Question: DiscoSNP++ limit number of cores?
0
gravatar for damiondooley
4.4 years ago by
Canada
damiondooley0 wrote:

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

snp processing • 990 views
ADD COMMENTlink modified 4.4 years ago • written 4.4 years ago by damiondooley0
1
gravatar for pierre.peterlongo
4.4 years ago by
France
pierre.peterlongo840 wrote:

Hi all,

 

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

 

Pierre
 

ADD COMMENTlink written 4.4 years ago by pierre.peterlongo840
1
gravatar for edrezen
4.4 years ago by
edrezen720
France
edrezen720 wrote:

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.

ADD COMMENTlink written 4.4 years ago by edrezen720
0
gravatar for pierre.peterlongo
4.4 years ago by
France
pierre.peterlongo840 wrote:

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

ADD COMMENTlink written 4.4 years ago by pierre.peterlongo840
0
gravatar for damiondooley
4.4 years ago by
Canada
damiondooley0 wrote:

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

ADD COMMENTlink written 4.4 years ago by damiondooley0
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