Sorry, here is the attachment
2014-07-21 16:18 GMT+02:00 Lorenzo Gontrani <lorenzo.gontrani.gmail.com>:
> 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
> necessary
>
--
==========================================
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
