Yes, that's definitely a messed up patch process...
On Wed, Apr 9, 2014 at 7:11 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> What bugfixes have been applied to your Amber 12? There are several
> bugfixes which are essential for proper functioning of the GPU code.
> Also, when you say 'the machine bearing the "good" program', do you
> mean that pmemd.cuda is able to run on that machine with no errors?
>
> -Dan
>
> On Wed, Apr 9, 2014 at 8:05 AM, Lorenzo Gontrani
> <lorenzo.gontrani.gmail.com> wrote:
> > Dear Amber experts, we have recently installed a GPU version of Amber12,
> > and we are experiencing problems in running a simulation on a system
> made
> > up of about 15000 atoms, after the initial minimization.
> > The MD engine do not even start after reading the restart structure and
> > velocities, giving the following error: "Error: invalid configuration
> > argument launching kernel kShake".
> >
> > >From a rapid inspection of the error routines, it seems that this
> > message regards
> > kshake.cu, that deals with the initial set-up of the process. No
> problem in
> > fact, is found when MPI is used, nor with a version of Amber11 we have on
> > another machine.
> > The non-working pmemd is installed on a machine having the following
> > graphic cards:
> >
> > +------------------------------------------------------+
> >
> > | NVIDIA-SMI 4.304.54 Driver Version: 304.54
> > |
> >
> |-------------------------------+----------------------+----------------------+
> > | GPU Name | Bus-Id Disp. | Volatile Uncorr.
> > ECC |
> > | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util
> Compute
> > M. |
> >
> |===============================+======================+======================|
> > | 0 Tesla S2050 | 0000:0F:00.0 Off |
> > 0 |
> > | N/A 58C P1 N/A / N/A | 0% 6MB / 2687MB | 0%
> > Default |
> >
> +-------------------------------+----------------------+----------------------+
> > | 1 Tesla S2050 | 0000:10:00.0 Off |
> > 0 |
> > | N/A 58C P1 N/A / N/A | 0% 6MB / 2687MB | 0%
> > Default |
> >
> +-------------------------------+----------------------+----------------------+
> >
> >
> > while the machine bearing the "good" program has
> >
> >
> > nvidia-smi
> > Wed Apr 9 16:00:56 2014
> > +------------------------------------------------------+
> >
> > | NVIDIA-SMI 5.319.37 Driver Version: 319.37
> > |
> >
> |-------------------------------+----------------------+----------------------+
> > | GPU Name Persistence-M| Bus-Id Disp.A | Volatile Uncorr.
> > ECC |
> > | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util
> Compute
> > M. |
> >
> |===============================+======================+======================|
> > | 0 Tesla C2075 Off | 0000:02:00.0 Off |
> > 0 |
> > | 30% 77C P0 83W / N/A | 10MB / 5375MB | 0%
> > Default |
> >
> +-------------------------------+----------------------+----------------------+
> > | 1 GeForce 210 Off | 0000:83:00.0 N/A |
> > N/A |
> > | N/A 33C N/A N/A / N/A | 62MB / 1023MB | N/A
> > Default |
> >
> +-------------------------------+----------------------+----------------------+
> >
> > Can anybody give us a clue on how to cope with this problem?
> >
> > Thanks a lot, kind regards
> >
> > Lorenzo Gontrani
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Apr 09 2014 - 08:30:03 PDT
