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Segmentation fault using gemma

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
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updated by dimpleadiwal050896 • dimpleadiwal050896 • written by ggman ggman

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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written by ashish ashish

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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written by ggman ggman

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

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written by ashish ashish

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

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written by dimpleadiwal050896 • dimpleadiwal050896

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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written by ggman ggman

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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written by Kevin Blighe Kevin Blighe

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