[slurm-users] Running pyMPI on several nodes

Tue Jul 16 07:46:26 UTC 2019

Hi,

I have now had the time to look at some of your suggestions.

First I tried running "srun -N1 hostname" via a sbatch-script, while 
having two nodes up and running.
"sinfo" yields that two nodes are up and idle prior to submitting the 
sbatch-script.
After submitting the job, I receive an error stating that:

"srun: error: Task launch for 86.0 failed on node lxclient11: Invalid 
node name specified.
srun: error: Application launch failed: Invalid node name specified
srun: Job step aborted: Waiting up to 32 seconds for job step to finish.
srun: error: TImed out waiting for job step to complete"

 From the log file at the client I get a more detailed error:
" Launching batch job 86 for UID 1000
[86.batch] error: Invalid host_index -1 for job 86
[86.batch] error: Host lxclient10 not in hostlist lxclient11
[86.batch] task_pre_launch: Using sched_affinity for tasks
rpc_launch_tasks: Invalid node list (lxclient10 not in lxclient11)"

My two nodes are called lxclient10 and lxclient11.
Why is my batch job launched with the UID 1000, shouldnt it be launched 
via the slurm-user (which in my case has the UID 64030)?
What is meant by that the different nodes are not in the nodeslist?
The two nodes and the server share the same setup of IP-addresses in the 
"/etc/hosts"-file.

-> This was resolved due to that lxclient10 was noted as down. Getting 
it back up, the submitting of the same sbatch-script, resulted in no error.
However running it on two nodes I get an error
"srun: error: Job Step 88.0 aborted before step completely launched.
srun: error: Job step aborted: Waiting up to 32 seconds for job step to 
finish.
srun: error: task 1 launched failed: Unspecifed error
srun: error: lxclient10: task 0: Killed"

And in the slurmctld.log-file from the client I get an error similiar to 
that prevously stated, that the pmix cannot bind UNIX socket 
/var/spool/slurmd/stepd.slurm.pmix.88.0: Address already in use (98)

I ran the lsof command, but I dont really know what I am looking after, 
I can see if I grep with the different nodenames that the two nodes have 
mounted the nfs-partition and that a link is established.

"As an aside, you have checked that your username exists on that compue 
server?      getent passwd par
Also that your home directory is mounted - or something substituting for 
your home directory?"
Yes, the user slurm exists on both nodes and have the same uid.

"Have you tried

         srun -N# -n# mpirun python3 ....

Perhaps you have no MPI environment being setup for the processes? 
  There was no "--mpi" flag in your "srun" command and we don't know if 
you have a default value for that or not.

"

In my slurm.conf-file I do specify that "MpiDefault=pmix" (And it can be 
seen in the logfile that there is something wrong with pmix, that the 
address already in use.)

One thing that struck my mind now is that I run these nodes as a pair of 
diskless nodes, whom boots and mounts the same filesystem which is 
supplied by a server. The run differen pids for different processes 
which should not affect one another(?), right?

Best regards,

Palle

On 2019-07-12 19:34, Pär Lundö wrote:
> Hi,
>
> Thank you so much for your quick responses!
> It is much appreciated.
> I dont have access to the cluster until next week, but I’ll be sure to 
> follow up on all of your suggestions and get back you next week.
>
> Have a nice weekend!
> Best regards
> Palle
>
> ------------------------------------------------------------------------
> *From:* "slurm-users" <slurm-users-bounces at lists.schedmd.com>
> *Sent:* 12 juli 2019 17:37
> *To:* "Slurm User Community List" <slurm-users at lists.schedmd.com>
> *Subject:* Re: [slurm-users] Running pyMPI on several nodes
>
> Par, by 'poking around' Crhis means to use tools such as netstat and 
> lsof.
> Also I would look as ps -eaf --forest to make sure there are no 
> 'orphaned' jusbs sitting on that compute node.
>
> Having said that though, I have a dim memory of a classic PBSPro error 
> message which says something about a network connection,
> but really means that you cannot open a remote session on that compute 
> server.
>
> As an aside, you have checked that your username exists on that compue 
> server?      getent passwd par
> Also that your home directory is mounted - or something substituting 
> for your home directory?
>
>
> On Fri, 12 Jul 2019 at 15:55, Chris Samuel < chris at csamuel.org 
> <mailto:chris at csamuel.org>> wrote:
>
>     On 12/7/19 7:39 am, Pär Lundö wrote:
>
>     > Presumably, the first 8 tasks originates from the first node (in
>     this
>     > case the lxclient11), and the other node (lxclient10) response as
>     > predicted.
>
>     That looks right, it seems the other node has two processes fighting
>     over the same socket and that's breaking Slurm there.
>
>     > Is it neccessary to have passwordless ssh communication
>     alongside the
>     > munge authentication?
>
>     No, srun doesn't need (or use) that at all.
>
>     > In addition I checked the slurmctld-log from both the server and
>     client
>     > and found something (noted in bold):
>
>     This is from the slurmd log on the client from the look of it.
>
>     > *[2019-07-12T14:57:53.771][83.0] task_p_pre_launch: Using sched
>     affinity
>     > for tasks lurm.pmix.83.0: Address already in use[98]*
>     > [2019-07-12T14:57:53.682][83.0] error: lxclient[0]
>     /pmix.server.c:386
>     > [pmix_stepd_init] mpi/pmix: ERROR: pmixp_usock_create_srv
>     > [2019-07-12T14:57:53.683][83.0] error: (null) [0] /mpi_pmix:156
>     > [p_mpi_hook_slurmstepd_prefork] mpi/pmix: ERROR:
>     pmixp_stepd_init() failed
>
>     That indicates that something else has grabbed the socket it wants
>     and
>     that's why the setup of the MPI ranks on the second node fails.
>
>     You'll want to poke around there to see what's using it.
>
>     Best of luck!
>     Chris
>     -- 
>       Chris Samuel  : http://www.csamuel.org/
>     <http://www.csamuel.org/>  :  Berkeley, CA, USA
>
-- 
Hälsningar, Pär
________________________________
Pär Lundö
Forskare
Avdelningen för Ledningssystem

FOI
Totalförsvarets forskningsinstitut
164 90 Stockholm

Besöksadress:
Olau Magnus väg 33, Linköping

Tel: +46 13 37 86 01
Mob: +46 734 447 815
Vxl: +46 13 37 80 00
par.lundo at foi.se
www.foi.se

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