how to set CPU with butterfly dependency RAM (bflyHeapSpaceMax) in trinity assembler?

Question

[seta]

Hi everybody,

I've heard that it's possible to set CPU with butterfly dependency RAM (bflyHeapSpaceMax) in Trinity software to overcome the RAM deficiency problem. Have anybody experience with it and how to set it, please let me know the exact command? your help and response is highly appreciated.

Answer 1

[rtliu]

Say you have 16 GB RAM but want to use 4 CPU to run Trinity assembly, you can pass 3G to --bflyHeapSpaceMax (default:10G)

Trinity --seqType fq --bflyHeapSpaceMax 3G --JM 10G --left reads_1.fq --right reads_2.fq --CPU 4

To show full usage of Trinity: Trinity --show_full_usage_info

[seta]

Thanks for your reply. As I found Trinity usually run on 4 or 6 CPU, isn't it? I have a 64 GB RAM and a big data (400 million PE reads). I'm concerned about low RAM, so I try to use your command to set CPU with butterfly dependency RAM (bflyHeapSpaceMax). Could you please let me know how much RAM should be pass to bflyHeapSpaceMax (default:10G). You say 3 GB for a computer 16 GB, what about for my situations (64 GB)? I will be glad to know what is the basic rule for this setting up in various computer with different RAM and CPU? Thanks for your feedback in advance.

[rtliu]

For 64GB RAM, I would use default 10G with no more than 6 CPU. The rule of thump is (number of CPU x bflyHeapSpaceMax) should be less than the RAM of the computer. Otherwise you will get Butterfly fails with java Error: Cannot create GC thread. Out of system resources.

[seta]

Hi rtilu,

Many thanks for clarifying me about it. So just

Trinity --seqType fq   --bflyHeapSpaceMax 10G  --JM 10G  --left reads_1.fq --right reads_2.fq  --CPU 4

will be fine? based on your great experience, could you please let me know in my situation (about 400 million PE reads and computer 64 GB RAM) how long Trinity to finish job? again thanks