glibc version problems

Compute nodes in partitions defq and interactive (as well as login nodes) have Centos version 6.5 with glibc version 2.12.

When you try to run a pre-build software that is built on a newer operating system, you will encounter the error, for example,

$ prefetch
./prefetch: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by ./prefetch)

Since glibc version on Centos version 6.5 nodes is 2.12, GLIBC_2.14 isn't available. It is possible to run this software if you use the compute nodes in partition centos7, which have Centos version 7.4 with glibc version 2.17. See ​here for more details.

See the alternate solution below if your software requires a glibc version greater than 2.17.

Work with Singularity Images

​Singularity allows you to run an application built for a different distribution of Linux than Cypress OS (Centos 6 or 7). Here we run Rockylinux 9.2 on Cypress using Singularity.

Run Rockylinux Images Interactively

Start an interactive session with centos7 partition.

 idev -t 8 --partition=centos7

Load Singularity module.

 module load singularity/3.9.0

Setup the environmental variables

 source /lustre/project/singularity_images/setup_cypress.sh

Run bash shell in Rockylinux Images,

 singularity shell -s /bin/bash /lustre/project/singularity_images/rockylinux-9.2.sif

You will get a command line prompt. Now the glibc version is 2.34.

Apptainer> ldd --version
ldd (GNU libc) 2.34
Copyright (C) 2021 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
Written by Roland McGrath and Ulrich Drepper.

You can use command line tools as you usually do on Centos6/7 nodes. module command also works but some of the modules may not work because of library incompatibility.

Run Scripts on Rockylinux in Bachjob

An example Slurm script.

#!/bin/bash
#SBATCH --job-name=Singularity # Job Name
#SBATCH --partition=centos7    # Partition must be centos7
#SBATCH --qos=normal           # Quality of Service normal or long
#SBATCH --time=0-01:00:00      # Wall clock time limit in Days-HH:MM:SS
#SBATCH --nodes=1              # Node count required for the job
#SBATCH --ntasks-per-node=1    # Number of tasks to be launched per Node
#SBATCH --cpus-per-task=1     # Number of threads per task (OMP threads 1-20)

# Load Singularity module
module load singularity/3.9.0

# Setup the environmental variables 
SingularityImageDir=/lustre/project/singularity_images
source $SingularityImageDir/setup_cypress.sh

# Run a command on RockyLinux 
singularity exec $SingularityImageDir/rockylinux-9.2.sif gcc --version

The example above runs gcc —version on RockyLinux. Submitting job is the same as you usually do. (See ​here.) When the job is finished, the log file should contain the output from gcc —version command, which will be:

gcc (GCC) 11.3.1 20221121 (Red Hat 11.3.1-4)
Copyright (C) 2021 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

If you want to run a bash script, assuming 'my_script.sh' is in the current working directory, modify the above as

singularity run $SingularityImageDir/rockylinux-9.2.sif /bin/bash -l -c ./my_script.sh

'my_script.sh' must be executable. You can make it by 'chmod' command (See ​here.)

chmod u+x my_script.sh

For example, 'my_script.sh' is

#!/bin/bash
module load intel-psxe/2016
echo "Hello world from $0 running in ${SINGULARITY_NAME}"
pwd
date
icc --version

When the job is finished, the log file will have:

Hello world from ./my_script.sh running in rockylinux-9.2.sif
/home/userid/test
Fri Jun  9 13:21:01 CDT 2023
icc (ICC) 16.0.0 20150815
Copyright (C) 1985-2015 Intel Corporation.  All rights reserved.

If you find missing packages in rockylinux-9.2.sif, please let us know.