Multiple threads on ubuntu server

Question

[oghzzang]

I am using Ubuntu 16.04 server. 88 threads, mem500Gb.

I used a program that supports multi-threads (number of threads=10)

In my case, it didn't use 10 CPUs. It is divided into a total of 10 processes and uses only 1 CPU.

I need any helps,,,

[Pierre Lindenbaum]

you asked many questions that got answers. Please review all your previous questions and validate the good answers . e.g: Questions about bam to fastq ; Differential Expression gene In Rna-Seq Experiment using mt.maxT ; get identical number of read1 and read2 aligned ; Parse allele database ; Have you ever obtained user guide of ExomeCNV? ; etc...

[oghzzang]

I reviewed and answered their comments. What do you mean?

[Mensur Dlakic]

What Pierre means is that you may want to consider upvoting and/or accepting the posts if they have been helpful to you. This gives an incentive to volunteers to share their expertise - although most of us don't do it for the votes - and also provides closure to threads. When others read these threads a year from now it is easier to find helpful comments if they are upvoted or accepted.

[oghzzang]

OMG. I got the function now. Many thanks!

[Mensur Dlakic]

To me this seems like a problem outside of your CPUs. If there is significant disk reading, and especially if disk writing, that your program is doing, that will be a bottleneck. In such a case it doesn't matter that you have plenty of threads, as they will be running with less than 100% because the disk is not fast enough to provide enough data (or offload the data).

I suggest you try a smaller number, maybe 4-5 threads, and see if that will get them all to run at 100%.

By the way, running "regular" programs as a root user is not good practice.

[oghzzang]

Many thanks,

I'll decrease the threads to run tools, and check the Disk I/O problem in my ubuntu server.

Best,

Oh.

[colindaven]

• please don't use sudo/root to run bioinformatics programs. Only use root to install software if needed. Else poorly written software (or a single incorrect command) can destroy your whole system
• There is a python program called glances which can help you to work out IO bottlenecks on linux.

[oghzzang]

I'll do that from now on. I'll use glances and check it. Thank you!