Re: [galaxy-dev] Scaling tools: data available? (Peter van Heusden)
If you are looking for a simple python program to log cpu% and memory of another executable, then analyze.py might do. Its in https://github.com/Public-Health-Bioinformatics/kipper/tree/master/RDP-test -case along with a few scripts that show examples of its use. Damion
On 02/21/2016 11:13 PM, Peter van Heusden wrote:
Hi there
We're researching the resource (CPU time and memory) requirements for RNA STAR at the moment. Specifically, we'd like to build up a database of input size to resource usage so that we can use this to feed a dynamic destination mapper (currently our STAR configuration uses a thumbsuck for RAM and CPU requirements that is not optimal but works in many cases).
Has anyone collected these metrics before? And more generally, is anyone collecting metrics for a range of bioinformatics tools? A database like this could be very useful!
Thanks! Peter
Thanks Damion We've got the collectl based metric collection stuff working and that dumps data in the Galaxy DB (which you can pull out using the API). Thanks, Peter On 17 March 2016 at 10:45, Dooley, Damion <Damion.Dooley@bccdc.ca> wrote:
If you are looking for a simple python program to log cpu% and memory of another executable, then analyze.py might do. Its in https://github.com/Public-Health-Bioinformatics/kipper/tree/master/RDP-test -case along with a few scripts that show examples of its use.
Damion
On 02/21/2016 11:13 PM, Peter van Heusden wrote:
Hi there
We're researching the resource (CPU time and memory) requirements for RNA STAR at the moment. Specifically, we'd like to build up a database of input size to resource usage so that we can use this to feed a dynamic destination mapper (currently our STAR configuration uses a thumbsuck for RAM and CPU requirements that is not optimal but works in many cases).
Has anyone collected these metrics before? And more generally, is anyone collecting metrics for a range of bioinformatics tools? A database like this could be very useful!
Thanks! Peter
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participants (2)
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Dooley, Damion -
Peter van Heusden