Yeah this one is tricky. In general we take the wildwest approach here,
but I've had users use --contiguous and their job takes forever to run.
I suppose one method would would be enforce that each job take a full
node and parallel jobs always have contiguous. As I recall Slurm will
preferentially fill up nodes to try to leave as large of contiguous
blocks as it can.
The other other option would be to use requeue to your advantage.
Namely just have a high priority queue only for large contiguous jobs
and it just requeues all the jobs it needs to to run. That would depend
on your single node/core users tolerances for being requeued.
-Paul Edmon-
On 06/08/2018 03:55 AM, John Hearns via Beowulf wrote:
Chris, good question. I can't give a direct asnwer there, but let me
share my experiences.
In the past I managed SGI ICE clusters and a large memory UV system
with PBSPro queuing.
The engineers submitted CFD solver jobs using scripts, and we only
allowed them to use a multiple of N cpus,
in fact there were queues named after lets say 2N or 4N cpu cores. The
number of cores were cunningly arranged to fit into
what SGI term an IRU, or everyone else would call a blade chassis.
We had job exclusivity, and engineers were not allowed to choose how
many CPUs they used.
This is a very efficient way to run HPC - as you have a clear view of
how many jobs fit on a cluster.
Yes, before you say it this does not cater for the mixed workload with
lots of single CPU jobs, Matlab, Python etc....
When the UV arrived I configured bladesets (placement sets) such that
the scheduler tried to allocate CPUs and memory from blades
adjacent to each other. Again much better efficiency. If I'm not wrong
you do that in Slurm by defining switches.
When the high core count AMDs came along again I configured blade sets
and the number of CPUs per job was increased to cope with
larger core count CPUs but again cunningly arranged to equal the
number of cores in a placement set (placement sets were configured to be
half, full or two IRUs)
At another place of employment recently we had a hugely mixed
workload, ranging from interactive graphics, to the Matlab type jobs,
to multinode CFD jobs. In addition to that we had different CPU
generations and GPUs in the mix.
That setup was a lot harder to manage and keep up the efficiency of
use, as you can imagine.
I agree with you about the overlapping partitions. If I was to arrange
things in my ideal worls, I would have a set of the latest generation CPUs
using the latest generation interconnect and reserve them for 'job
exclusive' jobs - ie parallel jobs, and leave other nodes exclusively for
one node or one core jobs.
Then have some mechanism to grow/shrink the partitions.
Ont thing again which I found difficult in my last job was users 'hard
wiring' the number of CPUs they use. In fact I have seen that quite
often on other projects.
What happens is that a new Phd or Postdoc or new engineer is gifted a
job submission script from someone who is leaving, or moving on.
The new person doesnt really understand why (say) six nodes with eight
CPU cores are requested.
But (a) they just want to get on and do the job (b) they are scared of
breaking things by altering the script.
So the number of CPUs doesnt change and with the latest generation
20plus cores on a node you get wasted cores.
Also having mixed generations of CPUs with different core counts does
not help here.
Yes I know we as HPC admins can easily adjust job scripts to mpirun
with N equal to the number of cores on a node (etc).
In fact when I have worked with users and showed them how to do this
it has been a source of satisfaction to me.
On 8 June 2018 at 09:21, Chris Samuel <ch...@csamuel.org
<mailto:ch...@csamuel.org>> wrote:
Hi all,
I'm curious to know what/how/where/if sites do to try and reduce
the impact of
fragmentation of resources by small/narrow jobs on systems where
you also have
to cope with large/wide parallel jobs?
For my purposes a small/narrow job is anything that will fit on
one node
(whether a single core job, multi-threaded or MPI).
One thing we're considering is to use overlapping partitions in
Slurm to have
a subset of nodes that are available to these types of jobs and
then have
large parallel jobs use a partition that can access any node.
This has the added benefit of letting us set a higher priority on
that
partition to let Slurm try and place those jobs first, before
smaller ones.
We're already using a similar scheme for GPU jobs where they get
put into a
partition that can access all 36 cores on a node whereas non-GPU
jobs get put
into a partition that can only access 32 cores on a node, so
effectively we
reserve 4 cores a node for GPU jobs.
But really I'm curious to know what people do about this, or do
you not worry
about it at all and just let the scheduler do its best?
All the best,
Chris
--
Chris Samuel : http://www.csamuel.org/ : Melbourne, VIC
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