Comments (2)
iCAMP uses some functions (e.g., big.matrix) from the R package bigmemory and parallel computing function (e.g., parLapply) from package parallel. I do not know which will cause file locking. Two possible reasons: (1) Many functions in iCAMP can set parallel computing thread number by the parameter 'nworker', e.g., in icamp.big. If the user sets nworker as a very large number (over CPU cores), it will occupy too many threads and make the computer not responsive at all. (2) The big.matrix function used in some iCAMP function (e.g., pdist.big) saves a relatively big file with suffix '.bin' somewhere in the harddisk, and the physical address will be saved in a '.desc' file; then, the data in '.bin' file will be used as if it is saved in memory, thus the calculation can go beyond the limit of memory. The '.bin' file occupies a certain place which will not work if physically changed (copy/paste) to another place. But this is unlikely to make computer not responsive.
I used iCAMP a lot on our Linux and Windows servers without problems as long as I limit the nworker (thread number) lower than the CPU core number. But I have not deployed it in HPC yet.
from icamp1.
I hope the problem has been solved. If no more questions, I will close this issue.
from icamp1.
Related Issues (20)
- Hi, professor Ning, I would like to ask you about the operation of iCAMP code HOT 2
- The issue with step"binps=iCAMP::ps.bin" HOT 2
- Error in UseMethod("is.rooted") HOT 3
- Error in checkForRemoteErrors(val) HOT 3
- Is it necessary to rarify the count data before starting iCAMP analysis ? HOT 5
- How to get the category information? HOT 2
- Stuck at phylogentic signal testing HOT 1
- icamp.bins - arguments imply differing number of rows HOT 2
- erro Now summarizing method=CbMPDiCbraya i=1 j=1. Sat Mar 9 23:34:20 2024 Error in oldname[j, 1:2] : subscript out of bounds HOT 11
- Protocols for using HPC? HOT 3
- requirement of the sample number HOT 2
- I couldn't the find the function 'big.mantel.correlog' HOT 1
- Error in utils::combn(sampik, 2) : n < m Calls: <Anonymous> ... lapply -> FUN -> t -> sapply -> lapply -> FUN -> <Anonymous>
- Fatal error: Exit code 1 () Now computing path. begin at Sat May 11 22:04:08 2024. Please wait... Error in checkForRemoteErrors(val) : 2 nodes produced errors; first error: subscript out of bounds Calls: ... clusterApply -> staticClusterAp
- How to build a bin level phylogenetic tree
- Interpretation questions
- Extremely fast phylogenetic distance computation
- Optimizing Binning: MeanR vs. RAsig.adj?
- icamp.big debug problem
- Problem creating filebacked matrix in the use of the pdist.big function.
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 icamp1.