Comments (2)
This is with d1a73a0 on a ubuntu 18.04 p3.16xlarge AWS instance
It appears to work with d5fd293. So it's definitely a regression related to changes this June for the overflow bugs in the repeatmasker.
Just looking at these commits, it would seem that the changes to the repeat masker here: d1a73a0 would also need to be applied to run_segalign??
It is very quickly reproduced:
wget -q http://public.gi.ucsc.edu/~hickey/debug/segalign_debug/hg38_without_alts_preprocessed.fa.pp.gz wget -q http://public.gi.ucsc.edu/~hickey/debug/segalign_debug/panTro6_preprocessed.fa.pp.gz gzip -d hg38_without_alts_preprocessed.fa.pp.gz gzip -d panTro6_preprocessed.fa.pp.gz
The segalign command
run_segalign panTro6_preprocessed.fa.pp hg38_without_alts_preprocessed.fa.pp --format=paf:minimap2 --step=2 --ambiguous=iupac,100,100 --ydrop=3000 --notransition
The crash
terminate called after throwing an instance of 'thrust::system::system_error' what(): trivial_device_copy D->H failed: cudaErrorInvalidValue: invalid argument /usr/local/bin/run_segalign: line 197: 35103 Aborted (core dumped) stdbuf -oL segalign $refPath $queryPath $DATA_FOLDER $optionalArguments
But
run_segalign
still returns 0!echo $? 0
The full log
Converting fasta files to 2bit format Executing: "segalign /home/ubuntu/work/panTro6_preprocessed.fa.pp /home/ubuntu/work/hg38_without_alts_preprocessed.fa.pp /home/ubuntu/work/output_13442/data_23960/ --format=paf:minimap2 --step=2 --ambiguous=iupac,100,100 --ydrop=3000 --notransition" Using 64 threads Using 8 GPU(s) Reading query file ... Reading target file ... Start alignment ... Sending reference block 0 ... Sending query block 0 with buffer 0 ... Sending query block 1 with buffer 1 ... Query block 0, interval 1/52 (0:10000000) with buffer 0 Query block 0, interval 3/52 (20000000:30000000) with buffer 0 Query block 0, interval 7/52 (60000000:70000000) with buffer 0 Query block 0, interval 10/52 (90000000:100000000) with buffer 0 Query block 0, interval 14/52 (130000000:140000000) with buffer 0 Query block 0, interval 17/52 (160000000:170000000) with buffer 0 Query block 0, interval 22/52 (210000000:220000000) with buffer 0 Query block 0, interval 26/52 (250000000:260000000) with buffer 0 Query block 0, interval 30/52 (290000000:300000000) with buffer 0 Query block 0, interval 35/52 (340000000:350000000) with buffer 0 Query block 0, interval 39/52 (380000000:390000000) with buffer 0 Query block 0, interval 42/52 (410000000:420000000) with buffer 0 Query block 0, interval 46/52 (450000000:460000000) with buffer 0 Query block 0, interval 48/52 (470000000:480000000) with buffer 0 Query block 0, interval 50/52 (490000000:500000000) with buffer 0 Query block 0, interval 2/52 (10000000:20000000) with buffer 0 Query block 0, interval 18/52 (170000000:180000000) with buffer 0 Query block 1, interval 4/60 (30000000:40000000) with buffer 1 Query block 0, interval 19/52 (180000000:190000000) with buffer 0 Query block 1, interval 10/60 (90000000:100000000) with buffer 1 Query block 0, interval 21/52 (200000000:210000000) with buffer 0 Query block 0, interval 23/52 (220000000:230000000) with buffer 0 Query block 0, interval 4/52 (30000000:40000000) with buffer 0 Query block 0, interval 24/52 (230000000:240000000) with buffer 0 Query block 0, interval 25/52 (240000000:250000000) with buffer 0 Query block 1, interval 12/60 (110000000:120000000) with buffer 1 Query block 0, interval 28/52 (270000000:280000000) with buffer 0 Query block 0, interval 8/52 (70000000:80000000) with buffer 0 Query block 0, interval 29/52 (280000000:290000000) with buffer 0 Query block 0, interval 31/52 (300000000:310000000) with buffer 0 Query block 0, interval 32/52 (310000000:320000000) with buffer 0 Query block 0, interval 9/52 (80000000:90000000) with buffer 0 Query block 0, interval 33/52 (320000000:330000000) with buffer 0 Query block 0, interval 34/52 (330000000:340000000) with buffer 0 Query block 0, interval 36/52 (350000000:360000000) with buffer 0 Query block 0, interval 5/52 (40000000:50000000) with buffer 0 Query block 0, interval 37/52 (360000000:370000000) with buffer 0 Query block 0, interval 38/52 (370000000:380000000) with buffer 0 Query block 0, interval 40/52 (390000000:400000000) with buffer 0 Query block 0, interval 11/52 (100000000:110000000) with buffer 0 Query block 0, interval 41/52 (400000000:410000000) with buffer 0 Query block 0, interval 43/52 (420000000:430000000) with buffer 0 Query block 0, interval 12/52 (110000000:120000000) with buffer 0 Query block 0, interval 44/52 (430000000:440000000) with buffer 0 Query block 0, interval 45/52 (440000000:450000000) with buffer 0 Query block 0, interval 13/52 (120000000:130000000) with buffer 0 Query block 0, interval 47/52 (460000000:470000000) with buffer 0 Query block 0, interval 15/52 (140000000:150000000) with buffer 0 Query block 0, interval 49/52 (480000000:490000000) with buffer 0 Query block 0, interval 16/52 (150000000:160000000) with buffer 0 Query block 0, interval 51/52 (500000000:510000000) with buffer 0 Query block 0, interval 52/52 (510000000:510113926) with buffer 0 Query block 1, interval 1/60 (0:10000000) with buffer 1 Query block 1, interval 2/60 (10000000:20000000) with buffer 1 Query block 1, interval 3/60 (20000000:30000000) with buffer 1 Query block 1, interval 5/60 (40000000:50000000) with buffer 1 Query block 1, interval 6/60 (50000000:60000000) with buffer 1 Query block 1, interval 7/60 (60000000:70000000) with buffer 1 Query block 0, interval 6/52 (50000000:60000000) with buffer 0 Query block 1, interval 8/60 (70000000:80000000) with buffer 1 Query block 1, interval 9/60 (80000000:90000000) with buffer 1 Query block 0, interval 20/52 (190000000:200000000) with buffer 0 Query block 1, interval 11/60 (100000000:110000000) with buffer 1 Query block 0, interval 27/52 (260000000:270000000) with buffer 0 terminate called after throwing an instance of 'thrust::system::system_error' what(): trivial_device_copy D->H failed: cudaErrorInvalidValue: invalid argument /usr/local/bin/run_segalign: line 197: 35103 Aborted (core dumped) stdbuf -oL segalign $refPath $queryPath $DATA_FOLDER $optionalArguments real 2m19.050s user 1m27.737s sys 1m50.123s real 2m19.072s user 2m25.897s sys 1m53.887s No alignment generated
@glennhickey I've recently run into the same problem. The driver scripts aren't catching all errors. I'm currently rewriting them in python to improve error handling.
from segalign.
Hi @richard-burhans,
Your PR #64 looks very interesting. I have a fork of SegAlign here that cactus uses.
My fork is identical to the master branch of this repo except for this commit ComparativeGenomicsToolkit@fe4b16f which I think I made to resolve this issue.
Anyway, I'm interested in incorporating your changes and any future developments into Cactus. So please considering PRing them to https://github.com/ComparativeGenomicsToolkit/SegAlign
Thanks!
from segalign.
Related Issues (20)
- couldn't find boost HOT 7
- Running on multi-fasta HOT 2
- "grep: *.err" and "m: cannot remove '*.segments'" errors HOT 2
- FAILURE: extra segments in file HOT 4
- SegAlign/progressivecactus errors on LSF HOT 1
- run_segalign_repeat_masker file HOT 2
- cudaErrorIllegalAddress: an illegal memory access was encountered HOT 1
- stdbuf: failed to run command ‘segalign’: No such file or directory HOT 2
- error during cmake HOT 1
- segalign_repeat_masker crashes HOT 3
- segaling_repeat_masker still crashes HOT 7
- segalign crashes while aligning final against final reference block HOT 1
- SegAlign crashes while running cactus on Terra HOT 3
- thrust::system::system_error | CUDA free failed: cudaErrorCudartUnloading
- Error: cudaMalloc of 256 bytes for sub_mat failed with error " the provided PTX was compiled with an unsupported toolchain. " HOT 1
- /usr/local/bin/run_segalign: line 60: segalign: command not found HOT 1
- AMD GPU support
- Output file size not correct HOT 1
- Support for linux-ppc64le?
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from segalign.