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
>
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> 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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Received on Wed Apr 09 2014 - 07:30:03 PDT
