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Question: ChIPQC : ChIPQCreport(experiment) swap memory overload
1
gravatar for ZheFrench
5 months ago by
ZheFrench10
ZheFrench10 wrote:

Hey,

I'm trying to generate a ChIPQCreport on my 21 samples described in my sample sheet for all chromosomes .

Memory use is increasing too fast, using all free memory and then it's going to swap memory which is also limited and then overload swap so the creation of the report will crash.

Is there a way to tell ChIPQC to use a directory on disk to write stuffs instead of using swap...or to tell don't use so much memory or so much cores...

Note that swap memory is not released after the crash and even when you kill R.

By the way,  I'm working on a system with 64GB and 32 cores. 

Linux  3.16.0-4-amd64 #1 SMP Debian 3.16.39-1 (2016-12-30) x86_64 GNU/Linux

R Version Information

  • Version: 3.3.1

  • Version_String :R version 3.3.1 (2016-06-21)

ChIPQC Version Information

  • Version: ChIPQC:1.10.3

 

 

 

ADD COMMENTlink modified 5 months ago by Thomas Carroll390 • written 5 months ago by ZheFrench10
2
gravatar for Thomas Carroll
5 months ago by
United Kingdom/London/MRC CSC Imperial College London
Thomas Carroll390 wrote:

 

Hi, it may have been that some of bigger files running in parallel were  causing it to run out memory.

Lowering the number of core will often solve this.

Best

Tom

 

 

 

 

 

 

 

ADD COMMENTlink written 5 months ago by Thomas Carroll390
1
gravatar for ZheFrench
5 months ago by
ZheFrench10
ZheFrench10 wrote:

Ok playing with register from BioCparallel by limiting the number of cores , you limit memory usage , it should make the trick. But anyway, it's buggy.

ADD COMMENTlink written 5 months ago by ZheFrench10
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