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 |
---------------------------------------------------------
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Received on Sat Jan 08 2011 - 09:00:02 PST
