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Subject: Re: [OMPI users] SLURM and OpenMPI
From: Ralph H Castain (rhc_at_[hidden])
Date: 2008-06-17 13:08:41


I can believe 1.2.x has problems in that regard. Some of that has nothing to
do with slurm and reflects internal issues with 1.2.

We have made it much more resistant to those problems in the upcoming 1.3
release, but there is no plan to retrofit those changes to 1.2. Part of the
problem was that we weren't using the --kill-on-bad-exit flag when we called
srun internally, which has been fixed for 1.3.

BTW: we actually do use srun to launch the daemons - we just call it
internally from inside orterun. The only real difference is that we use
orterun to setup the cmd line and then tell the daemons what they need to
do. The issues you are seeing relate to our ability to detect that srun has
failed, and/or that one or more daemons have failed to launch or do
something they were supposed to do. The 1.2 system has problems in that
regard, which was one motivation for the 1.3 overhaul.

I would argue that slurm allowing us to attempt to launch on a
no-longer-valid allocation is a slurm issue, not OMPI's. As I said, we use
srun to launch the daemons - the only reason we hang is that srun is not
returning with an error. I've seen this on other systems as well, but have
no real answer - if slurm doesn't indicate an error has occurred, I'm not
sure what I can do about it.

We are unlikely to use srun to directly launch jobs (i.e., to have slurm
directly launch the job from an srun cmd line without mpirun) anytime soon.
It isn't clear there is enough benefit to justify the rather large effort,
especially considering what would be required to maintain scalability.
Decisions on all that are still pending, though, which means any significant
change in that regard wouldn't be released until sometime next year.

Ralph

On 6/17/08 10:39 AM, "Sacerdoti, Federico"
<Federico.Sacerdoti_at_[hidden]> wrote:

> Ralph,
>
> I was wondering what the status of this feature was (using srun to
> launch orted daemons)? I have two new bug reports to add from our
> experience using orterun from 1.2.6 on our 4000 CPU infiniband cluster.
>
> 1. Orterun will happily hang if it is asked to run on an invalid slurm
> job, e.g. if the job has exceeded its timelimit. This would be trivially
> fixed if you used srun to launch, as they would fail with non-zero exit
> codes.
>
> 2. A very simple orterun invocation hangs instead of exiting with an
> error. In this case the executable does not exist, and we would expect
> orterun to exit non-zero. This has caused
> headaches with some workflow management script that automatically start
> jobs.
>
> salloc -N2 -p swdev orterun dummy-binary-I-dont-exist
> [hang]
>
> orterun dummy-binary-I-dont-exist
> [hang]
>
> Thanks,
> Federico
>
> -----Original Message-----
> From: Sacerdoti, Federico
> Sent: Friday, March 21, 2008 5:41 PM
> To: 'Open MPI Users'
> Subject: RE: [OMPI users] SLURM and OpenMPI
>
>
> Ralph wrote:
> "I don't know if I would say we "interfere" with SLURM - I would say
> that we
> are only lightly integrated with SLURM at this time. We use SLURM as a
> resource manager to assign nodes, and then map processes onto those
> nodes
> according to the user's wishes. We chose to do this because srun applies
> its
> own load balancing algorithms if you launch processes directly with it,
> which leaves the user with little flexibility to specify their desired
> rank/slot mapping. We chose to support the greater flexibility."
>
> Ralph, we wrote a launcher for mvapich that uses srun to launch but
> keeps tight control of where processes are started. The way we did it
> was to force srun to launch a single process on a particular node.
>
> The launcher calls many of these:
> srun --jobid $JOBID -N 1 -n 1 -w host005 CMD ARGS
>
> Hope this helps (and we are looking forward to a tighter orterun/slurm
> integration as you know).
>
> Regards,
> Federico
>
> -----Original Message-----
> From: users-bounces_at_[hidden] [mailto:users-bounces_at_[hidden]] On
> Behalf Of Ralph Castain
> Sent: Thursday, March 20, 2008 6:41 PM
> To: Open MPI Users <users_at_[hidden]>
> Cc: Ralph Castain
> Subject: Re: [OMPI users] SLURM and OpenMPI
>
> Hi there
>
> I am no slurm expert. However, it is our understanding that
> SLURM_TASKS_PER_NODE means the number of slots allocated to the job, not
> the
> number of tasks to be executed on each node. So the 4(x2) tells us that
> we
> have 4 slots on each of two nodes to work with. You got 4 slots on each
> node
> because you used the -N option, which told slurm to assign all slots on
> that
> node to this job - I assume you have 4 processors on your nodes. OpenMPI
> parses that string to get the allocation, then maps the number of
> specified
> processes against it.
>
> It is possible that the interpretation of SLURM_TASKS_PER_NODE is
> different
> when used to allocate as opposed to directly launch processes. Our
> typical
> usage is for someone to do:
>
> srun -N 2 -A
> mpirun -np 2 helloworld
>
> In other words, we use srun to create an allocation, and then run mpirun
> separately within it.
>
>
> I am therefore unsure what the "-n 2" will do here. If I believe the
> documentation, it would seem to imply that srun will attempt to launch
> two
> copies of "mpirun -np 2 helloworld", yet your output doesn't seem to
> support
> that interpretation. It would appear that the "-n 2" is being ignored
> and
> only one copy of mpirun is being launched. I'm no slurm expert, so
> perhaps
> that interpretation is incorrect.
>
> Assuming that the -n 2 is ignored in this situation, your command line:
>
>> srun -N 2 -n 2 -b mpirun -np 2 helloworld
>
> will cause mpirun to launch two processes, mapped byslot against the
> slurm
> allocation of two nodes, each having 4 slots. Thus, both processes will
> be
> launched on the first node, which is what you observed.
>
> Similarly, the command line
>
>> srun -N 2 -n 2 -b mpirun helloworld
>
> doesn't specify the #procs to mpirun. In that case, mpirun will launch a
> process on every available slot in the allocation. Given this command,
> that
> means 4 procs will be launched on each of the 2 nodes, for a total of 8
> procs. Ranks 0-3 will be placed on the first node, ranks 4-7 on the
> second.
> Again, this is what you observed.
>
> I don't know if I would say we "interfere" with SLURM - I would say that
> we
> are only lightly integrated with SLURM at this time. We use SLURM as a
> resource manager to assign nodes, and then map processes onto those
> nodes
> according to the user's wishes. We chose to do this because srun applies
> its
> own load balancing algorithms if you launch processes directly with it,
> which leaves the user with little flexibility to specify their desired
> rank/slot mapping. We chose to support the greater flexibility.
>
> Using the SLURM-defined mapping will require launching without our
> mpirun.
> This capability is still under development, and there are issues with
> doing
> that in slurm environments which need to be addressed. It is at a lower
> priority than providing such support for TM right now, so I wouldn't
> expect
> it to become available for several months at least.
>
> Alternatively, it may be possible for mpirun to get the SLURM-defined
> mapping and use it to launch the processes. If we can get it somehow,
> there
> is no problem launching it as specified - the problem is how to get the
> map!
> Unfortunately, slurm's licensing prevents us from using its internal
> APIs,
> so obtaining the map is not an easy thing to do.
>
> Anyone who wants to help accelerate that timetable is welcome to contact
> me.
> We know the technical issues - this is mostly a problem of (a)
> priorities
> versus my available time, and (b) similar considerations on the part of
> the
> slurm folks to do the work themselves.
>
> Ralph
>
>
> On 3/20/08 3:48 PM, "Tim Prins" <tprins_at_[hidden]> wrote:
>
>> Hi Werner,
>>
>> Open MPI does things a little bit differently than other MPIs when it
>> comes to supporting SLURM. See
>> http://www.open-mpi.org/faq/?category=slurm
>> for general information about running with Open MPI on SLURM.
>>
>> After trying the commands you sent, I am actually a bit surprised by
> the
>> results. I would have expected this mode of operation to work. But
>> looking at the environment variables that SLURM is setting for us, I
> can
>> see why it doesn't.
>>
>> On a cluster with 4 cores/node, I ran:
>> [tprins_at_odin ~]$ cat mprun.sh
>> #!/bin/sh
>> printenv
>> [tprins_at_odin ~]$ srun -N 2 -n 2 -b mprun.sh
>> srun: jobid 55641 submitted
>> [tprins_at_odin ~]$ cat slurm-55641.out |grep SLURM_TASKS_PER_NODE
>> SLURM_TASKS_PER_NODE=4(x2)
>> [tprins_at_odin ~]$
>>
>> Which seems to be wrong, since the srun man page says that
>> SLURM_TASKS_PER_NODE is the "Number of tasks to be initiated on each
>> node". This seems to imply that the value should be "1(x2)". So maybe
>> this is a SLURM problem? If this value were correctly reported, Open
> MPI
>> should work fine for what you wanted to do.
>>
>> Two other things:
>> 1. You should probably use the command line option '--npernode' for
>> mpirun instead of setting the rmaps_base_n_pernode directly.
>> 2. In regards to your second example below, Open MPI by default maps
> 'by
>> slot'. That is, it will fill all available slots on the first node
>> before moving to the second. You can change this, see:
>> http://www.open-mpi.org/faq/?category=running#mpirun-scheduling
>>
>> I have copied Ralph on this mail to see if he has a better response.
>>
>> Tim
>>
>> Werner Augustin wrote:
>>> Hi,
>>>
>>> At our site here at the University of Karlsruhe we are running two
>>> large clusters with SLURM and HP-MPI. For our new cluster we want to
>>> keep SLURM and switch to OpenMPI. While testing I got the following
>>> problem:
>>>
>>> with HP-MPI I do something like
>>>
>>> srun -N 2 -n 2 -b mpirun -srun helloworld
>>>
>>> and get
>>>
>>> Hi, here is process 0 of 2, running MPI version 2.0 on xc3n13.
>>> Hi, here is process 1 of 2, running MPI version 2.0 on xc3n14.
>>>
>>> when I try the same with OpenMPI (version 1.2.4)
>>>
>>> srun -N 2 -n 2 -b mpirun helloworld
>>>
>>> I get
>>>
>>> Hi, here is process 1 of 8, running MPI version 2.0 on xc3n13.
>>> Hi, here is process 0 of 8, running MPI version 2.0 on xc3n13.
>>> Hi, here is process 5 of 8, running MPI version 2.0 on xc3n14.
>>> Hi, here is process 2 of 8, running MPI version 2.0 on xc3n13.
>>> Hi, here is process 4 of 8, running MPI version 2.0 on xc3n14.
>>> Hi, here is process 3 of 8, running MPI version 2.0 on xc3n13.
>>> Hi, here is process 6 of 8, running MPI version 2.0 on xc3n14.
>>> Hi, here is process 7 of 8, running MPI version 2.0 on xc3n14.
>>>
>>> and with
>>>
>>> srun -N 2 -n 2 -b mpirun -np 2 helloworld
>>>
>>> Hi, here is process 0 of 2, running MPI version 2.0 on xc3n13.
>>> Hi, here is process 1 of 2, running MPI version 2.0 on xc3n13.
>>>
>>> which is still wrong, because it uses only one of the two allocated
>>> nodes.
>>>
>>> OpenMPI uses the SLURM_NODELIST and SLURM_TASKS_PER_NODE environment
>>> variables, starts with slurm one orted per node and tasks upto the
>>> maximum number of slots on every node. So basically it also does
>>> some 'resource management' and interferes with slurm. OK, I can fix
> that
>>> with a mpirun wrapper script which calls mpirun with the right -np
> and
>>> the right rmaps_base_n_pernode setting, but it gets worse. We want to
>>> allocate computing power on a per cpu base instead of per node, i.e.
>>> different user might share a node. In addition slurm allows to
> schedule
>>> according to memory usage. Therefore it is important that on every
> node
>>> there is exactly the number of tasks running that slurm wants. The
> only
>>> solution I came up with is to generate for every job a detailed
>>> hostfile and call mpirun --hostfile. Any suggestions for improvement?
>>>
>>> I've found a discussion thread "slurm and all-srun orterun" in the
>>> mailinglist archive concerning the same problem, where Ralph Castain
>>> announced that he is working on two new launch methods which would
> fix
>>> my problems. Unfortunately his email address is deleted from the
>>> archive, so it would be really nice if the friendly elf mentioned
> there
>>> is still around and could forward my mail to him.
>>>
>>> Thanks in advance,
>>> Werner Augustin
>>> _______________________________________________
>>> users mailing list
>>> users_at_[hidden]
>>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>
>
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