[slurm-users] slurm 17.11.2: Socket timed out on send/recv operation
Alessandro Federico
a.federico at cineca.it
Wed Jan 17 09:41:54 MST 2018
Hi John
thanks for the infos.
We are investigating the slowdown of sssd and I found some bug reports regarding slow sssd query
with almost the same backtrace. Hopefully an update of sssd could solve this issue.
We'll let you know if we found a solution.
thanks
ale
----- Original Message -----
> From: "John DeSantis" <desantis at usf.edu>
> To: "Alessandro Federico" <a.federico at cineca.it>
> Cc: "Slurm User Community List" <slurm-users at lists.schedmd.com>, "Isabella Baccarelli" <i.baccarelli at cineca.it>,
> hpc-sysmgt-info at cineca.it
> Sent: Wednesday, January 17, 2018 3:30:43 PM
> Subject: Re: [slurm-users] slurm 17.11.2: Socket timed out on send/recv operation
>
> Ale,
>
> > As Matthieu said it seems something related to SSS daemon.
>
> That was a great catch by Matthieu.
>
> > Moreover, only 3 SLURM partitions have the AllowGroups ACL
>
> Correct, which may seem negligent, but after each `scontrol
> reconfigure`, slurmctld restart, and/or AllowGroups= partition
> update,
> the mapping of UID's for each group will be updated.
>
> > So why does the UID-GID mapping take so long?
>
> We attempted to use "AllowGroups" previously, but we found (even with
> sssd.conf tuning regarding enumeration) that unless the group was
> local
> (/etc/group), we were experiencing delays before the AllowGroups
> parameter was respected. This is why we opted to use SLURM's
> AllowQOS/AllowAccounts instead.
>
> You would have to enable debugging on your remote authentication
> software to see where the hang-up is occurring (if it is that at all,
> and not just a delay with the slurmctld).
>
> Given the direction that this is going - why not replace the
> "AllowGroups" with either a simple "AllowAccounts=" or "AllowQOS="?
>
> > @John: we defined many partitions on the same nodes but in the
> > production cluster they will be more or less split across the 6K
> > nodes.
>
> Ok, that makes sense. Looking initially at your partition
> definitions,
> I immediately thought of being DRY, especially since the "finer"
> tuning
> between the partitions could easily be controlled via the QOS'
> allowed
> to access the resources.
>
> John DeSantis
>
> On Wed, 17 Jan 2018 13:20:49 +0100
> Alessandro Federico <a.federico at cineca.it> wrote:
>
> > Hi Matthieu & John
> >
> > this is the backtrace of slurmctld during the slowdown
> >
> > (gdb) bt
> > #0 0x00007fb0e8b1e69d in poll () from /lib64/libc.so.6
> > #1 0x00007fb0e8617bfa in sss_cli_make_request_nochecks ()
> > from /lib64/libnss_sss.so.2 #2 0x00007fb0e86185a3 in
> > sss_nss_make_request () from /lib64/libnss_sss.so.2 #3
> > 0x00007fb0e8619104 in _nss_sss_getpwnam_r ()
> > from /lib64/libnss_sss.so.2 #4 0x00007fb0e8aef07d in
> > getpwnam_r@@GLIBC_2.2.5 () from /lib64/libc.so.6 #5
> > 0x00007fb0e9360986 in _getpwnam_r (result=<optimized out>,
> > bufsiz=<optimized out>, buf=<optimized out>, pwd=<optimized out>,
> > name=<optimized out>) at uid.c:73 #6 uid_from_string
> > (name=0x1820e41
> > "g2bottin", uidp=uidp at entry=0x7fff07f03a6c) at uid.c:111 #7
> > 0x000000000043587d in get_group_members (group_name=0x10ac500 "g2")
> > at groups.c:139 #8 0x000000000047525a in _get_groups_members
> > (group_names=<optimized out>) at partition_mgr.c:2006 #9
> > 0x0000000000475505 in _update_part_uid_access_list
> > (x=0x7fb03401e650,
> > arg=0x7fff07f13bf4) at partition_mgr.c:1930 #10 0x00007fb0e92ab675
> > in
> > list_for_each (l=0x1763e50, f=f at entry=0x4754d8
> > <_update_part_uid_access_list>, arg=arg at entry=0x7fff07f13bf4) at
> > list.c:420 #11 0x000000000047911a in load_part_uid_allow_list
> > (force=1) at partition_mgr.c:1971 #12 0x0000000000428e5c in
> > _slurmctld_background (no_data=0x0) at controller.c:1911 #13 main
> > (argc=<optimized out>, argv=<optimized out>) at controller.c:601
> >
> > As Matthieu said it seems something related to SSS daemon.
> > However we don't notice any slowdown due to SSSd in our
> > environment.
> > As I told you before, we are just testing SLURM on a small 100
> > nodes
> > cluster before going into production with about 6000 nodes next
> > Wednesday. At present the other nodes are managed by PBSPro and the
> > 2
> > PBS servers are running on the same nodes as the SLURM controllers.
> > PBS queues are also configured with users/groups ACLs and we never
> > noticed any similar slowdown.
> >
> > Moreover, only 3 SLURM partitions have the AllowGroups ACL
> >
> > [root at mgmt01 slurm]# grep AllowGroups slurm.conf
> > PartitionName=bdw_fua_gwdbg Nodes=r040c03s0[1,2] Default=NO
> > DefMemPerCPU=3000 DefaultTime=00:30:00 MaxTime=00:30:00 State=UP
> > QOS=bdw_fua_gwdbg DenyQos=bdw_qos_special AllowGroups=g2
> > PartitionName=bdw_fua_gw Nodes=r040c03s0[1,2] Default=NO
> > DefMemPerCPU=3000 DefaultTime=00:30:00 MaxTime=48:00:00 State=UP
> > QOS=bdw_fua_gw DenyQos=bdw_qos_special AllowGroups=g2
> > PartitionName=bdw_fua_gwg2 Nodes=r040c03s0[1,2] Default=NO
> > DefMemPerCPU=3000 DefaultTime=00:30:00 MaxTime=168:00:00 State=UP
> > QOS=bdw_fua_gwg2 DenyQos=bdw_qos_special AllowGroups=g2
> >
> > So why does the UID-GID mapping take so long?
> >
> > @John: we defined many partitions on the same nodes but in the
> > production cluster they will be more or less split across the 6K
> > nodes.
> >
> > thank you very much
> > ale
> >
> > ----- Original Message -----
> > > From: "John DeSantis" <desantis at usf.edu>
> > > To: "Matthieu Hautreux" <matthieu.hautreux at gmail.com>
> > > Cc: hpc-sysmgt-info at cineca.it, "Slurm User Community List"
> > > <slurm-users at lists.schedmd.com>, "Isabella Baccarelli"
> > > <i.baccarelli at cineca.it> Sent: Tuesday, January 16, 2018 8:20:20
> > > PM
> > > Subject: Re: [slurm-users] slurm 17.11.2: Socket timed out on
> > > send/recv operation
> > >
> > > 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.hautreux at 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" <desantis at 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.federico at 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 at 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" <tcooper at sdsc.edu>
> > > > > > > To: "Slurm User Community List"
> > > > > > > <slurm-users at 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.federico at 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" <desantis at usf.edu>
> > > > > > > >> To: "Alessandro Federico" <a.federico at cineca.it>
> > > > > > > >> Cc: slurm-users at lists.schedmd.com, "Isabella
> > > > > > > >> Baccarelli"
> > > > > > > >> <i.baccarelli at cineca.it>, hpc-sysmgt-info at 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.federico at 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...
> > > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > >
> > > > >
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> > > > > Version: GnuPG v2
> > > > >
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> > > > >
> > >
> > >
> > >
> >
>
>
--
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...
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