sb, and a long helix, and found that the helix would collapse
in intrinsic solation unlike explicit solvation.  Is there a "good"
way to do intrinsic solvation simulations (like a very large # for
rvdw, rcoulomb), or some other force field such that long helices
behave well in intrinsic solvation?  It seems like the whole protein
wants scrunch up on itself.  Maybe my problem is that in the
simulation protein:protein interaction is too favored over
protein:solvent?

  Thanks,
  Matt

On Mon, Oct 24, 2011 at 2:44 PM, Szilárd Páll <szilard.pall at cbr.su.se> wrote:
> Hi Matt,
>
> Yes, you should use the "force-device=yes" option, the patch which was
> meant to update the list of compatible GPUs didn't make it for 4.5.5.
>
> Cheers,
> --
> Szilárd
>
>
>
> On Sun, Oct 23, 2011 at 10:24 PM, Matt Larson <larsonmattr at gmail.com> wrote:
>> I am having an error trying to use a compiled mdrun-gpu on my GPU setup here:
>>
>>
>> Fatal error:
>> The selected GPU (#0, GeForce GTX 580) is not supported by Gromacs!
>> Most probably you have a low-end GPU which would not perform well, or
>> new hardware that has not been tested with the current release. If you
>> still want to try using the device, use the force-device=yes option.
>> For more information and tips for troubleshooting, please check the GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>>
>>
>> ----
>>
>>  From what I can tell, the GTX 580 should be supported as of this
>> version of gromacs (4.5.5) - as it is listed in the supported cards.
>> I have openmm and CUDA libraries installed.
>>
>> - Openmm passes the test with
>> /usr/local/openmm/bin/TestReferenceHarmonicBondForce.
>> - NVIDIA driver is NVIDIA-Linux-x86_64-270.41.19
>> (devdriver_4.0_linux_64_270.41.19.run patched with the
>> nvidia_kernel-3.0-rc1.patch to let it be installed on ubuntu 11.10).
>> - the NVIDIA_GPU_Computing_SDK examples run.
>>
>>  I've also tried with the normal NVIDIA x86_64-280.13 driver, but same error.
>>
>>  From the gromacs GPU page
>> (http://www.gromacs.org/Downloads/Installation_Instructions/GPUs) it
>> is clear that the GTX 580 has been run with gromacs.
>>
>>  Should I use the "force-device" option to use GTX 580, or is there a
>> reason that gromacs doesn't think it has support for this GTX 580
>> card?
>>
>>  Thanks much,
>>  Matt Larson
>> --
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