Dear Ross Walker
Thanks for your reply.
The number of atom is including the water.
And I send the input files, please check our input files.
(com.sh is the script running our simulation.
in file and top file is parmtop file, an rst file is restart file after
minimize)
The message whcih I execute deviceQuery is below
=========================================
./deviceQuery Starting...
CUDA Device Query (Runtime API) version (CUDART static linking)
There is 1 device supporting CUDA
Device 0: "GeForce GTX 480"
CUDA Driver Version: 3.0
CUDA Runtime Version: 3.0
CUDA Capability Major revision number: 2
CUDA Capability Minor revision number: 0
Total amount of global memory: 1609760768 bytes
Number of multiprocessors: 15
Number of cores: 480
Total amount of constant memory: 65536 bytes
Total amount of shared memory per block: 49152 bytes
Total number of registers available per block: 32768
Warp size: 32
Maximum number of threads per block: 1024
Maximum sizes of each dimension of a block: 1024 x 1024 x 64
Maximum sizes of each dimension of a grid: 65535 x 65535 x 1
Maximum memory pitch: 2147483647 bytes
Texture alignment: 512 bytes
Clock rate: 1.40 GHz
Concurrent copy and execution: Yes
Run time limit on kernels: Yes
Integrated: No
Support host page-locked memory mapping: Yes
Compute mode: Default (multiple host
threads can use this device simultaneously)
deviceQuery, CUDA Driver = CUDART, CUDA Driver Version = 4243423, CUDA
Runtime Version = 3.0, NumDevs = 1, Device = GeForce GTX 480
PASSED
==============================================
Thank you
Best wishes,
Wookyung Yu
2010/5/28 Ross Walker <ross.rosswalker.co.uk>
> Hi Wookyung,
>
> > I use amber11, PMEMD.cuda using GTX480 graphic card.
> >
> > Sometimes, and special protein, MD is stopped, and leave this message.
> > "Error: the launch timed out and was terminated launching kernel
> > kPMEGetGridWeights"
> >
> > (I did explicit water simulation 2 proteins , one is 6820 atoms, and
> > the
> > other is 17800 atoms
> > The protein which has 6820 atoms has no problem,
> > but the protein which has 17800 atoms often has this problem.)
>
> Is this atom count of the protein or atom count including the water?
>
> Can you send me your input files please. Also can you run the deviceQuery
> command (download and compile the CUDA SDK and it is in CUDA_SDK/C/bin/)
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
>
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Received on Thu May 27 2010 - 22:00:03 PDT
