search

lbcb-sci / racon

Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads
MIT License
201 stars 34 forks source link

Illegal instruction (core dumped) #11

Closed ilyavs closed 4 years ago

ilyavs commented 4 years ago

Hi, I installed racon 1.4.10 using bioconda. Although I intend on using it on a cluster, I first tested it on the machine on which I ran the conda install command. Even though I ran it on the same machine I used for installing it, I still got the "Illegal instruction (core dumped)" error. The compiler on the machine is: gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-11) Will I have to compile racon from source on each of the cluster machines once I get it to work on the current one? I appreciate your help in getting racon to work on my system. Thanks, Ilya.

rvaser commented 4 years ago

Hi Ilya, try compiling from source on one of your machines and see if that executable works on others. I am not sure what exactly is causing the error, which CPU do you have? Does it support SSE4.1?

Best regards, Robert

ilyavs commented 4 years ago

Hi, I didn't change anything in the installation and ran it on the cluster. I think it crashed a couple of times with a similar error. However, once I requested larger amounts of memory (50Gb), it crashed less often (with the same error, at different stages). Could it be that the issue is related to available memory? Thanks, Ilya.

ilyavs commented 4 years ago

Another update, jobs that failed with 50Gb memory, completed successfully with 150Gb memory. Best, Ilya.

rvaser commented 4 years ago

The illegal instruction error is not tied to insufficient memory. Maybe you got a different node on the cluster that is compatible with the binary.

Best regards, Robert

ilyavs commented 4 years ago

Maybe. Anyway, seems to work in my current workflow. Thanks, Ilya.