Matthieu,
> I would bet on something like LDAP requests taking too much time
> because of a missing sssd cache.
Good point! It's easy to forget to check something as "simple" as user
look-up when something is taking "too long".
John DeSantis
On Tue, 16 Jan 2018 19:13:06 +0100
Matthieu Hautreux <matthieu.hautr...@gmail.com> wrote:
> Hi,
>
> In this kind if issues, one good thing to do is to get a backtrace of
> slurmctld during the slowdown. You should thus easily identify the
> subcomponent responsible for the issue.
>
> I would bet on something like LDAP requests taking too much time
> because of a missing sssd cache.
>
> Regards
> Matthieu
>
> Le 16 janv. 2018 18:59, "John DeSantis" <desan...@usf.edu> a écrit :
>
> > -----BEGIN PGP SIGNED MESSAGE-----
> > Hash: SHA512
> >
> > Ciao Alessandro,
> >
> > > setting MessageTimeout to 20 didn't solve it :(
> > >
> > > looking at slurmctld logs I noticed many warning like these
> > >
> > > Jan 16 05:11:00 r000u17l01 slurmctld[22307]: Warning: Note very
> > > large processing time from _slurm_rpc_dump_partitions:
> > > usec=42850604 began=05:10:17.289 Jan 16 05:20:58 r000u17l01
> > > slurmctld[22307]: Warning: Note very large processing time from
> > > load_part_uid_allow_list: usec=44861325 began=05:20:13.257 Jan 16
> > > 05:20:58 r000u17l01 slurmctld[22307]: Warning: Note very large
> > > processing time from _slurmctld_background: usec=44861653
> > > began=05:20:13.257
> >
> > And:
> >
> > > 271 Note very large processing time from
> > > _slurm_rpc_dump_partitions: 67 Note very large processing time
> > > from load_part_uid_allow_list:
> >
> > I believe these values are in microseconds, so an average of 44
> > seconds per call, mostly related to partition information. Given
> > that our configuration has the maximum value set of 90 seconds, I'd
> > again recommend another adjustment, perhaps to 60 seconds.
> >
> > I'm not sure if redefining your partitions will help, but you do
> > have several partitions which contain the same set of nodes that
> > could be condensed - decreasing the amount of partitions. For
> > example, the partitions bdw_all_serial & bdw_all_rcm could be
> > consolidated into a single partition by:
> >
> > 1.) Using AllowQOS=bdw_all_serial,bdw_all_rcm;
> > 2.) Setting MaxTime to 04:00:00 and defining a MaxWall via each QOS
> > (since one partition has 04:00:00 and the other 03:00:00).
> >
> > The same could be done for the partitions
> > skl_fua_{prod,bprod,lprod} as well.
> >
> > HTH,
> > John DeSantis
> >
> >
> > On Tue, 16 Jan 2018 11:22:44 +0100
> > Alessandro Federico <a.feder...@cineca.it> wrote:
> >
> > > Hi,
> > >
> > > setting MessageTimeout to 20 didn't solve it :(
> > >
> > > looking at slurmctld logs I noticed many warning like these
> > >
> > > Jan 16 05:11:00 r000u17l01 slurmctld[22307]: Warning: Note very
> > > large processing time from _slurm_rpc_dump_partitions:
> > > usec=42850604 began=05:10:17.289 Jan 16 05:20:58 r000u17l01
> > > slurmctld[22307]: Warning: Note very large processing time from
> > > load_part_uid_allow_list: usec=44861325 began=05:20:13.257 Jan 16
> > > 05:20:58 r000u17l01 slurmctld[22307]: Warning: Note very large
> > > processing time from _slurmctld_background: usec=44861653
> > > began=05:20:13.257
> > >
> > > they are generated in many functions:
> > >
> > > [root@r000u17l01 ~]# journalctl -u slurmctld --since='2018-01-16
> > > 00:00:00' | grep -oP 'Note very large processing time from \w+:'
> > > | sort | uniq -c 4 Note very large processing time from
> > > dump_all_job_state: 67 Note very large processing time from
> > > load_part_uid_allow_list: 67 Note very large processing time from
> > > _slurmctld_background: 7 Note very large processing time from
> > > _slurm_rpc_complete_batch_script: 4 Note very large processing
> > > time from _slurm_rpc_dump_jobs: 3 Note very large processing time
> > > from _slurm_rpc_dump_job_user: 271 Note very large processing
> > > time from _slurm_rpc_dump_partitions: 5 Note very large
> > > processing time from _slurm_rpc_epilog_complete: 1 Note very
> > > large processing time from _slurm_rpc_job_pack_alloc_info: 3 Note
> > > very large processing time from _slurm_rpc_step_complete:
> > >
> > > processing times are always around tens of seconds.
> > >
> > > I'm attaching sdiag output and slurm.conf.
> > >
> > > thanks
> > > ale
> > >
> > > ----- Original Message -----
> > > > From: "Trevor Cooper" <tcoo...@sdsc.edu>
> > > > To: "Slurm User Community List" <slurm-users@lists.schedmd.com>
> > > > Sent: Tuesday, January 16, 2018 12:10:21 AM
> > > > Subject: Re: [slurm-users] slurm 17.11.2: Socket timed out on
> > > > send/recv operation
> > > >
> > > > Alessandro,
> > > >
> > > > You might want to consider tracking your Slurm scheduler
> > > > diagnostics output with some type of time-series monitoring
> > > > system. The time-based history has proven more helpful at times
> > > > than log contents by themselves.
> > > >
> > > > See Giovanni Torres' post on setting this up...
> > > >
> > > > http://giovannitorres.me/graphing-sdiag-with-graphite.html
> > > >
> > > > -- Trevor
> > > >
> > > > > On Jan 15, 2018, at 4:33 AM, Alessandro Federico
> > > > > <a.feder...@cineca.it> wrote:
> > > > >
> > > > > Hi John
> > > > >
> > > > > thanks for the info.
> > > > > slurmctld doesn't report anything about the server thread
> > > > > count in the logs
> > > > > and sdiag show only 3 server threads.
> > > > >
> > > > > We changed the MessageTimeout value to 20.
> > > > >
> > > > > I'll let you know if it solves the problem.
> > > > >
> > > > > Thanks
> > > > > ale
> > > > >
> > > > > ----- Original Message -----
> > > > >> From: "John DeSantis" <desan...@usf.edu>
> > > > >> To: "Alessandro Federico" <a.feder...@cineca.it>
> > > > >> Cc: slurm-users@lists.schedmd.com, "Isabella Baccarelli"
> > > > >> <i.baccare...@cineca.it>, hpc-sysmgt-i...@cineca.it
> > > > >> Sent: Friday, January 12, 2018 7:58:38 PM
> > > > >> Subject: Re: [slurm-users] slurm 17.11.2: Socket timed out on
> > > > >> send/recv operation
> > > > >>
> > > > >> Ciao Alessandro,
> > > > >>
> > > > >>> Do we have to apply any particular setting to avoid
> > > > >>> incurring the problem?
> > > > >>
> > > > >> What is your "MessageTimeout" value in slurm.conf? If it's
> > > > >> at the default of 10, try changing it to 20.
> > > > >>
> > > > >> I'd also check and see if the slurmctld log is reporting
> > > > >> anything pertaining to the server thread count being over
> > > > >> its limit.
> > > > >>
> > > > >> HTH,
> > > > >> John DeSantis
> > > > >>
> > > > >> On Fri, 12 Jan 2018 11:32:57 +0100
> > > > >> Alessandro Federico <a.feder...@cineca.it> wrote:
> > > > >>
> > > > >>> Hi all,
> > > > >>>
> > > > >>>
> > > > >>> we are setting up SLURM 17.11.2 on a small test cluster of
> > > > >>> about 100
> > > > >>> nodes. Sometimes we get the error in the subject when
> > > > >>> running any SLURM command (e.g. sinfo, squeue, scontrol
> > > > >>> reconf, etc...)
> > > > >>>
> > > > >>>
> > > > >>> Do we have to apply any particular setting to avoid
> > > > >>> incurring the problem?
> > > > >>>
> > > > >>>
> > > > >>> We found this bug report
> > > > >>> https://bugs.schedmd.com/show_bug.cgi?id=4002 but it
> > > > >>> regards the previous SLURM version and we do not set debug3
> > > > >>> on slurmctld.
> > > > >>>
> > > > >>>
> > > > >>> thanks in advance
> > > > >>> ale
> > > > >>>
> > > > >>
> > > > >>
> > > > >
> > > > > --
> > > > > Alessandro Federico
> > > > > HPC System Management Group
> > > > > System & Technology Department
> > > > > CINECA www.cineca.it
> > > > > Via dei Tizii 6, 00185 Rome - Italy
> > > > > phone: +39 06 44486708
> > > > >
> > > > > All work and no play makes Jack a dull boy.
> > > > > All work and no play makes Jack a dull boy.
> > > > > All work and no play makes Jack...
> > > > >
> > > >
> > > >
> > > >
> > >
> >
> > -----BEGIN PGP SIGNATURE-----
> > Version: GnuPG v2
> >
> > iQEcBAEBCgAGBQJaXjxzAAoJEEmckBqrs5nB9FQH/Rq6avZRXV0r1qQhSBH514J6
> > vHWzGAgVSvBrpxFrtfu3aVTK6fk3bFahB9t2jtVJlg0HgO8dm3Gj6FMNo0nDyemD
> > NlIePvvXGwZYXeXlif+OtCTu/3fOqvuol1jX8/iXcG89Lm+HA92BhLKPYoqzWsK4
> > KQ/m8Mlj91Ei3GRZorZfyZrRrfAYNatIV2plmRaGWmuH39MEwQ0bF/qQhci/LAXB
> > xquAZWAVeSE1uWThXPS4sbzmHjNuenT9RqlGtgQOEMO4z/bHFQwmMVuxqfmS537h
> > /93icpAcWhJQ1bYe51ePykWk3Jkv901Z7Cr6bG1+hu2asN1loFzz38YugHUcfBs=
> > =VWA7
> > -----END PGP SIGNATURE-----
> >
