Dear Ross, thanks for the quick reply.
Overall, my simulation can be considered "non standard", since it is not a
protein nor a nucleic acid.
Though, you added a tutorial on ionic liquids recently..and I have been
using pmemd to study these systems for more than a year now.
It is surely a problem with my input, the same executable has no problems
for another system. The strange thing is that minimization runs without
problems, the fault occurs when NVT/NPT is switched on, and
that the problem does NOT happen if I use pmemd.cuda version 11 (on another
machine (older) with different graphic card, actually).
I generated the topology with a tleap script, after filling the cell with
packmol.
The files (mdin mdout inpcrd and prmtop) are attached.
Thanks a lot
Lorenzo
2014-07-21 15:39 GMT+02:00 Ross Walker <ross.rosswalker.co.uk>:
> Hi Lorenzo,
>
> This means something is funky with your topology file. Likely something is
> weird with the bonding or the atom ordering. The GPU code is more picky
> with such things than the CPU code. Can you send me your mdin, mdout,
> prmtop and inpcrd files please.
>
> Also how did you build your prmtop file / is there anything that might be
> considered non-standard with what you are trying to simulate?
>
> All the best
> Ross
>
>
> On 7/21/14, 3:45 AM, "Lorenzo Gontrani" <lorenzo.gontrani.gmail.com>
> wrote:
>
> >Dear Amber experts,
> >I woud be very happy if you could help me..
> >
> >I cannot run an NVT simulation with pmemd.cuda, I immediateIy (only step
> >number 0 is printed in mdout) obtain this cuda error, regarding kshake.cu
> :
> >
> >Error: invalid configuration argument launching kernel kShake
> >
> >No problem with serial or MPI versions.
> >
> >I checked if the code needs to be patched, but update_amber reports that
> >the code is updated.
> >
> >The output of nvidia_smi follows.
> >
> >+------------------------------------------------------+
> >
> >| 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 |
> >+-------------------------------+----------------------+------------------
> >----+
> >
> >
> >+-------------------------------------------------------------------------
> >----+
> >| Compute processes: GPU
> >Memory |
> >| GPU PID Process name
> >Usage |
> >|=========================================================================
> >====|
> >| No running compute processes
> >found |
> >+-------------------------------------------------------------------------
> >----+
> >
> >Any hints? Need for recompilation?
> >
> >Thanks everybody
> >--
> >==========================================
> > Lorenzo Gontrani
> > Research associate - EDXD group
> > University of Rome "La Sapienza"
> >
> > GSM +39 338 7615798
> > Email lorenzo DOT gontrani AT gmail DOT com
> > Webpage: http://webcaminiti/gontrani.html
> > =========================================
> > Rispetta l'ambiente: se non è necessario, non stampare
> > questa e-mail
> > Protect the environment: do not print this e-mail, unless
> > necessary
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>
>
>
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>
--
==========================================
Lorenzo Gontrani
Research associate - EDXD group
University of Rome "La Sapienza"
GSM +39 338 7615798
Email lorenzo DOT gontrani AT gmail DOT com
Webpage: http://webcaminiti/gontrani.html
=========================================
Rispetta l'ambiente: se non è necessario, non stampare
questa e-mail
Protect the environment: do not print this e-mail, unless
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Received on Mon Jul 21 2014 - 07:30:04 PDT
