[slurm-users] Running pyMPI on several nodes
Benson Muite
benson_muite at emailplus.org
Tue Jul 16 13:49:54 UTC 2019
Hi,
Does a regular MPI program run on two nodes? For example helloworld:
https://people.sc.fsu.edu/~jburkardt/c_src/hello_mpi/hello_mpi.c
https://people.sc.fsu.edu/~jburkardt/py_src/hello_mpi/hello_mpi.py
Benson
On 7/16/19 4:30 PM, Pär Lundö wrote:
> Hi,
> Thank you for your quick answer!
> I’ll look into that, but they share the same hosts-file and the
> DHCP-server sets their hostname.
>
> However I came across a setting in the slurm.conf-file ”Tmpfs” and
> there were a note regarding it in the guide of mpi at the slurms
> webpage. I implemented the proposed changes but still no luck.
>
> Best regards,
> Palle
>
> ------------------------------------------------------------------------
> *From:* "slurm-users" <slurm-users-bounces at lists.schedmd.com>
> *Sent:* 16 juli 2019 12:32
> *To:* "Slurm User Community List" <slurm-users at lists.schedmd.com>
> *Subject:* Re: [slurm-users] Running pyMPI on several nodes
>
> srun: error: Application launch failed: Invalid node name specified
>
> Hearns Law. All batch system problems are DNS problems.
>
> Seriously though - check out your name resolution both on the head
> node and the compute nodes.
>
>
> On Tue, 16 Jul 2019 at 08:49, Pär Lundö < par.lundo at foi.se
> <mailto:par.lundo at foi.se>> wrote:
>
> 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>
> <mailto:slurm-users-bounces at lists.schedmd.com>
> *Sent:* 12 juli 2019 17:37
> *To:* "Slurm User Community List"
> <slurm-users at lists.schedmd.com>
> <mailto: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 <tel:+46%2013%2037%2086%2001>
> Mob:+46 734 447 815 <tel:+46%20734%20447%20815>
> Vxl:+46 13 37 80 00 <tel:+46%2013%2037%2080%2000>
> par.lundo at foi.se <mailto:par.lundo at foi.se>
> www.foi.se <http://www.foi.se>
>
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