Thank you for that - I'm restricting things via limits.conf on the login
nodes at the moment, but have been considering using cgroups instead for
a while. So this is very useful :)
If we're sharing details, our setup currently is:
2x2 cluster not-quite-federations - prod and dev, each with a
'capability' and 'throughput' cluster.
The 'capability' system is homogeneous, and all nodes have low latency
interconnect; it prefers big jobs. The 'throughput' system is more
heterogeneous (it's where all the GPUs live, as well as some CPU only
nodes); it prefers small jobs.
(dev system has the same cluster config, but not the same resources,
obviously - it's for configuration testing, mostly, and for testing
upgrades)
Both 'federations' have one database server (server running mariadb and
slurmdbd) - so there's a 'prod' and a 'dev' database server.
All clusters have the same partitions & users & projects etc.
Each cluster has a dedicated hosts running slurmctld.
SLURM is installed locally - I build RPMs.
2 login nodes per prod cluster (only one overall for dev).
Apart from the actual worker nodes, all of these are VMs. I have no
secondary slurmctlds or anything as I'm more or less relying on the
VMWare cluster to handle this. (And we've done live migrations on the
VMWare end without problems.) The login nodes are doubled up as they get
rebooted for security updates regularly, so to ensure people can always
log in we double those up.
Login nodes are not (!) on the same OS release as cluster nodes - they
run the latest for security reasons. Software building etc happens on
'interactive' nodes (...a partition that oversubscribes by default).
Nodes mount application shares by hardware architecture (skylake,
broadwell, ...) - using autofs variables to pick up the correct share,
so applications have the same path on all nodes, but what's mounted is
the correct build for the local architecture. (Using Easybuild & lmod
for applications.)
Updates always need to be database first, of course (don't they always);
however,I can't quite confirm binaries not working with after upgrading
the database - we ran with a 20.11 database server & 20.02 everything
else for a fair while (the change in MPI behaviour had us downgrade
everything apart from the database), so I've only ever seen the '-M'
(and all accounting) not work during DB restarts.
They were meant to actually be federated, but it confused our users, so
I broke the federation again (but left the rest of the setup in place).
Tina
On 01/11/2021 10:35, Yair Yarom wrote:
cpu limit using ulimit is pretty straightforward with pam_limits and
/etc/security/limits.conf. On some of the login nodes we have a cpu
limit of 10 minutes, so heavy processes will fail.
The memory was a bit more complicated (i.e. not pretty). We wanted that
a user won't be able to use more than e.g. 1G for all processes
combined. Using systemd we added the file
/etc/systemd/system/user-.slice.d/20-memory.conf which contains:
[Slice]
MemoryLimit=1024M
MemoryAccounting=true
But we also wanted to restrict swap usage and we're still on cgroupv1,
so systemd didn't help there. The ugly part comes with a pam_exec to a
script that updates the memsw limit of the cgroup for the above slice.
The script does more things, but the swap section is more or less:
if [ "x$PAM_TYPE" = 'xopen_session' ]; then
_id=`id -u $PAM_USER`
if [ -z "$_id" ]; then
exit 1
fi
if [[ -e
/sys/fs/cgroup/memory/user.slice/user-${_id}.slice/memory.memsw.limit_in_bytes
]]; then
swap=$((1126 * 1024 * 1024))
echo $swap >
/sys/fs/cgroup/memory/user.slice/user-${_id}.slice/memory.memsw.limit_in_bytes
fi
fi
On Sun, Oct 31, 2021 at 6:36 PM Brian Andrus <toomuc...@gmail.com
<mailto:toomuc...@gmail.com>> wrote:
That is interesting to me.
How do you use ulimit and systemd to limit user usage on the login
nodes? This sounds like something very useful.
Brian Andrus
On 10/31/2021 1:08 AM, Yair Yarom wrote:
Hi,
If it helps, this is our setup:
6 clusters (actually a bit more)
1 mysql + slurmdbd on the same host
6 primary slurmctld on 3 hosts (need to make sure each have a
distinct SlurmctldPort)
6 secondary slurmctld on an arbitrary node on the clusters themselves.
1 login node per cluster (this is a very small VM, and the users
are limited both to cpu time (with ulimit) and memory (with systemd))
The slurm.conf's are shared on nfs to everyone in
/path/to/nfs/<cluster name>/slurm.conf. With symlink to /etc for
the relevant cluster per node.
The -M generally works, we can submit/query jobs from a login node
of one cluster to another. But there's a caveat to notice when
upgrading. slurmdbd must be upgraded first, but usually we have a
not so small gap between upgrading the different clusters. This
causes the -M to stop working because binaries of one version
won't work on the other (I don't remember in which direction).
We solved this by using an lmod module per cluster, which both
sets the SLURM_CONF environment, and the PATH to the correct slurm
binaries (which we install in /usr/local/slurm/<version>/ so that
they co-exists). So when the -M won't work, users can use:
module load slurm/clusterA
squeue
module load slurm/clusterB
squeue
BR,
On Thu, Oct 28, 2021 at 7:39 PM navin srivastava
<navin.alt...@gmail.com <mailto:navin.alt...@gmail.com>> wrote:
Thank you Tina.
It will really help
Regards
Navin
On Thu, Oct 28, 2021, 22:01 Tina Friedrich
<tina.friedr...@it.ox.ac.uk
<mailto:tina.friedr...@it.ox.ac.uk>> wrote:
Hello,
I have the database on a separate server (it runs the
database and the
database only). The login nodes run nothing SLURM related,
they simply
have the binaries installed & a SLURM config.
I've never looked into having multiple databases & using
AccountingStorageExternalHost (in fact I'd forgotten you
could do that),
so I can't comment on that (maybe someone else can); I
think that works,
yes, but as I said never tested that (didn't see much
point in running
multiple databases if one would do the job).
I actually have specific login nodes for both of my
clusters, to make it
easier for users (especially those with not much
experience using the
HPC environment); so I have one login node connecting to
cluster 1 and
one connecting to cluster 1.
I think the relevant bits of slurm.conf Relevant config
entries (if I'm
not mistaken) on the login nodes are probably:
The differences in the slurm config files (that haven't
got to do with
topology & nodes & scheduler tuning) are
ClusterName=cluster1
ControlMachine=cluster1-slurm
ControlAddr=/IP_OF_SLURM_CONTROLLER/
ClusterName=cluster2
ControlMachine=cluster2-slurm
ControlAddr=/IP_OF_SLURM_CONTROLLER/
(where IP_OF_SLURM_CONTROLLER is the IP address of host
cluster1-slurm,
same for cluster2)
And then the have common entries for the
AccountingStorageHost:
AccountingStorageHost=slurm-db-prod
AccountingStorageBackupHost=slurm-db-prod
AccountingStoragePort=7030
AccountingStorageType=accounting_storage/slurmdbd
(slurm-db-prod is simply the hostname of the SLURM
database server)
Does that help?
Tina
On 28/10/2021 14:59, navin srivastava wrote:
> Thank you Tina.
>
> so if i understood correctly.Database is global to both
cluster and
> running on login Node?
> or is the database running on one of the master Node and
shared with
> another master server Node?
>
> but as far I have read that the slurm database can also
be separate on
> both the master and just use the parameter
> AccountingStorageExternalHost so that both databases are
aware of each
> other.
>
> Also on the login node in slurm .conf file pointed to
which Slurmctld?
> is it possible to share the sample slurm.conf file of
login Node.
>
> Regards
> Navin.
>
>
>
>
>
>
>
>
> On Thu, Oct 28, 2021 at 7:06 PM Tina Friedrich
> <tina.friedr...@it.ox.ac.uk
<mailto:tina.friedr...@it.ox.ac.uk>
<mailto:tina.friedr...@it.ox.ac.uk
<mailto:tina.friedr...@it.ox.ac.uk>>> wrote:
>
> Hi Navin,
>
> well, I have two clusters & login nodes that allow
access to both. That
> do? I don't think a third would make any difference
in setup.
>
> They need to share a database. As long as the share
a database, the
> clusters have 'knowledge' of each other.
>
> So if you set up one database server (running
slurmdbd), and then a
> SLURM controller for each cluster (running
slurmctld) using that one
> central database, the '-M' option should work.
>
> Tina
>
> On 28/10/2021 10:54, navin srivastava wrote:
> > Hi ,
> >
> > I am looking for a stepwise guide to setup multi
cluster
> implementation.
> > We wanted to set up 3 clusters and one Login Node
to run the job
> using
> > -M cluster option.
> > can anybody have such a setup and can share some
insight into how it
> > works and it is really a stable solution.
> >
> >
> > Regards
> > Navin.
>
> --
> Tina Friedrich, Advanced Research Computing Snr HPC
Systems
> Administrator
>
> Research Computing and Support Services
> IT Services, University of Oxford
> http://www.arc.ox.ac.uk <http://www.arc.ox.ac.uk>
<http://www.arc.ox.ac.uk <http://www.arc.ox.ac.uk>>
> http://www.it.ox.ac.uk <http://www.it.ox.ac.uk>
<http://www.it.ox.ac.uk <http://www.it.ox.ac.uk>>
>
--
Tina Friedrich, Advanced Research Computing Snr HPC
Systems Administrator
Research Computing and Support Services
IT Services, University of Oxford
http://www.arc.ox.ac.uk <http://www.arc.ox.ac.uk>
http://www.it.ox.ac.uk <http://www.it.ox.ac.uk>
--
/| |
\/ |Yair Yarom | System Group (DevOps)
[] |The Rachel and Selim Benin School
[] /\ |of Computer Science and Engineering
[]//\\/ |The Hebrew University of Jerusalem
[// \\ |T +972-2-5494522 | F +972-2-5494522
// \ |ir...@cs.huji.ac.il <mailto:ir...@cs.huji.ac.il>
// |
--
/| |
\/ |Yair Yarom | System Group (DevOps)
[] |The Rachel and Selim Benin School
[] /\ |of Computer Science and Engineering
[]//\\/ |The Hebrew University of Jerusalem
[// \\ |T +972-2-5494522 | F +972-2-5494522
// \ |ir...@cs.huji.ac.il <mailto:ir...@cs.huji.ac.il>
// |
--
Tina Friedrich, Advanced Research Computing Snr HPC Systems Administrator
Research Computing and Support Services
IT Services, University of Oxford
http://www.arc.ox.ac.uk http://www.it.ox.ac.uk
