CODEWITHSUNDEEP
rlinuxslurm
Hailong Ji
Hailong Ji

Reputation: 53

error while loading shared libraries: libicuuc.so.50

I try to submit a R script to SLURM in CentOS 7, like this:

#!/bin/bash
#SBATCH -J test                   
#SBATCH -o test.out               
#SBATCH -p compute                
#SBATCH --qos=normal              
#SBATCH -N 1                      
#SBATCH --ntasks-per-node=8       
#SBATCH --cpus-per-task=1         
#SBATCH --job-name=rtest

Rscript --vanilla Rhelp.R

Then system will return a jobid, but the R script does not work. I can assure this script can run in command line. Then I have found in test.out, like this:

error while loading shared libraries: libicuuc.so.50: 
cannot open shared object file: No such file or directory

I am a freshman in SLURM and Linux, thx!

Upvotes: 3

Views: 12435

Answers (3)

EnthusiastiC
EnthusiastiC

Reputation: 155

With the module avail command from the head node you list all available modules and loaded modules are marked somehow depending on your OS; for me they are marked with (L). All you need to do is load those loaded modules from your file script each of which is invoked with the line module load path_to_module. Whereas, path_to_module is as is indicated with the previous command module avail. Or without resorting to module avail you could use module list for currently loaded modules.

Upvotes: 0

Dan
Dan

Reputation: 951

Just because it may be installed on the head node doesn't mean it's installed on the compute node(s). You could fire off the same ldconfig command in a Slurm job and view the results to confirm that's the case.

Upvotes: 0

damienfrancois
damienfrancois

Reputation: 59130

It looks like the libicu RPM package is not installed on the compute nodes.

Upvotes: 2

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