Re: [OMPI users] Unable to mpirun from within torque

[Gilles Gouaillardet]

Ralph,

i am not sure i am reading you correctly, so let me clarify.


i did not hack $PBS_NODEFILE for fun nor profit, i was simply trying to 
reproduce an issue i could not reproduce otherwise.

/* my job submitted with -l nodes=3:ppn=1 do not start if there are only 
two nodes available, whereas the same user job

starts on two nodes */

thanks for the explanation of the torque internals, my hack was 
incomplete and not a valid one, i do acknowledge it.


i re-read the email that started this thread and i found the information 
i was looking for


echo $PBS_NODEFILE
/var/lib/torque/aux//278.a00552.science.domain
cat $PBS_NODEFILE
a00551.science.domain
a00553.science.domain
a00551.science.domain 


so, assuming the enduser did not edit his $PBS_NODEFILE, and torque is 
correctly configured and not busted, then

Torque indeed always provides an ordered file - the only way you can get an 
unordered one is for someone to edit it
might be updated to

"Torque used to always provide an ordered file, but recent versions 
might not do that."


makes sense ?


Cheers,

Gilles


On 9/8/2016 4:57 PM, r...@open-mpi.org wrote:
Someone has done some work there since I last did, but I can see the issue. 
Torque indeed always provides an ordered file - the only way you can get an 
unordered one is for someone to edit it, and that is forbidden - i.e., you get 
what you deserve because you are messing around with a system-defined file :-)

The problem is that Torque internally assigns a “launch ID” which is just the 
integer position of the nodename in the PBS_NODEFILE. So if you modify that 
position, then we get the wrong index - and everything goes down the drain from 
there. In your example, n1.cluster changed index from 3 to 2 because of your 
edit. Torque thinks that index 2 is just another reference to n0.cluster, and 
so we merrily launch a daemon onto the wrong node.

They have a good reason for doing things this way. It allows you to launch a 
process against each launch ID, and the pattern will reflect the original qsub 
request in what we would call a map-by slot round-robin mode. This maximizes 
the use of shared memory, and is expected to provide good performance for a 
range of apps.

Lesson to be learned: never, ever muddle around with a system-generated file. 
If you want to modify where things go, then use one or more of the mpirun 
options to do so. We give you lots and lots of knobs for just that reason.



On Sep 7, 2016, at 10:53 PM, Gilles Gouaillardet <gil...@rist.or.jp> wrote:

Ralph,


there might be an issue within Open MPI.


on the cluster i used, hostname returns the FQDN, and $PBS_NODEFILE uses the 
FQDN too.

my $PBS_NODEFILE has one line per task, and it is ordered

e.g.

n0.cluster

n0.cluster

n1.cluster

n1.cluster


in my torque script, i rewrote the machinefile like this

n0.cluster

n1.cluster

n0.cluster

n1.cluster

and updated the PBS environment variable to point to my new file.


then i invoked

mpirun hostname



in the first case, 2 tasks run on n0 and 2 tasks run on n1
in the second case, 4 tasks run on n0, and none on n1.

so i am thinking we might not support unordered $PBS_NODEFILE.

as a reminder, the submit command was
qsub -l nodes=3:ppn=1
but for some reasons i ignore, only two nodes were allocated (two slots on the 
first one, one on the second one)
and if i understand correctly, $PBS_NODEFILE was not ordered.
(e.g. n0 n1 n0 and *not * n0 n0 n1)

i tried to reproduce this without hacking $PBS_NODEFILE, but my jobs hang in 
the queue if only two nodes with 16 slots each are available and i request
-l nodes=3:ppn=1
i guess this is a different scheduler configuration, and i cannot change that.

Could you please have a look at this ?

Cheers,

Gilles

On 9/7/2016 11:15 PM, r...@open-mpi.org wrote:
The usual cause of this problem is that the nodename in the machinefile is 
given as a00551, while Torque is assigning the node name as 
a00551.science.domain. Thus, mpirun thinks those are two separate nodes and 
winds up spawning an orted on its own node.

You might try ensuring that your machinefile is using the exact same name as 
provided in your allocation


On Sep 7, 2016, at 7:06 AM, Gilles Gouaillardet <gilles.gouaillar...@gmail.com> 
wrote:

Thanjs for the ligs

 From what i see now, it looks like a00551 is running both mpirun and orted, 
though it should only run mpirun, and orted should run only on a00553

I will check the code and see what could be happening here

Btw, what is the output of
hostname
hostname -f
On a00551 ?

Out of curiosity, is a previous version of Open MPI (e.g. v1.10.4) installled 
and running correctly on your cluster ?

Cheers,

Gilles

Oswin Krause <oswin.kra...@ruhr-uni-bochum.de> wrote:
Hi Gilles,

Thanks for the hint with the machinefile. I know it is not equivalent
and i do not intend to use that approach. I just wanted to know whether
I could start the program successfully at all.

Outside torque(4.2), rsh seems to be used which works fine, querying a
password if no kerberos ticket is there

Here is the output:
[zbh251@a00551 ~]$ mpirun -V
mpirun (Open MPI) 2.0.1
[zbh251@a00551 ~]$ ompi_info | grep ras
                 MCA ras: loadleveler (MCA v2.1.0, API v2.0.0, Component
v2.0.1)
                 MCA ras: simulator (MCA v2.1.0, API v2.0.0, Component
v2.0.1)
                 MCA ras: slurm (MCA v2.1.0, API v2.0.0, Component
v2.0.1)
                 MCA ras: tm (MCA v2.1.0, API v2.0.0, Component v2.0.1)
[zbh251@a00551 ~]$ mpirun --mca plm_base_verbose 10 --tag-output
-display-map hostname
[a00551.science.domain:04104] mca: base: components_register:
registering framework plm components
[a00551.science.domain:04104] mca: base: components_register: found
loaded component isolated
[a00551.science.domain:04104] mca: base: components_register: component
isolated has no register or open function
[a00551.science.domain:04104] mca: base: components_register: found
loaded component rsh
[a00551.science.domain:04104] mca: base: components_register: component
rsh register function successful
[a00551.science.domain:04104] mca: base: components_register: found
loaded component slurm
[a00551.science.domain:04104] mca: base: components_register: component
slurm register function successful
[a00551.science.domain:04104] mca: base: components_register: found
loaded component tm
[a00551.science.domain:04104] mca: base: components_register: component
tm register function successful
[a00551.science.domain:04104] mca: base: components_open: opening plm
components
[a00551.science.domain:04104] mca: base: components_open: found loaded
component isolated
[a00551.science.domain:04104] mca: base: components_open: component
isolated open function successful
[a00551.science.domain:04104] mca: base: components_open: found loaded
component rsh
[a00551.science.domain:04104] mca: base: components_open: component rsh
open function successful
[a00551.science.domain:04104] mca: base: components_open: found loaded
component slurm
[a00551.science.domain:04104] mca: base: components_open: component
slurm open function successful
[a00551.science.domain:04104] mca: base: components_open: found loaded
component tm
[a00551.science.domain:04104] mca: base: components_open: component tm
open function successful
[a00551.science.domain:04104] mca:base:select: Auto-selecting plm
components
[a00551.science.domain:04104] mca:base:select:(  plm) Querying component
[isolated]
[a00551.science.domain:04104] mca:base:select:(  plm) Query of component
[isolated] set priority to 0
[a00551.science.domain:04104] mca:base:select:(  plm) Querying component
[rsh]
[a00551.science.domain:04104] mca:base:select:(  plm) Query of component
[rsh] set priority to 10
[a00551.science.domain:04104] mca:base:select:(  plm) Querying component
[slurm]
[a00551.science.domain:04104] mca:base:select:(  plm) Querying component
[tm]
[a00551.science.domain:04104] mca:base:select:(  plm) Query of component
[tm] set priority to 75
[a00551.science.domain:04104] mca:base:select:(  plm) Selected component
[tm]
[a00551.science.domain:04104] mca: base: close: component isolated
closed
[a00551.science.domain:04104] mca: base: close: unloading component
isolated
[a00551.science.domain:04104] mca: base: close: component rsh closed
[a00551.science.domain:04104] mca: base: close: unloading component rsh
[a00551.science.domain:04104] mca: base: close: component slurm closed
[a00551.science.domain:04104] mca: base: close: unloading component
slurm
[a00551.science.domain:04109] mca: base: components_register:
registering framework plm components
[a00551.science.domain:04109] mca: base: components_register: found
loaded component rsh
[a00551.science.domain:04109] mca: base: components_register: component
rsh register function successful
[a00551.science.domain:04109] mca: base: components_open: opening plm
components
[a00551.science.domain:04109] mca: base: components_open: found loaded
component rsh
[a00551.science.domain:04109] mca: base: components_open: component rsh
open function successful
[a00551.science.domain:04109] mca:base:select: Auto-selecting plm
components
[a00551.science.domain:04109] mca:base:select:(  plm) Querying component
[rsh]
[a00551.science.domain:04109] mca:base:select:(  plm) Query of component
[rsh] set priority to 10
[a00551.science.domain:04109] mca:base:select:(  plm) Selected component
[rsh]
[a00551.science.domain:04109] [[53688,0],1] bind() failed on error
Address already in use (98)
[a00551.science.domain:04109] [[53688,0],1] ORTE_ERROR_LOG: Error in
file oob_usock_component.c at line 228
Data for JOB [53688,1] offset 0

========================   JOB MAP   ========================

Data for node: a00551   Num slots: 2    Max slots: 0    Num procs: 2
        Process OMPI jobid: [53688,1] App: 0 Process rank: 0 Bound: socket
0[core 0[hwt 0-1]], socket 0[core 1[hwt 0-1]], socket 0[core 2[hwt
0-1]], socket 0[core 3[hwt 0-1]], socket 0[core 4[hwt 0-1]], socket
0[core 5[hwt 0-1]], socket 0[core 6[hwt 0-1]], socket 0[core 7[hwt
0-1]], socket 0[core 8[hwt 0-1]], socket 0[core 9[hwt
0-1]]:[BB/BB/BB/BB/BB/BB/BB/BB/BB/BB][../../../../../../../../../..]
        Process OMPI jobid: [53688,1] App: 0 Process rank: 1 Bound: socket
1[core 10[hwt 0-1]], socket 1[core 11[hwt 0-1]], socket 1[core 12[hwt
0-1]], socket 1[core 13[hwt 0-1]], socket 1[core 14[hwt 0-1]], socket
1[core 15[hwt 0-1]], socket 1[core 16[hwt 0-1]], socket 1[core 17[hwt
0-1]], socket 1[core 18[hwt 0-1]], socket 1[core 19[hwt
0-1]]:[../../../../../../../../../..][BB/BB/BB/BB/BB/BB/BB/BB/BB/BB]

Data for node: a00553.science.domain    Num slots: 1    Max slots: 0    Num
procs: 1
        Process OMPI jobid: [53688,1] App: 0 Process rank: 2 Bound: socket
0[core 0[hwt 0-1]], socket 0[core 1[hwt 0-1]], socket 0[core 2[hwt
0-1]], socket 0[core 3[hwt 0-1]], socket 0[core 4[hwt 0-1]], socket
0[core 5[hwt 0-1]], socket 0[core 6[hwt 0-1]], socket 0[core 7[hwt
0-1]], socket 0[core 8[hwt 0-1]], socket 0[core 9[hwt
0-1]]:[BB/BB/BB/BB/BB/BB/BB/BB/BB/BB][../../../../../../../../../..]

=============================================================
[a00551.science.domain:04104] [[53688,0],0] complete_setup on job
[53688,1]
[a00551.science.domain:04104] [[53688,0],0] plm:base:receive update proc
state command from [[53688,0],1]
[a00551.science.domain:04104] [[53688,0],0] plm:base:receive got
update_proc_state for job [53688,1]
[1,0]<stdout>:a00551.science.domain
[1,2]<stdout>:a00551.science.domain
[a00551.science.domain:04104] [[53688,0],0] plm:base:receive update proc
state command from [[53688,0],1]
[a00551.science.domain:04104] [[53688,0],0] plm:base:receive got
update_proc_state for job [53688,1]
[1,1]<stdout>:a00551.science.domain
[a00551.science.domain:04109] mca: base: close: component rsh closed
[a00551.science.domain:04109] mca: base: close: unloading component rsh
[a00551.science.domain:04104] mca: base: close: component tm closed
[a00551.science.domain:04104] mca: base: close: unloading component tm

On 2016-09-07 14:41, Gilles Gouaillardet wrote:
Hi,

Which version of Open MPI are you running ?

I noted that though you are asking three nodes and one task per node,
you have been allocated 2 nodes only.
I do not know if this is related to this issue.

Note if you use the machinefile, a00551 has two slots (since it
appears twice in the machinefile) but a00553 has 20 slots (since it
appears once in the machinefile, the number of slots is automatically
detected)

Can you run
mpirun --mca plm_base_verbose 10 ...
So we can confirm tm is used.

Before invoking mpirun, you might want to cleanup the ompi directory in
/tmp

Cheers,

Gilles

Oswin Krause <oswin.kra...@ruhr-uni-bochum.de> wrote:
Hi,

I am currently trying to set up OpenMPI in torque. OpenMPI is build
with
tm support. Torque is correctly assigning nodes and I can run
mpi-programs on single nodes just fine. the problem starts when
processes are split between nodes.

For example, I create an interactive session with torque and start a
program by

qsub -I -n -l nodes=3:ppn=1
mpirun --tag-output -display-map hostname

which leads to
[a00551.science.domain:15932] [[65415,0],1] bind() failed on error
Address already in use (98)
[a00551.science.domain:15932] [[65415,0],1] ORTE_ERROR_LOG: Error in
file oob_usock_component.c at line 228
Data for JOB [65415,1] offset 0

========================   JOB MAP   ========================

Data for node: a00551   Num slots: 2    Max slots: 0    Num procs: 2
        Process OMPI jobid: [65415,1] App: 0 Process rank: 0 Bound: socket
0[core 0[hwt 0-1]], socket 0[core 1[hwt 0-1]], socket 0[core 2[hwt
0-1]], socket 0[core 3[hwt 0-1]], socket 0[core 4[hwt 0-1]], socket
0[core 5[hwt 0-1]], socket 0[core 6[hwt 0-1]], socket 0[core 7[hwt
0-1]], socket 0[core 8[hwt 0-1]], socket 0[core 9[hwt
0-1]]:[BB/BB/BB/BB/BB/BB/BB/BB/BB/BB][../../../../../../../../../..]
        Process OMPI jobid: [65415,1] App: 0 Process rank: 1 Bound: socket
1[core 10[hwt 0-1]], socket 1[core 11[hwt 0-1]], socket 1[core 12[hwt
0-1]], socket 1[core 13[hwt 0-1]], socket 1[core 14[hwt 0-1]], socket
1[core 15[hwt 0-1]], socket 1[core 16[hwt 0-1]], socket 1[core 17[hwt
0-1]], socket 1[core 18[hwt 0-1]], socket 1[core 19[hwt
0-1]]:[../../../../../../../../../..][BB/BB/BB/BB/BB/BB/BB/BB/BB/BB]

Data for node: a00553.science.domain    Num slots: 1    Max slots: 0    Num
procs: 1
        Process OMPI jobid: [65415,1] App: 0 Process rank: 2 Bound: socket
0[core 0[hwt 0-1]], socket 0[core 1[hwt 0-1]], socket 0[core 2[hwt
0-1]], socket 0[core 3[hwt 0-1]], socket 0[core 4[hwt 0-1]], socket
0[core 5[hwt 0-1]], socket 0[core 6[hwt 0-1]], socket 0[core 7[hwt
0-1]], socket 0[core 8[hwt 0-1]], socket 0[core 9[hwt
0-1]]:[BB/BB/BB/BB/BB/BB/BB/BB/BB/BB][../../../../../../../../../..]

=============================================================
[1,0]<stdout>:a00551.science.domain
[1,2]<stdout>:a00551.science.domain
[1,1]<stdout>:a00551.science.domain


if I login on a00551 and start using the hostfile generated by the
PBS_NODEFILE, everything works:

(from within the interactive session)
echo $PBS_NODEFILE
/var/lib/torque/aux//278.a00552.science.domain
cat $PBS_NODEFILE
a00551.science.domain
a00553.science.domain
a00551.science.domain

(from within the separate login)
mpirun --hostfile /var/lib/torque/aux//278.a00552.science.domain -np 3
--tag-output -display-map hostname

Data for JOB [65445,1] offset 0

========================   JOB MAP   ========================

Data for node: a00551   Num slots: 2    Max slots: 0    Num procs: 2
        Process OMPI jobid: [65445,1] App: 0 Process rank: 0 Bound: socket
0[core 0[hwt 0-1]], socket 0[core 1[hwt 0-1]], socket 0[core 2[hwt
0-1]], socket 0[core 3[hwt 0-1]], socket 0[core 4[hwt 0-1]], socket
0[core 5[hwt 0-1]], socket 0[core 6[hwt 0-1]], socket 0[core 7[hwt
0-1]], socket 0[core 8[hwt 0-1]], socket 0[core 9[hwt
0-1]]:[BB/BB/BB/BB/BB/BB/BB/BB/BB/BB][../../../../../../../../../..]
        Process OMPI jobid: [65445,1] App: 0 Process rank: 1 Bound: socket
1[core 10[hwt 0-1]], socket 1[core 11[hwt 0-1]], socket 1[core 12[hwt
0-1]], socket 1[core 13[hwt 0-1]], socket 1[core 14[hwt 0-1]], socket
1[core 15[hwt 0-1]], socket 1[core 16[hwt 0-1]], socket 1[core 17[hwt
0-1]], socket 1[core 18[hwt 0-1]], socket 1[core 19[hwt
0-1]]:[../../../../../../../../../..][BB/BB/BB/BB/BB/BB/BB/BB/BB/BB]

Data for node: a00553.science.domain    Num slots: 20   Max slots: 0    Num
procs: 1
        Process OMPI jobid: [65445,1] App: 0 Process rank: 2 Bound: socket
0[core 0[hwt 0-1]], socket 0[core 1[hwt 0-1]], socket 0[core 2[hwt
0-1]], socket 0[core 3[hwt 0-1]], socket 0[core 4[hwt 0-1]], socket
0[core 5[hwt 0-1]], socket 0[core 6[hwt 0-1]], socket 0[core 7[hwt
0-1]], socket 0[core 8[hwt 0-1]], socket 0[core 9[hwt
0-1]]:[BB/BB/BB/BB/BB/BB/BB/BB/BB/BB][../../../../../../../../../..]

=============================================================
[1,0]<stdout>:a00551.science.domain
[1,2]<stdout>:a00553.science.domain
[1,1]<stdout>:a00551.science.domain

I am kind of lost whats going on here. Anyone having an idea? I am
seriously considering this to be the problem of kerberos
authentification that we have to work with, but I fail to see how this
should affect the sockets.

Best,
Oswin
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