Hi all,
I can confirm that bugfix.12 seems to work and solved the the issue with NVIDIA GTX4XX cards!!!
I ran several short simulations (200ps each) using JAC-PME cuda benchmark and GTX470 card without any problems! Previously this was just impossible. The performance (ns/days) was identical to my last tests, but for GB it works better now - TRPCage 398 ns/day against 380 ns/days before.
Thank you for this bugfix!
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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Received on Sun Jan 09 2011 - 16:30:02 PST
