Sct toolbox illegal instruction error

SCT
1

Hi, I am running into a illegal instruction error when running the sct toolbox with the latest available docker image.
This issue only happens a virtual machine, I have tested the same image on physical machine and could run the batch_processing.sh to completion. I could reduce the issue to this:

 $ sct_check_dependencies 
   
   --
   Spinal Cord Toolbox (4.2.1)
   
   SCT info:
   - version: 4.2.1
   - path: /home/sct/sct_4.2.1
   OS: linux (Linux-3.10.0-1127.19.1.el7.x86_64-x86_64-with-debian-buster-sid)
   CPU cores: Available: 8, Used by SCT: 8
   RAM: MemTotal:        8006820 kB
   total        used        free      shared  buff/cache   available
   Mem:           7819         289        6704           8         824        7278
   Swap:          2047           1        2046
   Check Python executable.............................[OK]
     Using bundled python 3.6.10 |Anaconda, Inc.| (default, Jan  7 2020, 21:14:29) 
   [GCC 7.3.0] at /home/sct/sct_4.2.1/python/envs/venv_sct/bin/python
   Check if data are installed.........................[OK]
   Check if numpy is installed.........................[OK] (1.17.4)
   Check if cryptography is installed..................[OK] (2.8)
   Check if dipy is installed..........................[OK] (1.0.0)
   Check if futures is installed.......................[OK]
   Check if h5py is installed..........................[OK] (2.10.0)
   Check if Keras is installed.........................Illegal instruction

It looks like the issue has been addressed in newer versions according to https://github.com/neuropoly/spinalcordtoolbox/issues/2562.

Could you please update the docker hub with these newer version?
Thanks for the help

2

Hi @haz-edine,

Thank you for reaching out. We will likely stop maintaining our docker images because of the high maintenance requirement (issue opened here). However, could you please try to install the latest version of SCT from a fresh Docker container, as explained here?

3

Hi @jcohenadad, thanks for your support. I was able to install the latest version of SCT and can confirm that that issue is gone.

1 Like