From: James Starlight (jmsstarlight_at_gmail.com)
Date: Sun Nov 03 2013 - 08:04:02 CST
Its strange but no log file is found in the work directory and I could not
find a suitable option in the conf file for the log saving. :) Almost
that I have its the 645000 steps computed during 6 hours of simulation
(100k atoms protein in explicit water)
Also I'd be thankful for list of all possible swithes accompanied with the
namd2 terminal command
James
2013/11/3 Ajasja Ljubetič <ajasja.ljubetic_at_gmail.com>
>
> On 3 November 2013 09:38, James Starlight <jmsstarlight_at_gmail.com> wrote:
>
>> updating
>>
>> using namd2 +idlepoll +p4 +devices 0,1 ./restart.conf
>> I've launched simulation on both GPUs (according to thermal monitoring in
>> nvidia-settings) but only half of cpus were fully loaded.
>>
>> Yes, naturally. Look up what the +p4 switch does. (Also read up on
> hyperthreading)
>
> By the way how I could monitor real GPU loading as well as namd
>> performance ( in ns\days or GFlops )?
>>
>
> Try looking in the namd log file for the ns/days speed.
>
> And out of interest do report the ns/day of
>
> namd2 +idlepoll +p6 +devices 0 ./restart.conf
> vs
> namd2 +idlepoll +p6 +devices 0,1 ./restart.conf
>
> Regards,
> Ajasja
>
>
>>
>>
>> James
>>
>>
>> 2013/11/1 James Starlight <jmsstarlight_at_gmail.com>
>>
>>> Ok. I'll try to make some simulations of this configure. The main issue
>>> with which I can force is the possible conflict between that older cuda
>>> library (used from vmd) and more newest development driver ( 5.5 version)
>>> which comes from installed cuda-5.5.
>>>
>>> By the way how I could use both of the GPUs simultaneously ? Just use
>>> the below command?
>>>
>>> namd2 +idlepoll +p4 +devices 0,1 ./restart.conf
>>>
>>> Where 0 and 1 are the ids of my GPUs? Is there additional options for
>>> synchronization of the simulations in dual-GPU regime ?
>>>
>>> James
>>>
>>>
>>> 2013/10/31 Aron Broom <broomsday_at_gmail.com>
>>>
>>>> don't replace anything, just point to the version of the library in
>>>> your NAMD directory as you did. It should work fine.
>>>>
>>>>
>>>> On Thu, Oct 31, 2013 at 1:24 PM, James Starlight <
>>>> jmsstarlight_at_gmail.com> wrote:
>>>>
>>>>> Dear Namd users,
>>>>>
>>>>> I've build my new workstations consisted of two Titans with i6 (linux
>>>>> recognize it like 12 core process but actually it consist of 6 nodes)--047d7b6d95d08dc2a004ea464543--
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