Re: [HTCondor-users] Reserve all cores on a server?

[Greg Thain <gthain@xxxxxxxxxxx>]

On 04/12/2015 06:17 PM, Smithies, Russell wrote:

I have a problem where users are submitting jobs that are running programs with multiple threads but I’m not sure how to restrict this or to prevent other jobs running on the same server.

 

So the submit file could look like this:

 

Executable     =  run.sh

Universe       = vanilla

error          =  run.err.$(Cluster).$(Process)

output         = run.out.$(Cluster).$(Process)

log            =run.log

Queue 10

 

And run.sh contains some file checks and commands to exec eg.

 

blastn -query data.fastq -task megablast -num_threads 4 -db nt

 

You may very well get better throughput by running more blast jobs with -num_threads set to 1.

If, however, you really want to run with four threads, the job needs to tell HTCondor that it needs four cores by setting

Request_cpus = 4

in the submit file.

-greg