antsMultivariateTemplateConstruction2.sh error "GLIBC not found"

[YUZHENG6]

Operating system and version

Rocky Linux 8.7 (Green Obsidian)

CPU architecture

x86_64 (PC, Intel Mac, other Intel/AMD)

ANTs code version

2.5.2.post5-g3fa6cfb

ANTs installation type

ANTsX docker image (from DockerHub user antsx)

Summary of the problem

When running the command antsMultivariateTemplateConstruction2.sh, errors were reported "AverageImage GLIBC not found"

Commands to reproduce the problem.

!/bin/bash

SBATCH --job-name=antsTemplateConstruction

SBATCH --output=templateConstructionout%j.txt

SBATCH --error=templateConstructionerr%j.txt

SBATCH --ntasks=20

SBATCH --time=4-00:00:00

SBATCH --mem=250G

SBATCH --partition=gpu

SBATCH --gres=gpu:4

SBATCH --mail-user=nassare@crick.ac.uk

SBATCH --mail-type=ALL

antsMultivariateTemplateConstruction2.sh -d 3 -b 1 -n 0 -g 0.15 -q 200x200x100x50 -c 5 -u 50:00:00 -v 100G -o virgin20_ *.nii.gz

Output of the command with verbose output.

Data to reproduce the problem

Data temporarily unavailable

[cookpa]

This sounds like a system problem independent of the data. It should be reproducible by running AverageImages by itself

[cookpa]

Your system kernel might be too old for the docker image. Can you try an alternative install? Eg, these Centos 7 binaries

[YUZHENG6]

This sounds like a system problem independent of the data. It should be reproducible by running AverageImages by itself

I agree with that. And I also tried different versions of GCC. But results will show more errors as same as changed GLIBC version.

[YUZHENG6]

Your system kernel might be too old for the docker image. Can you try an alternative install? Eg, these Centos 7 binaries

Actually I used HPC of my insitute and that needs time to update whole system. Are there any other possible solutions to this system problem?

[cookpa]

Sorry, I didn't mean you should change the system, rather perhaps the ANTs binaries compiled for Centos 7 might work. They should be built with an older GLIBC

[cookpa]

I made a build using an older Debian, does this work for you? If so I can share the Dockerfile

docker pull cookpa/ants:buster

[YUZHENG6]

I made a build using an older Debian, does this work for you? If so I can share the Dockerfile

docker pull cookpa/ants:buster

Hi, I apologise for the late reply as I used the Ants you provided, submitted a new task and just got it processed! But in the "shapeupdatedtotemplate", it shows the error that " imagelist length is 18, expected 19". I submitted 19 image files. I'm wondering if it could be an error in processing one of the image files, rather than a problem with Ants, and I need to check with the HPC team.

[YUZHENG6]

I made a build using an older Debian, does this work for you? If so I can share the Dockerfile

docker pull cookpa/ants:buster

And I read the error log that shows the "slurm_load_jobs error: Invalid job id specified". I'm wondering if this could be the missing image file. But I read log of each jobs and that show "All_Command_lines_OK".

[cookpa]

Sounds like one image failed to register. It might be a slurm problem or something to do with that particular image, you have to find the logs and the job script for that image, and go from there.

Anyway, here's a Dockerfile that builds the most recent ANTs on debian:buster

Dockerfile_buster.txt