Entering edit mode
4.9 years ago
ggman
▴
80
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.
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.
I have gone up to 32 CPUs per task and 20 mem per cpu and it is still failing... I'm so confused.
I am sorry ggman but I have never used gemma. I cannot help you any more than that.
I have gone up to 32 CPUs per task and 20 mem per cpu and it is still failing... I'm so confused.
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.