This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How to qsub a task.sh (eg. blastn, bowties) that could launch multiple threads

As a biologist, I am very confused when I am using qsub to submit a task, how to qsub a task that could run in multiple threads, i.e., using -p in bowtie2, -a in blastn. After a exhaustive google search, I have tried -l nodes=1:ppn=8, -l ncpus=8, -pe pe_splots 8, all these parameters do not exist on our SGE server. The only one seems to work is qsub -pe orte 8, however, although 8 cores are assigned, bowtie2 and blastn only run in single threads, anyone could help me on this?

blastn bowtie2 sge qsub
• 5,443 views • link
updated by Ram Ram • written by Mingkun • Mingkun

2 answers

On our cluster "-pe smp 20", for example, would specify 20 threads. You should really ask the cluster administrator though, since he/she will be able to tell you exactly the right options.

• 1 views • link
written by Devon Ryan Devon Ryan

Thanks, I finally have -pe orte 8 successful running on my terminal now. I have a follow-up question, when I run multiple blastn on my own workstation, they shared the same memory load,i.e.,each of the 10 BLASTN task (using the same reference database NT) took 90% of MEM, whether the different BLASTN tasks could share the memory in the same way or not? or they have to be on the same physical node?

• 1 views • link
updated by Ram Ram • written by Mingkun • Mingkun

They'll need to be run on the same node to use the same memory. There's probably a qsub option to put things on the same node, read through man qsub.

• 1 views • link
written by Devon Ryan Devon Ryan

You need to tell blastn to use multiple threads (it is not clear from your post if you are doing that). Relevant option would be

-num_threads n

Similarly for bowtie

-p/--threads <int> number of alignment threads to launch

that number needs to match your qsub command -pe orte 8.

• 1 views • link
updated by Ram Ram • written by GenoMax GenoMax

I have done this, now it works.

• 0 views • link
written by Mingkun • Mingkun

Log in to answer this question.

More posts like this