DiscoSNP++ limit number of cores?

Question

[damiondooley]

I'm just wondering if there is a top-down way to limit the number of cores DiscoSNP++ is using? We operate in a shared environment that benefits from some unused cores. DiscoSNP (depending on # input files, right?) seems to consume as many cores as possible. I will look into limiting user/core ratio as an alternative but wondering if there is a more direct way?

Thanks,
Damion

Answer 1

[pierre.peterlongo]

Hi all,

The latest version (2.1.6) available here (sources) or here (binaries) has an option for limiting the number of cores.

Pierre

Answer 2

[edrezen]

Currently, it seems there is no way to set a specific number of cores with the script run_discoSnp++.sh, and by default, it takes all available cores, independently of the number of input files. It could be improved in a future version with a new argument for such a setting.

For the moment, you can modify the script by yourself and add directly -nb-cores X (where X is the number of cores to be used) at the end of the following lines:

• line holding the "dbgh5" command
• line holding the "kissnp2" command

For instance, it would be (for 4 cores):

$DISCO_BUILD_PATH/ext/gatb-core/bin/dbgh5 -in ... ... ...    -nb-cores 4
$DISCO_BUILD_PATH/tools/kissnp2/kissnp2 -in ... ... ...      -nb-cores 4

I have not tested this but I think it should work.

[pierre.peterlongo]

Hi Damion, Thanks

Erwan has specified by email we are preparing a new release including an option for controlling of the number of used threads.

Additionally the documentation of the VCF creation will be added, and the VCF creation itself will be improved.

Pierre

[damiondooley]

Ok, thanks folks for the feedback everyone. I was able to wait for the latest very speedily delivered enhancement to discoSnp for this.

Ciao,
Damion