GLIBC versions 2.14 not found

HPC Technical
1

Hi all,
I am new to baobab system. I am trying to run a parallel program in the baobab in debug mode but facing some issues:

  1. My original script is run with mpiexec. Can I use that or have to switch to srun (as mentioned in the)?
  2. I have loaded GCC, openmpi etc and I am trying to submit the script with either srun or mpiexec, I get this error:

version `GLIBC_2.14’ not found . A simple loading of the module glibc/2.17 causes a breakdown, if I load that I can’t type any command at all after that. For example, typing
‘module list’ gives :
/opt/lua/lua-5.3.5/bin/lua: error while loading shared libraries: __vdso_gettimeofday: invalid mode for dlopen(): Invalid argument

How can I safely update the version of GLIBC ?

Btw, it has been run successfully in the ‘lesta’ machines in the Astronomy department of Unige (there a spack module loading was essential. Is there something similar here?)

2

Hello Moupiya,

Indeed in CentOS 6.x , the GLIBC version is still 2.12 and cant’be updated easily.
Why do you need another version of GLIBC? If you are doing mpi stuff, please load for example the following package which contains the GCC compiler and openmpi:

module load foss/2018b

See compilers on Baobab.

Yes you should replace the mpiexec with srun (and don’t specify the number of worker, it’s picked automatically with the number of tasks.

I don’t know what spack is.

If you really need a version of GLIBC more recent, you should connect to the new login node (WIP: Migrate Baobab to CentOS7)

Best

3

Hello,

it looks i have the exact same problem in a quite particular situation.

I have the following modules loaded in my .bashrc file:

if [ -z "$BASHRC_READ" ]; then
  export BASHRC_READ=1
  module load foss/2016b
fi

I am compiling the Palabos library following the guide of the http://baobabmaster.unige.ch/enduser/src/enduser/applications.html#palabos

srun --cpus-per-task 16 --ntasks=1 --exclusive make

but when I try to run the produced excutable I also ecounter the glibc error:

./cavity2d: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by ./cavity2d)

After some trial and error it looks like compiling directly on the frontend (just running make) solves the problem.

I don’t know what is the problem here, but if srun solution does not work anymore, maybeit should be removed from the documentation.

EDIT: The error persists when I compile with the latest foss module as well.

Thank you for your help and best regards,
Orestis

4

Hello,

The issue is probably because you compiled Palabos from a node using CentOS 7 (*-EL7) and you are trying to run the binary on a CentOS 6 compute node.

You should either compile Palabos on a CentOS 6 node or only run Palabos on CentOS 7 nodes.