Re: Wrong energies in CUDA version

From: Jeff Wereszczynski (jmweresz_at_mccammon.ucsd.edu)
Date: Thu Jun 03 2010 - 21:25:45 CDT

Hi Francesco,

Thanks for pointing out my misreading of the pressure control part.

I tried installing the 2.3 cudatoolkit and recompiling and got the
same weird behavior, so it doesn't seem to be a problem with the CUDA
version.

Jeff

On Thu, Jun 3, 2010 at 1:10 PM, francesco oteri
<francesco.oteri_at_gmail.com> wrote:
> I think it is. I m currently running a simulation with the namd2.7b2 gpu
> version and
> i ve experienced no problem
>
>
> PS.Pressure control is supported, but only in the case of isotropic cell
> fluctuation (http://www.ks.uiuc.edu/Research/namd/2.7b2/ug/node70.html)
>
> 2010/6/3 Jeff Wereszczynski <jmweresz_at_mccammon.ucsd.edu>
>>
>> Hello NAMD List,
>>
>> I am trying to get a CUDA version of NAMD running.  We have access to
>> a GPU cluster with each node having 8 CPUs and either a Tesla C 1060
>> GPU or a Tesla C 2050, with the cuda 3.0 libraries installed.  I was
>> able to compile a namd executable using the with-cuda flag which runs
>> and detects the gpu, but the simulation quickly crashes with RATTLE
>> errors.  I tried to do a minimization and I observed that the energies
>> at step 0 were all correct except for the pressure, gpressure,
>> pressavg, and gpressvg columns.  As I continue the minimization these
>> terms fluctuate wildly and the potential energy of the system explodes
>> as the vdw terms increases drastically (atoms begin to overlap with
>> one another).
>>
>> I know pressure controls do not work in CUDA NAMD, but I am running
>> NVT so I would think that NAMD would ignore these terms.  I've tried
>> this with both 2.7b2 and the CVS version and got the same results.
>> Additionally, I tried this simulation (same input files) on a local
>> GPU with the pre-compiled binary and it worked fine (the simulation
>> progressed and the pressure values were normal).  One major difference
>> was on our local computer we had CUDA 2.3, whereas on this cluster
>> only 3.0 is available, could this be the cause of the problem?  Does
>> anyone have any ideas of other things I could try to get this to work?
>>
>> Thanks,
>> Jeff
>>
>
>
>
> --
> Cordiali saluti, Dr.Oteri Francesco
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:23:01 CST