search

jianyangqt / gcta

GCTA software
GNU General Public License v3.0
87 stars 26 forks source link

Segmentation fault error #96

Open mdickey7 opened 2 months ago

mdickey7 commented 2 months ago

Hi all, GCTA is currently installed on TAMU Grace cluster. However, when I run --make-grm I constantly get this error. It does not matter if I change the number of threads, I still get this error. The managers of Grace have tried to reinstall the package but this has not worked.

/var/spool/slurmd/job11243407/slurm_script: line 21: 209073 Segmentation fault (core dumped) gcta64 --threads 48 --bfile new.merged.norm.filtered --make-grm --autosome-num 42 --out wild.managed.relatedness

longmanz commented 2 months ago

Hi, How many samples do you have in your dataset? This error usually is driven by insufficient memory (which you can estimate following the point 2 in this thread: https://yanglab.westlake.edu.cn/software/gcta/#FAQ). If the required memory is too large for a single job, you may consider partitioning your job into small chunks by using the flag "--make-grm-part" (see details in this thread: https://yanglab.westlake.edu.cn/software/gcta/#MakingaGRM)

mdickey7 commented 2 months ago

Hi,

I have 100 total samples in my job that I am trying to run. The run I used previously did not have enough memory however, I just ran it using 2929G of memory and I still get the segmentation error. Then I tried to break it into three parts using the same allocation of 2929G of memory and I still get the segmentation error.

longmanz commented 2 months ago

Hi, Something is not right here. For a sample size of 100 it usually takes less 1GB. You might need to (greatly) reduce the number of variants when calculating the GRM.

Elijah-Ugoh commented 4 weeks ago

Hi,

I have 100 total samples in my job that I am trying to run. The run I used previously did not have enough memory however, I just ran it using 2929G of memory and I still get the segmentation error. Then I tried to break it into three parts using the same allocation of 2929G of memory and I still get the segmentation error.

Hello, Did you manage to find a solution. Currently experiencing the same issue.