[MUMmerGPU-devel] Cuda run-time error in MUMmerGPU-2.0

[Pankaj G. <pan...@st...>]

Hi,

I'm getting run-time error when I run MUMmerGPU-2.0 with a small
dataset. Here's the error I get:

*******************************************************
$ /opt/mummergpu-2.0/bin/release/mummergpu AE016877.fa
DeNovo_BacillusTotal.fasta >allRefsVsAllContigs.txt

TWO_LEVEL_NODE_TREE is 0
TWO_LEVEL_CHILD_TREE is 0
QRYTEX is 0
COALESCED_QUERIES is 0
REFTEX is 0
REORDER_REF is 0
NODETEX is 1
CHILDTEX is 1
MERGETEX is 0
REORDER_TREE is 1
RENUMBER_TREE is 1
Loading ref: AE016877.fa... 5411749 bp. [0.24514s]
Opening DeNovo_BacillusTotal.fasta...
Streaming reference pages against all queries
Stream will use 1 pages for 5411749 bases, page size = 5411749
Building reference texture...
  Creating Suffix Tree... 8920613 nodes [2.65961s]
  Renumbering tree... [1.05719s]
  Flattening Tree...  node: 4096x2208 children: 4096x2208 [4.75442s]
This tree will need 289406976 bytes on the board
The refstr requires 5415850 bytes
Beginning reference page 0x8ac8260
board free memory: 900464640 total memory: 1073020928
done
Loading query block... 69343 queries (53585598 bp), need 472451918 bytes
on the GPU (588864598 avail) [1.05587s]
done.
Allocating device memory for queries...         Processing queries C10_contig_1
to C9_contig_6702
        allocated 54282166 bytes
Matching queries C10_contig_1 - C9_contig_6702 against ref coords 1 -
5415848
Need 52271219 match coords for this result array
Allocating result array for 69343 queries (418169752 bytes) ...board
free memory: 550240256 total memory: 1073020928
done
Memory footprint is:
        queries: 54282166
        ref: 294822826
        results: 418169752
match kernel time= 11892.340820
Cuda error in file 'mummergpu.cu' in line 1144 : 6 (the launch timed out
and was terminated).
Trapped
**********************************************

My NVidia/CUDA/MUMmerGPU configuration is:

Graphics card: NVIDIA GeForce 9800 GT
NVidia Driver version: 195.36.15
CUDA toolkit version: 3.0
MUMmerGPU version: 2.0
GCC version: gcc-4.3
OS: Ubuntu 9.10 32-bit
**********************************************

Previously MUMmerGPU was working with the above dataset and
NVidia/CUDA/MUMmerGPU configuration, but recently it's been throwing the
above error. I would really appreciate any help in this regard.

Thanks for your help in advance!

Pankaj


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