Re: [AMBER] The good choice of the linux system for Amber 11 calculations on Tesla C2050 GPUs ?

From: Igor Marques <igor.dragon88.gmail.com>
Date: Thu, 2 Dec 2010 14:10:01 +0000

Dear Marek,

We have installed the nVidia drivers as recommended in the nVidia website.
See the instructions below:
 Install GPU machine

- Download NVIDIA driver, NVIDIA toolkit and NVIDIA GPU computing SDK from
http://developer.nvidia.com/object/cuda_3_2_downloads.html#Linux

- Follow the instructions on
http://developer.download.nvidia.com/compute/cuda/3_2_prod/docs/Getting_Started_Linux.pdf

- Write the script provided on Page 6 of the Manual into a file called
nvidia.bash

- Copy this script to /etc/init.d/ and run "update-rc.d nvidia.bash defaults


- Reboot and check if /dev/nvidia* were created

- Install Cuda Toolkit

- Install SDK.During make, some libraries are missing. Install them using
apt-get or make a symbolic link of installed libs
Regards,
      Igor Marques


2010/12/2 Marek Maly <marek.maly.ujep.cz>

> Dear Ian, Ross and Igor
>
> thanks a lot for your info !
>
> I have the last technical question regarding the Nvidia drivers.
>
> It is better/recommended to use
>
> #1
>
> "Developer Drivers for Linux (260.19.14) " available here:
>
> http://developer.nvidia.com/object/cuda_3_2_toolkit_rc.html
>
> #2
>
> or to install driver version "260.19.21 Certified"
>
> http://www.nvidia.com/object/linux-display-amd64-260.19.21-driver.html
>
>
> for the given purpose (just calculation on the given GPU) ?
>
> Thanks in advance for this last information,
>
> Best wishes,
>
> Marek
>
>
>
>
>
> Dne Wed, 01 Dec 2010 20:03:56 +0100 Gould, Ian R <i.gould.imperial.ac.uk>
> napsal/-a:
>
> > Hi Marek,
> >
> > I have been running my dual C2050 rig with Fedora 11 and it has been
> > very stable, have been running both cards flat out for runs which take 1
> > to 2 weeks to complete.
> >
> > Cheers
> > Ian
> >
> > Mediocrity knows nothing higher than itself, but talent instantly
> > recognizes genius.
> > Sir Arthur Conan Doyle
> > --
> > Dr Ian R Gould
> > Senior Lecturer Biological and Biophysical Chemistry
> > Imperial College London
> > Exhibition Road
> > London
> > SW7 2AY
> > E-mail i.gould.imperial.ac.uk
> > http://www3.imperial.ac.uk/people/i.gould
> > Tel +44 (0)207 594 5809
> >
> >
> >
> >
> > On 01/12/2010 18:50, "Marek Maly" <marek.maly.ujep.cz> wrote:
> >
> > Hello all,
> > I am just curious what linux (non commercial) system could be recommended
> > as the most suitable (well tested ...) for Amber 11 GPU calculations,
> > more
> > precisely
> > calc. on Tesla C2050 or if this question is not easy to answer, at least
> > which
> > linux system is let say not too much recommended.
> >
> > Although this question is probably not so relevant as the another
> > actually discussed ( motherboard dependence ...) also here
> > might be useful some positive or negative experiences/reccommendations
> > ...
> > although
> > it.s pretty possible that the answer on my question will be hardware
> > dependent.
> >
> > My motherboard is: Asus M4N98TD EVO - nForce 980a SLI
> > CPU: AMD Phenom II X4 955 Black Edition (HDZ955FBGMBOX)
> >
> > Thanks to all for any eventual comments/reccommendations !
> >
> > Best wishes,
> >
> > Marek
> >
> >
> >
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Received on Thu Dec 02 2010 - 06:30:04 PST
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