Entering edit mode
11 months ago
oghzzang
▴
50
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,,,
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...
I reviewed and answered their comments. What do you mean?
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.
OMG. I got the function now. Many thanks!
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.Many thanks,
I'll decrease the threads to run tools, and check the Disk I/O problem in my ubuntu server.
Best,
Oh.
glances
which can help you to work out IO bottlenecks on linux.I'll do that from now on. I'll use
glances
and check it. Thank you!