[slurm-users] Problem with permisions. CentOS 7.8

Tue Jun 2 17:19:08 UTC 2020

Mmm... What I did was install all rpms in the calculation nodes (similarly
as install all rpms in the controller node), but running on them slurmd
only.

I think you're aware that munge should be running in the calculation nodes,
the munge.key should be the same in all nodes, slurm configuration files
should be the same in all nodes. Directories and files should have the same
permissions as in the controller node, the slurm user should have the same
UID and GID as in the controller node. Pretty much install slurm in the
calculation nodes as if they were the controller node. The difference will
be that the slurm.conf will tell slurmctld which is the controller and
which are the calculation nodes.

Example:
ControlMachine=hostname
ControlAddr=XXX.XXX.XXX.0

# the calc nodes
NodeName=n[001-016] NodeAddr=XXX.XXX.XXX.[1-16] CPUs=28 RealMemory=64315
Sockets=2 CoresPerSocket=14 ThreadsPerCore=1 State=IDLE
PartitionName=slim Nodes=n[001-016] Default=YES MaxTime=INFINITE State=UP

El mar., 2 jun. 2020 a las 12:57, Ferran Planas Padros (<ferran.padros at su.se>)
escribió:

> Hi,
>
>
> Thanks for your answer,
>
>
> However, I am setting up a calculating node, not the master node, and thus
> I have not installed slurmctld on it.
>
>
> After some digging, I have found that all these files:
>
> /run/systemd/generator.late/slurm.service
>
> /run/systemd/generator.late/runlevel5.target.wants/slurm.service
>
> /run/systemd/generator.late/runlevel4.target.wants/slurm.service
>
> /run/systemd/generator.late/runlevel3.target.wants/slurm.service
>
> /run/systemd/generator.late/runlevel2.target.wants/slurm.service
>
> Which are a copy of each other and are generated by systemd-sysv-generator,
> point to the slurmctld.pid, not to the slurm.pid
>
>
> [Unit]
>
> Documentation=man:systemd-sysv-generator(8)
>
> SourcePath=/etc/rc.d/init.d/slurm
>
> Description=LSB: slurm daemon management
>
> Before=runlevel2.target
>
> Before=runlevel3.target
>
> Before=runlevel4.target
>
> Before=runlevel5.target
>
> Before=shutdown.target
>
> After=remote-fs.target
>
> After=network-online.target
>
> After=munge.service
>
> After=nss-lookup.target
>
> After=network-online.target
>
> Wants=network-online.target
>
> Conflicts=shutdown.target
>
>
> [Service]
>
> Type=forking
>
> Restart=no
>
> TimeoutSec=5min
>
> IgnoreSIGPIPE=no
>
> KillMode=process
>
> GuessMainPID=no
>
> RemainAfterExit=no
>
> *PIDFile=/var/run/slurmctld.pid*
>
> ExecStart=/etc/rc.d/init.d/slurm start
>
> ExecStop=/etc/rc.d/init.d/slurm stop
>
> ~
>
>
> How can I make it to avoid this? Besides editing the files manually, which
> will go back to the original after reboot.
>
>
> Thanks,
>
> Ferran
>
> ------------------------------
> *From:* slurm-users <slurm-users-bounces at lists.schedmd.com> on behalf of
> Rodrigo Santibáñez <rsantibanez.uchile at gmail.com>
> *Sent:* Tuesday, June 2, 2020 6:40:48 PM
> *To:* Slurm User Community List
> *Subject:* Re: [slurm-users] Problem with permisions. CentOS 7.8
>
> Yes, you have both daemons, installed with the slurm rpm.The slurmd (all
> nodes) communicates with slurmctld (runs in the main master node and,
> optionally, in a backup node).
>
> You do not need to run slurmd as the slurm user. Use `systemctld enable
> slurmctld` (and slurmd) followed by `systemclt start slurmctld`. Use
> restart instead of start if you change the configuration only if `sudo
> scontrol reconfigure` asks for it.
>
> If you run as root `slurmctld -Dvvvv` and `slurmd -Dvvvv` you'll see debug
> outputs to see further problems with configuration. The slurmd needs
> slurmctld running or will output "error: Unable to register: Unable to
> contact slurm controller (connect failure)"
>
> You should find the services here:
> -rw-r--r-- 1 root root 339 may 30 20:18
> /usr/lib/systemd/system/slurmctld.service
> -rw-r--r-- 1 root root 342 may 30 20:18
> /usr/lib/systemd/system/slurmdbd.service
> -rw-r--r-- 1 root root 398 may 30 20:18
> /usr/lib/systemd/system/slurmd.service
>
> Feel free to ask for more information,
> Best regards
>
> El mar., 2 jun. 2020 a las 11:12, Ferran Planas Padros (<
> ferran.padros at su.se>) escribió:
>
>>
>> Hi Ole,
>>
>>
>> Thanks for your answer and your time. I'd appreciate if you, or someone
>> else, could make a final look at my case.
>>
>> After your suggestions and comments, I have re-done the whole
>> installation for Munge and Slurm. I uninstalled and remoced all
>> previous rpms and restarted from scratch. Munge works with no problem,
>> however it does not happen the same with slurm (for which I have used the
>> instructions given in the link you attached)
>>
>>
>> - If I run /usr/bin/slurmd -D vvvvv as root user, I get the verbose until
>> the line 'slurmd: debug2: No acct_gather.conf file
>> (/etc/slurm/acct_gather.conf)' where the verbose stops. After I do
>> Ctrl+C, I get
>>
>>
>> slurmd: all threads complete
>>
>> slurmd: Consumable Resources (CR) Node Selection plugin shutting down ...
>>
>> slurmd: Munge cryptographic signature plugin unloaded
>>
>> slurmd: Slurmd shutdown completing
>>
>> - After that, if I run 'systemctl start slurmd' and 'systemctl status
>> slurmd', also as root user, I get:
>>
>> *●* slurmd.service - Slurm node daemon
>>
>>    Loaded: loaded (/etc/systemd/system/slurmd.service; enabled; vendor
>> preset: disabled)
>>
>>    Active: *active (running)* since Tue 2020-06-02 16:53:51 CEST; 33s ago
>>
>>   Process: 2750 ExecStart=/usr/sbin/slurmd -d /usr/sbin/slurmstepd
>> $SLURMD_OPTIONS (code=exited, status=0/SUCCESS)
>>
>>  Main PID: 2752 (slurmd)
>>
>>    CGroup: /system.slice/slurmd.service
>>
>>            └─2752 /usr/sbin/slurmd -d /usr/sbin/slurmstepd
>>
>>
>> Jun 02 16:53:51 roos21.organ.su.se systemd[1]: Starting Slurm node
>> daemon...
>>
>> Jun 02 16:53:51 roos21.organ.su.se systemd[1]: Can't open PID file
>> /var/run/slurm/slurmd.pid (yet?) after start: No such file or directory
>>
>> Jun 02 16:53:51 roos21.organ.su.se systemd[1]: Started Slurm node daemon.
>>
>> - Next, I kill the slurmd process, and I run, as slurm user, 'systemctl
>> start slurm'. Which does not work and returns the following in the
>> journalctl -xe:
>>
>>
>> Jun 02 16:56:01 roos21.organ.su.se systemd[1]: Starting LSB: slurm
>> daemon management...
>>
>> -- Subject: Unit slurm.service has begun start-up
>>
>> -- Defined-By: systemd
>>
>> -- Support: http://lists.freedesktop.org/mailman/listinfo/systemd-devel
>>
>> --
>>
>> -- Unit slurm.service has begun starting up.
>>
>> Jun 02 16:56:01 roos21.organ.su.se slurm[2805]: starting slurmd: [  OK  ]
>>
>> Jun 02 16:56:01 roos21.organ.su.se systemd[1]: Can't open PID file
>> /var/run/slurmctld.pid (yet?) after start: No such file or directory
>>
>> Jun 02 16:56:37 roos21.organ.su.se polkitd[1316]: *Unregistered
>> Authentication Agent for unix-process:2792:334647 (system bus name :1.46,
>> object path /org/freedesktop*
>>
>> Jun 02 16:56:38 roos21.organ.su.se sudo[2790]: pam_unix(sudo:session):
>> session closed for user slurm
>>
>> Something that I don't really understand because I have not installed
>> slurmctld. The slurmctld.service file does not even exist.
>>
>>
>> Any idea?
>>
>>
>> Many thanks,
>>
>> Ferran
>>
>>
>>
>> ------------------------------
>> *From:* slurm-users <slurm-users-bounces at lists.schedmd.com> on behalf of
>> Ole Holm Nielsen <Ole.H.Nielsen at fysik.dtu.dk>
>> *Sent:* Tuesday, June 2, 2020 12:03:27 PM
>> *To:* Slurm User Community List
>> *Subject:* Re: [slurm-users] Problem with permisions. CentOS 7.8
>>
>> Hi Ferran,
>>
>> Please install Slurm software in the standard way, see
>> https://wiki.fysik.dtu.dk/niflheim/Slurm_installation
>>
>> It seems that you have some unusual way to manage your Linux systems.  In
>> Stockholm and Sweden there are many Slurm experts at the HPC centers
>> which
>> might be able to help you more directly.
>>
>> Best regards,
>> Ole
>>
>> On 6/2/20 11:58 AM, Ferran Planas Padros wrote:
>> > I did a fresh installation with the EPEL repo, and installing munge
>> from
>> > it and it worked. To have the slurm user for munge was definitely a
>> > problem, but that is the set up we have on the CentOS 6. Now I've
>> learnt
>> > my lesson for future installations, thanks to everyone!
>> >
>> >
>> > Now, I have a follow up question, if you don't mind. I am now trying to
>> > run slurm, and it crashes:
>> >
>> >
>> > [root at roos21 ~]# systemctl status slurm.service
>> >
>> > *●*slurm.service - LSB: slurm daemon management
>> >
>> > Loaded: loaded (/etc/rc.d/init.d/slurm; bad; vendor preset: disabled)
>> >
>> > Active: *failed*(Result: protocol) since Tue 2020-06-02 11:45:33 CEST;
>> > 3min 33s ago
>> >
>> > Docs: man:systemd-sysv-generator(8)
>> >
>> >
>> > Jun 02 11:45:33 roos21.organ.su.se systemd[1]: Starting LSB: slurm
>> daemon
>> > management...
>> >
>> > Jun 02 11:45:33 roos21.organ.su.se slurm[18223]: starting slurmd: [OK]
>> >
>> > Jun 02 11:45:33 roos21.organ.su.se systemd[1]: Can't open PID file
>> > /var/run/slurmctld.pid (yet?) after start: No such file or directory
>> >
>> > Jun 02 11:45:33 roos21.organ.su.se systemd[1]: *Failed to start LSB:
>> slurm
>> > daemon management.*
>> >
>> > Jun 02 11:45:33 roos21.organ.su.se systemd[1]: *Unit slurm.service
>> entered
>> > failed state.*
>> >
>> > Jun 02 11:45:33 roos21.organ.su.se systemd[1]: *slurm.service failed.*
>> >
>> >
>> >
>> > The thing is that this is a computing node, not the master node, so
>> > slurmctld is not installed. Why do I get this error?
>> >
>> >
>> > Many thanks, and my apologies for this rather simple questions. I am a
>> > newbie on this.
>> >
>> >
>> > Best,
>> >
>> > Ferran
>> >
>> >
>> --------------------------------------------------------------------------
>> > *From:* slurm-users <slurm-users-bounces at lists.schedmd.com> on behalf
>> of
>> > Renata Maria Dart <renata at slac.stanford.edu>
>> > *Sent:* Friday, May 29, 2020 6:33:58 PM
>> > *To:* Ole.H.Nielsen at fysik.dtu.dk; Slurm User Community List
>> > *Subject:* Re: [slurm-users] Problem with permisions. CentOS 7.8
>> > Hi, don't know if this might be your problem but I ran into an issue
>> > on centos 7.8 where /var/run/munge was not being created at boottime
>> > because I didn't have the munge user in the local password file.  I
>> > have the munge user in AD and once the system is up I can start munge
>> > successfully, but AD wasn't available early enough during boot for the
>> > munge startup to see it.  I added these lines to the munge systemctl
>> > file:
>> >
>> > PermissionsStartOnly=true
>> > ExecStartPre=-/usr/bin/mkdir -m 0755 -p /var/run/munge
>> > ExecStartPre=-/usr/bin/chown -R munge:munge /var/run/munge
>> >
>> > and my system now starts munge up fine during a reboot.
>> >
>> > Renata
>> >
>> > On Fri, 29 May 2020, Ole Holm Nielsen wrote:
>> >
>> >> Hi Ferran,
>> >>
>> >> When you have a CentOS 7 system with the EPEL repo enabled, and you
>> have
>> >> installed the munge RPM from EPEL, then things should be working
>> correctly.
>> >>
>> >> Since systemctl tells you that Munge service didn't start correctly,
>> then it
>> >> seems to me that you have a problem in the general configuration of
>> your CentOS
>> >> 7 system.  You should check /var/log/messages and "journalctl -xe" for
>> munge
>> >> errors.  It is really hard for other people to guess what may be wrong
>> in your
>> >> system.
>> >>
>> >> My 2 cents worth: Maybe you could make a fresh CentOS 7.8 installation
>> on a
>> >> test system and install the Munge service (and nothing else) according
>> to
>> >> instructions in https://wiki.fysik.dtu.dk/niflheim/Slurm_installation.
>> This
>> >> *really* has got to work!
>> >>
>> >> /Ole
>> >>
>> >>
>> >> On 29-05-2020 10:23, Ferran Planas Padros wrote:
>> >>> Hello everyone,
>> >>>
>> >>>
>> >>> Here it comes everything I've done.
>> >>>
>> >>>
>> >>> - About Ole's answer:
>> >>>
>> >>> Yes, we have slurm as the user to control munge. Following your
>> comment, I
>> >>> have changed the ownership of the munge files and tried to start
>> munge as
>> >>> munge user. However, it also failed.
>> >>>
>> >>> Also, I first installed munge from a repository. I've seen your
>> suggestion of
>> >>> installing from EPEL. So I uninstalled and installed again. Same
>> result
>> >>>
>> >>> - About SELinux: It is disables
>> >>>
>> >>> - The output of ps -ef | grep munge is:
>> >>>
>> >>>
>> >>> root534051530 10:18 pts/000:00:00 grep --color=auto *munge*
>> >>>
>> >>>
>> >>> - The outputs of munge -n is:
>> >>>
>> >>>
>> >>> Failed to access "/var/run/munge/munge.socket.2": No such file or
>> directory
>> >>>
>> >>>
>> >>> - Same for unmunge
>> >>>
>> >>>
>> >>> - Output for sudo systemctl status --full munge
>> >>>
>> >>>
>> >>> *?*munge.service - MUNGE authentication service
>> >>>
>> >>> Loaded: loaded (/usr/lib/systemd/system/munge.service; enabled;
>> vendor preset:
>> >>> disabled)
>> >>>
>> >>> Active: *failed*(Result: exit-code) since Fri 2020-05-29 10:15:52
>> CEST; 4min
>> >>> 18s ago
>> >>>
>> >>> Docs: man:munged(8)
>> >>>
>> >>> Process: 5333 ExecStart=/usr/sbin/munged *(code=exited,
>> status=1/FAILURE)*
>> >>>
>> >>>
>> >>> May 29 10:15:52 roos21.organ.su.se systemd[1]: Starting MUNGE
>> authentication
>> >>> service...
>> >>>
>> >>> May 29 10:15:52 roos21.organ.su.se systemd[1]: *munge.service:
>> control process
>> >>> exited, code=exited status=1*
>> >>>
>> >>> May 29 10:15:52 roos21.organ.su.se systemd[1]: *Failed to start MUNGE
>> >>> authentication service.*
>> >>>
>> >>> May 29 10:15:52 roos21.organ.su.se systemd[1]: *Unit munge.service
>> entered
>> >>> failed state.*
>> >>>
>> >>> May 29 10:15:52 roos21.organ.su.se systemd[1]: *munge.service
>> failed.*
>> >>>
>> >>>
>> >>> - Regarding NTP, I get this message:
>> >>>
>> >>>
>> >>> Unable to talk to NTP daemon. Is it running?
>> >>>
>> >>>
>> >>> It is the same message I get in the nodes that DO work. All nodes are
>> sync in
>> >>> time and date with the central node
>> >>>
>> >>>
>> >>>
>> ------------------------------------------------------------------------
>> >>> *From:* slurm-users <slurm-users-bounces at lists.schedmd.com> on
>> behalf of Ole
>> >>> Holm Nielsen <Ole.H.Nielsen at fysik.dtu.dk>
>> >>> *Sent:* Friday, May 29, 2020 9:56:10 AM
>> >>> *To:* slurm-users at lists.schedmd.com
>> >>> *Subject:* Re: [slurm-users] Problem with permisions. CentOS 7.8
>> >>> On 29-05-2020 08:46, Sudeep Narayan Banerjee wrote:
>> >>>> also check:
>> >>>> a) whether NTP has been setup and communicating with master node
>> >>>> b) iptables may be flushed (iptables -L)
>> >>>> c) SeLinux to disabled, to check :
>> >>>> getenforce
>> >>>> vim /etc/sysconfig/selinux
>> >>>> (change SELINUX=enforcing to SELINUX=disabled and save the file and
>> reboot)
>> >>>
>> >>> There is no reason to disable SELinux for running the Munge service.
>> >>> It's a pretty bad idea to lower the security just for the sake of
>> >>> convenience!
>> >>>
>> >>> /Ole
>> >>>
>> >>>
>> >>>> On Fri, May 29, 2020 at 12:08 PM Sudeep Narayan Banerjee
>> >>>> <snbanerjee at iitgn.ac.in <mailto:snbanerjee at iitgn.ac.in
>> <snbanerjee at iitgn.ac.in>>> wrote:
>> >>>>
>> >>>>      I have not checked on the CentOS7.8
>> >>>>      a) if /var/run/munge folder does not exist then please double
>> check
>> >>>>      whether munge has been installed or not
>> >>>>      b) user root or sudo user to do
>> >>>>      ps -ef | grep munge
>> >>>>      kill -9 <PID> //where PID is the Process ID for munge (if the
>> >>>>      process is running at all); else
>> >>>>
>> >>>>      which munged
>> >>>>      /etc/init.d/munge start
>> >>>>
>> >>>>      please let me know the the output of:
>> >>>>
>> >>>>      |$ munge -n|
>> >>>>
>> >>>>      |$ munge -n | unmunge|
>> >>>>
>> >>>>      |$ sudo systemctl status --full munge
>> >>>>
>> >>>>      |
>> >>>>
>> >>>>      Thanks & Regards,
>> >>>>      Sudeep Narayan Banerjee
>> >>>>      System Analyst | Scientist B
>> >>>>      Indian Institute of Technology Gandhinagar
>> >>>>      Gujarat, INDIA
>> >>>>
>> >>>>
>> >>>>      On Fri, May 29, 2020 at 11:55 AM Bjørn-Helge Mevik
>> >>>>      <b.h.mevik at usit.uio.no <mailto:b.h.mevik at usit.uio.no
>> <b.h.mevik at usit.uio.no>>> wrote:
>> >>>>
>> >>>>          Ferran Planas Padros <ferran.padros at su.se
>> >>>>          <mailto:ferran.padros at su.se <ferran.padros at su.se>>> writes:
>> >>>>
>> >>>>           > I run the command as slurm user, and the /var/log/munge
>> >>>>          folder does belong to slurm.
>> >>>>
>> >>>>          For security reasons, I strongly advise that you run munged
>> as a
>> >>>>          separate user, which is unprivileged and not used for
>> anything else.
>> >>>>
>> >>>>          --          Regards,
>> >>>>          Bjørn-Helge Mevik, dr. scient,
>> >>>>          Department for Research Computing, University of Oslo
>>
>>
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