Segmentation fault using gemma
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5.0 years ago
ggman ▴ 90

Hi everyone,

I am receiving an interesting error when I run gemma for a MLMM gwas...

/var/spool/slurmd/slurm_script: line 27: 27058 Segmentation fault

Is this an issue with my file or a memory error? I have seen conflicting posts on biostars and was hoping to seek clarification.

gemma gwas • 2.9k views
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Segmentation fault is a memory error. You are trying to access memory you don't have access to. Change the maximum memory allowed and it will work. I have not used gemma, I am telling this from my experience of using STAR where this is a really common error.

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I have gone up to 32 CPUs per task and 20 mem per cpu and it is still failing... I'm so confused.

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I am sorry ggman but I have never used gemma. I cannot help you any more than that.

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Hello, were you able to rectify this. If yes, do tell. I am getting a similar error. Thank you

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I have gone up to 32 CPUs per task and 20 mem per cpu and it is still failing... I'm so confused.

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It usually relates to memory; however, a segmentation fault may still be called even if you have sufficient memory due to other system-specific reasons. Try it on a subset of your data to see if you can get it to run to completion that way. May help with debugging.

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