australianbiocommons / canu Goto Github PK
View Code? Open in Web Editor NEWCanu: structured documentation and results of testing / optimisation for Australian compute infrastructures
License: GNU General Public License v2.0
canu's People
Contributors
Stargazers
Watchers
Forkers
supernordcanu's Issues
CPU usage
Having run Canu on Rajin and Gadi in the past I have noticed that some jobs call multiple processes and and are not multi-threaded. The biggest offender is correction. I have dealt with this previously by altering the resource allocations of the seperate jobs. When running Canu on Gadi with this wrapper I still have this problem, resulting in a lot of wasted SU on gadi.
I dont know if anything can be done about this, but it is something to be aware of when using Canu.
CPU usage of a number of assemblies I was trialling:
CPU-usage Number-of-CPUS
10310801 cormhap_ 65 01:20:39 24:00:00 168GB 168GB 576GB 144
10310804 canu_E_v 05:00:00 4096MB 1
10313696 cor_E_le 60 00:24:25 24:00:00 195GB 195GB 576GB 144
10313697 canu_E_l 05:00:00 4096MB 1
10313777 cor_E_da 65 00:22:25 24:00:00 142GB 142GB 384GB 96
10313780 canu_E_d 05:00:00 4096MB 1
10313964 cormhap_ 46 00:20:19 00:00:00 998GB 998GB 1920GB 480
10313965 canu_E_m 05:00:00 4096MB 1
10313972 cor_E_pa 70 00:20:25 24:00:00 144GB 144GB 384GB 96
10313974 canu_E_p 05:00:00 4096MB 1
10314167 cor_E_fi 59 00:16:36 00:00:00 136GB 136GB 384GB 96
10314171 canu_E_f 05:00:00 4096MB 1
10314504 cor_E_pu 39 00:10:01 24:00:00 157GB 157GB 768GB 192
10314508 canu_E_p 05:00:00 4096MB 1
10314728 cor_E_sh 17 00:05:07 24:00:00 105GB 105GB 384GB 96
10314730 canu_E_s 05:00:00 4096MB 1
10314764 canu_E_p 05:00:00 4096MB 1
10314872 cor_E_cu 4 00:02:33 24:00:00 66.9GB 66.9GB 768GB 192
10314873 cormhap_ 36 00:02:32 24:00:00 276GB 276GB 960GB 240
10314875 canu_E_c 05:00:00 4096MB 1
10314876 canu_E_l 05:00:00 4096MB 1
Hard coded job limits
Hi,
Within jobwrapper.sh the walltime and jobfs limits have been hardcoded. These limits are not big enough to see many jobs through. Is there any reason why you have hard coded these limits?
jobfsMap["normal"]=8
jobfsMap["hugemem"]=29
echo "#PBS -lwalltime=24:00:00" >> $fname
Using your version of Canu requires me to highly monitor the assembly, frequently stop progress, and edit pbs scripts.
For now I have gone back to my own version of Canu which runs in remote mode. I would really like to use this version of canu as it would free up a lot of time, but in its current form can not.
Thanks.
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.