Thank you very much! I will try it tomorrow by GTX470 card and will share the results here. Indeed it will be very helpful most of the people that use GTX4XX and GTX5XX series cards to share their experience too.
Regards,
Filip
--- On Sat, 1/8/11, Ross Walker <ross.rosswalker.co.uk> wrote:
> From: Ross Walker <ross.rosswalker.co.uk>
> Subject: [AMBER] GPU Code Update
> To: "AMBER Mailing List" <amber.ambermd.org>
> Cc: "Duncan Poole" <dpoole.nvidia.com>, "Scott Le Grand" <SLeGrand.nvidia.com>, "Slaton Lipscomb" <lipscomb.slaton.gene.com>
> Date: Saturday, January 8, 2011, 6:57 PM
> To all those who are waiting for the
> latest update to the GPU code,
>
> Firstly I apologize for the day here but New Years of
> course bring new
> deadlines but I have now managed to put this together and
> it is posted on
> the AMBER website as bugfix.12. I would suggest that
> instead of just
> applying this bugfix you instead start from a completely
> new Amber 11 tree
> as follows:
>
> tar xvjf AmberTools-1.4.tar.bz2
> tar xvjf Amber11.tar.bz2
> export AMBERHOME=/path_to_/amber11
> cd $AMBERHOME
> wget http://ambermd.org/bugfixes/AmberTools/1.4/bugfix.all
> patch -p0 <bugfix.all
>
> rm -f bugfix.all
> wget http://ambermd.org/bugfixes/11.0/bugfix.all
> wget http://ambermd.org/bugfixes/11.0/apply_bugfix.x
> chmod 700 apply_bugfix.x
> ./apply_bugfix.x bugfix.all
>
> Then just build things again from scratch.
>
> The specifics of the bugfix are as follows:
>
> ********>Bugfix 12:
> Author: Ross Walker
> Date: 20 December 2010
>
> Program(s): pmemd.cuda
>
> Description: - This fixes a number of recently discovered
> bugs and possible
>
> performance issues with pmemd.cuda.
> Specifically it does the
>
> following:
>
>
> 1) Removes the dependence on CUDPP which
> could cause
>
> crashes on certain large simulations due to bugs in
>
> the CUDPP library.
>
>
> 2) Fixes problems with large simulations,
> 400K+ atoms
>
> crashing randomly with an allocation failure.
>
>
> 3) Fixes "ERROR: max
> pairlist cutoff must be less than unit
>
> cell max sphere radius!" bug allowing cutoffs larger
> than
>
> 8.0 to be used for both small and large systems.
>
>
> 4) Writes final performance info the the
> mdout file.
>
>
> 5) Possible (not fully tested) workaround
> for NVIDIA GTX4XX
>
> and GTX5XX series cards to avoid possible random
> hangs
>
> during PME simulations.
>
>
> 6) Tests for the use of non-power of 2 MPI
> tasks when running
>
> parallel GPU PME calculations. Update so that the
> code now
>
> quits with a suitable error message.
>
>
> 7) Minor performance improvements, mostly
> due to the use of a
>
>
> faster radixsort.
>
> Apply this patch in $AMBERHOME
>
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> ---------------------------------------------------------
> |
> Assistant Research Professor
> |
> | San Diego
> Supercomputer Center
> |
> |
> Adjunct Assistant Professor
> |
> | Dept. of Chemistry
> and Biochemistry
> |
> | University of
> California San Diego
> |
> |
> NVIDIA Fellow
>
> |
> | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk
> |
> ---------------------------------------------------------
>
> Note: Electronic Mail is not secure, has no guarantee of
> delivery, may not
> be read every day, and should not be used for urgent or
> sensitive issues.
>
>
>
>
>
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>
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Received on Sat Jan 08 2011 - 13:30:02 PST
