[slurm-users] Slurm missing non primary group memberships

[Aravindh Sampathkumar]

Hello all.

I'm seeing something strange related to group memberships and how it
bothers Slurm. Appreciate any ideas to understand what is going on.
It appears that only the primary group of the user is propagated when
Slurm runs a job. The additional group memberships vanish. This is not
expected behaviour. I'm wondering if I'm missing any configuration
with slurm.
navtp at console2:~> id
uid=29865(navtp) gid=510(finland)
groups=510(finland),508(nav),5001(ghpc) context=unconfined_u:unconfined_r:unconfined_t:s0-
s0:c0.c1023
navtp at console2:~> ssh c07b07 id
uid=29865(navtp) gid=510(finland)
groups=510(finland),508(nav),5001(ghpc) context=unconfined_u:unconfined_r:unconfined_t:s0-
s0:c0.c1023
navtp at console2:~> srun -p nav hostname
slurmstepd: error: couldn't chdir to `/usr/home/nav/finland/navtp': Permission denied: going to /tmp insteadc07b07.ghpc.au.dk

navtp at console2:~> srun -p nav id
slurmstepd: error: couldn't chdir to `/usr/home/nav/finland/navtp': Permission denied: going to /tmp insteaduid=29865(navtp) gid=510(finland) groups=510(finland)
context=system_u:system_r:unconfined_service_t:s0navtp at console2:~>

Our cluster uses FreeIPA and hence sssd to provide central identity
management.
As you can see, the user - navtp is part of finland, nav, and ghpc
groups. finland being primary group.
when I ssh into a node directly, the groups are configured correctly as
shown by ssh command.
But, through Slurm the additional groups vanish. This means that the
user now cannot access some directories they normally would. I believe
this is also the reason for the slurmstepd errors.
How can I make Slurm retain all group memberships? 

Thanks,
Aravindh

--
  Aravindh Sampathkumar
  aravindh at fastmail.com


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