Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

CUDAPolisher core dumps #21

Open
noncodo opened this issue Aug 21, 2020 · 1 comment
Open

CUDAPolisher core dumps #21

noncodo opened this issue Aug 21, 2020 · 1 comment

Comments

@noncodo
Copy link

noncodo commented Aug 21, 2020

I've been trying to get racon-gpu to run on my data (2x ~1kb contigs) but keep hitting a wall

$ racon -m 8 -x -6 -g -8 -c 1 reads.fastq aligned.paf dirtyCotigs.fa

Using 4 GPU(s) to perform polishing
Initialize device 0
Initialize device 1
Initialize device 2
Initialize device 3
[CUDAPolisher] Constructed.
[racon::Polisher::initialize] loaded target sequences 0.000031 s
[racon::Polisher::initialize] loaded sequences 22.377420 s
[racon::Polisher::initialize] loaded overlaps 3.298172 s
[racon::Polisher::initialize] aligning overlaps [====================] 12.168808 s
[racon::Polisher::initialize] transformed data into windows 2.449713 s
[racon::CUDAPolisher::polish] allocated memory on GPUs for polishing 6.232884 s
Floating point exception (core dumped)

Fiddling around with the parameters a bit, I get some more verbose output and seem to make it a bit further when specifying:
$ racon -c 1 --cudaaligner-batches 1 reads.fastq aligned.paf dirtyCotigs.fa

Using 4 GPU(s) to perform polishing
Initialize device 0
Initialize device 1
Initialize device 2
Initialize device 3
[CUDAPolisher] Constructed.
[racon::Polisher::initialize] loaded target sequences 0.000029 s
[racon::Polisher::initialize] loaded sequences 21.847521 s
[racon::Polisher::initialize] loaded overlaps 3.320273 s
GPU 0: Aligning with band width 46
GPU 1: Aligning with band width 46
GPU 2: Aligning with band width 46
GPU 3: Aligning with band width 46
[racon::CUDAPolisher::initialize] allocated memory on GPUs for alignment 6.027738 s
Alignment skipped by GPU: 1243722 / 1295352overlaps [=====>              ] 8.770285 s
[racon::Polisher::initialize] aligning overlaps [====================] 93.255284 s
[racon::Polisher::initialize] transformed data into windows 2.451490 s 121.277171 s
[racon::CUDAPolisher::polish] allocated memory on GPUs for polishing 5.430252 s
GPU Error:: invalid configuration argument /home/apps/racon-gpu/vendor/GenomeWorks/cudapoa/src/cudapoa_kernels.cuh 546

Aborted (core dumped)

Compiled with:
C/CXX compiler = GNU 7.5.0
CUDA v10.2

Running with: 4x RTX2080Ti

@schorlton
Copy link

Experiencing same thing (I think): NVIDIA-Genomics-Research/GenomeWorks#662
No response yet.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants