From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Mon Nov 04 2013 - 01:04:00 CST
The log file is what you see on the screen when starting namd like you did obviously. To get a file of it, append the command with >> my.log 2>> my.errors to redirect the output of stdout and stderr.
GPU load monitoring is only enabled on quadro and tesla series cards.
The easiest option to bypass the libcudart stuff is to use the charmrun ++runscript option. Save the following three lines to a file called runscript.sh in your namd folder and make it executable with "chmod +x runscript.sh", adapt the path to your namd location.
#!/bin/bash
export LD_LIBRARY_PATH=/your/namd/folder/:$LD_LIBRARY_PATH
$*
Now always start namd like "/your/namd/folder/charmrun +p6 ++runscript /your/namd/folder/runscript.sh /your/namd/folder/namd2 +idlepoll +devices 0,1 >> log 2>> errors"
Norman Geist.
> -----Ursprüngliche Nachricht-----
> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> Auftrag von James Starlight
> Gesendet: Sonntag, 3. November 2013 15:04
> An: Ajasja Ljubetič; Namd Mailing List
> Betreff: Re: namd-l: Two GPU-based workstation
>
> 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)=
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