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<p>Hi!</p>
<p>I have now had the chance to look into to this matter more
thoroughly and it seems that the problem was due to the fact that
the nodes are diskless and shared some data (e.g. "etc"-dir). I
removed that dependency and mounted each node to a unique set of
folders, which resolved the issue. Presumably, this can be done in
other ways unknown to me, but it helped me and I can now run
multiple nodes via MPI.</p>
<p>Thank you for your help!</p>
<p>Best regards,<br>
Pälle L<br>
</p>
<div class="moz-cite-prefix">On 2019-07-16 15:49, Benson Muite
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:6c81032b-5a45-3565-1df8-c9fc6a9192f2@emailplus.org">
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
<p>Hi,</p>
<p>Does a regular MPI program run on two nodes? For example
helloworld:</p>
<p><a class="moz-txt-link-freetext"
href="https://people.sc.fsu.edu/~jburkardt/c_src/hello_mpi/hello_mpi.c"
moz-do-not-send="true">https://people.sc.fsu.edu/~jburkardt/c_src/hello_mpi/hello_mpi.c</a><br>
</p>
<p><a class="moz-txt-link-freetext"
href="https://people.sc.fsu.edu/~jburkardt/py_src/hello_mpi/hello_mpi.py"
moz-do-not-send="true">https://people.sc.fsu.edu/~jburkardt/py_src/hello_mpi/hello_mpi.py</a><br>
</p>
<p>Benson<br>
</p>
<div class="moz-cite-prefix">On 7/16/19 4:30 PM, Pär Lundö wrote:<br>
</div>
<blockquote type="cite"
cite="mid:8972685e424e478bbf460e64e82d3407@foi.se">
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<div dir="ltr"
style="font-size:11.0pt;font-family:Calibri,Tahoma,Arial,Helvetica,sans-serif;color:black;">Hi,
</div>
<div dir="ltr"
style="font-size:11.0pt;font-family:Calibri,Tahoma,Arial,Helvetica,sans-serif;color:black;">Thank
you for your quick answer! </div>
<div dir="ltr"
style="font-size:11.0pt;font-family:Calibri,Tahoma,Arial,Helvetica,sans-serif;color:black;">I’ll
look into that, but they share the same hosts-file and the
DHCP-server sets their hostname. </div>
<div dir="ltr"
style="font-size:11.0pt;font-family:Calibri,Tahoma,Arial,Helvetica,sans-serif;color:black;"><br>
</div>
<div dir="ltr"
style="font-size:11.0pt;font-family:Calibri,Tahoma,Arial,Helvetica,sans-serif;color:black;">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. </div>
<div dir="ltr"
style="font-size:11.0pt;font-family:Calibri,Tahoma,Arial,Helvetica,sans-serif;color:black;"><br>
</div>
<div dir="ltr"
style="font-size:11.0pt;font-family:Calibri,Tahoma,Arial,Helvetica,sans-serif;color:black;">Best
regards, </div>
<div dir="ltr"
style="font-size:11.0pt;font-family:Calibri,Tahoma,Arial,Helvetica,sans-serif;color:black;">Palle
<br>
<br>
<hr> <b>From:</b> "slurm-users" <a
class="moz-txt-link-rfc2396E"
href="mailto:slurm-users-bounces@lists.schedmd.com"
moz-do-not-send="true"><slurm-users-bounces@lists.schedmd.com></a>
<br>
<b>Sent:</b> 16 juli 2019 12:32 <br>
<b>To:</b> "Slurm User Community List" <a
class="moz-txt-link-rfc2396E"
href="mailto:slurm-users@lists.schedmd.com"
moz-do-not-send="true"><slurm-users@lists.schedmd.com></a>
<br>
<b>Subject:</b> Re: [slurm-users] Running pyMPI on several
nodes <br>
<br>
</div>
<div dir="ltr">
<div>srun: error: Application launch failed: Invalid node name
specified <br>
</div>
<div><br>
</div>
<div>Hearns Law. All batch system problems are DNS problems.
</div>
<div><br>
</div>
<div>Seriously though - check out your name resolution both on
the head node and the compute nodes. </div>
<div><br>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Tue, 16 Jul 2019 at
08:49, Pär Lundö < <a href="mailto:par.lundo@foi.se"
moz-do-not-send="true"> par.lundo@foi.se</a>> wrote: <br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px
0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">
<div bgcolor="#FFFFFF">
<p>Hi,</p>
<p>I have now had the time to look at some of your
suggestions.</p>
<p>First I tried running "srun -N1 hostname" via a
sbatch-script, while having two nodes up and running. <br>
"sinfo" yields that two nodes are up and idle prior to
submitting the sbatch-script.<br>
After submitting the job, I receive an error stating
that:</p>
<p>"srun: error: Task launch for 86.0 failed on node
lxclient11: Invalid node name specified.<br>
srun: error: Application launch failed: Invalid node
name specified<br>
srun: Job step aborted: Waiting up to 32 seconds for job
step to finish.<br>
srun: error: TImed out waiting for job step to complete"</p>
<p><br>
</p>
<p>From the log file at the client I get a more detailed
error:<br>
" Launching batch job 86 for UID 1000 <br>
[86.batch] error: Invalid host_index -1 for job 86<br>
[86.batch] error: Host lxclient10 not in hostlist
lxclient11<br>
[86.batch] task_pre_launch: Using sched_affinity for
tasks<br>
rpc_launch_tasks: Invalid node list (lxclient10 not in
lxclient11)"<br>
</p>
<p>My two nodes are called lxclient10 and lxclient11.<br>
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)? <br>
What is meant by that the different nodes are not in the
nodeslist? <br>
The two nodes and the server share the same setup of
IP-addresses in the "/etc/hosts"-file.</p>
<p>-> 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.<br>
However running it on two nodes I get an error <br>
"srun: error: Job Step 88.0 aborted before step
completely launched.<br>
srun: error: Job step aborted: Waiting up to 32 seconds
for job step to finish.<br>
srun: error: task 1 launched failed: Unspecifed error<br>
srun: error: lxclient10: task 0: Killed"</p>
<p>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)</p>
<p>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.</p>
<p>"As an aside, you have checked that your username
exists on that compue server? getent passwd par<br>
Also that your home directory is mounted - or something
substituting for your home directory?"<br>
Yes, the user slurm exists on both nodes and have the
same uid.<br>
<br>
"Have you tried <br>
<br>
<br>
srun -N# -n# mpirun python3 .... <br>
<br>
<br>
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. <br>
</p>
"
<p>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.)<br>
</p>
<p>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?</p>
<p><br>
</p>
<p>Best regards,</p>
<p>Palle<br>
</p>
<div class="gmail-m_5257842815186023450moz-cite-prefix">On
2019-07-12 19:34, Pär Lundö wrote: <br>
</div>
<blockquote>
<div dir="ltr"
style="font-size:11pt;font-family:Calibri,Tahoma,Arial,Helvetica,sans-serif;color:black">Hi,
</div>
<div dir="ltr"
style="font-size:11pt;font-family:Calibri,Tahoma,Arial,Helvetica,sans-serif;color:black"><br>
</div>
<div dir="ltr"
style="font-size:11pt;font-family:Calibri,Tahoma,Arial,Helvetica,sans-serif;color:black">Thank
you so much for your quick responses! </div>
<div dir="ltr"
style="font-size:11pt;font-family:Calibri,Tahoma,Arial,Helvetica,sans-serif;color:black">It
is much appreciated. </div>
<div dir="ltr"
style="font-size:11pt;font-family:Calibri,Tahoma,Arial,Helvetica,sans-serif;color:black">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. </div>
<div dir="ltr"
style="font-size:11pt;font-family:Calibri,Tahoma,Arial,Helvetica,sans-serif;color:black"><br>
</div>
<div dir="ltr"
style="font-size:11pt;font-family:Calibri,Tahoma,Arial,Helvetica,sans-serif;color:black">Have
a nice weekend! </div>
<div dir="ltr"
style="font-size:11pt;font-family:Calibri,Tahoma,Arial,Helvetica,sans-serif;color:black">Best
regards </div>
<div dir="ltr"
style="font-size:11pt;font-family:Calibri,Tahoma,Arial,Helvetica,sans-serif;color:black">Palle
<br>
<br>
<hr> <b>From:</b> "slurm-users" <a
class="gmail-m_5257842815186023450moz-txt-link-rfc2396E"
href="mailto:slurm-users-bounces@lists.schedmd.com"
target="_blank" moz-do-not-send="true">
<slurm-users-bounces@lists.schedmd.com></a> <br>
<b>Sent:</b> 12 juli 2019 17:37 <br>
<b>To:</b> "Slurm User Community List" <a
class="gmail-m_5257842815186023450moz-txt-link-rfc2396E"
href="mailto:slurm-users@lists.schedmd.com"
target="_blank" moz-do-not-send="true">
<slurm-users@lists.schedmd.com></a> <br>
<b>Subject:</b> Re: [slurm-users] Running pyMPI on
several nodes <br>
<br>
</div>
<div dir="ltr">
<div>Par, by 'poking around' Crhis means to use tools
such as netstat and lsof. </div>
<div>Also I would look as ps -eaf --forest to make
sure there are no 'orphaned' jusbs sitting on that
compute node. </div>
<div><br>
</div>
<div>Having said that though, I have a dim memory of a
classic PBSPro error message which says something
about a network connection, </div>
<div>but really means that you cannot open a remote
session on that compute server. </div>
<div><br>
</div>
<div>As an aside, you have checked that your username
exists on that compue server? getent passwd par
</div>
<div>Also that your home directory is mounted - or
something substituting for your home directory? </div>
<div><br>
</div>
</div>
<br>
<div class="gmail_quote">
<div class="gmail_attr" dir="ltr">On Fri, 12 Jul 2019
at 15:55, Chris Samuel < <a
href="mailto:chris@csamuel.org" target="_blank"
moz-do-not-send="true"> chris@csamuel.org</a>>
wrote: <br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px
0px 0.8ex;padding-left:1ex;border-left:1px solid
rgb(204,204,204)"> On 12/7/19 7:39 am, Pär Lundö
wrote: <br>
<br>
> Presumably, the first 8 tasks originates from
the first node (in this <br>
> case the lxclient11), and the other node
(lxclient10) response as <br>
> predicted. <br>
<br>
That looks right, it seems the other node has two
processes fighting <br>
over the same socket and that's breaking Slurm
there. <br>
<br>
> Is it neccessary to have passwordless ssh
communication alongside the <br>
> munge authentication? <br>
<br>
No, srun doesn't need (or use) that at all. <br>
<br>
> In addition I checked the slurmctld-log from
both the server and client <br>
> and found something (noted in bold): <br>
<br>
This is from the slurmd log on the client from the
look of it. <br>
<br>
> *[2019-07-12T14:57:53.771][83.0]
task_p_pre_launch: Using sched affinity <br>
> for tasks lurm.pmix.83.0: Address already in
use[98]* <br>
> [2019-07-12T14:57:53.682][83.0] error:
lxclient[0] /pmix.server.c:386 <br>
> [pmix_stepd_init] mpi/pmix: ERROR:
pmixp_usock_create_srv <br>
> [2019-07-12T14:57:53.683][83.0] error: (null)
[0] /mpi_pmix:156 <br>
> [p_mpi_hook_slurmstepd_prefork] mpi/pmix:
ERROR: pmixp_stepd_init() failed <br>
<br>
That indicates that something else has grabbed the
socket it wants and <br>
that's why the setup of the MPI ranks on the second
node fails. <br>
<br>
You'll want to poke around there to see what's using
it. <br>
<br>
Best of luck! <br>
Chris <br>
-- <br>
Chris Samuel : <a
href="http://www.csamuel.org/" rel="noreferrer"
target="_blank" moz-do-not-send="true">
http://www.csamuel.org/</a> : Berkeley, CA, USA
<br>
<br>
</blockquote>
</div>
</blockquote>
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