Hi Marcus, Thank you for your reply. Your comments regarding the oom_killer sounds interesting. Looking at the slurmd logs on the serial nodes I see that the oom_killer is very active on a typical day, and so I suspect you're likely on to something there. As you might expect memory is configured as a resource on these shared nodes and users should take care to request sufficient memory for their job. More often than none I guess that users are wrongly assuming that the default memory allocation is sufficient.
Best regards, David ________________________________ From: Marcus Wagner <wag...@itc.rwth-aachen.de> Sent: 06 November 2019 09:53 To: David Baker <d.j.ba...@soton.ac.uk>; slurm-users@lists.schedmd.com <slurm-users@lists.schedmd.com>; juergen.s...@uni-ulm.de <juergen.s...@uni-ulm.de> Subject: Re: [slurm-users] Running job using our serial queue Hi David, if I remember right (we have disabled swap for years now), swapping out processes seem to slow down the system overall. But I know, that if the oom_killer does its job (killing over memory processes), the whole system is stalled until it has done its work. This might be the issue, your users see. Hwloc at least should help the scheduler to decide, where to place processes, but if I remember right, slurm has to be built with hwloc support (meaning at least hwloc-devel has to be installed). But this part is more guessing, than knowing. Best Marcus On 11/5/19 11:58 AM, David Baker wrote: Hello, Thank you for your replies. I double checked that the "task" in, for example, taskplugin=task/affinity is optional. In this respect it is good to know that we have the correct cgroups setup. So in theory users should only disturb themselves, however in reality we find that there is often a knock on effect on other users' jobs. So, for example, users have complained that their jobs sometimes stall. I can only vaguely think that something odd is going on at the kernel level perhaps. One additional thing that I need to ask is... Should we have hwloc installed our compute nodes? Does that help? Whenever I check which processes are not being constrained by cgroups I only ever find a small group of system processes. Best regards, David ________________________________ From: slurm-users <slurm-users-boun...@lists.schedmd.com><mailto:slurm-users-boun...@lists.schedmd.com> on behalf of Marcus Wagner <wag...@itc.rwth-aachen.de><mailto:wag...@itc.rwth-aachen.de> Sent: 05 November 2019 07:47 To: slurm-users@lists.schedmd.com<mailto:slurm-users@lists.schedmd.com> <slurm-users@lists.schedmd.com><mailto:slurm-users@lists.schedmd.com> Subject: Re: [slurm-users] Running job using our serial queue Hi David, doing it the way you do it, is the same way, we do it. When the Matlab job asks for one CPU, it only gets on CPU this way. That means, that all the processes are bound to this one CPU. So (theoretically) the user is just disturbing himself, if he uses more. But especially Matlab, there are more things to do. I t does not suffice to add '-singleCompThread' to the commandline. Matlab is not the only tool, that tries to use all cores, it finds on the node. The same is valid for CPLEX and Gurobi, both often used from Matlab. So even, if the user sets '-singleCompThread' for Matlab, that does not mean at all, the job is only using one CPU. Best Marcus On 11/4/19 4:14 PM, David Baker wrote: Hello, We decided to route all jobs requesting from 1 to 20 cores to our serial queue. Furthermore, the nodes controlled by the serial queue are shared by multiple users. We did this to try to reduce the level of fragmentation across the cluster -- our default "batch" queue provides exclusive access to compute nodes. It looks like the downside of the serial queue is that jobs from different users can interact quite badly. To some extent this is an education issue -- for example matlab users need to be told to add the "-singleCompThread" option to their command line. On the other hand I wonder if our cgroups setup is optimal for the serial queue. Our cgroup.conf contains... CgroupAutomount=yes CgroupReleaseAgentDir="/etc/slurm/cgroup" ConstrainCores=yes ConstrainRAMSpace=yes ConstrainDevices=yes TaskAffinity=no CgroupMountpoint=/sys/fs/cgroup The relevant cgroup configuration in the slurm.conf is... ProctrackType=proctrack/cgroup TaskPlugin=affinity,cgroup Could someone please advise us on the required/recommended cgroup setup for the above scenario? For example, should we really set "TaskAffinity=yes"? I assume the interaction between jobs (sometimes jobs can get stalled) is due to context switching at the kernel level, however (apart from educating users) how can we minimise that switching on the serial nodes? Best regards, David -- Marcus Wagner, Dipl.-Inf. IT Center Abteilung: Systeme und Betrieb RWTH Aachen University Seffenter Weg 23 52074 Aachen Tel: +49 241 80-24383 Fax: +49 241 80-624383 wag...@itc.rwth-aachen.de<mailto:wag...@itc.rwth-aachen.de> www.itc.rwth-aachen.de<https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.itc.rwth-aachen.de&data=01%7C01%7CD.J.Baker%40soton.ac.uk%7Ccf7d7c5b2f294965e06f08d7629f3040%7C4a5378f929f44d3ebe89669d03ada9d8%7C0&sdata=%2FKhU1fdr86GJemYcUWEzW23zh2LALjgLXntiB5MXy%2FA%3D&reserved=0> -- Marcus Wagner, Dipl.-Inf. 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