Comments (7)
I have to look into the issue more carefully, not sure why/when it happens, but it happened more than once already. @a-slide do you have any idea?
from nanocompore.
Ok, it looks like I figured it out. On my system numpy is built against openBlas, which by default is multithreaded. The result is that the np.array() call in __process_references() spawns multiple threads (and every worker process does the same).
Since we are using multiprocessing, the solution seems to be to disable multithreading for openBlas and mkl before importing numpy:
import os
os.environ["MKL_NUM_THREADS"] = "1"
os.environ["MKL_THREADING_LAYER"] = "sequential"
os.environ["NUMEXPR_NUM_THREADS"] = "1"
os.environ["OMP_NUM_THREADS"] = "1"
I'm currently testing whether it works as it should.. will commit as soon as I'm sure all is fine.
from nanocompore.
I did not notice, but my version is actually also build against OpenBlas.
I had a quick look as well and it looks like the method you describe should work but you might want to include that as well
os.environ['OPENBLAS_NUM_THREADS'] = '1'
from nanocompore.
Not completely fixed apparently.
Numpy is still causing issues in a cluster environment.
An option to explore might be to use this package to set the number of threads:
https://github.com/joblib/threadpoolctl
from nanocompore.
This should be fixed by #94 but I haven't tested it yet. Did you?
from nanocompore.
I think it's fixed
from nanocompore.
But it's not, reopening.
from nanocompore.
Related Issues (20)
- 'event_l' referenced before assignment HOT 4
- nanocompore sampcomp defunct
- About SK1 transcriptome reference and m6A sites for Yeast HOT 1
- eventalign_collapse error HOT 9
- Where is the fold change value HOT 3
- samcomp
- Script for generating the "sharkfin plot of the p-values compared with Log Odds Ratio" HOT 6
- SampCompDB error HOT 1
- dbm.error: db file doesn't exist; use 'c' or 'n' flag to create a new db HOT 21
- plot position is giving an error HOT 5
- cluster_counts interpretation HOT 1
- Issues on reproducing the synthetic oligo results from the nanocompore paper HOT 3
- Request for demo data & getting ValueError: 'read_name' is not in list when running nanocompore eventalign_collapse with nanopolishComp data HOT 11
- nanocompore to be used for SHAPEseq data HOT 1
- returns numpy error while intsalling nanocompore on Ubuntu 22.04 HOT 2
- miCLIP dataset HOT 2
- A question about the result HOT 1
- nanocompore-sampcomp-References found in index: 0 HOT 2
- nanocompore sampcomp output question. HOT 5
- Problems with save_to_bed. And questions with bed file annotation HOT 1
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 nanocompore.