singularity : GLIBC_2.34 not found

dbpatankar · 2022-05-08 07:18:28

Hi,

I have installed salome_meca 2021 container image using singularity on my arco-linux machine. So far it worked without any issue and I was able to use it. But now may be after an upgrade the salome_meca is unable to start. Here follows what happens and what I know about the issue :

1. When I run it in GPU mode, I get the GLIBC_2.34 error message

$./salome_meca-lgpl-2021.0.0-2-20211014-scibian-9
/usr/bin/nvidia-smi
**************************************
INFO : Running salome_meca in GPU mode
**************************************
runSalome running on digvijay-gl552vx
Searching for a free port for naming service: 2812 - OK
Searching Naming Service  + found in 0.1 seconds 
Searching /Kernel/Session in Naming Service  ++++SALOME_Session_Server: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /.singularity.d/libs/libGLX.so.0)
Traceback (most recent call last):
  File "/opt/salome_meca/Salome-V2021-s9/modules/KERNEL_V9_7_0/bin/salome/orbmodule.py", line 181, in waitNSPID
    os.kill(thePID,0)
ProcessLookupError: [Errno 3] No such process

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/opt/salome_meca/appli_V2021/bin/salome/runSalome.py", line 694, in useSalome
    clt = startSalome(args, modules_list, modules_root_dir)
  File "/opt/salome_meca/appli_V2021/bin/salome/runSalome.py", line 639, in startSalome
    session=clt.waitNSPID("/Kernel/Session",mySessionServ.PID,SALOME.Session)
  File "/opt/salome_meca/Salome-V2021-s9/modules/KERNEL_V9_7_0/bin/salome/orbmodule.py", line 183, in waitNSPID
    raise RuntimeError("Process %d for %s not found" % (thePID,theName))
RuntimeError: Process 8691 for /Kernel/Session not found


--- Error during Salome launch ---

2. When I run it in software rendering mode, it starts properly though rendering is not proper:

$./salome_meca-lgpl-2021.0.0-2-20211014-scibian-9 --soft
*****************************************************
INFO : Running salome_meca in software rendering mode
*****************************************************
runSalome running on digvijay-gl552vx
Searching for a free port for naming service: 2813 - OK
Searching Naming Service  + found in 0.1 seconds 
Searching /Kernel/Session in Naming Service  +++++++++++ found in 5.5 seconds 
Start SALOME, elapsed time :   6.1 seconds
****************************************************************
     Warning: module GHS3DPLUGIN is improperly configured!
     Module GHS3DPLUGIN will not be available in GUI mode!
****************************************************************
****************************************************************
     Warning: module GHS3DPRLPLUGIN is improperly configured!
     Module GHS3DPRLPLUGIN will not be available in GUI mode!
****************************************************************
****************************************************************
     Warning: module BLSURFPLUGIN is improperly configured!
     Module BLSURFPLUGIN will not be available in GUI mode!
****************************************************************
****************************************************************
     Warning: module NETGENPLUGIN is improperly configured!
     Module NETGENPLUGIN will not be available in GUI mode!
****************************************************************
****************************************************************
     Warning: module HYBRIDPLUGIN is improperly configured!
     Module HYBRIDPLUGIN will not be available in GUI mode!
****************************************************************
****************************************************************
     Warning: module GMSHPLUGIN is improperly configured!
     Module GMSHPLUGIN will not be available in GUI mode!
****************************************************************
****************************************************************
     Warning: module HexoticPLUGIN is improperly configured!
     Module HexoticPLUGIN will not be available in GUI mode!
****************************************************************

3. I can get into the container shell and inspect the environment:

Singularity> ldd --version
ldd (Debian GLIBC 2.24-11+deb9u4) 2.24
Copyright © 2016 Free Software Foundation, Inc.
Ce logiciel est libre; voir les sources pour les conditions de
reproduction. AUCUNE garantie n'est donnée; tant pour des raisons
COMMERCIALES que pour RÉPONDRE À UN BESOIN PARTICULIER.
Écrits par Roland McGrath et Ulrich Drepper.

The container has GLIBC_2.24. My system has GLIBC_2.35. Not sure which GLIBC is causing this issue. It most likely appears to be from container but then not sure how it worked earlier.

singularity version is 3.9.0

I also checked the container image with Fedora 35 and Ubuntu 22.04 and they all give GLIBC_2.34 error whereas Ubuntu 18.04 works well. So is this an issue with GLIBC on host machine?

As far as I know, the newer GLIBC should have older GLIBC binaries.

Can someone point to a solution to this?

CharlesM · 2022-05-14 12:45:56

Hello, have you found a solution ?

I am experiencing the same issue. (Glibc_ 2.34) Crashing in GPU, rendering problems in software rendering.
(For example, when it works, I cannot edit in text mode in the aster-study module. )

dbpatankar · 2022-05-14 17:57:25

CharlesM wrote:

Hello, have you found a solution ?

Not yet! Forced to stick to Ubuntu 18.04 for now until this gets resolved. Although I have no idea how thats going to happen because I was using it without any issue until a few weeks ago.

amit_code_aster · 2022-06-11 05:17:35

Hi dbpatankar and CharlesM

I got the same error on Fedora 36.
Another user @aurelius_nero also faced the same issue on Fedora 35. He solved it by installing nvidia-container-toolkit from NVIDIA website.
I also tried this solution and it worked for me also. The link to @aurelius_nero's post on this forum is https__://code-aster.org/forum2/viewtopic.php?id=26213 (remove __ as links are not allowed).

You can install `nvidia_container-toolkit` from the official NVIDIA repository https:__//nvidia.github.io/libnvidia-container/ (remove __ as links are not allowed). The repository also has instructions for how to install on Ubuntu 22.04.

Regards,
amit_code_aster

osman · 2022-07-09 04:26:52

I have ubuntu 22.04, nvidia rtx-3070Ti and the installation of nvidia-container-toolkit solved the problem of salome-meca only working with --soft option. Now, it works without --soft. Thanks for the info. This should be mentioned in the FAQ.

mpex · 2022-08-12 03:36:21

I'm experiencing a similar issue, though I don't have an NVIDIA GPU so I suspect the previously mentioned solutions will not work. Any suggestions?

*****************************************************
INFO : Running salome_meca in software rendering mode
*****************************************************
runSalome running on laptop
Searching for a free port for naming service: 2810 - OK
Searching Naming Service + found in 0.1 seconds
Searching /Kernel/Session in Naming Service +++SALOME_Session_Server: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /.singularity.d/libs/libGLX.so.0)
Traceback (most recent call last):
File "/opt/salome_meca/Salome-V2021-s9/modules/KERNEL_V9_7_0/bin/salome/orbmodule.py", line 181, in waitNSPID
os.kill(thePID,0)
ProcessLookupError: [Errno 3] No such process

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/opt/salome_meca/appli_V2021/bin/salome/runSalome.py", line 694, in useSalome
clt = startSalome(args, modules_list, modules_root_dir)
File "/opt/salome_meca/appli_V2021/bin/salome/runSalome.py", line 639, in startSalome
session=clt.waitNSPID("/Kernel/Session",mySessionServ.PID,SALOME.Session)
File "/opt/salome_meca/Salome-V2021-s9/modules/KERNEL_V9_7_0/bin/salome/orbmodule.py", line 183, in waitNSPID
raise RuntimeError("Process %d for %s not found" % (thePID,theName))
RuntimeError: Process 25480 for /Kernel/Session not found

--- Error during Salome launch ---

Humberto · 2022-08-12 23:57:49

Using Arch Linux
Dual GPU Inel + Nvidia
Same issue.
Works with --soft

**************************************
INFO : Running salome_meca in GPU mode
**************************************
runSalome running on archlinux
Searching for a free port for naming service: 2819 - OK
Searching Naming Service  + found in 0.1 seconds 
Searching /Kernel/Session in Naming Service  ++SALOME_Session_Server: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /.singularity.d/libs/libGLX.so.0)
Traceback (most recent call last):
  File "/opt/salome_meca/Salome-V2021-s9/modules/KERNEL_V9_7_0/bin/salome/orbmodule.py", line 181, in waitNSPID
    os.kill(thePID,0)
ProcessLookupError: [Errno 3] No such process

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/opt/salome_meca/appli_V2021/bin/salome/runSalome.py", line 694, in useSalome
    clt = startSalome(args, modules_list, modules_root_dir)
  File "/opt/salome_meca/appli_V2021/bin/salome/runSalome.py", line 639, in startSalome
    session=clt.waitNSPID("/Kernel/Session",mySessionServ.PID,SALOME.Session)
  File "/opt/salome_meca/Salome-V2021-s9/modules/KERNEL_V9_7_0/bin/salome/orbmodule.py", line 183, in waitNSPID
    raise RuntimeError("Process %d for %s not found" % (thePID,theName))
RuntimeError: Process 137243 for /Kernel/Session not found

Last edited by Humberto (2022-08-12 23:59:13)

amit_code_aster · 2022-09-06 12:29:09

Hi @Humberto.

A solution that worked for me on Fedora 36 is

1. Search for a file named `nvliblist.conf` in your installation. It should be under your Singularity installation directory somewhere.
2. Make a back-up of this file `mv nvliblist.conf nvliblist.conf.bak`.
3. Open the file `nvliblist.conf` using a text editor.
4. Delete the lines `libGLX.so.0`, `libglx.so.0`, and `libGLdispatch.so`.

Try running the Salome container again, it should work this time.

Reference: https: //github.com/apptainer/apptainer/issues/598

tomg · 2022-09-17 11:22:42

Hello,

I had the same problem with running in GPU mode:

/lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /.singularity.d/libs/libGLX.so.0)

I do not know if its a fix but if I commented the line in file /etc/singularity/nvliblist.conf with libGLX.so then Salome-Meca is running fine even in GPU mode. Colors seems a bit brighter but otherwise I have not noticed any other problems.

I am using Ubuntu 22 like distro (Linux Mint 21) and only thing I additionally installed were nvidia-drivers and latest singularity-ce deb package from sylabs github (package manager also automatically installed runc package).

I have to mention that with the same setup GPU mode works fine for me if ran on Mint 20 and that I have nvidia graphics card. Nvidia-container toolkit and so on mentioned on the other threads there did not work for me so I did not install them at all.

So what I did:
sudo nano /etc/singularity/nvliblist.conf

and there I edited the line with libGLX.so to:
#libGLX.so

Hope this will be helpful.

Tomas

#1 2022-05-08 07:18:28

singularity : GLIBC_2.34 not found

#2 2022-05-14 12:45:56

Re: singularity : GLIBC_2.34 not found

#3 2022-05-14 17:57:25

Re: singularity : GLIBC_2.34 not found

#4 2022-06-11 05:17:35

Re: singularity : GLIBC_2.34 not found

#5 2022-07-09 04:26:52

Re: singularity : GLIBC_2.34 not found

#6 2022-08-12 03:36:21

Re: singularity : GLIBC_2.34 not found

#7 2022-08-12 23:57:49

Re: singularity : GLIBC_2.34 not found

#8 2022-09-06 12:29:09

Re: singularity : GLIBC_2.34 not found

#9 2022-09-17 11:22:42

Re: singularity : GLIBC_2.34 not found

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